ARTICLE | doi:10.20944/preprints202009.0459.v1
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; coronavirus; drug repositioning; pathway enrichment
Online: 19 September 2020 (11:34:12 CEST)
The COVID-19 global pandemic has created dire consequences with an alarming rate of morbidity and mortality. There are not yet vaccine or efficacious treatment options to combat the causative SARS-CoV-2 infection. This paper describes the identification of potentially repurposable drugs for COVID-19 treatment by conducting pathway enrichment analysis on publicly available Gene Expression Omnibus datasets. We first determined SARS-CoV-2 infection-induced alterations of host gene expressions and pathways. We then identified drugs or compounds that target and counter virus-triggered cellular perturbations, suggesting their potential repurposing for COVID-19 treatment. The key findings are that SARS-CoV-2 infection in host cells induces mitochondrial dysfunction, inhibits oxidative phosphorylation, and activates several immune response and pro-inflammatory pathways. Triptolide, the major bioactive component of a traditional Chinese medicine herb, may rescue mitochondrial dysfunction by activating oxidative phosphorylation. Further in vitro and in vivo studies are necessary to verify these results prior to clinical application.
ARTICLE | doi:10.20944/preprints201810.0268.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Turner’s syndrome; chromosomal aneuploidy; amniotic fluid; cell-free RNA; ingenuity pathway analysis
Online: 12 October 2018 (12:07:26 CEST)
Genetic disorders are quite a major topic of discussion and debate in the recent world of biological sciences. Turner’s syndrome is one such disorder caused by a chromosome aneuploidy and it has characteristic symptoms in the patient or the affected individual. The amniotic fluid is a complex biological material found in the amniotic sac of pregnant women and they can provide valuable knowledge and understanding of the pathogenesis of this particular chromosomal abnormality. In this study, global gene expression analysis of cell-free RNA in amniotic fluid supernatant was used to detect genes/organ systems which may be significant in the pathophysiology of Turner’s syndrome. The cell-free RNA from the amniotic fluid of five mid-trimester Turner’s syndrome fetuses and five euploid female fetuses matched for age of gestation were extracted, amplified and hybridized onto Affymetrix U33 Plus 2.0. array. The paired t-test was used to identify the significantly differentially regulated genes. Biological interpretation was conducted using ingenuity pathway analysis and BioGPS gene expression atlas. Of the genes, XIST was especially downregulated and SHOX was not expressed differentially. One of the most highly represented organ systems was the hematologic/immune system, differentiating the transcriptome of Turner’s syndrome from other chromosomal aneuploidies that are discussed in this area of science. The differences in the transcriptome of the Turner’s syndrome are due to genome-wide dysregulation. The hematologic/immune system differences are significant in early-onset autoimmune dysfunction. There are other genes which have been identified that are associated with the cardiovascular and the skeletal system, as these are often seen to be affected in the female patients with turner’s syndrome. Hopefully, such knowledge gained from this study will help us to understand the deeper mechanisms of this disorder and the possible treatments of this disease.
ARTICLE | doi:10.20944/preprints202006.0261.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: adverse outcome pathway; toxicity pathway; computational toxicology
Online: 21 June 2020 (11:10:34 CEST)
Background: Targeted methods that dominated toxicological research until recently did not allow for screening of all molecular changes involved in toxic response. Therefore, it is difficult to infer if all major mechanisms of toxicity have already been discovered, or if some of them are still overlooked. Objectives: To identify molecular mechanisms sensitive to chemical exposures in an unbiased manner. Methods: We used data on 641,516 unique chemical-gene interactions from the Comparative Toxicogenomic Database. Only data from high-throughput gene expression experiments with human, rat or mouse cells/tissues were extracted. The total number of chemical-gene interactions was calculated for every gene, and used as a measure of gene sensitivity to chemical exposures. These values were further used in enrichment analyses to identify molecular mechanisms sensitive to chemical exposures. Results: Remarkably, use of different input subsets with non-overlapping lists of chemical compounds identified largely the same genes and molecular pathways as most sensitive to chemical exposures, indicative of an unbiased nature of our analysis. One of the most important findings of this study is that almost every known molecular mechanism may be affected by chemical exposures. Predictably, xenobiotic metabolism pathways and mechanisms of cellular response to stress and damage were among the most sensitive. Additionally, our analysis identified a range of highly sensitive molecular pathways, which are not widely recognized by modern toxicology as major targets of toxicants, including lipid metabolism pathways, longevity regulation cascade and cytokine mediated signaling. Discussion: Molecular mechanisms identified as the most sensitive to chemical exposures are relevant for significant public health problems, such as aging, cancer, metabolic and autoimmune disease. Thus, public health system will likely benefit from future research focus on these sensitive molecular mechanisms. Additionally, approach used in this study may guide identification of priority adverse outcome pathways (AOP) for in-vitro and in-silico toxicity testing methods.
ARTICLE | doi:10.20944/preprints202310.0025.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: Ellagic acid; cisplatin; hepatotoxicity; Nrf2/HO-1 pathway; NF-κB pathway
Online: 2 October 2023 (03:19:16 CEST)
Cisplatin (CDDP), an important chemotherapeutic agent, could result in potential hepatotoxicity, but the precious molecular mechanisms remain unclear. In this study, the protective effect of ellagic acid (EA) on CDDP exposure-induced hepatotoxicity and underlying molecular mechanisms were investigated using a mouse model. Mice were randomly divided into control, CDDP model, EA100 (i.e., EA 100 mg/kg/day), and CDDP plus EA 25, 50, and 100 mg/kg/day. Mice in all CDDP-treated groups were intraperitoneally injected with CDDP 20 mg/kg/day for 2 days. In all EA co-treatments, mice were orally administrated with EA for 7 days. Our results found that, compared to the control group, CDDP treatment resulted in liver dysfunction, oxidative stress, and hepatocyte necrosis, which are effectively revised by EA supplementation in a dose-dependent manner. Meanwhile, EA supplementation inhibited CDDP-induced the elevation of caspases-9 and -3 activities in the liver tissues of mice. Furthermore, EA supplementation significantly downregulated CDDP exposure-induced the increases of NF-κB, IL-1β, TNF-α, and IL-6 proteins and mRNAs, while further upregulated the expression of Nrf2, and HO-1 proteins and mRNAs. Taken together, our results reveal that EA supplementation could ameliorate CCDP-induced liver injury in mice via the opposite regulation of Nrf2/HO-1 and NF-kB pathways.
REVIEW | doi:10.20944/preprints202009.0276.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Citral; essential oil; integrated pest management; insect-repellent; lemongrass; MEP pathway; mevalonate pathway
Online: 13 September 2020 (11:30:41 CEST)
Lemongrass (Cymbopogon flexuosus) is an aromatic perennial grass grown extensively for its essential oil. Lemongrass oil is chiefly a mixture of various cyclic and acyclic bioactive monoterpenes. We reviewed lemongrass oil and its biosynthesis in the present chapter along with its biochemical composition. Furthermore, we attempted to explore both the possible routes for essential oil biosynthesis in lemongrass, i.e. mevalonate and non-mevalonate pathways and how these pathways interwind with each other. Lemongrass oil has high commercial potential in medicinal, cosmetic, food and energy industries. Regarding the pharmacological properties, a wide array of biological activities has been observed in lemongrass oil such as antimicrobial, insecticidal, analgesic and anti-cancer properties as well as its efficacy as insect-repellent. The later sections were dedicated for the analysis of insecticidal property of the lemongrass oil and the mechanism working behind this phenomenon where it was observed that in addition to synergistic effects, various components of lemongrass oil can also induce specific neurotoxic and cytotoxic responses in the insects.
REVIEW | doi:10.20944/preprints202307.1284.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Cancer; tumourigenesis; drug resistance; signalling pathways; Wnt/β-catenin pathway; JAK/STAT pathway; PI3K/Akt/mTOR pathway; RAS/RAF/MAPK/ERK signalling
Online: 19 July 2023 (09:14:02 CEST)
One of the leading causes of death worldwide, in both man and woman, is cancer. Despite the significant development in therapeutic strategies, the inevitable emergence of drug resistance limits the success and impedes the curative outcome. Intrinsic and acquired resistance are common mechanisms responsible for cancer relapse. Several factors crucially regulate tumourigenesis and resistance, including physical barriers, tumour microenvironment (TME), heterogeneity, genetic and epigenetic alterations, the immune system, tumour burden, growth kinetics and undruggable targets. Moreover, transforming growth factor-beta (TGF-β), Notch, epidermal growth factor receptor (EGFR), integrin-extracellular matrix (ECM), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), phosphoinositol-3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR), wingless-related integration site (Wnt)/β-catenin), Janus kinase/signal transducers and activators of transcription (JAK/STAT) and RAS/RAF/mitogen-activated protein kinase (MAPK) signalling pathways are some of the key players that have a pivotal role in drug resistance mechanisms. To guide future cancer treatments and improve results, a deeper comprehension of drug resistance pathways is necessary. This review will cover both intrinsic and acquired resistance and give a comprehensive overview of recent research on mechanisms that enable cancer cells to bypass barriers put by treatments, and like “satellite navigation”, find alternative routes to carry on their “journey” to cancer progression.
ARTICLE | doi:10.20944/preprints202305.0844.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Peptidomimetic; VEGFR2; Angiogenesis; Tumor suppression; PI3K/Akt/mTOR signaling pathway; PLCγ/ERK signaling pathway
Online: 11 May 2023 (10:57:38 CEST)
Vascular endothelial growth factor receptor 2 (VEGFR2) mediates VEGFA signaling mainly through the PI3K/AKT/mTOR and PLCγ/ERK1/2 pathways. Here we unveil a peptidomimetic (VGB3) based on the interaction between VEGFB and VEGFR1 that unexpectedly binds and neutralizes VEGFR2. Investigation of the cyclic and linear structures of VGB3 using receptor binding and cell proliferation assays, molecular docking, and evaluation of antiangiogenic and antitumor activities in the 4T1 mouse mammary tumor model showed that loop formation is essential for peptide functionality. VGB3 inhibited proliferation and tubulogenesis of human umbilical vein endothelial cells (HUVECs), accounting for the abrogation of VEGFR2, p-VEGFR2 and, subsequently, PI3K/AKT/mTOR and PLCγ/ERK1/2 pathways. In 4T1 cells, VGB3 inhibited cell proliferation, VEGFR2 expression and phosphorylation, PI3K/AKT/mTOR pathway, FAK/Paxillin, and epithelial-to-mesenchymal transition cascade. The apoptotic effects of VGB3 on HUVE and 4T1 cells were inferred from annexin-PI and TUNEL staining and activation of P53, caspase-3, caspase-7, and PARP1, which mechanistically occurred through the intrinsic pathway mediated by Bcl2 family members, Cytochrome c, Apaf-1 and caspase-9, and extrinsic pathway via death receptors and caspase-8. These data indicate that binding regions shared by VEGF family members may be important in developing novel pan-VEGFR inhibitors that are highly relevant in the pathogenesis of angiogenesis-related diseases.
ARTICLE | doi:10.20944/preprints202305.0500.v1
Subject: Computer Science And Mathematics, Computer Vision And Graphics Keywords: no-reference image quality assessment; dual-stream networks; contrast sensitivity; ventral pathway; dorsal pathway
Online: 8 May 2023 (09:49:49 CEST)
Blind image quality assessment (BIQA) aims to evaluate image quality in a way that closely matches human perception. To achieve this goal, the strengths of deep learning and the characteristics of human visual system (HVS) can be combined. In this paper, inspired by the ventral pathway and dorsal pathway of HVS, a dual-pathway convolutional neural network is proposed for BIQA task. The proposed method consists of two pathways: “what” pathway, which mimics the ventral pathway of HVS to extract the content features of distorted images, and the “where” pathway, which mimics the dorsal pathway of HVS to extract the global shape features of distorted images. Then, the features from the two pathways are fused and mapped to an image quality score. Additionally, the gradient images weighted by the contrast sensitivity are used as the input to the “where” pathway, allowing it to extract global shape features that are more sensitive to human perception. Moreover, a dual-pathway multi-scale feature fusion module is designed to fuse the multi-scale features of the two pathways, enabling the model to capture both global features and local details, thus improving the overall performance of the model. The experiments conducted on six databases show that the proposed method achieves the state-of-the-art performance.
REVIEW | doi:10.20944/preprints201908.0229.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: paracellular permeability; tight junction; Pore Pathway; Leak Pathway; occludin; ZO-1; ZO-2; claudin
Online: 22 August 2019 (03:58:59 CEST)
The epithelial cell tight junction structure is the site of the transepithelial movement of solutes and water between epithelial cells (paracellular permeability). Paracellular permeability can be divided into two distinct pathways, the Pore Pathway mediating the movement of small ions and solutes and the Leak Pathway mediating the movement of large solutes. Claudin proteins form the basic paracellular permeability barrier and mediate the movement of small ions and solutes via the Pore Pathway. The Leak Pathway remains less understood. Several proteins have been implicated in mediating the Leak Pathway, including occludin, ZO proteins, tricellulin, and actin filaments, but the proteins comprising the Leak Pathway remain unresolved. The properties of the Leak Pathway, such as its molecular mechanism, its regulation, and whether or not it has a size limit, remain controversial. This review will trace the evolution of the Leak Pathway concept from its origins, will discuss the current information about the properties of the Leak Pathway, and will discuss recent research suggesting a possible molecular basis for the Leak Pathway. Based on these findings, we propose a model for the molecular mechanism underlying the Leak Pathway and its regulation.
ARTICLE | doi:10.20944/preprints202204.0082.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Caco2/HT-29 cells; lipopolysaccharide(LPS); mucins; focal adhesion pathway; ECM receptor in-teraction pathway
Online: 8 April 2022 (14:04:17 CEST)
Endotoxins are toxic substances that widely exist in the environment and can enter the intestine with food and other substances. Intestinal epithelial cells are protected by a mucus layer that contains MUC2 as its main structural component. However, a detailed understanding of the mechanisms involved in the function of the mucus barrier in endotoxin penetration is lacking. Here, we established the most suitable proportion of Caco-2/HT-29 co-culture cells as a powerful tool to evaluate the intestinal mucus layer. Our findings significantly advance current knowledge as focal adhesion and ECM-receptor interaction were identified as the two most significantly implicated pathways in MUC2 small interfering RNA (siRNA)-transfected Caco-2/HT-29 co-culture cells after 24 h of LPS stimulation. When the mucus layer was not intact, LPS was found to damage the tight junctions of Caco-2/HT29 co-cultured cells. Furthermore, LPS was demonstrated to inhibit the integrin-mediated focal adhesion structure and damage the matrix network structure of the extracellular and actin microfilament skeletons. Ultimately, LPS inhibited the interactive communication between the extracellular matrix and the cytoskeleton for 24 h in the siMUC2 group compared with the LPS(+) and LPS(-) groups. Overall, we recognized the potential of MUC2 as a tool for barrier function in several intestinal bacterial diseases.
ARTICLE | doi:10.20944/preprints202010.0373.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Fungi; ergosterol pathway; dermatophytes; chelerythrine; sanguinarine
Online: 19 October 2020 (11:10:30 CEST)
The ergosterol pathway is a prime antifungal target. The minimum inhibitory concentration (MIC) assay is a simple research tool that determines the lowest concentration at which a novel antimicrobial with limited scope to determine the mechanism of action for a drug. In this study, we show that by adding hydrogen peroxide, an oxidative stressor, or glutathione (GSH), an antioxidant, to modify a commonly performed MIC assay allowed us to screen selectively for new antifungal drugs that target ergosterol biosynthesis in fungi. A human pathogen, Microsporum gypseum, was used as a test organism. When exposed to ergosterol targeting drugs, the hydrogen peroxide treatment significantly decreased fungal survival by reducing ergosterol in the cell wall, whereas GSH increased survival of M. gypseum. Further, by performing a series of experiments with M. gypseum, it was determined that the oxidative stress from hydrogen peroxide causes cell death at different developmental stages. These findings allow us to describe a simple, high-throughput method for simultaneously screening new antifungal drugs for activity and effects on the ergosterol pathway. By using this tool, two isoquinoline alkaloids were discovered to be potent inhibitors of ergosterol biosynthesis by reducing the amount of ergosterol without affecting the expression of 1,3-β-glucan.
ARTICLE | doi:10.20944/preprints201906.0130.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: breast cancer; Wnt pathway; TCF1; NHERF1
Online: 14 June 2019 (05:00:53 CEST)
Wnt pathway is involved in breast cancer (BC) progression. Our aim was to evaluate the expression of some components of the Wnt pathway (β-catenin, FZD4, LRP5, LRP6 and TCF1) in order to detect potential associations with NHERF1 protein. In addition, we assessed their impact on patients’clinical outcome. We evaluated 220 primary BC samples by immunohistochemistry (IHC) and protein localization by immunofluorescence. We found a significant correlation between NHERF1 and FZD4, LRP5, LRP6 and TCF1. Univariate analysis showed that β-catenin (p<0.0001), FZD4 (p=0.0001), LRP5, LRP6 and TCF1 over-expression (p<0.0001 respectively) was related to poor disease free survival (DFS). A Kaplan-Meier analysis confirmed univariate data and showed a poor DFS for cNHERF1+/FZD4+ (p=0.0007), cNHERF1+/LRP5+ (p=0.0002), cNHERF1+/LRP6+ (p<0.0001) and cNHERF1+/TCF1+ phenotypes (p=0.0034). In multivariate analysis, TCF1 and β-catenin expression were independent prognostic variable of worse DFS (p=0.009 and p=0.027, respectively). In conclusion, we found that β-catenin, FZD4, LRP5, LRP6 and TCF1 overexpression was associated to poor prognosis. Furthermore, we first identified TCF1 as independent prognostic factor of poor outcome, indicating it as a new potential biomarker for BC patients management. In addition, Wnt pathway proteins expression, both alone and in association with NHERF1, suggests original associations of biological significance for new studies.
ARTICLE | doi:10.20944/preprints201905.0020.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: Euglena; central metabolic pathway; subcellular location
Online: 5 May 2019 (12:41:30 CEST)
Euglenids are a group of algae of great interest for biotechnology, with a large and complex metabolic capability. To study the metabolic network, it is necessary to know the subcellular locations of the component enzymes, but despite a long history of research into Euglena, the subcellular locations of many major pathways are only poorly defined. Euglena is phylogenetically distant from other commonly studied algae, they have secondary plastids bounded by three membranes, and they can survive after destruction of their plastids. These unusual features make it difficult to assume that the subcellular organization of the metabolic network will be equivalent to that of other photosynthetic organisms. Moreover, we show here that the presence of the secondary chloroplast means that it is not possible to make reliable predictions of the subcellular locations of enzymes in Euglena using existing informatics tools. In order to generate a model of the central metabolic pathway operating in Euglena we analysed biochemical and proteomic information from a variety of sources to assess the subcellular location of relevant enzymes. We use these assignments to propose the compartmentation of the core metabolic pathways in Euglena, a prerequisite for the further study of the metabolic network of Euglena. This model of the metabolic network shows that, other than photosynthesis, all major pathways present in the chloroplast are duplicated elsewhere in the cell, and that several biosynthetic pathways confined to plastids in higher plants are localized elsewhere in Euglena. Our model demonstrates how this organism can synthesise all the metabolites required for growth from simple carbon inputs, and can survive in the absence of chloroplasts.
ARTICLE | doi:10.20944/preprints202304.1105.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: citrate cycle; fructose and mannose pathway; glycolysis/gluconeogenesis pathway; Il17b; Ngf; Nfe2l2; pmm1; pmm2; pyruvate metabolism; Slc2a1
Online: 28 April 2023 (04:22:40 CEST)
The high morbidity and mortality rate of the pulmonary arterial hypertension (PAH) is partially explained by the metabolic deregulation associated with the disease. The present study identified statistically significant increase of the glucose transporter solute carrier family 2 (Slc2a1), beta nerve growth factor (Ngf), and nuclear factor erythroid derived 2, like 2 (Nfe2l2) on three standard PAH rat models and their healthy counterpart. PAH was induced by subjecting the animals to hypoxia (HO group) or by injecting them with monocrotaline in either normal (CM) or hypoxic (HM) atmospheric conditions. The Western blot and double immunofluorescent experiments were complemented with the gene expression profiling of the animal lungs analyzed from the perspective of the Genomic Fabric Paradigm. We found substantial remodeling of the genomic fabrics of the citrate cycle, pyruvate metabolism, glycolysis/gluconeogenesis and fructose and manose pathways. According to the novel transcriptomic distance criterion, the most comprehensive measure of the transcriptomic alteration, glycolysis/gluconeogenesis was the most affected functional pathway in all three PAH models. PAH decoupled the coordinated expression of many metabolic genes and replaced Pmm2 with Pmm1 in the center of the fructose and mannose metabolism. Our data show that metabolic dysregulation is a major pathogenic factor of the PAH.
REVIEW | doi:10.20944/preprints202011.0563.v2
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Chromosomal instability; FA pathway; Radial figures; TGF pathway; MYC; p53; Bone marrow failure; cancer; physical abnormalities; infertility.
Online: 22 December 2020 (10:58:20 CET)
Abstract: Fanconi anemia (FA), a chromosomal instability syndrome, is caused by inherited pathogenic variants in any of 22 FANC genes, that cooperate in the FA/BRCA pathway. This pathway regulates the repair of DNA interstrand crosslinks (ICLs) through homologous recombination. In FA proper repair of ICLs is impaired, and accumulation of toxic DNA double strand breaks occurs. In order to repair this type of DNA damage, FA cells activate alternative error-prone DNA repair pathways, that may lead to the formation of gross structural chromosome aberrations of which radial figures are the hallmark of FA and their segregation during cell division are the origin of subsequent aberrations like translocations, dicentrics and acentric fragments. The deficiency in DNA repair has pleiotropic consequences in the phenotype of patients with FA, including developmental alterations, bone marrow failure and an extreme risk to develop cancer. The mechanisms leading to the physical abnormalities during embryonic development have not been clearly elucidated, however FA has features of premature aging with chronic inflammation mediated by pro-inflammatory cytokines, that results in tissue attrition, selection of malignant clones and cancer onset. Moreover, the effect of the FA/BRCA pathway in germinal cells, evidenced by infertility in patients with FA attests of chromosomal instability and cell death also occurring in the germinal compartment.
ARTICLE | doi:10.20944/preprints202011.0709.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Sphingosine-1-phosphate receptor analogue; fingolimod phosphate; neuroprotection; mitochondrial damage; glycolytic pathway; pentose phosphate pathway; REDOX homeostasis.
Online: 30 November 2020 (08:31:50 CET)
Imbalance in the oxidative status in neurons, along with mitochondrial damage, are common characteristics in some neurodegenerative diseases. The maintenance in energy production is crucial to face and recover from the oxidative damage and the coexistence of different sources of energy production, such as mitochondrial and glycolytic ATP, allows faster adaptative mechanisms to situations of high energy demand and may help in the maintenance of neuronal function in stress situations. Fingolimod phosphate is a drug with neuroprotective and antioxidant actions, used in the treatment of Multiple Sclerosis. This work has been performed in a model of oxidative damage on neuronal cell cultures exposed to menadione, in presence or absence of fingolimod phosphate. We have studied the mitochondrial function and several pathways related with glucose metabolism, including oxidative, glycolytic and pentose phosphate in neuronal cells cultures. Our results showed a beneficial effect on neuronal survival probably based in the recovery of all, oxidative balance, glycolysis and pentose phosphate, promoted by fingolimod phosphate. These effects are mediated, at least in part by the interaction with its specific receptor. These actions would make this drug a potential tool to the treatment of neurodegenerative processes, either to slow progression or alleviate symptoms.
ARTICLE | doi:10.20944/preprints202310.0078.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: transcriptomics; metabolomics; drought stress; rehydration; genes; pathway
Online: 3 October 2023 (05:34:06 CEST)
Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis–antenna proteins, nitrogen metabolism, plant–pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to the water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5′-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomato to enhance drought tolerance.
REVIEW | doi:10.20944/preprints202306.1180.v3
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: PCa; AR; ADT; TLK1 signaling; pathway inhibition
Online: 25 June 2023 (03:56:10 CEST)
Androgen deprivation therapy (ADT) has been the mainstay of prostate cancer (PCa) treatment, with success in developing more effective inhibitors of androgen synthesis and antiandrogens in clinical practice. However, hormone deprivation and AR ablation have caused an increase in ADT-insensitive PCas’ associated with poor prognosis. Resistance to ADT arises through various mechanisms, and most castration-resistant PCas’ still rely on the androgen axis, while others become truly androgen receptor (AR)-independent. Our research identified the human tousled-like kinase 1 (TLK1) as a crucial early mediator of PCa cell adaptation to ADT, promoting androgen-independent growth, inhibiting apoptosis, and facilitating cell motility and metastasis. Although explicit, the growing role of TLK1 biology in PCa has remained under-represented and elusive. In this review, we aim to highlight the diverse functions of TLK1 in PCa, shed light on the molecular mechanisms underlying the transition from androgen-sensitive (AS) to an androgen-insensitive (AI) disease mediated by TLK1, and explore potential strategies to counteract this process. Targeting TLK1 and its associated signaling could prevent PCa progression to the incurable metastatic castration-resistant PCa (mCRPC) stage and provide a promising approach to treating PCa.
REVIEW | doi:10.20944/preprints202305.1855.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: sarcoidosis; advanced pulmonary fibrosis; signaling; molecular pathway
Online: 26 May 2023 (04:55:01 CEST)
Sarcoidosis is a multisystemic disease of unknown etiology characterized by the formation of granulomas in various organs, especially lung and mediastinal hilar lymph nodes. The clinical course and manifestations are unpredictable: spontaneous remission can occur in approximately two thirds of patients; up to 20% of patients have chronic course of the lung disease (called Ad-vanced Pulmonary Sarcoidosis) resulting in progressive loss of lung function, sometimes life-threatening that can lead to respiratory failure and death. The immunopathology mechanism leading from granuloma formation to the fibrosis in APS still remains elusive. Recent studies have provided new insights into the genetics factors and immune components involved in the clinical manifestation of the disease. In this review we aim to summarize the clinical-prognostic charac-teristics and molecular pathways which are believed to be associated with the development of APS
REVIEW | doi:10.20944/preprints202201.0186.v2
Subject: Social Sciences, Behavior Sciences Keywords: Habituation; Genelist; Molecular pathway; Cognition; Neurodevelopmental disorders
Online: 6 May 2022 (08:58:50 CEST)
Habituation is the most ancient and fundamental form of learning. As a firewall that protects our brain from sensory overload, it is indispensable for higher cognitive processes. Studies in humans and animal models provide a growing body of evidence that habituation is affected in autism and related monogenic neurodevelopmental disorders (NDDs). An integrated application of habituation assessment in NDDs and their animal models has currently unexploited potential for fundamental neuroscience and medical care.With the aim to gain mechanistic insights, we systematically retrieved genes that have been demonstrated in the literature to underlie habituation. We identified 258 evolutionarily conserved genes across species, describe the biological processes they converge on, and highlight regulatory pathways and drugs that may alleviate the habituation deficits associated with their dysregulation. We also summarize current habituation paradigms and extract the most decisive arguments from the literature that support the crucial role of habituation for cognition in health and disease. We conclude that habituation is a conserved, quantitative, cognition- and disease-relevant process that can connect preclinical and clinical work, and hence is a powerful tool to advance research, diagnostics,’’ and treatment of NDDs.
REVIEW | doi:10.20944/preprints202201.0134.v1
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: TRYCATs; MDD; MDE; Suicidal behavior; Kynurenine pathway
Online: 11 January 2022 (10:39:25 CET)
Kynurenine or tryptophan catabolite (TRYCAT) pathway contributes to the pathophysiology of major depression disorder (MDD) and major depressive episodes (MDE) in bipolar disorder and suicidal behaviors. The consequences of the overactivation of this pathway large reduced tryptophan (TRP) levels in peripheral blood and the CNS and increased levels of neurotoxic TRYCATs including kynurenine (KYN), 3-hydroxy kynurenine (3HK), quinolinic acid (QA), xanthurenic acid (XA), and picolinic acid (PA). However, other TRYCATs are protective, such as kynurenic acid (KA) and anthranilic acid (AA). Inflammation and cell-mediated immune activation along with oxidative and nitrosative stress (O&NS) may stimulate the first and rate-limiting enzyme of this pathway, namely indoleamine-2,3-dioxygenase (IDO). Therefore, during depression, balancing neuroprotective versus neurotoxic TRYCATs and balancing activation of the immune response system (IRS) versus the compensatory immune response system is crucial for achieving better treatment outcomes. Furthermore, targeting the causes of TRYCAT pathway activation (immune activation and O&NS) is probably the most effective strategy to treat depression. In the present review, we aim to provide a comprehensive explanation of the impact of TRYCATs in terms of pathophysiology and treatment of MDD and MDE.
ARTICLE | doi:10.20944/preprints202103.0742.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Salinity; wheat; organellar antioxidant; SOS pathway; RBOH
Online: 30 March 2021 (13:49:12 CEST)
The response of salt tolerant wheat genotype (Kharchia 65), and sensitive cultivars (HD2687, HD2009, WL711) to vegetative stage salinity stress (for 4 weeks) were studied at 1.1 (control), 9.1 (S1) and 14.2 (S2) dSm-1 salinity levels. Based on relative change in Membrane stability, PSII efficiency, retention of chlorophyll and carotenoid contents, Kharchia 65 showed better tolerance to salinity than other genotypes considered. To understand the role of different component mechanisms, expression of genes involved in ion exclusion, antioxidant defence and compatible osmolyte synthesis were analysed. Expression of SOS1 (plasma membrane Na+/H+ antiporter), NHX (vacuolar Na+/H+ antiporter), Ionic (sodium exclusion) and tissue tolerance (Sodium compartmentation, compatible solute accumulation and antioxidant defence) mechanisms were analysed in leaves of the genotypes after 4 weeks of salinity stress. Expression assay and the content of respective constituents indicated that apart from the well-known ion exclusion ability, Kharchia 65 also showed high level of tissue tolerance resulting in high early vigour and maintenance of growth rate afterwards. In Kharchia 65, sensing of salinity stress at plasma membrane activates NADPH Oxidase (RBOH) genes and generate ROS at apoplast. Apoplastic ROS triggers calcium influx and activates calcium signaling genes of SOS pathway (SOS1 and NHX). ROS generated from organelles chloroplast, peroxisome and mitochondria triggers cellular oxidative burst. ROS and calcium activates MAPK genes and downstream transcription factors, NAC and bZIP. MAPK signaling induces cellular antioxidant and compatible osmolyte biosynthesis and imparts tissue tolerance to salinity.
ARTICLE | doi:10.20944/preprints202005.0495.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Hedgehog pathway; Smoothened; Promoter; Methylation; Transcription factors
Online: 31 May 2020 (19:14:59 CEST)
Background: The hedgehog (HH) signaling pathway is a key regulator of embryonic patterning, tissue regeneration, stem cell renewal, and cancer growth. The smoothened (SMO) protein regulates the HH signaling pathway and has demonstrated oncogenic activity. Methods: To clarify the role of the HH signaling pathway in tumorigenesis, the expression profile of key HH signaling molecules, including SMO, PTCH1, GLI1, GLI2, and GLI3, were determined in thirty-three cancer cell lines. We performed a computational analysis of the upstream region of the SMO gene to identify the regulatory elements. Results: Three potential CpG islands and several putative SMO promoter elements were identified. Luciferase reporter assays mapped key SMO promoter elements, and functional binding sites for SP1, AP1, CREB, and AP-2a transcription factors in the core SMO promoter region were confirmed. A hypermethylated SMO promoter was identified in several cancer cell lines suggesting an important role for epigenetic silencing of SMO expression in certain cancer cells. Discussion: These results have important implications for our understanding of regulatory mechanisms controlling HH pathway activity and the molecular basis of SMO gene function. Moreover, this study may prove valuable for future research aimed at producing therapeutic downregulation of SMO expression in cancer cells.
ARTICLE | doi:10.20944/preprints202002.0423.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ITF2_TCF4; chemotheraoy resistance; NSCLC; HOXD9; Wnt pathway
Online: 28 February 2020 (11:58:28 CET)
Despite often leading to platinum resistance, platinum-based chemotherapy continues to be the standard treatment for many epithelial tumors. In this study we analyze and validated the cytogenetic alterations that arise after treatment in four lung and ovarian paired cisplatin-sensitive/resistant cell lines by 1-million array-CGH and qRT-PCR methodologies. RNA-sequencing, functional transfection assays and gene-pathway activity analysis were used to identify genes with a potential role in the development of this malignancy. Results were further explored in 55 lung and ovarian primary tumors and control samples and in two extensive in silico databases. Long-term cell exposure to platinum induces the frequent deletion of ITF2 gene. Its expression re-sensitizes tumor cells to platinum and recovers the levels of Wnt/β-catenin transcriptional activity. ITF2 expression was also frequently downregulated in epithelial tumors, predicting a worse overall survival. We also identified an inverse correlation between ITF2 and HOXD9 expression, revealing that NSCLC patients with lower expression of HOXD9 have a better overall survival rate. We define the implication of ITF2 as a molecular mechanism behind the development of cisplatin resistance probably through the activation of the Wnt-signaling pathway. This data highlights the possible role of ITF2 and HOXD9 as novel therapeutic targets for platinum resistant tumors.
REVIEW | doi:10.20944/preprints201805.0404.v2
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: microbiota; kynurenine pathway; serotonin; inflammation; gut motility
Online: 22 June 2018 (06:29:42 CEST)
The human gastrointestinal tract is inhabited by trillions of commensal bacteria collectively known as the gut microbiota. Our recognition of the significance of the complex interaction between the microbiota, and its host has grown dramatically over the past years. A balanced microbial community is a key regulator of the immune response, and metabolism of dietary components, which in turn, modulates several brain processes impacting mood and behavior. Consequently, it is likely that disruptions within the composition of the microbiota would remotely affect the mental state of the host. Here, we discuss how intestinal bacteria and their metabolites can orchestrate gut-associated neuroimmune mechanisms that influence mood and behavior leading to depression. In particular, we focus on microbiota-triggered gut inflammation and its implications in shifting the tryptophan metabolism towards kynurenine biosynthesis while disrupting the serotonergic signaling. We further investigate the gaps to be bridged in this exciting field of research in order to clarify our understanding of the multifaceted crosstalk in the microbiota-gut-brain interphase, bringing about a novel microbiota-targeted therapeutics for mental illnesses.
ARTICLE | doi:10.20944/preprints201804.0344.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Chevron-Phillips; chromium; trimerization; polymerization; reaction pathway
Online: 26 April 2018 (16:55:12 CEST)
In the present work, effect of basic components on the energy pathway of ethylene oligomerization by landmark Chevron-Phillips catalyst has been explored in detail using density functional theory (DFT). Studied factors were chosen considering the main components of Chevron-Phillips catalyst, i.e. ligand, cocatalyst and halocarbon compounds, comprising i) the type of alkyl substituents in pyrrole ligand as methyl, iso-propyl, tert-butyl, and phenyl, as well as the simple hydrogen, and the electronwithdrawing fluoro and trifluoromethyl; ii) the number of Cl atoms in Al-compound (as AlMe2Cl, AlMeCl2 and AlCl3) which indicates halocarbon amount and iii) cocatalyst type as alkylboron, alkylaluminium, or alkylgallium. Besides main ingredients, solvent effect, from toluene or methylcyclohexane, on oligomerization pathway was explored as well. In this regard, the full catalytic cycles for the main product (1-hexene) formation as well as side reactions, i.e. 1-butene release and chromacyclononane formation, were calculated on the basis of the metallacycle based mechanism. Based on results, a modification on the Chevron-Phillips catalyst system, to reach higher 1-hexene selectivity and activity, is suggested.
ARTICLE | doi:10.20944/preprints202311.0013.v1
Subject: Biology And Life Sciences, Toxicology Keywords: Bisphenol A; Bisphenol S; Bisphenol F; Atopic dermatitis; DNA methylation; JAK-STAT signaling pathway; PI3K-AKT signaling pathway
Online: 1 November 2023 (04:02:06 CET)
Bisphenol is a chemical substance widely used in plastic products and food containers. In this study, we observed a relationship between DNA methylation and atopic dermatitis (AD) in the peripheral blood mononuclear cells (PBMCs) of pregnant women exposed to bisphenol A (BPA) and its alternatives, bisphenol S (BPS) and bisphenol F (BPF). DNA methylation is an epigenetic mechanism that regulates gene expression, which can be altered by environmental factors, and affects the onset and progression of diseases. We found that genes belonging to the JAK-STAT and PI3K-AKT signaling pathways were hypomethylated in the blood of pregnant women exposed to bisphenols. These genes play important roles in skin barrier function and immune responses, and may influence AD. Therefore, we suggest that not only BPA but also BPS and BPF, which are used as alternatives, can have a negative impact on AD through epigenetic mechanisms.
ARTICLE | doi:10.20944/preprints202210.0242.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: pheromones; androstenone; mouse deer; metabolic pathway; reproduction; hormones
Online: 18 October 2022 (02:44:00 CEST)
Two putative boar pheromones (Androstenone and Androstenol) were discovered in endangered mouse deer during captive breeding program. This study further examined the molecular characteristics, pheromone synthesis pathway, and the functional role of these pheromones in reproduction of mouse deer. CYP17A1 and CYB5 genes were cloned and expressed in HEK-293, COS-7 cell lines and gonads of mouse deer to investigate CYP17A1 gene’s andien-β-synthase activity towards synthesis of sex pheromones in mouse deer. An enzyme immunoassay was also developed and standardized to measure the fecal androstenone during reproductive cycles of mouse deer. Results showed that mouse deer’s CYP17A1 gene possesses andien-β-synthase activity and could transform pregnenolone into 5,16-androstadien-3β-ol. The expression of CYP17A1 gene upregulated in the testis and ovary, compared to other tissues in mouse deer. Significantly elevated pheromones and estrogens were recorded prior to delivery and postpartum estrus / mating in mouse deer. Further, there were weak correlations between fecal pheromones and estrogens/ androgens in mouse deer during breeding season. The findings suggest that the boar pheromones might play a direct role in the reproductive activities of mouse deer which might be used for breeding of mouse deer elsewhere.
REVIEW | doi:10.20944/preprints202209.0458.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: kynurenine pathway; inflammatory biomarkers; inflammation; ADHD; neurobiology; kynurenine
Online: 29 September 2022 (08:11:33 CEST)
Attention deficit hyperactivity disorder (ADHD) is a prevalent neurodevelopmental disorder that can diminish the quality of life of both children and adults in academic, occupational, and social contexts. The kynurenine pathway (KP) contains a set of enzymatic reactions involved in tryptophan (TRP) degradation. It is known to be associated with the risk of developing ADHD. This review will address the KP and underlying mechanism of inflammation in ADHD. Potential inflammatory biomarkers reported in the most recent studies are summarized. Although a strong neuroimmunological basis has been established due to advances of recent neurobiological research, the pathophysiology of ADHD remains unclear.
ARTICLE | doi:10.20944/preprints202207.0067.v1
Subject: Medicine And Pharmacology, Cardiac And Cardiovascular Systems Keywords: restenosis; foam cells; NLRP3 inflammasome; MAPK signaling pathway
Online: 5 July 2022 (08:15:38 CEST)
The accumulation of foam cells in arterial intima and the accompanied chronic inflammation are considered major causes of neoatherosclerosis and restenosis. However, both the underlying mechanism and effective treatment for the disease are yet to be uncovered. In this study, we combined transcriptome profiling of restenosis artery tissue and bioinformatic analysis to reveal that NLRP3 inflammasome is markedly upregulated in restenosis and that several restenosis re-lated DEGs are also targets of mulberry extract, a natural dietary supplement used in traditional Chinese medicine to improve liver vitality. Further pathway enrichment analysis identified MAPK signaling pathway to be involved in the inflammatory response of foam cells. Consistently, immunofluorescence microscopy shows co-localization of NLRP3 with CD68+ macrophages. We then evaluated the efficacy of mulberry extract in inhibiting both the formation of foam cells and their inflammatory response. We demonstrated that mulberry extract suppresses the formation of ox-LDL induced foam cells, possibly by upregulating the cholesterol efflux genes ABCA1 and ABCG1 to inhibit intracellular lipid accumulation. In addition, mulberry extract dampens NLRP3 inflammasome activation by stressing the MAPK signaling pathway. Collectively, our mecha-nistic and functional studies unveil the therapeutic value of mulberry extract in neoatherosclerosis and restenosis treatment by regulating lipid metabolism and inflammatory response of foam cells.
REVIEW | doi:10.20944/preprints202111.0127.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Apoptosis; preclinical research; diabetes type 2; HIPPO pathway
Online: 8 November 2021 (11:45:49 CET)
Diabetes mellitus is a heterogeneous disease of complex etiology and pathogenesis. Hyperglycemia leads to many serious complications, but also directly initiates the process of β cell apoptosis. A potential strategy for the preservation of pancreatic β cells in diabetes may be to inhibit the implementation of pro-apoptotic pathways or to enhance the action of pancreatic protective factors. The HIPPO signaling pathway is proposed and selected as a target to manipulate the activity of its core proteins in therapy - basic research. MST1 and LATS2 as major upstream signaling kinases of the Hippo pathway are considered as target candidates for pharmacologically induced tissue regeneration and inhibition of apoptosis. Manipulating the activity of components of the HiPPO pathway offers a wide range of possibilities, and thus is a potential tool in the treatment of diabetes and the regeneration of β cells. Therefore, it is important to fully understand the processes involved in apoptosis in diabetic states and to fully characterize the role of this pathway in diabetes. Therapy consisting in slowing down or stopping the mechanisms of apoptosis may be an important direction of diabetes treatment shortly.
ARTICLE | doi:10.20944/preprints202011.0311.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: autism genetics; family microarrays; pathway enrichment; network biology
Online: 10 November 2020 (12:33:35 CET)
The genetic heterogeneity of autism has stymied the search for causes and cures. Whole-genomic studies on large numbers of families have helped identify combinations of inherited and de novo signal. In the present work, we re-analyze DNA microarrays using a novel strategy that takes prior knowledge of genetic relationships into account and that was designed to boost signal important to our understanding of the molecular basis of autism. Our strategy was designed to identify significant genomic variation within a priori defined biological concepts and improves signal detection while lessening the severity of multiple test correction seen in standard analysis of genome-wide association data. Upon application of our approach using 3,244 biological concepts, we detected genomic variation in 68 biological concepts with significant association to autism in comparison to family-based controls. These concepts clustered naturally into a total of 19 classes, principally including cell adhesion, cancer, and immune response. The top-ranking concepts contained high percentages of genes already suspected to play roles in autism or in a related neurological disorder. In addition, many of the sets associated with autism at the DNA level also proved to be predictive of changes in gene expression within a separate population of autistic cases, suggesting that the signature of genomic variation may also be detectable in blood-based transcriptional profiles. This cross-validation with gene expression data from individuals with autism coupled with the enrichment within autism-related neurological disorders supported the possibility that the mutations play important roles in the onset of autism and should be given priority for further study. Our work provides new leads into the genetic underpinnings of autism and highlights the importance of reanalysis of genomic studies of complex disease using prior knowledge of genetic organization.
ARTICLE | doi:10.20944/preprints201805.0076.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Oral cancer; mTOR pathway; secreted glycoprotein; drug resistance
Online: 3 May 2018 (12:47:14 CEST)
Oral cancer is a major public health burden worldwide. The lack of biomarkers for early diagnosis has increased the difficulty in managing this disease. Recent studies have reported that neutrophil gelatinase-associated lipocalin (NGAL), a secreted glycoprotein, is upregulated in various tumors. In our study we found that NGAL was significantly downregulated in primary malignant and metastatic tissues of oral cancer compared to normal tissues. The downregulation of NGAL was strongly correlated with the degree of differentiation and stage (I-IV), and can serve as a prognostic biomarker for oral cancer. Tobacco carcinogens were also found to be involved in the downregulation of NGAL. Mechanistic studies revealed that knockdown of NGAL increased oral cancer cell proliferation, survival, and migration, and also induced resistance against cisplatin. Silencing of NGAL activated mTOR signaling and reduced autophagy by the LKB1-AMPK-p53-Redd1 signaling axis. Moreover, cyclin-D1, Bcl-2, and MMP-9 were upregulated, and caspase-9 was downregulated, suggesting that silencing of NGAL increases oral cancer cell proliferation, survival, and migration. Thus, from our study it is evident that downregulation of NGAL activates the mTOR pathway and helps in the progression of oral cancer.
ARTICLE | doi:10.20944/preprints201608.0011.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: curcumin; furazolidone; oxidative stress; DNA damage; mitochondrial pathway
Online: 2 August 2016 (05:59:38 CEST)
Furazolidone (FZD) is a synthetic nitrofuran with the antiprotozoal and antibacterial activity. The proper mechanism of FZD induced toxicity is still unclear. This study aimed to investigate the protective effect of curcumin on FZD induced oxidative stress, DNA injury and apoptosis in human hepatocyte L02 cells. The results showed that curcumin treatment significantly ameliorated FZD induced cytotoxicity, characterized by decreasing the production of reactive oxygen species (ROS) and malondialdehyde, as well as increasing superoxide dismutase, catalase activities and glutathione contents. Moreover, curcumin pretreatment significantly inhibited FZD induced the loss of mitochondrial membrane potential, the activation caspase-9 and -3 and apoptosis. Comet assay showed that curcumin attenuated FZD induced DNA injury in a dose-dependent manner. Correspondingly, curcumin markedly reversed the up-regulation of p53, Bax, caspase-9 and -3 mRNA expressions and the down-regulation of Bcl-2 mRNA (all p<0.05 or 0.01). These results reveal that curcumin protects against FZD induced oxidative stress, DNA injury and cell apoptosis via inhibiting oxidative stress and mitochondrial pathway, which may be attributed to ROS scavenging and anti-oxidative ability of curcumin. Importantly, our study highlights that curcumin may be a potential way to prevent FZD-mediated oxidative DNA injury and apoptosis in human or animals.
ARTICLE | doi:10.20944/preprints202004.0053.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: calcium signaling; chemokine signaling; gap junction; NOD-like receptor signaling; oli-neu cells; pannexin1; PI3K-Akt pathway; thyroid hormone pathway
Online: 6 April 2020 (12:36:20 CEST)
We profiled the transcriptomes of primary mouse cortical astrocytes cultured alone or co-cultured with immortalized precursor oligodendrocytes. The experimental set-up (insert systems) prevented formation of gap junction channels but allowed free exchange of the two culture media. The study complements our previously published reports that the genomic fabrics of major functional pathways in oligodendrocytes are substantially remodeled by the proximity of non-touching astrocytes. Here, we present new analysis indicating that the transcriptomic landscape of astrocytes likewise changes significantly in the proximity of non-touching oligodendrocytes. The research was stimulated by the reported transcriptomic similarity between the brains of Cx43KO and Cx32KO mice, both substantially different from that of the Cx36KO mice. Since the three connexins are expressed in different cell types (Cx43 in astrocytes, Cx32 in oligodendrocytes and Cx36 in neurons), altogether these findings support the idea of a “panglial transcriptomic syncytium” in the mouse brain. Going further, our results suggest that integration in a heterocellular tissue modulates not only the expression profile but also the expression control and networking of the genes in each cell phenotype.
ARTICLE | doi:10.20944/preprints202310.0736.v1
Subject: Medicine And Pharmacology, Complementary And Alternative Medicine Keywords: antiproliferation; apoptosis; breast cancer; chrysin; WNT/β-catenin pathway
Online: 11 October 2023 (13:23:48 CEST)
Chrysin, a flavonoid compound, has attracted interest as a therapeutic agent due to its anti-inflammatory, antidiabetic, antidepressant, and particularly its anticancer properties. Although studies have presented findings regarding the anticancer properties of chrysin, research on its molecular mechanisms of action remains largely insufficient. This research aimed to deeply investigate chrysin's effects on the breast cancer cell line, MDA-MB-231, in terms of proliferation, invasion, colony formation, and apoptosis. The XTT test results confirmed chrysin's cytotoxic effect on MDA-MB-231 cells, indicating a 48-hour IC50 value of 115.77 µM. Chrysin induced apoptosis in cells, as evidenced by Annexin V assay, and also reduced their colony-forming and invasion. Gene expression analyses showed elevated levels of APC, AXIN1, AXIN2, GSK3A, GSK3B, CK1α, CTNNB1, as well as apoptosis-related genes CASP3, -7, -9, and BAX. This increase was corroborated by the observed rise in protein levels of caspase 3/7 and GSK3B. Moreover, molecular docking results showed that chrysin interacted with genes in the WNT/β-catenin pathway and exhibited drug-like ADME properties. In conclusion, chrysin exhibits potential anticancer effects against MDA-MB-231 cells. It is hoped that these findings will advance preclinical and clinical studies on chrysin's potential in breast cancer treatment.
ARTICLE | doi:10.20944/preprints202308.1713.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: fresh-cut Gastrodia elata; melatonin; ROS metabolism; phenylpropanoid pathway
Online: 24 August 2023 (07:22:18 CEST)
The application of melatonin (MT) has been shown to improve the quality during the storage of fruits and vegetables. The primary objective of this study is to investigate the effects of MT on the quality of fresh-cut Gastrodia elata during low temperature (4°C) storage. The results indicate that MT treatment could suppress the respiratory rate and malondialdehyde content of fresh-cut G. elata, while also slowing down the decline in total acidity and total soluble solids. The treatment with MT reduced the superoxide anions and hydrogen peroxide production, inhibited the activity and expression of peroxidase and polyphenol oxidase. Additionally, it led to increased activity and expression of antioxidant-related enzymes, including superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase, monodehydroascorbate reductase, and dehydroascorbate reductase, while also resulted in elevated levels of ascorbic acid and glutathione. Furthermore, the treatment with MT induced an increase in total phenolic and flavonoid content of fresh-cut G. elata and enhanced the activity and expression of key enzymes involved in phenylpropanoid pathway (phenylalanine ammonia-lyase, cinnamate-4-hydroxylase, 4-coumarate: CoA ligase). In summary, MT enhances the antioxidant capacity by activating both ROS metabolism and phenylpropanoid pathway, thus maintaining the quality of fresh cut G. elata.
ARTICLE | doi:10.20944/preprints202308.0670.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: zebrafish; BMP4; antiviral innate immunity; IFN; p38 MAPK pathway
Online: 8 August 2023 (11:39:28 CEST)
Bone Morphogenetic Proteins (BMPs) are a group of structurally and functionally related signaling molecules that comprise a subfamily, belonging to the TGF-β superfamily. Most BMPs play roles in the regulation of embryonic development, stem cell differentiation, tumor growth and some cardiovascular and cerebrovascular diseases. Although evidences are emerging for the antiviral immunity of a few BMPs, more BMPs are needed to determine whether this function is universal. Here we identified the zebrafish bmp4 ortholog, whose expression is up-regulated by challenge with virus or its mimic poly(I:C). Overexpression of bmp4 in EPC cells significantly decreased the viral titer of GCRV-infected cells. Moreover, compared to wild type zebrafish, viral load and mortality were significantly increased in both larvae and adults of bmp4-/- mutant zebrafish infected with GCRV virus. We further demonstrated that Bmp4 promotes the phosphorylation of Tbk1 and Irf3 through p38 MAPK pathway, thereby inducing the production of type I IFNs in response to virus infection. These data suggest that Bmp4 runs an important role in the host defense against virus infection. Our study expands the understanding of BMP protein functions and opens up new targets for the control of viral infection.
ARTICLE | doi:10.20944/preprints202102.0602.v1
Subject: Medicine And Pharmacology, Orthopedics And Sports Medicine Keywords: Knee Osteoarthrit; miR-27b-3p; TrkB/CREB; pathway; BDNF
Online: 26 February 2021 (09:38:28 CET)
Knee Osteoarthritis (KOA) is a chronic disease characterized by progressive disability and joint pain. Meniscus chondrocytes apoptosis is the main cause of reduced chondrocyte number and self-repair function. The purpose of this study was to investigate the role of miR-27b-3p in KOA.In this study, we found that the expression of miR-27b-3p was downregulated in cultured IL-1β treated chondrocyte and cartilage tissues in KOA. KOA overexpression evidently reduced IL-1β induced chondrocyte apoptosis and caspase-3 and caspase-9 expression.The upregulated iNOS and COX-2 mRNA and proteins expression was also inhibited by miR-27b-3p mimics. The expression of nitric oxide, PGE2, TNF-α and IL-6 was also inhibited by miR-27b-3p mimics. The target gene of miR-27b-3p was confirmed to be BDNF. TrkB/CREB pathway was proved to be the downstream pathway of miR-27b-3p/BDNF axis.The apoptotic cell percentage and nitric oxide, PGE2, TNF-α and IL-6 expression was induced by BDNF+IL-1β. This induction was inhibited by miR-27b-3p mimics. The cartilage tissues stained with safranin O results showed miR-27b-3p greatly decreased KOA induced cartilage degradation. The expression of BDNF、TrkB and p-CREB was inhibited by len-miR-27b-3p. MiR-27b-3p also reduced the expression of TNF-α、IL-6 and Bax, and increased Bcl-2 expression. These results indicated miR-27b-3p could applied to inhibit the development of KOA and miR-27b-3p/BDNF/TrkB/CREB pathway could serve as novel treatment target to handle KOA.
ARTICLE | doi:10.20944/preprints202101.0130.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Geniposide; NF-ĸB; IEC-6; Signaling pathway; Cell migration
Online: 8 January 2021 (08:35:25 CET)
The nuclear factor-ĸB (NF-ĸB) transcriptional system is a major effector pathway involved in inflammatory responses. Previous studies found that a Gardenia decoction (GD) inhibited the expression of NF-κB in a lipopolysaccharide (LPS)-stimulated mouse intestinal injury model. Herein, we hypothesized that geniposide (GE), a component of Gardenia jasminoides Ellis, also exerts anti-inflammatory effects and inhibits NF-ĸB activity in LPS-induced intestinal epithelial cells (IEC-6). IEC-6 cells were stimulated with LPS, following which the effects of GE on NF-ĸB signaling in the IEC-6 cells were examined by western blotting to detect IĸB phosphorylation/degradation. The expression of NF-κB was determined by immunofluorescence assay (IFA). Enzyme-linked immunosorbent assay (ELISA) was used to detect the inhibitory effect of GE on the release of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interleukin-1β (IL-1β) activated by LPS in IEC-6 cells. In addition, the migration ability of IEC-6 cells was observed by the scratch method. These results showed that GE dose-dependently downregulated levels of the proinflammatory cytokines TNF-α, IL-6 and IL-1β that had been upregulated by LPS and suppressed the phosphorylation of IĸB and NF-ĸB induced by LPS. Our findings indicated that GE could reduce LPS-induced NF-ĸB signaling and proinﬂammatory expression in IEC-6 cells and significantly enhance the migration of IEC-6 cells. Moreover, GE inhibited the expression of NF-κB, nuclear transfer, and transcriptional activity in IEC-6 cells. GE could block the synthesis of inflammatory factors of IEC-6 cells by inhibiting activation of the IĸB/NF-κB signaling pathway induced by LPS.
ARTICLE | doi:10.20944/preprints202011.0497.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: ONC201; colorectal cancer cells; DDIT3; CHOP; BAK/BAX pathway
Online: 19 November 2020 (08:42:43 CET)
The imipramine ONC201 exerts a novel anti-proliferative activity over a wide spectrum of cancer cell types. ONC201 activates integrated stress response pathway that is associated with induction of Damage Inducible Transcript 3 (DDIT3, also known as C/EBP homologous protein or CHOP). We questioned whether the ONC201/CHOP crosstalk is regulated by diverse signaling pathways in non-metastatic versus metastatic cancer cell lines. Therefore, the Dukes' type B colorectal adenocarcinoma non-metastatic (SW480) and metastatic (LS-174T) cell lines were treated with ONC201. Cell proliferation and apoptosis were evaluated by MTT assay, flow cytometry analysis, gene expression was assessed by Affymetrix microarray, and key regulatory proteins were validated by Western blot assays. Unlike LS-174T cells, SW480 cells were resistant to ONC201 treatment. Gene ontology pathway enrichment analysis of differentially expressed genes revealed substantial differences between LS-174T and SW480 responsiveness to ONC201 treatment. In both cell lines, CHOP expression was upregulated in response to ONC201 treatment, however, its upstream regulatory mechanisms were not identical. Although, PERK, ATF6 and IRE1 ER-stress pathways were found to upregulated CHOP in both cell types, the BAK/BAX pathway was a notable regulator of CHOP in the metastatic LS-174T cells alone. In addition, CHOP RNA splicing profiles were varied between the two cell lines, which was further modified in response to ONC201 treatments. In conclusion, we delineated the signaling mechanisms regulating the expression of CHOP in non-metastatic versus metastatic colorectal cells in response to ONC201 treatment. The observed differences were related to cellular plasticity and metabolic reprogramming.
REVIEW | doi:10.20944/preprints202004.0294.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: signaling pathway; microRNA; long-noncoding RNA; chemoresistence; cervical cancer
Online: 17 April 2020 (08:12:52 CEST)
Cervical cancer is known as one of the most important cancers in women worldwide. Chemotherapy is a standard treatment for advanced/recurrent cervical cancer in which the prognosis of the disease is really poor and the 1-year survival chance in these patients is maximally 20%. However, resistance to anticancer drugs is a major problem in treating cancer. Cervical cancer stem cells are considered as a fundamental cause of chemo and radio-resistance and also relapse after primary successful treatment. Signaling pathways include a wide range of molecular mechanisms contribute to drug resistance. Recently, microRNAs (miRNAs) are announced as a group of molecular biomarkers involving in response to chemotherapy in cancer patients. As the miRNAs, there are some long non-coding RNAs (LncRNAs) which their aberrant expression is considered as a biomarker for monitoring chemoresistance. In this review, we summarized current reports about the involvement of signaling pathways during chemoresistance in cervical cancer. Then, genes that have been demonstrated their involvement during drug resistance in cervical cancer were tabulated. Further, miRNAs that have been reported as biomarkers during treatment are listed. By bioinformatic analysis, we predictedmiR-335-5p and miR-16-5p as the most potential biomarkers for monitoring resistance to chemotherapy. Finally, long non-coding RNAs that have been introduced in recent studies as novel biomarkers during the response to chemotherapy were mentioned.
ARTICLE | doi:10.20944/preprints201809.0274.v1
Subject: Chemistry And Materials Science, Food Chemistry Keywords: rice bran; rice genes; rice cultivars; metabolic pathway; metabolomics
Online: 15 September 2018 (19:34:43 CEST)
Rice (Oryza sativa L.) processing yields ~60 million metric tons of bran annually. Rice genes producing bran metabolites of nutritional and human health importance were assessed across 17 diverse cultivars from seven countries using non-targeted metabolomics and resulted in 378-430 metabolites. Gambiaka cultivar had the highest number and Njavara had the lowest number of metabolites. The 71 rice bran compounds of significant variation by cultivar included 21 amino acids, seven carbohydrates, two metabolites from cofactors and vitamins, 33 lipids, six nucleotides, and two secondary metabolites. Tryptophan, -ketoglutarate, γ-tocopherol/β-tocopherol and γ-tocotrienol are example bran metabolites with extensive cultivar variation and genetic information. 34 rice bran components that varied between cultivars linked to 535 putative biosynthetic genes using to the OryzaCyc 4.0, Plant Metabolic Network database. Rice genes responsible for bran composition with animal and human health importance is available for rice breeding programs to utilize in crop improvement.
ARTICLE | doi:10.20944/preprints201804.0158.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Cholera toxin; exosomes; endocytic pathway; Caveolin-1; GM1 ganglioside
Online: 12 April 2018 (05:58:31 CEST)
Here we first report, how cholera toxin (CT) A subunit (CTA), the bacterial enzyme moiety responsible of cell signaling alteration, can take over the exosomal pathway, spread extracellularly and be transmitted in a cell population. A first evidence for long-term transmission of CT toxic effect via extracellular vesicles was obtained in CHO cells. To follow CT intracellular route towards exosome secretion we adopted a strategy apt to convert multivesicular body (MVB) derived exosomes in traceable fluorescent vectors. CT treated Me665 cells, a human melanoma cell line highly expressing caveolin-1 (Cav-1) and GM1, were used to purify and characterize fluorescent exosomes. Our results clearly show association of CT with exosomes together with typical exosomal markers and the HSP90 and PDI molecules, the required membrane translocation elements of CTA to the cytoplasm. Confocal microscopy proved direct CT containing fluorescent exo transfer into CHO cells coupled with the morphological cell change characteristic of CT action. Moreover, direct assessment of cAMP levels in Me665 cells treated with CT containing exo showed an efficient induction of cAMP increase comparable with CT alone. From our results, we can infer that CT can exploit exosome-mediated cell communication to target and extend its pathophysiological action throughout cell tissues.
ARTICLE | doi:10.20944/preprints202310.1510.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Drosophila; signaling pathway; domesticated retroviral gag gene; immunity; ammonium persulphate
Online: 24 October 2023 (08:35:20 CEST)
Background: The molecular domestication of the gag gene of retrotransposons and retroviruses gave rise to the Gagr gene in the genome of Drosophila. The Gagr protein has a conservative structure in all Drosophila species, suggesting an essential function. As we previously shown, the Gagr gene may play a part in immune response and processes linked to stress reactions. Methods: Tub-GAL4>UAS-Gagr flies, which had the Gagr gene knockdown in all tissues, were compared with the control hybrid Tub-GAL4>w1118. Gagr gene function was verified by RNA-sequencing followed by RT-PCR and physiological tests. Results: In contrast to the control strain, we observed that flies with the Gagr gene knockdown had a shorter lifespan, but the mutant strain was more resistant to heat stress. Also, the Gagr knockdown strain had higher level of transcription of the immune response genes, according to a transcriptome analysis. It has been shown that the ammonium persulfate used to induce stress causes the Toll, Jal-STAT, and Jnk/MAPK signaling pathways to become activated, which results in a systemic response in numerus tissues in the control strain. Conversely, the Gagr gene mutant strain exhibits low expression of the stress response. Enrichment of the molecular function of genes overexpressed under ammonium persulfate stress in the control strain, but not in the Gagr knockdown mutant, revealed a category with 19 transcription factors involved in the control of organism development, morphogenesis and the functioning of the central nervous system. Their expression pattern and the Gagr gene's expression pattern match. The data obtained demonstrates the importance Gagr is to maintaining both the body's immune system and homeostasis.
ARTICLE | doi:10.20944/preprints202309.0531.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: pharmacogenomics; network analysis; multilayer networks; community detection; pathway enrichment analysis
Online: 7 September 2023 (11:49:09 CEST)
Over the years, network analysis became a promising strategy to analyze complex system, i.e. systems composed by a large number of interacting elements. In particular, multilayer networks have emerged as a powerful framework for modelling and analysing complex systems with multiple types of interactions. Network analysis can be applied to pharmacogenomics to gain insights into the interactions between genes, drugs, and diseases. By integrating network analysis techniques with pharmacogenomic data, the goal consists to uncover complex relationships and identify key genes to use in pathway enrichment analysis to figure out biological pathways involved in drug response and adverse reactions. In this study, we model omics, diseases and drugs data together through the multilayer network representation. Then, we mined the multilayer network with a community detection algorithm by obtaining top communities. After that, we used the identified list of genes from the communities to perform pathway enrichment analysis (PEA) to figure out the biological function affected form the selected genes. The results show that the genes forming the top community have the multiple roles through different pathways.
ARTICLE | doi:10.20944/preprints202306.1381.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: pre-hospital pathway; COVID-19; hospitalisation; healthcare system; pandemic preparedness
Online: 20 June 2023 (03:32:42 CEST)
Context. During the COVID-19 pandemic, patient care was mainly organised around the hospital. Pre-hospital care has, to our knowledge, never been evaluated. Objective: To evaluate the impact of pre-hospital pathways on hospitalisation during the last part of the pandemic. Design. This was a monocentric retrospective analysis of prospectively collected medical records. Data from patients admitted to our institute between 1 February and 7 March 2022 were analysed. Main Outcome Measure(s): The primary outcomes were defined as the number of hospitalisations, resuscitations, and deaths at the time of interview and in the subsequent 30 days. The main explanatory variables were times from onset of symptoms to care, age, gender, News2 score, comorbidities, and pre-hospital pathways and their duration. Results: Three pre-hospital pathways have been identified: a pathway in which the patient consults a general practitioner for a test (PHP1); a pathway in which the patient consulted for care (PHP2); and no pre-hospital pathway and direct admission to hospital (PHP3). Factors independently associated with outcome (hospitalisation) were being male (OR 95% CI; 2.21 [1.01–4.84], p=0,04), News2 score (OR 95% CI; 2.04 [1.65–2.51], p<0.001), obesity (OR 95% CI; 3.45 [1.48–8.09], p=0.005), D-dimers > 0.5 µg/ml (OR 95% CI; 3.45 [1.47–8.12], p=0.005), prolonged time from symptoms to hospital care (PHP duration) (OR 95% CI; 1.07 [1.01–1.14], p=0.03). All things being equal, patients with a “PHP2” pre-hospital pathway had a higher probability of hospitalisation compared to those with a “PHP3” pre-hospital pathway (OR 95% CI; 4.31 [1.48–12.55], p=0.007). Conclusions. Along with recognised risk factors such as gender, News 2 score, and obesity, the patient’s pre-hospital pathway is an important risk factor associated with hospitalisation.
ARTICLE | doi:10.20944/preprints202305.1304.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: drug resistance; cisplatin; arsenic; tumor microenvironment; microRNA; molecular pathway network
Online: 18 May 2023 (08:41:46 CEST)
To reveal the relationship between metallodrugs and cancer malignancy, molecular networks of anti-cancer drugs were analyzed. Molecular networks in several types of cancers were analyzed in Ingenuity Pathway Analysis (IPA). Analysis of carboplatin revealed the causal network in diffuse large B-cell lymphoma. Analysis of 12 analyses of cisplatin treatment identified causal networks including camptothecin and NUPR1. The causal network of camptothecin, which includes PTEN, FAS, and IRF1, was inactivated in diffuse-type GC and activated in intestinal-type GC. Upstream regulator analysis of cisplatin revealed an increase in FAS, BTG2, SESN1 and CDKN1A, and the involvement of the tumor microenvironment pathway. Upstream regulators of cisplatin-treated lung adenocarcinoma included a histone deacetylase inhibitor, trichostatin A (TSA). Causal network of arsenic was inactivated in diffuse-type GC and activated in intestinal-type GC, and included ERK, EGFR, SRC, IKK and TP53. Prediction of RNA-RNA interactions with the causal network of arsenic identified 10 microRNAs including mir-101, mir-103, and mir-22. The results revealed the involvement of EMT in arsenic treatment. Analysis of oxaliplatin, a platinum drug, revealed that the SPINK1 pancreatic cancer pathway is inactivated in ischemic cardiomyopathy. The study showed the importance of the relationship between platinum drugs or arsenic trioxide and the tumor microenvironment in the treatment of resistant cancer in humans.
ARTICLE | doi:10.20944/preprints202302.0099.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: manganese; cGAS-STING pathway; RNA virus; antiviral function; redundant mechanisms
Online: 6 February 2023 (10:01:21 CET)
The innate immune system is the first line of host defense sensing viral infection. Manganese (Mn) has recently been found to be involved in the activation of innate immune DNA sensing cGAS-STING pathway and subsequent anti-DNA virus function. However, whether Mn2+ mediates host defense against RNA viruses is still unclear. In the current study, we demonstrated that Mn2+ exhibited antiviral effects against various animal and human viruses including RNA viruses such as PRRSVs and the VSV as well as a DNA virus such as the HSV1 in a dose-dependent manner. Moreover, cGAS and STING were both investigated in the Mn2+ mediated antiviral roles using the knockout cells made by CRISPR-Cas9 approach. Unexpectedly, the results revealed that neither cGAS knockout nor STING knockout had any effect on Mn2+ mediated antiviral functions. Nevertheless, we verified that Mn2+ promoted the activation of cGAS-STING signaling pathway. These findings suggest that Mn2+ has broad spectrum antiviral activities in a cGAS-STING pathway independent manner. This study also provides significant insights into redundant mechanisms participating in the Mn2+ antiviral functions and also indicates new target for Mn2+ antiviral therapeutics.
ARTICLE | doi:10.20944/preprints202206.0385.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: UxuR; ExuR; Ashwell pathway; uxuAB; fliC; proteome; motility; biofilm formation
Online: 28 June 2022 (10:42:44 CEST)
ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to the uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in significantly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and inhibition of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins.This suggests that the roles of proteins predicted as homologs are far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate activation of both was not so prominent. During growth on glucose, the maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests thus suggesting involvement of UxuR in the regulation of bacterial motility and biofilm formation.
ARTICLE | doi:10.20944/preprints202201.0359.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: JAK/STAT3 signaling pathway; Meridianin derivatives; Isothiouronium; Anti-tumor activity
Online: 24 January 2022 (14:06:38 CET)
Hyperactivation of Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) signaling is an attractive therapeutic target for tumor therapy. Herein, forty-eight novel meridianin derivatives were designed and synthesized, and their anti-tumor activity were evaluated in vitro both for activity optimization and structure-activity relationship (SAR) study. The results indicated that most derivatives exhibited significantly improved anti-tumor activity, especially for compound 6e. The compound 6e contains an isothiouronium linked by an alkyl chain consisting of 6 carbon atoms with IC50 ranging from 1.11 to 2.80 μM on various cancer cell lines. Consistently, 6e dose dependently induced the apoptosis of A549 and DU145 cells, in which STAT3 are constitutively active. Western blotting assays indicated that the phosphorylation levels of JAK1, JAK2 and STAT3 were inhibited by 6e at 5 μM without significant change in total STAT3 level. Moreover, 6e also suppressed the expressions of STAT3 downstream genes, including c-Myc, Cyclin D1 and Bcl-XL at 10 μM. An additional in vivo study revealed that 6e at the dose of 10 mg/kg could potently inhibit the DU145 xenograft tumor without obvious body-weight loss. These results clearly indicate that 6e could be a potential anti-tumor agent by targeting JAK/STAT3 signaling pathway.
ARTICLE | doi:10.20944/preprints202109.0105.v1
Subject: Medicine And Pharmacology, Obstetrics And Gynaecology Keywords: endometrial cancer; tumor microenvironment; Wnt/β-catenin pathway; SATB1; SATB2
Online: 6 September 2021 (14:29:35 CEST)
Wnt/β-catenin signaling pathway plays an established role in various diseases and is considered a hallmark of endometrial cancer (EC). Special AT-rich sequence-binding protein 1 and 2 (SATB1 and SATB2) are nuclear matrix-associated proteins involved in chromatin remodeling and regulation of gene expression. SATB1 promotes the progression of numerous types of cancers, whereas SATB2 acts as a tumor suppressor. Despite a recent progress in our knowledge about EC, the exact mechanisms that control their proliferation and metastatic potential still remain unknown. The aim of our study was to investigate the association between Wnt3A, β-catenin, SATB1 and SATB2 protein level and the clinicopathological features of EC patients. 92 EC patients, aged 37-84, were enrolled to our study. The immunoexpression of WNT3A was found in specimens from all EC patients, β-catenin was expressed in 97% of the cases, SATB1 in 87%. The significant association between Wnt3a expression and tumor grade was found; moreover mean IRS for Wnt3a turned out to be significantly lower in high-grade tumors than in low-grade malignancies (p=0.038). In turn, immunoexpression of β-catenin varied significantly across FIGO stages and was associated with the presence of lymph node metastases. Mean IRS for β-catenin in patients with lymph node metastases was significantly lower than in those without (p = 0.028). The Kaplan-Meier analyses demonstrated a stepwise impairment of cancer overall survival with increasing SATB1 expression. In conclusion, both Wnt/β-catenin signaling pathway and SATB1 contribute to progression of EC. Downregulation of β-catenin may predispose to lymphatic spread of EC. In turn, downregulation of Wnt3a seems to be characteristic for high-grade tumors, but probably does not play a role in formation of lymph node metastases. The important role of SATB1 as a predictor of poor survival and could be helpful in establishing a more accurate prognosis in endometrial cancer patients.
Subject: Business, Economics And Management, Accounting And Taxation Keywords: course pathway modeling; student-centered classroom; course evaluation; course design
Online: 10 February 2021 (09:01:23 CET)
Student-centered teaching practices such as active learning continue to gain momentum in college science education. Many instructors committed to these innovative practices transform their classroom beyond the standard lecture. Nevertheless, widespread implementation of these practices is limited because the learning benefits for students are often attained through increased instructional complexity to which many instructors cannot commit. When co-instructors are teaching the course, the level of commitment to building a student-centered classroom may be even more profound. For these reasons, new tools are needed to help instructors and co-instructors plan, organize, evaluate, and communicate their classroom innovations. Pathway modeling is a tool with potential to fill this gap. Unlike curriculum mapping -- which identifies academic content gaps, redundancies, and misalignments by examining a series of courses within a plan of study – course pathway modeling creates a visual map of a single course and reveals how teaching practices influence short-, mid-, and long-term student learning outcomes. This essay demonstrates how course pathway modeling can help co-instructors better represent the complexity of student-centered teaching practices. We include guides for creating course pathway models and discuss how this approach offers the potential to improve curricular design, course evaluation, student assessment, and communication between co-instructors.
REVIEW | doi:10.20944/preprints202010.0338.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Urothelial carcinoma; immune checkpoint inhibitors; immunotherapy; tumor microenvironment; metabolic pathway
Online: 16 October 2020 (08:00:41 CEST)
Cisplatin-based chemotherapy has long been viewed as the first-line chemotherapy for advanced and metastatic urothelial carcinoma (UC). However, many patients with UC have been classified as “cisplatin-ineligible patient”, which requires alternative chemotherapy due to their poor responses. In fact, vast majority of those who initially responded to cisplatin-based chemotherapy eventually progressed. Understanding of UC tumor immunology provided an immunopathogenic bases for immune checkpoint inhibitors, targeting PD-1 and CTLA-4, to treat cisplatin ineligible metastatic UC and patients with platinum-refractory metastatic UC. In 2020, data from the trail further showed that PD-L1 inhibitors benefit prolonged survival and progression-free survival as maintenance therapy. Besides immune-targeting therapies, manipulation of tumor microenvironment via metabolic pathways alternation, such as inhibiting tumor glycolysis, lactate accumulation and exogenous glutamine uptake, has been investigated in the past few years. In this comprehensive review, we started by introducing traditional chemotherapy of UC, and summarized current evidences supporting the use of immune checkpoint inhibitors and highlighted ongoing clinical trials. Lastly, we reviewed the tumor metabolic characteristic and the anti-tumor treatments targeting metabolic pathways.
Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; COVID-19; coronavirus; signaling pathway; molecular alteration
Online: 21 September 2020 (04:17:24 CEST)
Emerging viruses description have grown at an unprecedented rate since the beginning of the 21st century. The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its related illness, Coronavirus Disease 2019 (COVID-19) has been reported as the third highly pathogenic coronavirus introducing itself into human population in the current era after the SARS-CoV and Middle East Respiratory Syndrome (MERS-CoV). Molecular and cellular studies considering the pathogenesis of this novel coronavirus are still in the early stages of research, however, regarding the similarity of SARS-CoV-2 and other coronaviruses, it could be hypothesized that the NF-κB, Cytokine regulation, ERK, and TNF-α signaling pathways are the more likely causes of inflammation upon onset of COVID-19. There are several drugs prescribed and used to alleviate the activity of these inflammatory cellular signaling pathways which might be beneficial for developing novel therapeutic modalities against COVID-19. In this review, we briefly summarized the alteration of cellular signaling pathways affected by coronavirus infection, particularly SARS-CoV and MERS-CoV and tabulated the current therapeutic agents approved for previous human diseases.
REVIEW | doi:10.20944/preprints202008.0699.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: heterologous production; shikimic acid pathway; phenolic acids; flavonoids; anthocyanins; stilbenes
Online: 31 August 2020 (05:02:19 CEST)
Secondary phenolic metabolites are defined as valuable natural products synthesized by different organisms that are not essential for growth and development. These compounds play an essential role in plant defense mechanisms, and an important role in the pharmaceutical, cosmetics, food, and agricultural industries. Despite the vast chemical diversity of natural compounds, their content in plants is very low, in consequence, it eliminates the possibility of the production of these interesting secondary metabolites from plants. Therefore, microorganisms are widely used as cell factories by industrial biotechnology to the production of different non-native compounds. Among microorganisms commonly used in biotechnological applications, yeasts are prominent host for the diverse secondary metabolite biosynthetic pathways. Saccharomyces cerevisiae is often regarded as the better host organism for the heterologous production of phenolics compounds, especially if the expression of different plant genes is necessary.
REVIEW | doi:10.20944/preprints202007.0123.v1
Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: causal interactions; databases; interoperability; biological pathway; logical modeling; computational biology
Online: 7 July 2020 (09:50:40 CEST)
Causal molecular interactions represent key building blocks used in computational modeling, where they facilitate the assembly of regulatory networks. These regulatory networks can then be used to predict biological and cellular behavior by system perturbations and in silico simulations. Today, broad sets of these interactions are being made available in a variety of biological knowledge resources. Moreover, different visions, based on distinct biological interests, have led to the development of multiple ways to describe and annotate causal molecular interactions. Therefore, data users can find it challenging to efficiently explore resources of causal interaction and to be aware of recorded contextual information that ensures valid use of the data. This manuscript presents a review of public resources collecting causal interactions and the different views they convey, together with a thorough description of the export formats established to store and retrieve these interactions. Our goal is to raise awareness amongst the targeted audience, i.e., logical modelers, but also any scientist interested in molecular causal interactions, about existing data resources and how to get familiar with them.
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: neural differentiation; regulatory motif; feedback regulation; signaling pathway; mathematical models
Online: 24 December 2019 (11:20:25 CET)
Computational simulation using mathematical models is a useful method for understanding the complex behavior of a living system. The majority of studies using mathematical models to reveal biological mechanisms uses one of the two main approaches: the bottom-up or the top-down approach. When we aim to analyze a large-scale network, such as a comprehensive knowledge-integrated model of a target phenomenon, for example a whole-cell model, the variation of analyses is limited to particular kind of analysis because of the size and complexity of the model. To analyze a large-scale regulatory network of neural differentiation, we developed a hybrid method that combines both approaches. To construct a mathematical model, we extracted network motifs, subgraph structures that recur more often in a metabolic network or gene regulatory network than in a random network, from a large-scale regulatory network, detected regulatory motifs among them, and combined these motifs. We confirmed that the model reproduced the known dynamics of HES1 and ASCL1 before and after differentiation, including oscillation and equilibrium of their concentrations. The model also reproduced the effects of overexpression and knockdown of the Id2 gene. Our model suggests that the characteristic change in HES1 and ASCL1 expression in the large-scale regulatory network is controlled by a combination of four feedback loops, including a large loop which has not been focused on. The model extracted by our hybrid method has the potential to reveal the critical mechanisms of neural differentiation. The hybrid method is applicable to other biological events.
ARTICLE | doi:10.20944/preprints201910.0063.v1
Subject: Biology And Life Sciences, Plant Sciences Keywords: lilium sp.; in vitro protocol; conventional pathway; bulb production; timeline
Online: 7 October 2019 (11:16:43 CEST)
Lily–belong to the genus Lilium is one of the top cut flowers worldwide. Production and propagation of bulblets in vitro is an important approach for high-volume production, but not proved satisfactory. Hence, the aim of this study was to describe and compare the performances of morphological characteristics of the lily bulb in vivo produced by in vitro and conventional culture method and compare the production timelines in vitro vs conventional culture method. In results, it seems clear that in vitro re-culture of lily bulblet was able to be sustained and maintained its growth and so, ontogenic development after their performance in soil. Our results demonstrate that in the conventional pathway, the course of bulblet growth to bulb and ontogenic development took 3–4 growing seasons to reach the adult flowering phase. On the other hand, along with the re-culture in vitro, the course of bulb growth and ontogenic development took 1–2 growing seasons to reach the adult flowering phase because of the increasing initial bulb size and advancement of ontogenic development. Other than bulblet production through bulb scale explant, this study represents the first report on the method of in vitro bulb production of lily through re-culture by in vitro pathway with a comparison of the timelines and ontogenic development obtained from in vitro versus conventional pathway.
REVIEW | doi:10.20944/preprints202308.1473.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Mob4,; Cell proliferation, neurogenesis, spermatogenesis, Hippo pathway, STRIPAK, MOB-like protein
Online: 21 August 2023 (12:12:00 CEST)
Signaling modules that integrate the diverse extra- and intracellular inputs to control cell proliferation are essential during both development and adult stages to guarantee organism homeostasis. Mobs are small adaptor proteins that participate in several of these signalling pathways. Here we review recent advances unraveling Mob4 cellular functions, a highly conserved non-catalytic protein, that plays a diversity of roles in cell proliferation, sperm cell differentiation and simultaneously is involved in synapse formation and neural development. In addition, the gene is often overexpressed in a wide range of tumors and is linked to poor clinical outcomes. Nevertheless, Mob4 molecular functions remain poorly defined, although it integrates the core structure of STRIPAK, a kinase/phosphatase protein complex, that can act upstream of the Hippo pathway. In this review we focus on the recent findings of Mob4 functions, that have begun to clarify its critical role on cell proliferation and development of tissues and individuals.
ARTICLE | doi:10.20944/preprints202303.0355.v1
Subject: Arts And Humanities, Literature And Literary Theory Keywords: glioblastoma; biomarker selection; metabolomics; pathway analysis; personalized therapy; network analysis; inflammationomics
Online: 20 March 2023 (09:09:49 CET)
The most aggressive primary malignant brain tumor in adults is glioblastoma (GBM), which has poor overall survival (OS). There is a high relapse rate among patients with GBM despite maxi-mally safe surgery, radiation therapy, temozolomide (TMZ), and aggressive treatment. Hence, there is an urgent and unmet clinical need for new approaches to managing GBM. The current study identified modules (MYC, EGFR, PIK3CA, SUZ12, and SPRK2) involved in GBM disease through the NeDRex plugin. Furthermore, hub genes were identified in a comprehensive interaction network containing 7,560 proteins related to GBM disease and 3,860 proteins associated with signaling pathways involved in GBM. By integrating the results of the aforementioned analyses and performing centrality analysis again, eleven key genes involved in GBM disease were identi-fied. ProteomicsDB or Gliovis databases were used for determining the gene expression in normal or tumor brain tissue. The NetworkAnalyst and the mGWAS-Explorer tools identified miRNAs, SNPs, and metabolites associated with these 11 genes. Moreover, a literature review of recent studies revealed other lists of metabolites related to GBM disease. The enrichment analysis of iden-tified genes, miRNAs, and metabolites associated with GBM disease was done using ExpressAna-lyst, miEAA, and MetaboAnalyst tools. Further investigation of metabolite roles in GBM was done through the pathway, joint pathway, and network analyses. The results of this study identified 11 genes (UBC, HDAC1, CTNNB1, TRIM28, CSNK2A1, RBBP4, TP53, APP, DAB1, PINK1, and RELN), five miRNAs (hsa-mir-221-3p, hsa-mir-30a-5p, hsa-mir-15a-5p, hsa-mir-130a-3p, hsa-let-7b-5p), six metabolites (HDL, N6-acetyl-L-lysine, cholesterol, formate, N, N-dimethylglycine/xylose and X2. piperidinone) and 15 distinct signaling pathways that play an indispensable role in the GBM disease development. To establish early diagnostic methods and plan personalized GBM treatment strategies, the identified top genes-miRNAs and metabolite signatures can be targeted.
REVIEW | doi:10.20944/preprints202207.0436.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: SUMO; MSC; osteoblast; chondrocyte; osteoclast; signaling pathway; arthritis; osteosarcoma; developmental disorders
Online: 28 July 2022 (09:04:33 CEST)
The modification of proteins by small ubiquitin-related modifier (SUMO) molecules, SUMOylation, is a key post-translational modification involved in a variety of biological processes such as chromosomes organization, DNA replication and repair, transcription, nuclear transport, and cell signaling transduction. In recent years, emerging evidence has shown that SUMOylation regulates the development and homeostasis of the skeletal system, with its dysregulation causing skeletal diseases, suggesting that SUMOylation pathways may serve as a promising therapeutic target. In this review, we summarize the current understanding of the molecular mechanisms by which SUMOylation pathways regulate skeletal cells in the physiological and disease contexts.
REVIEW | doi:10.20944/preprints202110.0026.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Halotolerant/halophilic fungi; Hortaea werneckii; Wallemia ichthyophaga; HOG signal transduction Pathway
Online: 1 October 2021 (14:52:54 CEST)
Sensing and responding to changes in NaCl concentration in hypersaline environments is vital for cell survival. We have identified and characterized key components of the high-osmolarity glycerol (HOG) signal transduction pathway, which is crucial in sensing hypersaline conditions in the extremely halotolerant black yeast Hortaea werneckii and in the obligate halophilic fungus Wallemia ichthyophaga. Both organisms were isolated from solar salterns, their predominating ecological niche. The identified components included homologous proteins of both branches involved in sensing high osmolarity (SHO1 and SLN1) and the homologues of mitogen-activated protein kinase module (MAPKKK Ste11, MAPKK Pbs2, and MAPK Hog1). Functional complementation of the identified gene products in S. cerevisiae mutant strains revealed some of their functions. Structural protein analysis demonstrated important structural differences in the HOG pathway components between halotolerant/halophilic fungi isolated from solar salterns, salt-sensitive S. cerevisiae, the extremely salt-tolerant H. werneckii, and halophilic W. ichthyophaga. Known and novel gene targets of MAP kinase Hog1 were uncovered particularly in halotolerant H. werneckii. Molecular studies of many salt-responsive proteins confirm unique and novel mechanisms of adaptation to changes in salt concentration.
Subject: Chemistry And Materials Science, Biomaterials Keywords: bismuth selenide nanoparticles; photothermal killing; apoptosis; autophagy; stress-related signaling pathway
Online: 10 May 2021 (10:52:30 CEST)
With a highly efficient optical absorption capability, bismuth selenide (Bi2Se3) nanomaterial can be used as an outstanding photothermal agent for anti-tumor treatment and shows promise in the field of nanotechnology-based biomedicine. However, little research has been done on the relevant mechanism underlying the photothermal killing effect of Bi2Se3 nanomaterial. Herein, the photothermal effects of Bi2Se3 nanoparticles on A549 cells were explored with emphasis put on autophagy. Firstly, we characterized the structure and physicochemical property of the synthesized Bi2Se3 and confirmed their excellent photothermal conversion efficiency (35.72%), photostability, biocompatibility and ability of photothermal killing on A549 cells. Enhanced autophagy was detected in Bi2Se3-exposed cells under an 808 nm laser. Consistently, an elevated expression ratio of LC3-II to LC3-I, a marker of autophagy occurrence, was induced in Bi2Se3-exposed cells upon NIR irradiation. Meanwhile, the expression of cleaved-PARP was increased in the irradiated cells dependently on the exposure concentrations of Bi2Se3 nanoparticles. Pharmacological inhibition of autophagy by 3-methyladenine (3-MA) further strengthened the photothermal killing effect of Bi2Se3. Meanwhile, stress-related signaling pathways including p38 and SAPK/JNK were activated coupled with the attenuated PI3K/Akt signaling. Our study figures out that autophagy and the activation of stress-related signaling pathways were involved in the photothermal killing of cancerous cells by Bi2Se3, which provides a more understanding of photothermal nanomaterials.
REVIEW | doi:10.20944/preprints202008.0455.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Hedgehog signaling pathway; GLI family; protein arginine methyl transferase; signal transduction
Online: 20 August 2020 (09:58:05 CEST)
The glioma-associated oncogene (GLI) family consists of GLI1, GLI2, and GLI3 in mammals, and is the effector in the Hedgehog signaling pathway. This family has important roles in the development and homeostasis of various tissues. To achieve these roles, the GLI family has widespread outputs. GLI activity is therefore strictly regulated at multiple levels, including via post-translational modifications for context-dependent GLI target gene expression. Conversely, dysregulated GLI activation has strong links with a variety of cancers. The protein arginine methyl transferase (PRMT) family is also associated with embryogenesis, homeostasis, and cancer via epigenetic modifications and signal transduction. In the PRMT family, PRMT1, PRMT5, and PRMT7 reportedly regulate GLI1 and GLI2 activity. PRMT1 methylates GLI1 to upregulate its activity and target gene expression. Cytoplasmic PRMT5 methylates GLI1 and is involved in GLI1 protein stabilization. In contrast, nucleic PRMT5 interacts with MENIN to suppress growth arrest-specific protein 1 expression, which assists Hedgehog ligand binding to Patched, indirectly resulting in downregulated GLI1 activity. PRMT7-mediated GLI2 methylation upregulates its activity through the dissociation of GLI2 and Suppressor of Fused. Therefore, PRMT1, PRMT5, and PRMT7 regulate GLI activity at multiple levels, and PRMT-mediated GLI dysregulation may be involved in cancer formation.
ARTICLE | doi:10.20944/preprints201909.0045.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Prostate cancer, post-GWAS, functional variants, pathway analysis, upstream analysis, Oncomine
Online: 4 September 2019 (14:13:15 CEST)
Understanding the role of risk regions identified by genome-wide association studies (GWAS) have made considerable progress lately referred to the post-GWAS era. Annotation of the genes to the GWAS and fine-mapped functional variants, and understanding their biological pathway/gene networks enrichments is expected to give rich dividend by elucidating the mechanisms underlying prostate cancer. To this aim, we compiled and analysed currently available post-GWAS data on genes identified through GWAS and validated through experimental studies in prostate cancer to investigate molecular biological pathways enriched for assigned functional genes. The results highlight some well-known cancer signalling pathways, antigen presentation process and enrichment in cell growth and development gene networks suggesting prostate cancer may result from the accumulation of the effects of functional variants through multiple gene sets and pathways. The upstream analysis identifies critical transcription factors, which supplements the results regarding the regulatory role of the post-GWAS genes. We also identified the common genes between post-GWAS and three well-annotated prostate cancer Oncomine data in patient samples in order to uncover possible main genes in prostate cancer development/progression. Post-GWAS generated knowledge of gene networks and pathways, if analysed further and targeted appropriately, will have an important impact on clinical management of the disease.
ARTICLE | doi:10.20944/preprints201802.0013.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: pancreatic cancer; proteomics; PI3K pathway; precision medicine; predictor of therapeutic response
Online: 2 February 2018 (06:57:47 CET)
In metastatic pancreatic cancer patients non eligible to surgery, signal-targeted therapies so far failed to show a significant amelioration of survival. These therapeutic options were tested in Phase II/III clinical trials mostly in combination with the reference treatment Gemcitabine. These innovative therapies aim at annihilating the oncogene dependency; they also aim at renormalizing the tumoral stroma to allow immune cell function or re-vascularisation. Transcriptomics and genomics large scale analysis show the great heterogeneity of pancreatic cancers and failed to clearly delineate specific oncogene dependency besides oncogenic Kras. In this review, we will describe the most recent proteomic data in pancreatic tumors and its metastasis, which could help at identifying their major signalling dependencies, as well as explain why they are intrinsically resistant to signal-targeted therapies. We will also discuss why PI3K signalling, as a paradigm of pro-tumorigenic cell signalling and of tumoral adaptative resistance to drugs, is a relevant target in this context.
REVIEW | doi:10.20944/preprints201802.0011.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Pancreatic cancer, proteomics, PI3K pathway, precision medicine, predictor of therapeutic response
Online: 1 February 2018 (17:16:04 CET)
In metastatic pancreatic cancer patients non eligible to surgery, signal-targeted therapies so far failed to show a significant amelioration of survival. These therapeutic options were tested in Phase II/III clinical trials mostly in combination with the reference treatment Gemcitabine. These innovative therapies aim at annihilating the oncogene dependency; they also aim at renormalizing the tumoral stroma to allow immune cell function or re-vascularisation. Transcriptomics and genomics large scale analysis show the great heterogeneity of pancreatic cancers and failed to clearly delineate specific oncogene dependency besides oncogenic Kras. In this review, we will describe the most recent proteomic data in pancreatic tumors and its metastasis, which could help at identifying their major signalling dependencies, as well as explain why they are intrinsically resistant to signal-targeted therapies. We will also discuss why PI3K signalling, as a paradigm of pro-tumorigenic cell signalling and of tumoral adaptative resistance to drugs, is a relevant target in this context.
ARTICLE | doi:10.20944/preprints201706.0120.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: sinulariolide; human bladder cancer; migration; invasion; PI3K/AKT/mTOR signaling pathway
Online: 27 June 2017 (06:23:44 CEST)
Sinulariolide, a natural product extracted from cultured-type soft coral Sinularia flexibilis, possesses bioactivity against the movement of several types of cancer cell. However, the molecular pathway of its effects on human bladder cancer remain poorly understood. Using a human bladder cancer cell line as an in vitro model, this study investigated the underlying mechanism of sinulariolide against cell migration/invasion in TSGH-8301 cells. We found that sinulariolide inhibited TSGH-8301 cell migration/invasion, and the effect was concentration-dependent. Furthermore, the protein expressions of matrix metalloproteinases (MMPs) MMP-2 and MMP-9, as well as urokinase, were significantly decreased after 24-h sinulariolide treatment. Meanwhile, the increased expressions of tissue inhibitors of metalloproteinases (TIMPs) TIMP-1 and TIMP-2 were in parallel with an increased concentration of sinulariolide. Finally, the expressions of several key phosphorylated proteins in the mTOR signaling pathway were also downregulated by sinulariolide treatment. Our results demonstrated that sinulariolide has significant effects against TSGH-8301 cell migration/invasion, and its effects were associated with decreased levels of MMP-2/-9 and urokinase expression, as well as increased TIMP-1/TIMP-2 expression. The inhibitory effects were mediated by reducing phosphorylation proteins of the PI3K, AKT and mTOR signaling pathway. The findings suggested that sinulariolide is a good candidate for advanced investigation with the aim of developing a new drug for the treatment of human bladder cancer.
ARTICLE | doi:10.20944/preprints201609.0074.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: hepatocellular carcinoma; hepatitis B virus X protein; Notch1 pathway; ERK; AKT
Online: 21 September 2016 (09:49:13 CEST)
Hepatitis B virus (HBV) is the dominant risk factor for hepatocellular carcinoma (HCC). HBV X protein (HBx) plays crucial roles in HCC carcinogenesis. HBx interferes with several signaling pathways including Notch1 pathway in HCC. In our study, we found that Notch1 was highly expressed in HCC especially in large HCC. Notch1 and HBx co-localized in HCC and their levels were positively correlated with each other. Notch1 expression was more elevated in HepG2.2.15 than that in HepG2. HBx activated Notch1 pathway in HepG2.2.15. Repression of HBx and Notch1 pathway attenuated the growth of HepG2.2.15. Notch1, ERK and AKT pathways were inhibited after a γ-secretase inhibitor treatment. Dual-specificity phosphatase 1 (DUSP1) and phosphatase and tensin homolog (PTEN) were up-regulated after the γ-secretase inhibitor treatment and Hes1 inhibition. Luciferase reporter assays showed that Hes1 repressed the promoters of DUSP1 and PTEN and this was reverted by γ-secretase inhibitor treatment. Western blotting demonstrated that DUSP1 dephosphorylated pERK and PTEN dephosphorylated pAKT. Collectively, we reported a link among HBx, Notch1 pathway, DUSP1/PTEN, and ERK/AKT pathways, which influenced HCC cell survival and could be a therapeutic target for HCC.
REVIEW | doi:10.20944/preprints202307.1175.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: ω-Amidase; L-glutamine; L-glutamate; L-glutamine addiction; glutaminase II; GLS1; GLS2; glutamine transaminase; GTωA pathway; α-ketoglutaramate; α-ketoglutarate; asparaginase II pathway; asparaginase, α-ketosuccinamate
Online: 18 July 2023 (08:55:27 CEST)
Many cancers utilize L-glutamine as a major energy source. This “L-glutamine addiction” involves a well-characterized pathway whereby L-glutamine is hydrolyzed by a glutaminase (GLS) to L-glutamate, which is then converted to α-ketoglutarate, the carbons of which enter the tricarboxylic acid (TCA) cycle. However, mammalian tissues/cancers possess a rarely mentioned alternative pathway (the glutaminase II pathway): L-Glutamine is transaminated to α-ketoglutaramate (KGM), followed by ω-amidase (ωA)-catalyzed hydrolysis of KGM to α-ketoglutarate. Uncertainty may prevail over the name glutaminase II which may be confused with the enzyme named glutaminase 2 (GLS2). Thus, we recently suggested a new name for the glutaminase II pathway, namely the glutamine transaminase-ω-amidase (GTωA) pathway. Herein, we 1) evaluate three recent articles that mention L-glutamine addiction, but not the GTωA pathway, 2) summarize the metabolic importance of the GTωA pathway, including its role in closing the methionine salvage pathway, and 3) as a source of anaplerotic α-ketoglutarate. An advantage of the GTωA pathway [i.e., L-glutamine + α-keto acid + H2O α-ketoglutarate + L-amino acid + +NH4] is that it is irreversible and that there is no net change in redox status, permitting α-ketoglutarate production during hypoxia. Finally, we discuss possible clinical benefits of GTωA pathway inhibitors.
REVIEW | doi:10.20944/preprints202310.0988.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: Colorectal cancer stem cells; LGR5; Wnt signaling pathway; Single-cell omics technology
Online: 17 October 2023 (05:48:24 CEST)
Once discovered, cancer stem cells have become a hot topic in the research of cancer therapy. These cells possess stem cell-like self-renewal and differentiation capacities and are important factors that dominate cancer metastasis, therapy- resistance and recurrence. What's worse, their own characteristics make them difficult to be eliminated. Colorectal cancer is the third most common cancer and the second leading cause of cancer death worldwide. Targeting colorectal cancer stem cells (CRCSCs) can inhibit colorectal cancer metastasis, enhance therapeutic efficacy, and reduce recurrence. Here, we introduced the origin, marker proteins, identification, cultivation and research techniques of CRCSCs, summarized the signaling pathways that regulate the stemness of CRCSCs, such as Wnt, JAK/STAT3, Notch, and Hh signaling pathway. In addition to these, we also reviewed anti-CRCSC drugs targeting signaling pathways，markers，and other regulators in recent years. These will help researchers gain insight into the current agents targeting to CRCSCs, explore new cancer drugs, and propose potential therapy.
BRIEF REPORT | doi:10.20944/preprints202307.2067.v1
Subject: Biology And Life Sciences, Aquatic Science Keywords: Litopenaeus vannamei; Suppressor of cytokine signaling; Gene expression; JAK-STAT signaling pathway
Online: 31 July 2023 (10:48:31 CEST)
Suppressors of cytokine signaling (SOCS) genes are essential negative regulators that modulate cytokine signaling and play key roles in numerous biological processes, including immune responses. In this study, we cloned the complementary DNA (cDNA) sequences of two SOCS genes, designated as LvSOCS6 and LvSOCS7, from the white-leg shrimp, Litopenaeus vannamei. LvSOCS6 encoded a polypeptide of 463 amino acids (aa), spanning 1,392 base pairs (bp), while LvSOCS7 encodes a significantly larger polypeptide of 955 aa, encompassing 2,868 bp. Both LvSOCS proteins exhibited conserved domains associated with SOCS, including a centralized Src homology 2 (SH2) domain and a C-terminal SOCS box. Phylogenetic analysis revealed that the deduced aa sequences of LvSOCS6 and LvSOCS7 cluster within the invertebrate type I SOCS family, indicating their evolutionary relatedness. Tissue distribution analysis demonstrated ubiquitous expression of both LvSOCS genes across all examined tissues, with LvSOCS6 showing heightened expression in the gills and LvSOCS7 exhibiting a remarkable preference for the gills and stomach. Notably, mRNA expression patterns of LvSOCS genes following LPS and poly (I:C) stimulations exhibit significant upregulations, while PGN stimulation yields incongruous results across the experimented tissues. Interestingly, concurrent with the diminished expression of LvSOCS6 and LvSOCS7, there is a significant elevation in mRNA expression levels of LvSTAT, a vital component of the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway. These findings shed light on the potential involvement of the newly discovered type I SOCS genes in regulating the JAK/STAT pathway and assuming pivotal roles in orchestrating the innate immune responses in L. vannamei defense mechanisms.
ARTICLE | doi:10.20944/preprints202307.1464.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: bovine skeletal muscle satellite cells; sodium butyrate; mitophagy; apoptosis; mTOR signaling pathway
Online: 21 July 2023 (05:18:58 CEST)
Sodium butyrate (NaB) is one of the short-chain fatty acids and is notably produced in large amounts from dietary fiber in the gut. Recent evidence suggests that NaB induces cell proliferation and apoptosis. The skeletal muscle is rich in plenty of mitochondrial. However, it is unclear how NaB acts on host muscle cells and whether it is involved in mitochondria-related functions in myocytes. The present study aimed to investigate the role of NaB treatment on the proliferation, apoptosis, and mitophagy of bovine skeletal muscle satellite cells (BSCs). The results showed that NaB inhibited the proliferation and promoted apoptosis of BSCs, and promoted mitophagy in a time and dose-dependent manner in BSCs. In addition, 1mM NaB increased the mitochondrial ROS level, decreased the mitochondrial membrane potential (MMP), increased the number of autophagic vesicles in mitochondria, and increased the mitochondrial DNA(mtDNA) and ATP level. The effects of the mTOR pathway on BSCs were investigated, and the results showed that 1mM NaB inhibited the mRNA and protein expression of mTOR and genes AKT1, FOXO1, and EIF4EBP1 in the mTOR signaling pathway, while the addition of PP242, an inhibitor of the mTOR signaling pathway, also inhibited mRNA and protein expression levels of mTOR, AKT1, FOXO1, and EIF4EBP1, and promoted mitophagy and apoptosis, which were consistent with the effect of NaB treatment. In conclusion, NaB might promote mitophagy and apoptosis in BSCs by inhibiting the mTOR signaling pathway. Our results would expand the knowledge of sodium butyrate on bovine skeletal muscle cell state and mitochondrial function.
REVIEW | doi:10.20944/preprints202306.1650.v1
Subject: Biology And Life Sciences, Other Keywords: Esophageal cancer; Targeted drug therapies; Pathway targeting; Drug resistance; Patient survival rates
Online: 23 June 2023 (09:44:00 CEST)
Esophageal cancer is a formidable challenge in the realm of cancer treatment. Conventional methods such as surgery, chemotherapy, and immunotherapy have demonstrated limited success rates in managing this disease. In response, targeted drug therapies have emerged as a promising strategy to improve outcomes for patients. These therapies aim to disrupt specific pathways involved in the growth and development of esophageal cancer cells. This review explores various drugs used to target specific pathways, including cetuximab and monoclonal antibodies (gefitinib) that target the epidermal growth factor receptor (EGFR), trastuzumab that targets human epidermal growth factor receptor 2 (HER-2), drugs targeting the vascular endothelial growth factor receptor (VEGFR), mTOR inhibitors, and cMET inhibitors. Additionally, the article discusses the impact of drug resistance on the effectiveness of these therapies, highlighting factors such as cancer stem cells, cancer-associated fibroblasts, immune-inflammatory cells, cytokines, hypoxia, and growth factors. While drug targeting approaches do not provide a complete cure for esophageal cancer due to drug resistance and associated side effects, they offer potential for improving patient survival rates.
REVIEW | doi:10.20944/preprints202306.0602.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Chemotherapy Resistance; Molecular Targeting; Signalling Pathway; Metastasis; Apoptosis; Tumor Microenvironment; Cancer Stemness
Online: 8 June 2023 (07:37:41 CEST)
Cancer is a devastating disease, causing tremendous morbidity and mortality each year. Cancer can be considered as a genetic disease in the sense that instabilities in protooncogenes and tumor suppressor genes are among the hallmarks of cancer progression and metastasis. However, a particular cancer can express different proteins in different patients, making cancer a heterogeneous disease. This heterogeneity in part influences treatment resistance and failure. Therefore, it is crucial to understand the mechanism by which cancer cells develop and enhance resistance to different agents. This review aims to present the general paradigm and recent updates on cancer cell resistance to different antitumor agents. It demonstrates that tumor resistance results from a myriad of factors, including tumor microenvironment, supporting immune cells, and cancer stem cells. This interaction contributes to cancer cells overcoming the therapeutic effects of different classes of antitumor agents, such as cytotoxic chemotherapeutics, targeted agents, and immunotherapies. With the development of advanced molecular analysis, specialized genomic assessment has assisted clinicians and researchers in choosing selected agents combating cancer cells. Together, this approach can potentially reduce treatment toxicity, health system burden, and financial costs while improving patient quality of life. Understanding the exact mechanism of drug resistance in cancer cells can open the way to new effective and less toxic therapeutics.
REVIEW | doi:10.20944/preprints202306.0220.v1
Subject: Chemistry And Materials Science, Biomaterials Keywords: hydrogel-forming microneedles; transdermal drug delivery; controlled release; permeation pathway; environmental response
Online: 2 June 2023 (15:57:01 CEST)
Transdermal drug delivery (TDD) is one of the key approaches for treating diseases, avoiding first-pass effects, reducing systemic adverse drug reactions and improving patient compliance. Microneedling, iontophoresis, electroporation, laser ablation and ultrasound facilitation are often used to improve the efficiency of TDD. Among them, microneedling is a relatively simple and efficient means of drug delivery. Microneedles usually consist of micron-sized needles (50-900 μm in length) in arrays that can successfully penetrate the stratum corneum and deliver drugs in a minimally invasive manner below the stratum corneum without touching the blood vessels and nerves in the dermis, improving patient compliance. Hydrogel-forming microneedles (HFMNs) are safe, non-toxic, no residual matrix material, high drug loading capacity, controlled drug release and are suitable for long-term, multiple drug delivery. This work reviewed the characteristics of skin structure and transdermal drug delivery; introduced TDD strategies based on hydrogel microneedles; summarised the characteristics of HFMNs TDD systems and the evaluation methods of HFMNs; and the application of HFMNs drug delivery systems in disease treatment. The HFMNs drug delivery system has a wide scope for development, but the translation to clinical application still has more challenges.
REVIEW | doi:10.20944/preprints202305.1990.v1
Subject: Biology And Life Sciences, Aging Keywords: Tryptophan; Kynurenine pathway; Aging; older adults; Inflammation; Osteoporosis; Sarcopenia; Frailty; Biomarkers; Osteosarcopenia
Online: 29 May 2023 (07:32:17 CEST)
Tryptophan is an essential nutrient required to produce niacin (vitamin B3), which is needed for energy metabolism and DNA production. Alterations in tryptophan metabolism could have significant effects on aging and musculoskeletal health. The kynurenine pathway, the main catabolic route of tryptophan, is modulated by inflammatory factors, which are increased in older persons, a process known as inflammaging. Osteoporosis, sarcopenia, osteosarcopenia and frailty have also been linked with chronic increased levels of inflammatory factors. Due to the disruption of the kynurenine pathway by chronic inflammation and/or changes in the gut microbiota, serum levels of toxic kynurenines are increased and have been associated with osteoporosis, sarcopenia and frailty. In contrast, anabolic end products of this pathway, such as picolinic acid, have demonstrated a beneficial effect on bone and muscle. In addition, recent studies have shown that physical activity can modulate this pathway by promoting the secretion of anabolic kynurenines. According to the evidence collected, kynurenines could have a promising role as biomarkers for osteoporosis sarcopenia, osteosarcopenia and frailty in older persons. In addition, some of these metabolites could become important targets for developing new pharmacological treatments for these conditions.
ARTICLE | doi:10.20944/preprints202304.0580.v1
Subject: Biology And Life Sciences, Insect Science Keywords: herbivore-induced plant defense; signaling pathway; intraguild predation; jasmonoyl-isoleucine; abscisic acid
Online: 19 April 2023 (09:31:48 CEST)
The fall armyworm (FAW), Spodoptera frugiperda, has become one of the most important pests on corn in China since it invaded in 2019. Although FAW has not been reported to cause widespread damage to rice plants in China, it has been sporadically found feeding in the field. If FAW infests rice in China, the fitness of other insect pests on rice may be influenced. However, how FAW and other insect pests on rice interact remains unknown. In this study, we found that the infestation of FAW larvae on rice plants prolonged the developmental duration of the brown planthopper (BPH, Nilaparvata lugens (Stål)) eggs, and plants damaged by gravid BPH females did not induce defenses that influenced the growth of FAW larvae. Moreover, co-infestation by FAW larvae on rice plants did not influence the attractiveness of volatiles emitted from BPH-infested plants to Anagrus nilaparvatae, an egg parasitoid of rice planthoppers. FAW larvae were able to prey on BPH eggs laid on rice plants and grew faster compared to those larvae that lacked available eggs. Studies revealed that the delay in development of BPH eggs on FAW-infested plants was probably related to the increase in levels of jasmonoyl-isoleucine, abscisic acid and the defensive compounds in the rice leaf sheaths on which BPH eggs were laid. These findings indicate that if FAW invades rice plants in China, the population density of BPH may be decreased by intraguild predation and induced plant defenses, whereas the population density of FAW may be increased.
ARTICLE | doi:10.20944/preprints202301.0247.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: statin; natural compounds; Bcl2 family proteins; intrinsic apoptosis pathway; caspase dependent apoptosis
Online: 13 January 2023 (09:29:40 CET)
Glioblastoma multiforme (GBM) is one of the deadliest cancers. Temozolomide (TMZ) is the most common chemotherapy used for GBM patients. Recently, combination chemotherapy strategies have more effective antitumor effects and focus on slowing down the development of chemotherapy resistance. A combination of TMZ and cholesterol lowering medications (statins) is currently under investigation in in vivo and clinical trials. In our current investigation, we have used a triple combination therapy of TMZ, Simvastatin (Simva), and Acetylshikonin (ASH) and investigated its apoptotic mechanism in GBM cell lines (U87 and U251). We used viability, apoptosis, reactive oxygen species (ROS), mitochondrial membrane potential (MMP), caspase-3/-7, acridine orange (AO) and immunoblotting autophagy assays. Our results showed that TMZ/Simva/ASH combination therapy significantly induced more apoptosis compared to TMZ, Simva, ASH, and TMZ/Simva treatments in GBM cells. Apoptosis via TMZ/Simva/ASH treatment induced mitochondrial damage (increase of ROS, decrease of MMP) and induced caspase-3/7 activation in both GBM cell lines. Compared to all single treatments and the TMZ/Simva treatment, TMZ/Simva/ASH significantly increased positive acidic vacuole organelles. We further confirmed that the increase of AVOs during the TMZ/Simva/ASH treatment was due to partial inhibition of autophagy flux (accumulation of LC3β-II and decrease in p62 degradation) in GBM cells. Our investigation also showed that TMZ/Simva/ASH-induced cell death was depended on autophagy flux as further inhibition of autophagy flux increased TMZ/Simva/ASH-induced cell death in GBM cells. Finally, our results showed that TMZ/Simva/ASH treatment potentially depends on an increase of Bax expression in GBM cells. Our current investigation might open new avenues for more effective treatment of GBM but further investigations are required for better identification of the mechanisms.
ARTICLE | doi:10.20944/preprints202301.0009.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Acanthamoeba keratitis; transcriptome analysis; immune status; differentially expressed genes; SLAMF7/STAT6 pathway
Online: 3 January 2023 (07:33:07 CET)
Acanthamoeba keratitis (AK) is a blinding corneal infection caused by the protozoan Acanthamoeba. The long-term course of AK suggests the host immunity could not kill Acanthamoeba rapidly. The immune status is still unclear in the late stage of AK. The comparative transcriptome analysis was made based on the bulk RNA sequencing of cornea tissues from AK patients and donors. Differentially expressed genes and enriched signaling pathways were calculated. CIBERSORT algorithm was used for Immune infiltration analysis of cornea tissue between AK and normal controls. A total of 2668 differentially expressed genes, including 1477 upregulated genes and 1191 downregulated genes, were detected. Gene Ontology analysis revealed that the pathways were significantly enriched in leukocyte migration, regulation of T cell activation, the external side of plasma membrane, collagen-containing extracellular matrix, immune receptor activity and cytokine binding. KEGG pathway analysis showed that the pathways were significantly enriched in the cytokine-cytokine receptor interaction, hematopoietic cell lineage and Staphylococcus aureus infection pathway. The immune infiltration profiles varied little between AK and normal controls. Compared with normal tissue, cornea tissue of AK contained a higher proportion of M0 macrophages and CD8 T cells, while resting memory CD4 T cells contributed to a relatively lower portion (P < 0.05). Finally, the expression levels of cell markers and SLAMF7/STAT6 pathway were confirmed by histopathology examinations, RT-qPCR and western blot.
ARTICLE | doi:10.20944/preprints202207.0378.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: FHB; plant metabolomic; plant-pathogen interaction; barley; wheat; Brachypodium distachyon; pathway enrichment
Online: 26 July 2022 (03:22:55 CEST)
Background: Fusarium head blight (FHB) is a serious fungal disease of crop plants due to substantial yield reduction and production of mycotoxins in the infected grains. The breeding progress in increasing resistance with maintaining a high yield is not possible without a thorough examination of the molecular basis of plant immunity responses; Methods: LC-MS based metabolomics approaches powered by three-way ANOVA and differentially accumulated metabolites (DAMs) selection, correlation network and functional enrichment were conducted on grains of resistant and susceptible to FHB genotypes of barley and wheat as well as model grass Brachypodium distachyon (Bd) still poorly known at metabolomic level; Results: We selected common and genotype-specific DAMs in response to F. culmorum inoculation. Immunological reaction at metabolomic level was strongly diversified between resistant and susceptible genotypes. DAMs common for all tested species from porphyrins, flavonoids and phenylpropanoids metabolic pathways were highly correlated and reflects conservativeness in FHB response in Poaceae family. Resistant related DAMs belonged to different structural classes including tryptophan derived metabolites, pirimidines, amino acids proline and serine as well as phenylpropanoids and flavonoids. Physiological response to F. culmorum of Bd was close to barley and wheat genotypes however, metabolomic changes were strongly diversified. Conclusions: Combined targeted and untargeted metabolomics provides comprehensive knowledge about significant elements of plant immunity with potential of being molecular biomarkers of enhance resistance to FHB in grass family. Thorough examination of Bd21 metabolome in juxtaposition with barley and wheat diversified genotypes facilitate their setting as model grass for plant-microbe interaction.
ARTICLE | doi:10.20944/preprints202207.0375.v1
Subject: Biology And Life Sciences, Virology Keywords: Enterovirus; vemurafenib; RAF; MAPK signaling pathway; genome replication; virus assembly; VP0 cleavage
Online: 25 July 2022 (12:25:13 CEST)
Enterovirus A71 (EV-A71) infection is a major cause of hand, foot and mouth disease (HFMD) which may be occasionally associated with severe neurological complications. There are currently a lack of treatment options for EV-A71 infection. The Raf-MEK-ERK signaling pathway, in addition to its critical importance in the regulation of cell growth, differentiation and survival, has been shown to be essential for virus replication. In this study, we investigated the anti-EV-A71 activity of vemurafenib, a clinically approved B-Raf inhibitor used in the treatment of late stage melanoma. Vemurafenib exhibits potent anti-EV-A71 effect in cytopathic effect inhibition and viral load reduction assays, with half maximal effective concentration (EC50) at nanomolar concentration. Mechanistically, vemurafenib interrupts both EV-A71 genome replication and assembly. These findings expand the list of potential antiviral candidates of anti-EV-A71 therapeutics.
ARTICLE | doi:10.20944/preprints202108.0019.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: leptin; JAK/STAT pathway; myocardial infarction; hemodynamics; arrhythmias; dyslipidaemia; inflammation; cardiac remodeling
Online: 2 August 2021 (11:24:57 CEST)
Hyperleptinemia potentiates the effects of many atherogenic factors, such as inflammation, platelet aggregation, migration, hypertrophy, proliferation of vascular smooth muscle cells, and endothelial cell dysfunction. The present study analysed the eﬀects of long-term hyperleptinemia in an in vivo myocardial ischemia-reperfusion model to demonstrate whether the in vivo deleterious effect also affects cardiac structure and function. Rats by were subcutaneously administered leptin for 8 days to estimate the involvement of the JAK/STAT pathway. Data from 58 male Wistar rats were included in the final analysis. Myocardial infarction (MI) was modelled by the 30-minute ligation of the main left coronary artery followed by 120-minute reperfusion. Hemodynamic measurements, electrocardiography monitoring, echocardiography, myocardial infarct size and area at risk, blood biochemical parameters, leptin, IL-6, TNF-alpha, FGF-21, and cardiomyocyte morphology were measured. Statistical analyses were performed using IBM SPSS Statistics v.26. Seven-day hyperleptinemia in rats led to increased an blood pressure and heart rate, myocardial hypertrophy, impaired LV function, an increased frequency of ischemic arrhythmias, dyslipidaemia, systemic inflammation, and an increased size of induced myocardial infarction. The blockade of the JAK/STAT signalling pathway effectively reversed the negative effects of leptin, including increased blood pressure and total cholesterol.
Subject: Physical Sciences, Acoustics Keywords: thermonuclear function; pathway model; reaction rate probability integral; H-function; Mellin transform
Online: 6 May 2021 (12:33:07 CEST)
The closed forms of the non-resonant thermonuclear function in the Maxwell-Boltzmann and Tsallis case with depleted tail are obtained in generalized special functions. The results are written in terms of H-function of two variables. The importance of the results in this paper lies in the fact that the reaction rate probability integrals in Maxwell-Boltzmann and Tsallis cases are not obtained by the conventional method of approximation or by means of a single variable transform technique but by means of a two variable transform method. The Behaviour of the depleted non-resonant thermonuclear functions are examined using graphs. The results in the paper are of much interest to astrophysicists and statisticians in their further work in this area.
ARTICLE | doi:10.20944/preprints202105.0064.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: pancreas; tissue slices; beta cells; calcium imaging; amplifying pathway; forskolin; Epac2A KO
Online: 5 May 2021 (13:34:10 CEST)
Beta cells couple stimulation by glucose with insulin secretion and impairments in this coupling play a central role in diabetes mellitus. To clarify the effect of cAMP and the role of Epac2A in intracellular calcium signals and intercellular coupling, we performed functional multicellular calcium imaging in beta cells in mouse pancreas tissue slices after stimulation with glucose and forskolin in wild-type and Epac2A knock-out mice. Increased cAMP evoked calcium signals in otherwise sub-stimulatory glucose and beta cells from Epac2A knock-out mice displayed a faster activation. During the plateau phase, beta cells from Epac2A knock-out mice displayed a slightly higher active time in response to glucose compared with wild-type littermates, and increased cAMP increased the active time via a large increase in oscillation frequency and small decrease in oscillation duration in both Epac2A knock-out and wild-type mice. Functional network properties during stimulation with glucose did not differ in Epac2A knock-out mice, but the presence of Epac2A was crucial for the protective effect of increased cAMP in preventing a decline in beta cell functional connectivity with time. Finally, increased cAMP prolonged beta cell activity during deactivation in an Epac2A-independent manner.
ARTICLE | doi:10.20944/preprints202012.0496.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Hungateiclostridium thermocellum; adaptive laboratory evolution; RNA-seq; cellulosomal genes; EMP pathway; monosaccharides
Online: 21 December 2020 (10:36:00 CET)
Hungateiclostridium thermocellum ATCC 27405 is a promising bacterium with a robust ability to degrade lignocellulosic biomass complexes, including crystalline cellulose components, through a multienzyme cellulosomal system. In contrast, it exhibits poor growth on simple monosaccharides such as fructose and glucose. This phenomenon raises many important questions concerning its glycolytic pathways and sugar transport systems. Until now, the detailed mechanisms of H. thermocellum adaptation to growth on monosaccharides have been poorly explored. In this study, adaptive laboratory evolution was applied to train the bacterium on monosaccharides, and genome resequencing was used to detect the genes that had mutated during adaptation. RNA-seq data of the 1st-generation culture growing on either fructose or glucose revealed that several glycolytic genes in the EMP pathway were expressed at lower levels in these cells than in cellobiose-grown cells. After 8 generations of culture on fructose and glucose, the evolved H. thermocellum strains grew faster and yielded greater biomass than the nonadapted strains. Genomic screening also revealed several mutation events in the genomes of the evolved strains, especially in genes responsible for sugar transport and central carbon metabolism. Consequently, these genes could be applied as targets for further metabolic engineering to improve this bacterium for bioindustrial usage.
REVIEW | doi:10.20944/preprints202008.0369.v2
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Extreme capsule; uncinate fasciculus; IFOF; ventral pathway of language; bottle neck; DTI
Online: 7 September 2020 (10:26:24 CEST)
On review of neuroscience literature extreme capsule considered as a whiter matter tract. Nevertheless it is not clear that extreme capsule itself is a association fiber pathway or is o bottleneck for passing other association fiber. By a systematic search with investigating anatomical position, dissection, connectivity and cognitive role of extreme capsule it can be argued that extreme capsule probably is a bottleneck for passing uncinated fasciculus (UF) and inferior fronto – occipital fasciculus(IFOF), And its different role of language processing is duo to different tract that passing it.
Subject: Medicine And Pharmacology, Ophthalmology Keywords: HLA; Uveitis; Birdshot; Antigen Presentation Pathway; Autoimmune Disease; Inflammation; ERAP1 and ERAP2
Online: 30 August 2020 (17:39:55 CEST)
HLA class I alleles constitute established risk factors for non-infectious uveitis and preemptive genotyping of HLA class I alleles is standard practice in the diagnostic work-up. The HLA-A29 serotype is indispensable to Birdshot Uveitis (BU) and renders this enigmatic eye condition a unique model to better understand how the antigen processing and presentation machinery contributes to non-infectious uveitis or chronic inflammatory conditions in general. This review will discuss salient points regarding the protein structure of HLA-A29 using and how key amino acid positions impact the peptide binding preference and interaction with T cells. We discuss to what extent the risk genes ERAP1 and ERAP2 uniquely affect HLA-A29 and how the discovery of a HLA-A29-specific submotif may impact autoantigen discovery. We further provide a compelling argument to solve the long-standing question why BU only affects HLA-A29-positive individuals from Western-European ancestry by exploiting data from the 1000 Genomes Project. We combine novel insights from structural and immunopeptidomic studies and discuss the functional implications of genetic associations across the HLA class I antigen presentation pathway to refine the etiological basis of Birdshot Uveitis.
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: pathway optimization; machine learning tools; enzyme activity prediction; promoter classification; expression tuning
Online: 26 August 2020 (04:05:47 CEST)
Successful engineering of a microbial host for efficient production of a target product from a given substrate can be viewed as an extensive optimization task. Such a task involves the selection of high activity enzymes as well as their gene expression regulatory control elements (i.e., promoters and ribosome binding sites). Finally, there is also the need to tune expression of multiple genes along a heterologous pathway to relieve constraints from rate-limiting step and help reduce metabolic burden on cells from unnecessary over-expression of high activity enzymes. While the aforementioned tasks could be performed through combinatorial experiments, such an approach incurs significant cost, time and effort, which is a handicap that can be relieved by application of modern machine learning tools. Such tools could attempt to predict high activity enzymes from sequence, but they are currently most usefully applied in classifying strong promoters from weaker ones as well as combinatorial tuning of expression of multiple genes. This perspective reviews the application of machine learning tools to aid metabolic pathway optimization through identifying challenges in metabolic engineering that could be overcome with the help of machine learning tools.
HYPOTHESIS | doi:10.20944/preprints202004.0171.v1
Subject: Biology And Life Sciences, Virology Keywords: Coronavirus; COVID-19 outbreak; SARS-CoV; ESCRT pathway; FGI-104 quinolone; chloroquine;
Online: 10 April 2020 (13:22:27 CEST)
Although phylogenetic analysis shows coronaviruses (CoV) share similar genome sequences, CoVs encode different number of proteins (5 to 14). The newly isolated viruses harbour more proteins than the old ones. Therefore, identifying the functional protein unites will benefits to understand the molecular interactions of the virus, and then identify molecular targets for antiviral drug. Here, the comparative in-silico analysis of 33 coronavirus proteomes show that coronaviruses harbour diverse number of protein functional motifs. Coronaviruses harbour wide-range of motifs including those involved in integrin-binding and ESCRT pathway before virus budding. For example, SARS-CoV-2, but not SARS-CoV-1, encodes PPxY motif, which is required for virus entry and budding of HIV, influenza and adenoviruses. The quinolone inulding the antiviral FGI-104 is able to block ESCRT pathway and viral budding and has been used against HIV, HCV and Ebola virus.
ARTICLE | doi:10.20944/preprints201910.0154.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: papillary thyroid cancer; germline mutations; whole genome sequencing; predisposition markers; pathway analysis
Online: 13 October 2019 (17:07:34 CEST)
Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. We performed whole genome sequencing on 23 affected and 3 unaffected family members from five NMTC-prone families and prioritized the identified variants using our Familial Cancer Variant Prioritization Pipeline (FCVPPv2). In total, 31 coding variants and 39 variants located in upstream, downstream, 5′ or 3′ untranslated regions passed FCVPPv2 filtering. Altogether, 210 genes affected by variants that passed the first three steps of the FCVPPv2 were analyzed using Ingenuity Pathway Analysis software. These genes were enriched in tumorigenic signaling pathways mediated by receptor tyrosine kinases and G-protein coupled receptors, implicating a central role of PI3K/AKT and MAPK/ERK signaling in familial NMTC. Our approach can facilitate the identification and functional validation of causal variants in each family as well as the screening and genetic counseling of other individuals at risk of developing NMTC.
ARTICLE | doi:10.20944/preprints201907.0018.v1
Subject: Medicine And Pharmacology, Dermatology Keywords: atopic dermatitis; AD; dermatology; target identification; pathway identification; bioinformatics; protein-protein networks
Online: 1 July 2019 (12:47:49 CEST)
The exploration and identification of targets and pathways for Atopic dermatitis (AD) treatment and diagnosis are critical for AD control. The conventional target exploration approach such as the literature review is not satisfying in terms of efficiency and accuracy. Recently, the bioinformatic approach is drawing attention for its unique advantage of high-volume data analysis for target and pathway exploration; Open Targets Platform is the targets source for this study to extract top 200 high-rank proteins from 3122 AD associated proteins. STRING, Cytoscape, CytoHubba, ClueGo, and CluePedia function had been applied for data analysis. The KEGG Mapper search & colour pathway was the pathway map resource for identified pathways; 23 key hub genes (VDR, KIT, BCL2L11, NFKBIA, KRAS, IL13, JAK2, STAT3, IL21, IL4R, REL, PDGFRB, FOXP3, RARA, RELB, EGFR, IL21R, MYC, CREBBP, NR3C1, IL2, JAK1, and KITLG). Additionally, 8 correlated pathways and the biological process had been identified; Through this study, a viable approach for target and pathway exploration had been presented. The identified AD targets and pathways will be tested for upcoming research for traditional Chinese medicinal herb interactions
ARTICLE | doi:10.20944/preprints201703.0237.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: valproic acid; doxorubicin; reactive oxygen species; autophagy; cell death; caveolae endocytosis pathway
Online: 31 March 2017 (12:08:53 CEST)
We evaluated the mono- and combination-therapy effects of valproic acid (VPA) and doxorubicin (DOX) in hepatocellular carcinoma (HCC) and identified a specific and efficient, synergistic anti-proliferative effect of the VPA and DOX combination in HCC cells, especially HepG2 cells; this effect was not apparent in MIHA cells, a normal hepatocyte cell line. The calculation of the coefficient of drug interaction confirmed the significant synergistic effect of the combination treatment. Concurrently, the synergistic apoptotic cell death caused by the VPA and DOX combination treatment was confirmed by Hoechst nuclear staining and western blot analysis of caspase-3 and poly (ADP-ribose) polymerase (PARP) activation. Co-treatment with VPA and DOX enhanced reactive oxygen species (ROS) generation and autophagy, which were clearly attenuated by ROS and autophagy inhibitors, respectively. Furthermore, as an indication of the mechanism underlying the synergistic effect, we observed that DOX internalization, which was induced in the VPA and DOX combination-treated group, occurred via by the caveolae-mediated endocytosis pathway. Taken together, our study uncovered the potential effect of the VPA and DOX combination treatment with regard to cell death, including induction of cellular ROS, autophagy, and the caveolae-mediated endocytosis pathway. Therefore, these results present novel implications in drug delivery research for the treatment of HCC.
ARTICLE | doi:10.20944/preprints202311.1383.v1
Subject: Biology And Life Sciences, Horticulture Keywords: soil improvement; endophytic bacteria; rhizosphere soil bacteria; metabolic pathway; functional bacteria; nitrogen cycle
Online: 22 November 2023 (06:42:52 CET)
Soil improvement methods can result in changes in the microbial community in blueberry soil. However, there have been few reports on the impacts of different soil improvement methods on the microbial function, particularly on endophytic microbe. In this study, we analyzed the response of microbial community composition, microbial function and nitrogen (N) cycle to different improvement methods using high throughput sequencing. We aimed to investigate the best soil improvement method from a microbial perspective. The results showed that the highest microbial diversity was observed in the T4 treatment (peat combined with mushroom bran), followed by the T2 treatment (peat combined with acidified rice husk) both in the rhizosphere and roots. The dominant phyla were Proteobacteria and Actinobacteria, which were most abundance in the T4 and T1 (peat combined with sulfur) treatments in the rhizosphere soil, respectively, but showed the opposite trend in the root endophytic bacterial community. Interestingly, Acidobacterium and Paludibaculum, belonging to the Acidobacteria phylum, were found to have the highest influence according to the correlation network analysis. And these bacteria were most abundant in the T2 treatment in the rhizosphere soil. The rhizosphere soil microbial communities were clustered into two categories: one for T1 and T2 treatments, and another for T3 (mushroom bran) and T4 treatments. Compared to the other treatments, the T1 treatment had the most significant impact on microbial functional pathways in the blueberry roots. T2 treatment promoted the growth of N fixation functional bacteria both in the rhizosphere soil and roots. At the module level, the T2 treatment increased the relative abundance of N fixation and decreased the relative abundance of assimilating nitrate reduction reaction (ANRA), dissimilating nitrate reduction reaction (DNRA), denitrification and completed nitrification in the blueberry rhizosphere soil. Additionally, the T2 treatment increased the abundance of root endophytic microbes involved in N fixation. Overall, our findings suggest that the addition of peat combined with acidified rice husk is the optimal soil improvement method for blueberry cultivation.
ARTICLE | doi:10.20944/preprints202306.0342.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: chromone derivatives; oral squamous cell carcinoma; tumor-specificity; keratinocyte toxicity; neurotoxicity; signaling pathway
Online: 5 June 2023 (15:45:48 CEST)
Background. Many anticancer drugs used in clinical practice cause adverse events such as oral mucositis, neurotoxicity, and extravascular leakage. We have reported that two 3-styrylchromone derivatives, 7-methoxy-3-[(1E)-2-phenylethenyl]-4H-1-benzopyran-4-one (compound A) and 3-[(1E)-2-(4-hydroxyphenyl)ethenyl]-7-methoxy-4H-1-benzopyran-4-one (compound B) showed the highest tumor-specificity against human oral squamous cell carcinoma (OSCC) cell lines among 291 related compounds. After confirming their superiority by comparing their tumor specificity with newly synthesized 65 derivatives, we investigated the neurotoxicity of these compounds, in comparison with 4 popular anticancer drugs. Methods: Tumor-specificity (TSM, TSE, TSN) was evaluated as the ratio of mean CC50 for human normal oral mesenchymal (gingival fibroblast, pulp cell), oral epithelial cells (gingival epithelial progenitor), and neuronal cells (PC-12, SH-SY5Y, LY-PPB6, differentiated PC-12) to OSCC cells (Ca9-22, HSC-2), respectively. Results: Compounds A and B showed one-order of magnitude higher TSM as compared with newly synthesized derivatives, confirming its prominent tumor-specificity. Docetaxel showed one order of magnitude higher TSM, but two order of magnitude lower TSE than compounds A and B. Compounds A and B showed higher TSM, TSE and TSN values than doxorubicin, 5-FU and cisplatin, damaging OSCC cells at concentrations that do not affect the viability of normal epithelial and neuronal cells. QSAR prediction based on the Tox21 database suggested that compounds A and B may inhibit the signaling pathway of estrogen-related receptors.
ARTICLE | doi:10.20944/preprints202103.0336.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Myalgic Encephalomyelitis/chronic fatigue syndrome; Wnt pathway; inflammation; neuro-immune; oxidative stress; biomarkers
Online: 12 March 2021 (08:46:45 CET)
End-stage renal disease (ESRD) is associated with fatigue and physio-somatic symptoms. The aims of this study are to delineate the associations between severity of fatigue and physio-somatic symptoms and glomerular filtration rate, inflammatory biomarkers, and Wnt/catenin-pathway proteins. The Wnt-pathway related proteins β-catenin, Dickkopf-related protein 1 (DKK1), R-spondin-1, and sclerostin were measured by ELISA technique in 60 ESRD patients and 30 controls. The Fibromyalgia and Chronic Fatigue Syndrome (FF) Rating Scale was used to assess severity of FF symptoms. ESRD is characterized by a significant increase in the total FF score, muscle tension, fatigue, sadness, sleep disorders, GI symptoms, and a flu-like malaise. The total FF score was significantly correlated with serum levels of urea, creatinine, phosphate, and copper (positively), and β-catenin, eGFR, hemoglobin, albumin, and zinc (inversely). The total FF score was associated with the number of total dialysis and weekly dialysis sessions, and these dialysis characteristics were more important in predicting FF scores than eGFR measurements. Partial Least Squares analysis showed that the FF score comprised two factors which are differently associated with biomarkers: a) 43.0% of the variance in fatigue, GI symptoms, muscle tension, sadness, and insomnia is explained by hemoglobin, albumin, zinc, β-catenin, and R-spondin-1; and b) 22.3% of the variance in irritability, concentration and memory impairments by increased copper and cations/chloride ratio, and male sex. ESRD patients show high levels of fatigue and physio-somatic symptoms which are associated with hemodialysis and mediated by dialysis-induced changes in inflammatory pathways, the Wnt/catenin pathway, and copper.
ARTICLE | doi:10.20944/preprints202004.0016.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: glaucoma; retina ganglion cell degeneration; microarray; genes coordination; notch signaling pathway; complement cascade
Online: 23 February 2021 (12:44:20 CET)
Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the retinal ganglion cells (RGCs). There has been little progress in developing efficient strategies for neuroprotection in glaucoma. We profiled the retina transcriptome of Lister Hooded rats at 2 weeks after optic nerve crush (ONC) and analyzed the data from the Genomic Fabric Paradigm (GFP) to bring additional insights into the molecular mechanisms of the retinal remodeling after induction of RGC degeneration. GFP considers for the expression of each gene 3 independent characteristics: level, variability and correlation with each other gene. Thus, the 17,657 quantified genes our study generated a total of 155,911,310 values to analyze. This represents 8,830x more data per condition than a traditional transcriptomic analysis. ONC led to a 57% reduction in RGC numbers as detected by retrograde labeling with DiI. We observed a higher Relative Expression Variability after ONC. Gene expression stability was used as a measure of transcription control and disclosed a robust reduction in the number of very stably expressed genes. Predicted Protein-Protein interaction (PPI) analysis with STRING revealed axon and neuron projection as mostly decreased processes, consistent with RGC degeneration. Conversely, immune response PPIs were found among up-regulated genes. Enrichment analysis showed that Complement Cascade and Notch Signaling Pathway, as well as Oxidative Stress and Kit Receptor Pathway were affected after ONC. To expand our studies of altered molecular pathways, we examined the pair-wise coordination of gene expressions within each pathway and within the entire transcriptome using Pearson correlations. ONC increased the number of synergistically coordinated pairs of genes and the number of similar profiles mainly in Complement Cascade and Notch Signaling Pathway. This deep bioinformatic study provides novel insights beyond the regulation of individual gene expression and discloses changes in the control of expression of Complement Cascade and Notch Signaling functional pathways that may be relevant for both RGC degeneration and remodeling of the retinal tissue after ONC.
ARTICLE | doi:10.20944/preprints202008.0322.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: TAP1; transcriptional expression; methylation analysis; survival analysis; co-expression; pathway analysis; health informatics
Online: 14 August 2020 (11:17:29 CEST)
Transporter associated with antigen processing 1 (TAP1) gene codes for a transporter protein, which is responsible for tumor antigen presentation in the MHC I or HLA complex. A defect in the gene results in an inadequate tumor tracking. TAP1 may also influence multi drug resistance, which is an extreme threat in providing treatment by drugs which are chemotherapeutic. The gene of TAP1 was analyzed bioinformatically. It gave us prognostic data as a confirmation of whether it should be used as a biomarker. The expression level and pattern analysis were conducted using ONCOMINE, GENT2 and GEPIA2 online platforms. Samples with different clinical outcomes were investigated for expression and promoter methylation analysis was done in cancer vs normal tissues using UALCAN. The copy number alteration and mutation frequency and expression in different cancer studies were analyzed using cBioPortal. The PrognoScan and KM plotter survival analysis of significant data (p-value<0.05) was representing graphically. Pathway and Gene ontology analysis of gene correlated to TAP1 gene was presented using bar charts. After arranging the data in a single panel and correlating expression to prognosis, understanding mutational and alterations and comparing pathways, TAP1 may be a potential novel target to evade a threat against chemotherapy and the study gives new aspects to consider for immunotherapy in human breast, lung, liver and ovarian cancer.
REVIEW | doi:10.20944/preprints201912.0165.v2
Subject: Biology And Life Sciences, Food Science And Technology Keywords: glucose; pentose phosphate pathway; NADPH; redox balance; glycogen; glycolysis; stress resistance; insulin resistance
Online: 30 January 2020 (12:49:19 CET)
A human organism depends on stable glucose blood levels in order to maintain the metabolic needs. Glucose is considered as the most important energy source and glycolysis is postulated as a backbone pathway. However, when glucose supply is limited, ketone bodies and amino acids can be used to produce enough ATP. In contrast, for the functioning of pentose phosphate pathway (PPP) glucose is essential and cannot be substituted by other metabolites. PPP generates and maintains levels of NADPH needed for reduction of oxidized glutathione and protein thiols, synthesis of lipids and DNA as well as for xenobiotic detoxification, regulatory redox signaling and counteracting infections. Flux of glucose into a PPP, particularly under extreme oxidative and toxic challenges is critical for survival, whereas the glycolytic pathway is primarily activated when glucose is abundant, and there is lack of NADP+ that is required for activation of glucose-6 phosphate dehydrogenase. An important role of glycogen stores in resistance to oxidative challenges is discussed. Current evidences explain disruptive metabolic effects and detrimental health consequences of chronic nutritional carbohydrate overload and provides new insights into positive metabolic effects of intermittent fasting, caloric restriction, exercise, and ketogenic diet through modulation of redox homeostasis.