REVIEW | doi:10.20944/preprints202209.0364.v1
Subject: Life Sciences, Molecular Biology Keywords: breast cancer; Nerve Growght Factor (NGF); TrkA; p75NTR; NGFR; pro-NGF; angiogenesis; invasion; metastasis; diagnosis; prognosis; treatment
Online: 23 September 2022 (09:18:12 CEST)
Breast cancer represents the most frequent cancer and the leading cause of cancer death among women. Thus, the prevention and early diagnosis of breast cancer appears to be of primary urgency as well as the development of new treatments able to improve its prognosis. Nerve Growth Factor (NGF) is a neurotrophic factor that plays a key role in the regulation of neuronal functions thought the binding to the Tropomyosin receptor kinase A (TrkA) and the Nerve Growth Factor receptor or Pan-Neurotrophin Receptor 75 (NGFR/p75NTR). Also, its precursor (pro-NGF) can extert biological activity by forming a trimeric complex with NGFR/p75NTR and sortilin or by binding to TrkA receptors with low affinity. Both in vitro and in vivo studies showed that NGF is synthesized and released by breast cancer cells and has mitogen, antiapoptotic and angiogenic effects on these cells through the activation of different signaling cascades that involve TrkA and NGFR/p75NTR receptors. Conversely, pro-NGF signaling has been related to breast cancer invasion and metastasis. Other studies suggested that NGF and its receptors could represent a good diagnostic and prognostic tool, as well as promising therapeutic targets for breast cancer. Here, we comprehensively summarize and systematically review the current experimental evidence on this topic.
ARTICLE | doi:10.20944/preprints202209.0290.v1
Subject: Life Sciences, Molecular Biology Keywords: Sulfatide; cerebroside sulfotransferase; ventricular enlargement; Alzheimer’s disease; brain MRI; aquaporins
Online: 20 September 2022 (03:56:30 CEST)
Alzheimer’s disease (AD) is a neurodegenerative disease characterized by progressive memory loss and a decline in activities of daily life. Ventricular enlargement has been associated with worse performance on global cognitive tests and AD. Our previous studies demonstrated that brain sulfatides, myelin-enriched lipids, are dramatically reduced in subjects at the earliest clinically recognizable AD stages via an apolipoprotein E (APOE)-dependent and isoform-specific process. Herein, we provided pre-clinical evidence that sulfatide deficiency is causally associated with brain ventricular enlargement. Specifically, taking advantage of genetic mouse models of global and adult-onset sulfatide deficiency, we demonstrated that sulfatide losses cause ventricular enlargement without significantly affecting hippocampal or whole brain volumes using histological and magnetic resonance imaging approaches. Mild decreases in sulfatide content and mild increases in ventricular areas were also observed in human APOE4 compared to APOE2 knock-in mice. Finally, we provided Western blot and immunofluorescence evidence that aquaporin-4, the most prevalent aquaporin channel in the central nervous system (CNS) that provides fast water transportation and regulates cerebrospinal fluid in the ventricles, is significantly increased under sulfatide-deficient conditions, while other major brain aquaporins (e.g., aquaporin-1) are not altered. In short, we unraveled a novel molecular mechanism that may contribute to ventricular enlargement in AD.
ARTICLE | doi:10.20944/preprints202209.0260.v1
Subject: Life Sciences, Molecular Biology Keywords: Mollusks; gastropods; Zooplankton; Plankton; Pacific Ocean; larvae; DNA barcoding
Online: 19 September 2022 (04:57:36 CEST)
The life cycles and biodiversity of Pacific coast gastropods were analyzed by videomicroscopy and DNA barcoding of indi-viduals collected from tide pools and in plankton nets from a variety of shore stations. In many species (Families Calyptrae-idae, Cerithiopsidae, Strombidae, Vermetidae, Columbellidae, Nassariidae, Olivellidae, Hermaeidae, Onchidorididae, Gas-tropteridae, Haminoeidae), the free-swimming veligers were recovered from plankton collections; in Roperia poulsoni (family Muricidae) veligers were usually recovered from egg sacs where they had been retained although some escapees were found in plankton collections; in Pteropurpura festiva (family Muricidae) free-living veligers were also found; and in Atlanta californiensis (family Atlantidae) both veligers and adults were obtained from plankton collections making this a holoplank-tonic species. The results confirm that DNA barcoding using the COI barcode is a useful strategy to match life-cycle stages within species as well as to identify species and to document the level of biodiversity within the gastropods.
REVIEW | doi:10.20944/preprints202209.0227.v1
Subject: Life Sciences, Molecular Biology Keywords: Amyotrophic lateral sclerosis (ALS); neurodegeneration; neuroinflammation; neuromuscular disease; autoimmunity; the clonotypic immune system
Online: 15 September 2022 (08:51:54 CEST)
Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disease, characterized by progressive degeneration of upper and lower motor neurons in the cortex and spinal cord. Although the pathogenesis of ALS remains unclear, evidence on the role of the clonotypic immune system is growing. Adaptive immunity cells often appear changed in number or activation profile peripherally and centrally. However, their role in ALS appears conflicting. Data, from human and animal model studies, currently reported in literature show that each subset of lymphocytes and their mediators may mediate a protective or toxic mechanism in ALS, affecting both its progression and risk of death. In the present review article and attempt is made to shed light on the actual role of the cellular clonotypic immunity in ALS by integrating recent clinical studies and experimental observations.
ARTICLE | doi:10.20944/preprints202209.0091.v1
Subject: Life Sciences, Molecular Biology Keywords: calorie restriction; aging; inflammation; autophagy; senescence.; skeletal muscle
Online: 6 September 2022 (11:01:40 CEST)
Calorie restriction (CR), defined as a reduction of the total calorie intake of 30% to 60% without malnutrition, is the only nutritional strategy that has proven to extend lifespan, prevent or delay the onset of age-associated diseases, and delay the functional decline in a wide range of species. However, little is known about the effects of CR when started early in life. We sought to analyze the effects of CR in the skeletal muscle of young Wistar rats. For this, 3-month-old male and female rats were subjected to 40% CR or fed ad libitum for 3 months. Gastrocnemius muscles were used to extract RNA and total protein. Western blot and RT-qPCR were performed to evaluate the expression of key markers/pathways modulated by CR and affected by aging. CR decreased body and skeletal muscle weight in both sexes. No differences were found in most senescence, antioxidant, and nutrient sensing pathways analyzed. However, we found a sexual dimorphism in markers of oxidative stress, inflammation, apoptosis, and mitochondrial function in response to CR. Our data show that young female rats treated with CR exhibit similar expression patterns of key genes/pathways associated with healthy aging when compared to old animals treated with CR, while in male rats these effects are reduced. Additional studies are needed to understand how early or later life CR exerts positive effects on health- and lifespan.
ARTICLE | doi:10.20944/preprints202208.0527.v1
Subject: Life Sciences, Molecular Biology Keywords: Glutamate dehydrogenase; allosteric regulation; leucine; ADP; potassium; acetylation; thiamine triphosphate
Online: 31 August 2022 (02:39:02 CEST)
Glutamate dehydrogenase (GDH) plays a key role in the metabolism of glutamate, an important compound at a cross-road of carbon and nitrogen metabolism and a relevant neurotransmitter. Despite being one of the first discovered allosteric enzymes, GDH still poses challenges for structural characterization of its allosteric sites. Only the structures with ADP, and at low (3.5 Å) resolution, are available for mammalian GDH complexes with allosteric activators. Here we aim at deciphering structural basis for the GDH allosteric activation, using bovine GDH as a model. For the first time we report a mammalian GDH structure in a ternary complex with the activators leucine and ADP, co-crystallized with potassium ion. An improved 2.4 Å resolution of the GDH complex with ADP is also presented. The ternary complex with leucine and ADP differs from the binary complex with ADP by the conformation of GDH C-terminus, involved in the leucine binding and subunit interactions. The potassium site, identified in this work, may mediate interactions between the leucine and ADP binding sites. Our data provide novel insights into the mechanisms of GDH activation by leucine and ADP, linked to the enzyme regulation by (de)acetylation.
ARTICLE | doi:10.20944/preprints202208.0482.v1
Subject: Life Sciences, Molecular Biology Keywords: African buffaloes; bovine tuberculosis; cfp-10; esat-6; hsp65; nontuberculous mycobacteria; rpoB; Syncerus caffer
Online: 29 August 2022 (09:48:58 CEST)
Diagnosis of bovine tuberculosis (bTB) may be confounded by immunological cross-reactivity to Mycobacterium bovis antigens when animals are sensitised by certain nontuberculous mycobacteria (NTMs). Therefore, this study aimed to investigate NTM species diversity in African buffalo (Syncerus caffer) respiratory secretions and tissue samples, using a combination of novel molecular tools. Oronasal swabs were collected opportunistically from 120 immobilised buffaloes in historically bTB-free herds. In addition, bronchoalveolar lavage fluid (BALF; n=10) and tissue samples (n=19) were obtained during post-mortem examination. Mycobacterial species were identified directly from oronasal swab samples using the Xpert MTB/RIF Ultra qPCR (14/120 positive) and GenoType CMdirect (104/120 positive). In addition, all samples underwent mycobacterial culture, and PCRs targeting hsp65 and rpoB were performed. Overall, 55 NTM species were identified in 36 mycobacterial culture-positive swab samples with presence of esat-6 or cfp-10 detected in 20 of 36 isolates. The predominant species were M. avium complex and M. komanii. Nontuberculous mycobacteria were also isolated from 6 of 10 culture-positive BALF and 4 of 19 culture-positive tissue samples. Our findings demonstrate that there is a high diversity of NTMs present in buffaloes, and further investigation should determine their role in confounding bTB diagnosis in this species.
ARTICLE | doi:10.20944/preprints202208.0462.v1
Subject: Life Sciences, Molecular Biology Keywords: Hypoxia; Extracellular vesicles; Breast Cancer; Cell Invasion
Online: 26 August 2022 (14:08:23 CEST)
Hypoxia, a condition of low oxygenation frequently found in triple-negative breast tumors (TNBC), promotes extracellular vesicle (EV) secretion and favors cell invasion, a complex process in which cell morphology is altered, dynamic focal adhesion spots are created, and ECM is re-modeled. Here, we investigated the invasive properties triggered by TNBC-derived hypoxic small EV (SEVh) in vitro in cells cultured under hypoxic and normoxic conditions, using pheno-typical and proteomic approaches. SEVh characterization demonstrated increased protein abundance and diversity over normoxic SEV (SEVn), with enrichment in pro-invasive pathways. In normoxic cells, SEVh promotes invasive behavior through pro-migratory morphology, in-vadopodia development, ECM degradation and matrix metalloprotease (MMP) secretion. Pro-teome profiling of normoxic cells exposed to SEVh determined enrichment in metabolic processes and cell cycle, modulating cell health to escape apoptotic pathways. In hypoxia, SEVh was re-sponsible for proteolytic and catabolic pathway inducement, interfering with integrin availabil-ity and gelatinase expression. Overall, our results demonstrate the importance of hypoxic signal-ing via SEV in tumors for the early establishment of metastasis.
ARTICLE | doi:10.20944/preprints202208.0413.v1
Subject: Life Sciences, Molecular Biology Keywords: translation initiation; canonical and noncanonical translation initiation codons; protein translation; oncogene; oncogenesis; tumorigenesis; cancer
Online: 24 August 2022 (05:30:03 CEST)
Ribosome profiling and mass spectroscopy have identified canonical and noncanonical translation initiation codons (TICs) that are upstream of the main translation initiation site and used to translate oncogenic proteins. Here, we use a Kozak Similarity Score algorithm to find that nearly all of these TICs have flanking nucleotides closely matching the Kozak sequence. Remarkably, the nucleotides flanking alternative noncanonical TICs are frequently closer to the Kozak sequence than the nucleotides flanking TICs used to translate the gene’s main protein. Of note, the 5’ untranslated region (5‘UTR) of cancer-associated genes with an upstream TIC tend to be significantly longer than the same region in genes not associated with cancer. The presence of a longer than typical 5’UTR increases the likelihood of ribosome binding to upstream noncanonical TICs, and may be a distinguishing feature of a number of genes overexpressed in cancer. Noncanonical TICs that are located in the 5’UTR, although thought disadvantageous and suppressed by evolution, may translate oncogenic proteins because of their flanking nucleotides
ARTICLE | doi:10.20944/preprints202208.0343.v1
Subject: Life Sciences, Molecular Biology Keywords: 14-3-3; interactome; protein-protein interaction; mitochondria; metabolism; protein quality control; homeostasis; left ventricule; network
Online: 18 August 2022 (10:54:49 CEST)
Rationale: The 14-3-3 protein family is known to interact with many proteins in non-cardiac cell types to regulate multiple signaling pathways, particularly those relating to energy and protein homeostasis; and the 14-3-3 network is a therapeutic target of critical metabolic and proteostatic signaling in cancer and neurological diseases. Although the heart is critically sensitive to nutrient and energy alterations, and multiple signaling pathways coordinate to maintain the cardiac cell homeostasis, neither the structure of cardiac 14-3-3 protein interactome, nor potential functional roles of 14-3-3 protein-protein interactions (PPIs) in heart has been explored. Objective: To establish the comprehensive landscape and characterize the functional role of cardiac 14-3-3 PPIs. Methods and Results: We evaluated both RNA expression and protein abundance of 14-3-3 isoforms in mouse heart, followed by co-immunoprecipitation of 14-3-3 proteins and mass spectrometry in left ventricle. We identified 52 proteins comprising the cardiac 14-3-3 interactome. Multiple bioinformatic analyses indicated that more than half of the proteins bound to 14-3-3 are related to mitochondria; and the deduced functions of the mitochondrial 14-3-3 network are to regulate cardiac ATP production via interactions with mitochondrial inner membrane proteins, especially those in mitochondrial complex I. Binding to ribosomal proteins, 14-3-3 proteins likely coordinate protein synthesis and protein quality control. Localizations of 14-3-3 proteins to mitochondria and ribosome were validated via immunofluorescence assays. The deduced function of cardiac 14-3-3 PPIs is to regulate cardiac metabolic homeostasis and proteostasis. Conclusions: Thus, the cardiac 14-3-3 interactome may be a potential therapeutic target in cardiovascular metabolic and proteostatic disease states, as it already is in cancer therapy.
ARTICLE | doi:10.20944/preprints202208.0323.v1
Online: 17 August 2022 (11:29:02 CEST)
The hematopoietic transcription factor Ikaros (IKZF1) regulates normal B cell development and functions as a tumor suppressor in precursor B cell acute lymphoblastic leukemia (B-ALL). MicroRNAs (miRNAs) are small regulatory RNAs that through post-transcriptional gene regulation play critical roles in intracellular processes including cell growth in cancer. However, the role of Ikaros in the regulation of miRNA expression in developing B cells is unknown. In this study, we examined the Ikaros-regulated miRNA targets using patient-derived IKZF1-mutated B-ALL xenograft-derived cell lines. Inducible expression of wild-type Ikaros (the Ik1 isoform) caused B-ALL growth arrest and exit from the cell cycle. Global miRNA expression analysis revealed a total of 31 miRNAs regulated by IK1, and ChIP-seq analysis showed that Ikaros bound to several Ik1-responsive miRNA genes. Examination of the prognostic significance of miRNA expression in B-ALL indicate that the IK1-regulated miRNAs hsa-miR-26b, hsa-miR-130b and hsa-miR-4649 are significantly associated with outcome in B-ALL. Our findings establish a potential regulatory circuit between the tumor-suppressor Ikaros and the oncogenic miRNA networks in IKZF1-mutated B-ALL. These results indicate that Ikaros regulates the expression of a subset of miRNAs, of which several may contribute to B-ALL growth.
REVIEW | doi:10.20944/preprints202208.0285.v1
Online: 16 August 2022 (09:52:17 CEST)
Regardless of the advances in our ability to detect early and treat breast cancer, it is still one of the common types of malignancy worldwide, with the majority of patients decease upon metastatic disease. Nevertheless, due to these advances, we have extensively characterized the drivers and molecular profiling of breast cancer and further dividing it into subtypes. These subgroups are based on immunohistological markers (Estrogen Receptor-ER, Progesterone Receptor-PR and Human Epidermal Growth Factor Receptor 2-HER-2) and transcriptomic signatures, with distinct therapeutic approaches and regiments. These therapeutic approaches include targeted therapy (HER-2+), endocrine therapy (HR+) or chemotherapy (TNBC) with optional combination radiotherapy, depending on clinical stage. Technological and scientific advances in the identification of molecular pathways that contribute to therapy-resistance and establishment of metastatic disease, have provided the rationale for revolutionary targeted approaches against Cyclin-Dependent Kinases 4/6 (CDK4/6), PI3 Kinase (PI3K), Poly ADP Ribose Polymerase (PARP) and Programmed Death-Ligand 1 (PD-L1), among others. In this review, we focus on the comprehensive overview of epidemiology and current standard of care treatment of metastatic breast cancer, along with ongoing clinical trials. Towards this goal, we utilized available literature from PubMed and ongoing clinical trial information from clinicaltrials.gov to reflect the up to date and future treatment options for metastatic breast cancer.
REVIEW | doi:10.20944/preprints202208.0263.v1
Subject: Life Sciences, Molecular Biology Keywords: Neural stem cells; Reprogramming; Neurons; MicroRNA; Somatic cells; Trans-Differentiation; miRNA
Online: 15 August 2022 (12:00:33 CEST)
Brain stem cells (neural stem cells or NSCs) and neurons of a chosen kind reprogramming is a potential technique for cell therapy. It is possible to reprogram non-neuronal cells, for example, by using a predetermined group of factors, nuclear transfer, and the induced transcriptional factors (TFs) expression in a related lineage of cells, and non-coding microRNAs (miRNAs). Researchers have additionally been attempting to improve reprogramming methods, whether it is by employing unique sets of biomolecules and particular TFs or by delivering relevant miRNA and Biomolecules. The technique of miRNA mediated is intriguing for its capability to quickly create a range of biologically desirable cell types for therapy from different lineages of cells. Current findings have made significant advancements towards changing the somatic cells to diverse particular neuronal subgroups with greater efficiency, using reprogramming of miRNA-mediated neural cells, despite the fact that the precise processes need to be discovered. To further understand how miRNAs might direct somatic cells to become neural, we need to look at the latest research on their function in neural reprogramming over the differentiated cells. Recent findings on the role of miRNAs in the initiation of cell reprogramming and the determination of the neuronal subtype's destiny are the primary focus of this comprehensive overview. Furthermore, we cover the far more latest results concerning certain miRNAs' activity in controlling different phases of neuronal differentiation, which contributes in comprehending the interaction network of miRNAs and their receptors.
ARTICLE | doi:10.20944/preprints202208.0191.v1
Subject: Life Sciences, Molecular Biology Keywords: bacterial genomics; de novo assembly; Oxford Nanopore Technologies; Snakemake
Online: 10 August 2022 (04:37:01 CEST)
With the advancement of long-read sequencing technologies and their more widespread use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also the need for measuring completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run all these programs, I developed two workflows for the workflow management system Snakemake for bacterial genome assembly and evaluation of assemblies, which provide end users with an easy-to-run method for both tasks. The workflows are available as open source software under the MIT license at https://github.com/pmenzel/ont-assembly-snake and https://github.com/pmenzel/score-assemblies.
ARTICLE | doi:10.20944/preprints202207.0442.v1
Subject: Life Sciences, Molecular Biology Keywords: COVID-19; molecular diagnostic; SARS-CoV-2; Real-time PCR
Online: 29 July 2022 (03:10:47 CEST)
RT-PCR tests have become the gold standard for detecting the SARS-CoV-2 virus in the context of the COVID-19 pandemic. Because of the extreme number of cases in periodic waves of infection, there is a severe financial and logistical strain on diagnostic laboratories. For this reason, alternative implementations, and validations of academic protocols, that employ the lowest cost and most widely available equipment and reagents found in different regions, is essential. In this study, we report an alternative implementation of the EUA 2019-nCoV CDC assay which uses a previously characterized duplex PCR reaction for the N1 and RNAse P target regions and an additional uniplex reaction for the N2 target region. Taking advantage of the Abbott m2000 Sample Preparation System and NEB Luna Universal Probe One-Step RT-qPCR kit, some of the most widely available and lowest cost nucleic acid extraction and amplification platforms, this modified test shows a state-of-the-art analytical and clinical sensitivities and specificities, when compared with the Seegene Allplex-SARS-CoV-2 assay. This implementation has the potential to be verified and implemented by diagnostic laboratories around the world to guarantee low-cost RT-PCR tests that can take advantage of widely available equipment and reagents.
ARTICLE | doi:10.20944/preprints202207.0409.v1
Subject: Life Sciences, Molecular Biology Keywords: QNBC (Quadruple negative breast cancer); AR (Androgen receptor); AA (African American); CA (Caucasian); BC (Breast cancer)
Online: 27 July 2022 (04:07:32 CEST)
Background: We previously found that QNBC tumors are more frequent in African Americans compared to TNBC tumors. To characterize this subtype further, we sought to determine the miRNA-mRNA profile in QNBC patients based on race. Methods: Both miRNA and mRNA expression data were analyzed from TCGA and validated using datasets from the METABRIC, TCGA proteomic, and survival analysis by KMPLOT. Results: miRNA-mRNAs which include FOXA1 and MYC (mir-17/20a targets); GATA3 and CCNG2 (mir-135b targets); CDKN2A, CDK6, and B7-H3 (mir-29c targets); and RUNX3, KLF5, IL1-β, and CTNNB1 (mir-375 targets) were correlated with basal-like and immune subtypes in QNBC patients and associated with a worse survival. Conclusion: Thus, QNBC tumors have an altered gene signature implicated in racial disparity and poor survival.
ARTICLE | doi:10.20944/preprints202207.0127.v1
Subject: Life Sciences, Molecular Biology Keywords: Epigenetic regulation; Histone demthylases; JMJC; IDR; biomolecular condensates
Online: 7 July 2022 (12:59:29 CEST)
JmjC-family of lysine demethylases (JMJC-KDMs) plays an essential role controlling gene expression and chromatin structure. In most cases, their function has been attributed to the demethylase activity. However, accumulating evidence demonstrates that these proteins play roles distinct from histone demethylation. This raises the possibility that they might share domains that contribute to their functional outcome. Here, we show that the JMJC-KDMs contain low complexity domains as well as intrinsically disordered regions, which in some cases reached 70% of the protein. Our data revealed that PHF2, KDM2A and KDM4B cluster by phase-separation in vitro and in vivo. Moreover, our molecular analysis demonstrated that these domains are important to regulate transcription, suggesting that clustering via phase -separation is a common feature that JMJC-KDMs utilize, in addition to their catalytic activity, to facilitate their functional responses. Our study uncovers a novel potential function for the JMJC-KDM family that sheds light on the mechanisms to achieve the competent concentration of molecules in time and space within the cell nucleus.
REVIEW | doi:10.20944/preprints202207.0125.v1
Subject: Life Sciences, Molecular Biology Keywords: hybridization; sexuality; asexuality; biotype; species; sex determination; ploidy level; Carassius auratus complex
Online: 7 July 2022 (09:56:49 CEST)
Sexual vs asexual reproduction—unisexual vs bisexual populations—diploid vs polyploid biotypes—genetic vs environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. Two Carassius entities with completely different biological characteristics exist: one globally widespread and invasive Carassius gibelio, and the other C. carassius with decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance advantages of highly invasive and disadvantages of threatened species. For example, benefits of a wide-ranged colonization can lead toward extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and importance of the Carassius genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in Carassius may be applied in conservation efforts to sustain threatened populations in their native ranges. Also, the review focuses on consequences of co-occurrence of native and non-native species and outlines future perspectives of Carassius research.
REVIEW | doi:10.20944/preprints202207.0099.v1
Subject: Life Sciences, Molecular Biology Keywords: mass spectrometry; substrate-trapping assay; BioID; POLDIP2; LRPPRC; GRSF1; PNPT1; MTIF2; ataxia
Online: 6 July 2022 (15:26:30 CEST)
In the matrix of bacteria/mitochondria/chloroplasts, Lon acts as the degradation machine for soluble proteins. In stress periods, however, proteostasis and survival depend on the strongly conserved Clp/Hsp100 family. Currently, the targets of ATP-powered unfoldases/disaggregases ClpB and ClpX, and of peptidase ClpP heptameric rings, are still unclear. Trapping experiments and proteome profiling in multiple organisms triggered confusion, so we analyzed the consistency of ClpP-trap targets in bacteria. We also provide meta-analyses of protein interactions in humans, to elucidate where Clp family members are enriched. Furthermore, meta-analyses of mouse complexomics are provided. Genotype-phenotype correlations confirmed our concept. Trapping, proteome, and complexome data retrieved consistent coaccumulation of ClpXP with GFM1 and TUFM orthologs. ClpX shows broad interaction selectivity encompassing mitochondrial translation elongation, RNA granule, and nucleoid; ClpB preferentially attaches to mitochondrial RNA granule and translation initiation components; ClpP is enriched with them all, and associates with release/recycling factors. Mutations in ClpP cause Perrault syndrome, with phenotypes similar to defects in mtDNA/mtRNA. Thus, we propose that ClpB and ClpXP are crucial to counteract misfolded insoluble protein assemblies that contain nucleotide-phosphates. This insight is relevant to improve ClpP-modulating drugs that block bacterial growth, and for the treatment of human infertility, deafness and neurodegeneration.
ARTICLE | doi:10.20944/preprints202207.0030.v1
Online: 4 July 2022 (04:39:27 CEST)
Rett syndrome (RTT) is a rare disease and one of the most abundant causes for intellectual disa-bilities in females. Single mutations in the gene coding for methyl-CpG-binding protein 2 (MECP2), are responsible for the disease. MeCP2 regulates gene expression as a transcriptional regulator as well as through epigenetic imprinting and chromatin condensation. Consequently, numerous biological pathways on multiple levels are influenced however, the exact molecular pathways from genotype to phenotype are currently not fully elucidated. Treatment of RTT is purely symptomatic where no curative options for RTT have yet to reach the clinic. The paucity of this is mainly due to an incomplete understanding of the underlying pathophysiology of the dis-order with no clinically useful common disease drivers, biomarkers or therapeutic targets being identified. With the premise of identifying universal and robust disease drivers and therapeutic targets, here we interrogated a range of RTT transcriptomic studies spanning different species, models and MECP2 mutations. A meta-analysis using RNA sequencing data from brains of RTT mouse models human post-mortem brain tissue and patient-derived induced pluripotent stem cells (iPSC) neurons was performed using Weighted Gene Correlation Network Analysis (WGC-NA). This study identified a module of genes common to all datasets with the following ten hub genes driving the expression ATRX, ADCY7, ADCY9, SOD1, CACNA1A, PLCG1, CCT5, RPS9, BDNF and MECP2. Here we discuss the potential benefits of these genes as therapeutic targets.
ARTICLE | doi:10.20944/preprints202207.0025.v1
Subject: Life Sciences, Molecular Biology Keywords: Bulinus; Schistosoma haematobium; urogenital schistosomiasis
Online: 1 July 2022 (17:58:08 CEST)
The freshwater snail genus Bulinus plays a vital role in transmitting parasites of the Schistosoma haematobium group. A hybrid schistosome between S. haematobium and S. mattheei has been recently detected using DNA-based identification methods in school children along the Lake Malawi shoreline in Mangochi District. This finding raised the need for contemporary revaluation of local interactions between schistosomes and snails, with a particular focus on snail species within the Bulinus africanus group. In 2017 and 2018, malacological surveys sampled several freshwater sites in Mangochi District. Collected snails (n= 250) were characterised using cytochrome oxidase subunit 1 gene (cox1), with DNA barcoding of the ‘Folmer’ region and a rapid PCR-RFLP typing assay with double digestion with HaeIII and SacI restriction enzymes. DNA cox1 sequence analysis, with phylogenetic tree construction, suggested the presence of at least three Bu. africanus group taxa in Lake Malawi, Bu. globosus, alongside first reports of Bu. africanus and Bu. angolensis, which can be differentiated by PCR-RFLP methods. In addition, A total of 30 of the 106 Bu. africanus group snails (28.30%) were positive to the Schistosoma-specific screen using real-time PCR methods. This study provides new insight into the recent changes in the epidemiology of urogenital schistosomiasis as likely driven by a new diversity of Bu. africanus group snails within the lake
REVIEW | doi:10.20944/preprints202207.0024.v1
Subject: Life Sciences, Molecular Biology Keywords: post-translation modifications; CK2; Huntington’s Disease; Kinase Inhibition; HTT phosphorylation
Online: 1 July 2022 (17:47:10 CEST)
Huntington’s Disease (HD) is a devastating neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the HTT gene, for which no disease modifying therapies are currently available. Much of the recent research has focused on developing therapies to directly lower HTT expression, and while promising, these therapies have presented several challenges regarding administration and efficacy. Another promising therapeutic approach is the modulation of HTT post-translational modifications (PTMs) that are dysregulated in disease and have shown to play a key role in HTT toxicity. Among all PTMs, modulation of HTT phosphorylation has been proposed as an attractive therapeutic option due to the possibility of orally administering specific kinase effectors. One of the kinases described to participate in HTT phosphorylation is Protein Kinase CK2. CK2 has recently emerged as a target for the treatment of several neurological and psychiatric disorders, although its role in HD remains controversial. While pharmacological studies in vitro inhibiting CK2 resulted in reduced HTT phosphorylation and increased toxicity, genetic approaches in mouse models of HD have provided beneficial effects. In this review we discuss potential therapeutic approaches related to the manipulation of HTT-PTMs with special emphasis on the role of CK2 as a therapeutic target in HD.
ARTICLE | doi:10.20944/preprints202207.0009.v1
Subject: Life Sciences, Molecular Biology Keywords: co-expression network, water deprivation, drought, systems biology, network centrality, computational simulation, Arabidopsis, transcriptional regulation
Online: 1 July 2022 (08:15:36 CEST)
Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on the plants, a systems biology-based approach is necessitated, entailing the generation of co-expression networks, identification of highly-priority transcription factors (TFs) dynamic mathematical modeling, and computational simulations. Here, we studied a high-resolution drought transcriptome of Arabidopsis. We revealed distinct temporal transcriptional signatures and demonstrated the involvement of specific biological pathways. Generation of a large-scale co-expression network followed by network centrality analyses identified 117 TFs that possess critical properties of hubs, bottlenecks, and high clustering coefficients nodes. Dynamic transcriptional regulatory modeling on integrated TF-target and transcriptome datasets uncovered major transcriptional events during the course of drought stress. Mathematical transcriptional simulations allowed us to ascertain the activation status of major TFs as well as the transcriptional intensity and amplitude of their target genes. Finally, we validated our predictions by providing experimental evidence of gene expression under drought stress for a set of four TFs and their major target genes using qRT-PCR. Taken together, we provided a systems-level perspective on the dynamic transcriptional regulation during drought stress in Arabidopsis and uncovered numerous novel TFs that can potentially be used in future genetic crop engineering programs.
REVIEW | doi:10.20944/preprints202206.0403.v1
Subject: Life Sciences, Molecular Biology Keywords: Endothelium; Endothelium dysfunction; Newer omics technologies; network medicine; biomarkers and therapeutic targets
Online: 29 June 2022 (09:48:20 CEST)
The endothelium has multiple functions from maintaining vascular homeostasis, providing nutrition and oxygen to tissues, to evocating inflammation, under adverse conditions, and determining endo-thelial barrier disruption resulting in dysfunction. Endothelial dysfunction represents the typical condition associated with the pathogenesis of all the diseases of cardiovascular system, as well as of diseases of all the other human body’s systems, also including sepsis, acute respiratory distress syn-drome and COVID-19 respiratory distress. Such evidence is leading to identifying potential bi-omarkers and therapeutic targets for preserving, reverting, or restoring endothelium integrity and functionality by early treating its dysfunction. Here, it stresses some strategies for achieving these goals, even if diverse challenges exist and require a significant bench work associated with an in-creased number of clinical studies.
ARTICLE | doi:10.20944/preprints202206.0385.v1
Subject: Life Sciences, 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/preprints202206.0372.v1
Online: 28 June 2022 (04:08:17 CEST)
The TREX1 exonuclease degrades DNA to prevent aberrant nucleic acid sensing through the cGAS-STING pathway, and dominant Aicardi-Goutières Syndrome type 1 (AGS1) represents one of numerous TREX1-related autoimmune diseases. Monoallelic TREX1 mutations were identified in patients showing early-onset cerebrovascular disease, ascribable to small vessel disease, and CADASIL-like neuroimaging. We report the clinical-neuroradiological features of two patients with AGS-like (Patient A) and CADASIL-like (Patient B) phenotypes carrying the heterozygous p.A136V and p.R174G TREX1 variants, respectively. Genetic findings, obtained by a customized panel including 183 genes associated with monogenic stroke, were combined with interferon signature testing and biochemical assays to determine the mutations’ effects in vitro. Comprehensive studies revealed no pathological impact on TREX1 enzymatic function for the p.A136V variant. The p.R174G variant modestly altered exonuclease activity consistently with perturbation of substrate interaction rather than catalysis, which represents the first robust enzymological data for a TREX1 variant identified in a CADASIL-like patient. In conclusion, functional analysis allowed us to interpret the impact of TREX1 variants on patients’ phenotypes. Whilst Patient A’s manifestations are not related to p.A136V variant, Patient B’s phenotype is likely related to the p.R174G variant. Further functional investigations of TREX1 variants found in CADASIL-like patients are warranted to establish a causal link and interrogate the molecular disease mechanism.
ARTICLE | doi:10.20944/preprints202206.0310.v1
Subject: Life Sciences, Molecular Biology Keywords: astroglial injury; GFAP; calpain; caspase; biomarkers; traumatic brain injury
Online: 22 June 2022 (08:28:02 CEST)
Glial fibrillary acidic protein (GFAP) is the major intermediate filament III protein of astroglia cells which is upregulated in traumatic brain injury (TBI). Here we reported that GFAP is truncated at both the C- and N-terminals by cytosolic protease calpain to GFAP breakdown products (GBDP) of 46-40K then 38K following pro-necrotic (A23187) and pro-apoptotic (staurosporine) challenges to primary cultured astroglia or neuron-glia mixed cells. In addition, with another pro-apoptotic challenge (EDTA) where caspases are activated but not calpain, GFAP was fragmented internally, generating a C-terminal GBDP of 20 kDa. Following controlled cortical impact in mice, GBDP of 46-40K and 38K were formed from day 3 to 28 post-injury. Purified GFAP protein treated with calpain-1 and -2 generates (i) major N-terminal cleavage sites between A-56 and A-75, and (ii) major C-terminal cleavage sites between T-383 and Q-388, producing a limit fragment of 38K. Caspase-6 treated GFAP was cleaved at D-78, R-79, D-266 and A-267, where GFAP was relatively resistant to caspase-3. We also derived a GBDP-38K N-terminal-specific antibody which only labels injured astroglia cell body in both cultured astroglia and mouse cortex and hippocampus after TBI. As a clinical translation, we observed that CSF samples collected from severe human TBI have elevated levels of GBDP-38K as well as two C-terminally released GFAP peptides (DGEVIKES and DGEVIKE). Thus, in addition to intact GFAP, both the GBDP-38K as well as unique GFAP released C-terminal proteolytic peptides species might have the potential in tracking brain injury progression.
ARTICLE | doi:10.20944/preprints202206.0177.v1
Subject: Life Sciences, Molecular Biology Keywords: Deuterium-depleted water (DDW); deuterium-depleted organic compounds (DDOC); anticancer drug development; D/H ratio; production of metabolic water; ketogenic diet
Online: 13 June 2022 (09:49:32 CEST)
Research with deuterium-depleted water (DDW) in the last two decades proved that deuterium/hydrogen ratio has a key role in cell cycle regulation and cellular metabolism. The present study aimed to investigate the possible effect of deuterium-depleted organic compounds (DDOC) alone and in combination with DDW on cancer growth in two in vivo mouse models. To produce DDOC, drinking water of laying hens was replaced with DDW (25 ppm) for 6 weeks, resulting in 60 ppm D level in dried egg yolk that was used as deuterium-depleted food additive. In one model, 4T1, a cell line with high metastatic capacity to the lung, was inoculated in the mice’s mammary pad. After three weeks of treatment with DDW and/or DDOC, the tumor volume in the lungs was smaller in all treated groups vs. controls with natural D level. Tumor growth and survival in mice transplanted with MCF-7 breast cancer cell line showed that the anticancer effect of DDW was enhanced by food containing the deuterium-depleted yolk. The study confirmed the importance of D/H ratio not only in consumed water but also in metabolic water produced by the mitochondria while oxidizing nutrient molecules. This is in line with the concept that initiation of cell growth requires the cells to generate a higher D/H ratio, but DDW, DDOC, or the naturally low-D lipids in a ketogenic diet, have significant effect on tumor growth by preventing the cells from raising D/H ratio to the threshold.
ARTICLE | doi:10.20944/preprints202206.0016.v1
Subject: Life Sciences, Molecular Biology Keywords: lipids; regulation; microalgae; transcription factors
Online: 1 June 2022 (11:09:11 CEST)
Microalgae biomass is considered a promising alternative feedstock for biodiesel production due to its high productivity of neutral lipids, specially under abiotic stress conditions. Among the unicellular microalgae that show this characteristic, Chlamydomonas reinhardtii appears as one of the most important model species that have increased lipids production under abiotic stress conditions. In this study, we show that cells cultivated under mixotrophic condition supplemented with 0.1 M of NaCl rapidly raises their amount of neutral lipids in C. reinhardtii without reduction of their cellular growth rate, being therefore a promising condition for biomass towards bioenergy production. The nuclear proteome of these cells was investigated where we identified 323 proteins with an enrichment of almost 60% of nuclear proteins in the total dataset. We found 61 proteins differentially regulated upon salt treatment, including proteins annotated in functional categories related to translation and nucleosome assembly functions, among others. Additionally, we identified Transcription factor proteins (TFs) and analyzed their likely Transcription factors-binding regulatory elements identifying target genes related to lipids metabolism and kinase functions, indicating possible regulatory pathways of lipids biosynthesis. Together these data can help understand regulatory nuclear mechanisms leading to an increase of lipids in the first 24h of salt stress 0.1M NaCl.
ARTICLE | doi:10.20944/preprints202205.0364.v1
Subject: Life Sciences, Molecular Biology Keywords: Hemoglobin switch; BGLT3-lncRNA expression; chromatin conformation; LRF/ZBTB7A overexpression
Online: 26 May 2022 (10:39:49 CEST)
Hemoglobin switch from fetal (HbF) to adult (HbA) has been studied intensively as an essential model for gene’s expression regulation, but also as a beneficial therapeutic approach for β-hemoglobinopathies, towards the objective of reactivating HbF. Transcription factor LRF (Leukemia/lymphoma-related), encoded from ZBTB7A gene has been implicated in fetal hemoglobin silencing, though has a wide range of functions that have not been fully clarified. We thus established LRF/ZBTB7A-overexpressing and ZBTB7A-knockdown K562 (human erythroleukemia cell line) clones and hemoglobin production was evaluated pre- and post-induction. Related effects on the process of hemoglobin switch from fetal to adult were also assessed. Transgenic K562 clones were further developed and studied under the influence of epigenetic chromatin regulators, such as DNA methyl transferase 3 (DNMT3) and Histone Deacetylase 1 (HDAC1), to evaluate LRF’s potential disturbance upon aberrant epigenetic background and provide valuable information of the preferable epigenetic frame, in which LRF unfolds its action on the β-type globin’s expression. ChIP-seq analysis demonstrated that LRF binds το γ-globin genes (HBG2/1) and apparently associates BCL11A for their silencing, but also, during erythropoiesis induction LRF binds BGLT3 gene promoting BGLT3-lncRNA production through the γ-δ intergenic region of β-type globin’s locus, triggering the transcriptional events from γ- to β-globin switch.
REVIEW | doi:10.20944/preprints202205.0340.v1
Subject: Life Sciences, Molecular Biology Keywords: herbivore-associated elicitors; plant defense; secondary metabolites; signaling metabolites; pattern recognition receptors
Online: 25 May 2022 (03:53:53 CEST)
Insect herbivores have a wide range of life cycles and feeding habits, making them extremely diverse. With their host plants, they form close relationships and suppress their defense mecha-nisms. Molecular elicitors are the key bio-elements in detection and recognition of attacking enemies in tissue consumption. Insect oral secretion, frass, and fluid of egg deposition contain bio-logical active molecules called herbivore-associated elicitors (HAEs) are recognized by pattern recognition receptors (PRRs). However, in insect herbivores, little is known about the molecular basis of signal transduction and regulation of plant resistance. Many plants distinguish insect feeding from wounding by HAEs presenting in their oral secretions (OS) and induce local and systemic responses against arthropod feeding. PRRs perceive HAEs in the oral secretion of cater-pillars in a species-specific manner to elicit exclusive defense responses. HAEs-PRRs interactions induce plant resistance by reprogramming plant metabolism and transcriptional machinery. Quantitative, timely, and coordinated plant response initiate early signalling events including Ca+2, reactive oxygen species (ROS) and mitogen-activated protein kinases (MAPKs). We have discussed how early signalling cascades converge into the accumulation of phytohormones that regulate down-stream special metabolites against herbivores. In this review, we have drawn a hypothetical model of PPRs-HAEs mediated induced responses in plants and discussed how PRRs-HAEs interactions based on molecular mechanism that elicit short- and long-term induced defenses in plants. The identification of plant target insect herbivore PRRs-HAEs interactions will help to explore the fundamental molecular mechanisms of host manipulation and may generate prospects to develop novel pest resistance strategies.
ARTICLE | doi:10.20944/preprints202205.0318.v1
Subject: Life Sciences, Molecular Biology Keywords: HIV; cryptococcal meningitis; HIV-1 viral load; cerebrospinal fluid (CSF) viral escape; Botswana
Online: 24 May 2022 (04:20:08 CEST)
Cerebrospinal fluid (CSF) viral escape has been poorly described among people with HIV-associated cryptococcal meningitis. We determined the prevalence of CSF viral escape and HIV-1 viral load (VL) trajectories in individuals treated for HIV-associated cryptococcal meningitis. A retrospective longitudinal study was performed using paired CSF and plasma collected prior to and during the antifungal treatment of 83 participants recruited at the Botswana site of the phase-3 AMBITION-cm trial (2018-2021). HIV-1 RNA levels were quantified then CSF viral escape (CSF HIV-1 RNA ≥ 0.5 log10 higher than plasma) and HIV-1 VL trajectories were assessed. CSF viral escape occurred in 20/62 (32.3%; 95% confidence interval [CI]: 21.9%-44.6%), 13/52 (25.0%; 95% CI: 15.2%-38.2%) and 1/33 (3.0%; 95% CI: 0.16%-15.3%) participants at days 1, 7 and 14 respectively. CSF viral escape was significantly lower on day 14 compared to days 1 and 7, p=0.003 and p=0.02, respectively. HIV-1 VL de-creased significantly from day 1 to day 14 post antifungal therapy in the CSF but not in the plasma (OR, 0.56; 95% CI: 0.41-0.77; p<0.001). CSF viral escape is high among individuals presenting with HIV-associated cryptococcal meningitis; however, antifungal therapy may reverse this, highlighting the importance of rapid initiation of antifungal therapy in these patients.
REVIEW | doi:10.20944/preprints202205.0014.v2
Subject: Life Sciences, Molecular Biology Keywords: COVID-19; SARS-CoV-2; Diabetes; Neurological dysfunction; Cardiovascular complications; Pulmonary dysfunction; Renal dysfunction; bone loss; Eye disease; Gastrointestinal complications
Online: 23 May 2022 (11:00:06 CEST)
Since the discovery of the Coronavirus disease 2019 (COVID-19) outbreak, a vast majority of studies have been carried out that confirmed the worst outcome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in people with preexisting health conditions, including diabetes, obesity, hypertension, cancer, and cardiovascular diseases. Likewise, diabetes itself is one of the leading causes of global public health concerns that impose a heavy global burden on public health as well as socio-economic development. Both diabetes and SARS-CoV-2 infection have their independent ability to induce the pathogenesis and severity of multi-system organ dysfunction, while the co-existence of these two culprits can accelerate the pathophysiology and magnify the severity of the diseases. However, the exact pathophysiology of multi-system organ failure in diabetic patients after SARS-CoV-2 infection is still obscure. This review summarized the organ-specific possible molecular mechanisms of SARS-CoV-2 and diabetes-induced pathophysiology of several diseases of multiple organs, including the lungs, heart, kidney, brain, eyes, gastrointestinal system, and bones, and subsequent manifestation of multi-system organ failure.
REVIEW | doi:10.20944/preprints202205.0289.v1
Subject: Life Sciences, Molecular Biology Keywords: mitochondria; reactive species; eustress; distress; bioenergetic; microbiota
Online: 23 May 2022 (09:41:06 CEST)
From oxidative eustress and distress, to bioenergetic metabolism, and cell death, the reactive species interactome (RSI) and mitochondria are two connected metabolisms that require further investigation improving redox medicine. The step before, finding new clues needs a comprehensive discussion of the two metabolisms, and their relationship. Here, the review focuses on the RSI-mitochondria axis, from mitochondrial roles to crosstalk between mitochondria and other organelles, and the major implication of the RSI in mitochondrial roles. Specifically, the review discussed the apoptosis-necroptosis-ferroptosis death traingle, mitochondrial protein quality control system, calcium homeostasis, and mitochondrial metabolome. Through mitochondrial diseases, and mitochondrial dysfunction associated with diseases, the RSI-mitochondria axis is proposed as a brand-new perspective, including with the involvement of bacterial microbiota, on redox signaling, and redox medicine.
ARTICLE | doi:10.20944/preprints202205.0224.v1
Subject: Life Sciences, Molecular Biology Keywords: age-related macular degeneration; light-induced photoreceptor degeneration; anti-inflammatory drug; toll-like receptor 4
Online: 17 May 2022 (08:03:11 CEST)
Age-related macular degeneration is a progressive retinal disease that is associated with factors such as oxidative stress, decreased phagocytic activity, and inflammation. In this study, we evaluated the protective effects of SIG-1451, a non-steroidal anti-inflammatory drug developed for treating atopic dermatitis and known to inhibit toll-like receptor 4, on light-induced photoreceptor degeneration. SIG-1451 was intraperitoneally injected into rats once a day before exposure to 1000 lx light for 24 h; one day later, optical coherence tomography showed a decrease in retinal thickness, and electroretinogram (ERG) amplitude was also found to have decreased 3 d after light exposure. Moreover, SIG-1451 protected against this decrease in retinal thickness and increase in ERG am-plitude. One day after light exposure, upregulation of inflammatory response-related genes was observed, and SIG-1451 was found to inhibit this upregulation. Iba-1, a microglial marker, was suppressed in SIG-1451-injected rats. To investigate the molecular mechanism underlying these effects, we used lipopolysaccharide (LPS)-stimulated rat immortalised Müller cells. The upregu-lation of C-C motif chemokine 2 by LPS stimulation was significantly inhibited by SIG-1451 treatment, and western blot analysis revealed a decrease in phosphorylated I-κB levels. These results indicate that SIG-1451 protects photoreceptor cells by attenuating light damage progression through inhibiting inflammatory responses.
ARTICLE | doi:10.20944/preprints202205.0184.v1
Subject: Life Sciences, Molecular Biology Keywords: amyloid precursor protein; photothrombotic stroke; ischemia; alpha-secretase; beta-secretase; gamma-secretase
Online: 13 May 2022 (08:39:09 CEST)
Photothrombotic stroke (PTS) stimulates the level of N- and C-terminal fragments of Amyloid precursor protein (APP) growth in the cytoplasm of ischemic penumbra cells not earlier but at 24 hours. Here we have shown that APP fragments are visualized in thin unmyelinated fibers of neurons, in containing mitochondria large fibers and in synapses but absent in the nuclei. At 24 hours after PTS, some elements of the destroyed tissue accumulated a significant amount of APP protein. The level of ADAM10 α-secretase decreased on the first day after PTS in the rat brain cortex and ADAM-10 co-localized with the lipid raft marker caveolin-1. PTS caused no changes in the level of β-secretase BACE1 either on the first day after PTS or in the early recovery period. The expression of proteins of the γ-secretase complex: presenilin-1 and nicastrin increased in astrocytes, but not in penumbra neurons after PTS. The β-secretase inhibitor LY2886721 did not affect the infarct size of the mouse cerebral cortex and the level of apoptosis of cells in the perifocal region after PTS. Whereas the inhibitor of γ-secretase DAPT reduced the expression of glial fibrillary acidic protein (GFAP) in astrocytes, prevented the growth of apoptosis of mouse cerebral cortex cells reducing the infarct volume on the 7th and 14th days after PTS. DAPT may be considered as a drug for stroke therapy.
REVIEW | doi:10.20944/preprints202205.0166.v1
Subject: Life Sciences, Molecular Biology Keywords: Antimicrobial Peptides (AMPs); Alzheimer’s Disease (AD); infectious hypothesis; beta-amyloid (Ab); lactoferrin; defensins; cystatins; thymosin β4; histatin 1; statherin
Online: 12 May 2022 (09:40:33 CEST)
Alzheimer's Disease (AD) represents the most frequent type of dementia in elderly people. There are two major forms of the disease: sporadic (SAD) - whose causes are not completely understood - and familial (FAD) - with clear autosomal dominant inheritance. The two main hallmarks of AD are extracellular deposits of amyloid-beta (Ab) peptide and intracellular deposits of the hyperphosphorylated form of the tau protein (P-tau). An ever-growing body of research supports the infectious hypothesis of sporadic forms of AD. Indeed, it has been documented that some pathogens, such as herpesviruses and certain bacterial species, are commonly present in AD patients, prompting recent clinical research to focus on the characterization of Antimicrobial Peptides (AMPs) in this pathology. Literature also demonstrates that Ab can be considered itself as an AMP thus representing a type of innate immune defense peptide that protect the host against a variety of pathogens. Beyond Ab, other proteins with antimicrobial activity, such as lactoferrin, defensins, cystatins, thymosin β4, LL37, histatin 1 and statherin have been shown to be involved in AD. Here we have summarized and discussed these findings and explored the diagnostic and therapeutic potential of AMPs in AD.
REVIEW | doi:10.20944/preprints202205.0141.v1
Subject: Life Sciences, Molecular Biology Keywords: Cigarette smoking; e-cigarette smoking; mitochondria; fusion; fission
Online: 10 May 2022 (12:54:42 CEST)
Toxins present in cigarette and e-cigarette smoke constitute a significant cause of illnesses and are known to have fatal health impacts. Specific mechanisms by which toxins present in smoke impair cell repair are still being researched and are of prime interest for developing more effective treatments. Current literature suggests toxins present in cigarette smoke and aerosolized e-vapor trigger abnormal intercellular responses, damage mitochondrial function, and consequently disrupt the homeostasis of the organelle’s biochemical processes by increasing reactive oxidative species. Increased oxidative stress sets off a cascade of molecular events, disrupting optimal mitochondrial morphology and homeostasis. Furthermore, smoking-induced oxidative stress may also amalgamate with other health factors to contribute to various pathophysiological processes. An increasing number of studies show that toxins may affect mitochondria even though exposure to secondhand or thirdhand smoke. This review assesses the impact of toxins present in tobacco smoke and e-vapor on mitochondrial health, networking, and critical structural processes including mitochondria fission, fusion, hyperfusion, fragmentation, and mitophagy. The efforts are focused on discussing current evidence linking toxins present in first, second, and thirdhand smoke to mitochondrial dysfunction
REVIEW | doi:10.20944/preprints202205.0117.v1
Subject: Life Sciences, Molecular Biology Keywords: Transposon; Cancer; Neurological Disease; Evolution; LINE; SINE; ERV
Online: 9 May 2022 (10:50:37 CEST)
Transposable elements (TEs) ubiquitously exist in the human genome, and some have the ability to copy and paste themselves to other locations, resulting in new insertions. Organisms have evolved with mechanisms and machineries to repress such activity. TEs are also co-opted for beneficial functions by the host and are thus maintained in the genome. During the lifetime of humans, aberrant TE activity might cause or contribute towards diseases including neurological conditions such as Alzheimers Disease (AD) and cancer. While inflammatory pathways linked to TEs may be a part of the disease pathology, on the other hand altered TE activity involving inflammatory pathways could be recognised by disease suppression mechanisms. For this reason, TEs could be targeted for therapeutic applications aiming to prevent TE activity or reduce initial inflammatory pathways as well as to activate disease suppression mechanisms. In this review, we describe the contributory and potential preventative roles of TEs in neurological conditions and cancer from a molecular and evolutionary perspective. Evolutionary paradigms both at the unicellular and organismal level aid understanding the role of TEs in disease. These observations could pave the way for the development of novel therapeutic approaches targeting TEs.
ARTICLE | doi:10.20944/preprints202205.0081.v1
Subject: Life Sciences, Molecular Biology Keywords: fatty acid; RNAseq; transcriptome; immune response; Huntington's disease; metabolism; hepatic tissue; Longissimus lomborum; biomedical model
Online: 6 May 2022 (13:58:59 CEST)
The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal model for metabolic diseases in human. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n=17 and SOY3.0, n=18) and 36 samples of skeletal muscle (SOY1.5, n=18 and SOY3.0, n=18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune process, and pathways associated with the oxidative stress, type 2 diabetes and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet.
BRIEF REPORT | doi:10.20944/preprints202205.0018.v2
Online: 6 May 2022 (11:55:20 CEST)
The rapid emergence and worldwide detection of the SARS-CoV-2 omicron variant underscore the importance of robust genomic surveillance systems and prompt information sharing among global public health partners. The Omicron variant has rapidly replaced the delta variant as a dominating SARS-CoV-2 variant because of natural selection, favoring the variant with higher infectivity and more strong vaccine breakthrough ability. Also known as B.1.1.529, Omicron has four sub-variants, BA.1, BA.2, BA.3, and BA.4. Among them, BA.1 is the currently prevailing sub-variant, BA.2 is found to be able to alarmingly re-infect patients initially infected by omicron BA.1. BA.3 sub-variants is a combination of mutations of BA.1 and BA.2, especially in the spike protein. Today emerging is the BA.4, herein described and first detected in Italy, harboring a new mutation, specifically a deletion in the ORF 1 ab gene, corresponding to KSF141_del in non-structural protein 1 (nsp1), a critical virulence factor able to suppress host translation. The bioinformatics comparison analysis with the other three sub-variants pointed out that the deletion was not present previously and was never reported until now. Therefore, we can speculate that omicron BA.4; will become a new dominating “variant of concern” and might also break vaccine protection . On the other hand, we show that other proteins are mutated in the BA.4 in particular, seven mutations are recognized in the nucleocapsid (N) protein, the capability of five different types of rapid antigenic tests to recognize it.
ARTICLE | doi:10.20944/preprints202205.0008.v1
Subject: Life Sciences, Molecular Biology Keywords: Chronic Myeloid Leukaemia; BCR/ABL; CRISPR; Gene therapy; CRISPR-Trap.
Online: 4 May 2022 (12:30:11 CEST)
Chronic myeloid leukaemia (CML) is a haematological neoplasm driven by the BCR/ABL fusion oncogene. The monogenic aspect of the disease and the feasibility of ex vivo therapies in haematological disorders make CML an excellent candidate for gene therapy strategies. The ability to abolish any coding sequence by CRISPR-Cas9 nucleases offers a powerful therapeutic opportunity to CML patients. However, a definitive cure can only be achieved when only CRISPR-edited cells are selected. A gene-trapping approach combined with CRISPR technology would be an ideal approach to ensure this. Here, we have developed a CRISPR-Trap strategy that efficiently inserts a donor gene trap (SA-CMV-Venus) cassette into the BCR-ABL1-specific fusion point in the CML K562 human cell line. The trapping cassette interrupts the on-cogene coding sequence and expresses a reporter gene that enables the selection of edited cells. Quantitative expression analyses showed significantly higher level of expression of the BCR-Venus allele coupled with a drastically lower level of BCR/ABL expression in Venus+ cell fractions. Functional in vitro experiments showed cell proliferation arrest and apoptosis in selected Venus+ cells. Finally, xenograft experiments with the selected Venus+ cells showed a large reduction in tumour growth, thereby demonstrating a therapeutic benefit in vivo. This study is a proof of concept for the therapeutic potential of a CRISPR-Trap system as a novel strategy for gene elimination in haematological neoplasms.
ARTICLE | doi:10.20944/preprints202205.0001.v1
Subject: Life Sciences, Molecular Biology Keywords: ovarian cancer; ALDH1A1; cancer stem cells; senescence; chemotherapy resistance
Online: 2 May 2022 (09:39:22 CEST)
Ovarian cancer is a deadly disease attributed to late-stage detection as well as recurrence and development of chemoresistance. Ovarian cancer stem cells (OCSCs) are hypothesized to be largely responsible for emergence of chemoresistant tumors. Although chemotherapy may initially succeed at decreasing the size and number of tumors, it leaves behind residual malignant OCSCs. In this study, we demonstrate that Aldehyde dehydrogenase 1A1 (ALDH1A1) is essential for the survival of OCSCs. We identified a novel ALDH1A1 inhibitor, compound 974, and used 974 as a tool to decipher the mechanism of stemness regulation by ALDH1A1. Treatment of OCSCs with 974 significantly inhibited ALDH activity, expression of stemness genes, spheroid, and colony formation. In vivo limiting dilution assay demonstrated that 974 significantly inhibited CSC frequency. Transcriptomic sequencing of cells treated with 974 revealed significant downregulation of genes related to stemness and chemoresistance as well as senescence and senescence associated secretory phenotype (SASP). We confirmed that 974 inhibited senescence and stemness induced by platinum-based chemotherapy in functional assays. Overall, these data establish that ALDH1A1 is essential for OCSCs survival and ALDH1A1 inhibition sup-presses chemotherapy induced senescence and stemness. Targeting ALDH1A1 using small molecule inhibitors in combination with chemotherapy therefore presents a promising strategy to pre-vent ovarian cancer recurrence and has potential for clinical translation.
ARTICLE | doi:10.20944/preprints202204.0248.v1
Subject: Life Sciences, Molecular Biology Keywords: granulosa cells; heat stress; integrated analysis; transcriptomics; metabolomics; differentially ex-pressed genes; metabolites; signaling pathways; metabolic pathways; cancer pathways
Online: 27 April 2022 (05:08:15 CEST)
Previous studies reported the physical, transcriptomics and metabolomics changes in in-vitro acute heat stressed bovine granulosa cells. Granulosa cells exhibited transient proliferation senescence, oxidative stress, increased rate of apoptosis, and decline in steroidogenic activity. This study performs joint integration and network analysis of metabolomics and transcriptomics data to further narrow down and elucidate the role of differentially expressed genes, important metab-olites and relevant cellular and metabolic pathways in acute heat-stressed granulosa cells. Among significant (Raw P-value <0.05) metabolic pathways where metabolites and genes did converge, this study found Vitamin B6 metabolism, Glycine, serine and threonine metabolism, Phenylalanine metabo-lism, Arginine biosynthesis, Tryptophan metabolism, Arginine and proline metabolism, Histidine metabolism, and Glyoxylate and dicarboxylate metabolism. Important significant convergent bio-logical pathways included, ABC transporters and Protein digestion and absorption, while func-tional signaling pathways included cAMP, mTOR, and AMPK signaling pathways together with Ovarian steroidogenesis pathway. Among caner pathways, the most important pathway was Central carbon metabolism in cancer. Through multiple analysis query, Progesterone, Serotonin, citric acid, Pyridoxal, L-Lysine, Succinic acid, L-Glutamine, L-Leucine, L-Threonine, L-Tyrosine, Vitamin B6, Choline, and CYP1B1, MAOB, VEGFA, WNT11, AOX1, ADCY2, ICAM1, PYGM, SLC2A4, SLC16A3, HSD11B2 and NOS2 appeared to be important enriched metabolites and genes, respectively. These genes, metabolites, metabolic, cellular and cell signaling pathways com-prehensively elucidate the mechanisms underlying the intricate fight between death and survival in acute heat-stressed bovine granulosa cells, and essentially help further our understanding and future quest of research in this direction.
ARTICLE | doi:10.20944/preprints202204.0245.v1
Subject: Life Sciences, Molecular Biology Keywords: meiosis-I; zygotene-pachytene; homologous recombination; H3K9ac; acetyl-tubulin; Twinkle helicase; RMND1; tRNA /rRNA processing; cGAS-STING signaling
Online: 27 April 2022 (02:55:32 CEST)
Human Perrault syndrome (PRLTS) is defined by autosomal recessive inheritance with primary ovarian insufficiency and early hearing loss. Most PRLTS disease proteins modulate mitochondrial transcription or translation. Among the genetic causes are ClpP mutations, which trigger also complete azoospermia, whose cellular and molecular underpinnings are unknown. Here, the ClpP-null mouse model was studied by global transcriptomics, proteomics, RT-qPCR, immunoblots, tissue fractionation, testis histology, and was crossed with STING/IFNAR mutants. Spermatogenesis showed accumulated early spermatocytes, versus deficits of desynapsis and kinetochore factors; excess Dazl/Stra8 and acetylSMC3, versus deficient SHCBP1L, were molecular correlates. Spermiogenesis showed few round spermatids, tsHMG/TFAM in elongated spermatids was absent; transcripts for tail/acrosome factors were downregulated from start. Nuclear anomalies included a failed Rec8 induction, early BRDT deficiency, histone H3 cleavage, and cGAMP increase, among antiviral responses typical of ClpP-mutants. However, deletion of downstream innate immune signals STING/IFNAR failed to reestablish fertility. As mitochondrial triggers, we observed accumulation of ClpX, with PTCD1, POLDIP2, GRSF1, ALKBH7, DNAJA3, AURKAIP1, VWA8, and Perrault proteins ERAL1, PEO1, HARS2, partially showing nuclear redistribution. ClpP-depletion is known to cause extra-mitochondrial release of mispacked mtDNA/mtRNA/protein complexes. Now we define nuclear inflammatory responses and meiotic arrest as consequences, similar to observations in mito-mice and mutator-mice.
ARTICLE | doi:10.20944/preprints202204.0208.v1
Subject: Life Sciences, Molecular Biology Keywords: sulfate deficiency; Arabidopsis thaliana; Solanum lycopersicum; Triticum aestivum; LSU; response to low sulfur; abiotic stress; sulfur nutrition
Online: 22 April 2022 (03:32:19 CEST)
LSU (RESPONSE TO LOW SULFUR) proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. However, little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant species with whole genome sequence available. Phylogenetic analysis revealed that LSU genes belong to a Spermatophyta-specific gene family, and their homologs are distributed in three major groups, two for dicotyledons and one group for monocotyledons. Moreover, we analyzed the expression of LSU genes in one representative species of each phylogenetic group (wheat, tomato and Arabidopsis) and found a conserved response to S-deficiency, suggesting that these genes might play a key role in S stress responses. Accordingly, Arabidopsis lsu2 knockout mutant plants showed increased levels of internal sulfate content and lower levels of expression of different key genes involved in S deficiency and metabolism like SDI2 and APR3. In summary, our results indicate that LSU genes are evolutionarily conserved in angiosperms and that specific members of this family might play an important role regulation of S transport and assimilation.
HYPOTHESIS | doi:10.20944/preprints202204.0124.v1
Subject: Life Sciences, Molecular Biology Keywords: Senescence; EMT; NF-κB; Inflammation; Epigenetics; Aging
Online: 13 April 2022 (10:22:37 CEST)
The origin of cancer remains one of the most important enigmas in modern biology. This paper presents a hypothesis for the origin of carcinomas in which cellular aging and inflammation enable the recovery of cellular plasticity that may ultimately result in cancer. The process is described as the result of dedifferentiation undergone by epithelial cells in hyperplasia due to replicative senescence towards a mesenchymal cell state with potential cancerous behavior. In support of the hypothesis, the molecular, cellular, and histopathological evidence was critically reviewed and reinterpreted when necessary to postulate a plausible generic model for the origin and progression of carcinomas. In addition, the implications of this theoretical framework for the current strategies of cancer treatment are discussed against recent evidence of the molecular events underlying the epigenetic switches involved in the resistance of breast carcinomas. Subsequently, is proposed an epigenetic landscape for their progression and a potential mechanism to restrain the degree of dedifferentiation and malignant behavior. Finally, is suggested a novel understanding of the involution and carcinogenesis of tissues associated with aging as a perspective that might inspire integrative approaches in the study and management of chronic diseases.
REVIEW | doi:10.20944/preprints202204.0117.v1
Subject: Life Sciences, Molecular Biology Keywords: cold stress; wheat; hormonal; reactive oxygen species; epigenetic regulation
Online: 13 April 2022 (07:35:35 CEST)
Cold stress is a major environmental factor affecting the growth, development, and productivity of various crop species. With the current trajectory of global climate change, low temperatures are becoming more frequent and can significantly decrease crop yield. Wheat (Triticum aestivum L.) is the first crop to be domesticated and is the most popular cereal crop in the world. Due to a lack of systematic research on cold response pathways and gene regulatory networks, the underlying molecular mechanisms of cold signal transduction in wheat are poorly understood. This study reviews recent progress in wheat, including the ICE-CBF-COR signaling pathway in cold stress and the effects of cold stress on hormonal pathways, reactive oxygen species (ROS), and epigenetic regulation. This review also highlights outstanding issues that are crucial for understanding the interactions between wheat and low-temperature conditions.
REVIEW | doi:10.20944/preprints202204.0055.v1
Subject: Life Sciences, Molecular Biology Keywords: cell; biology; aging; medicine; transcription; activity; neurons; brain; immune system; muscle
Online: 7 April 2022 (04:24:23 CEST)
In several mammalian species including humans, complex stimulation patterns such as cognitive challenge and physical exercise lead to improvements in organ function, organism health and performance, as well as possibly longer lifespans. The hypothesis is presented here that activity-dependent transcriptional programs, induced by these environmental stimuli, temporarily and lightly de-differentiate somatic cells such as neurons and muscle cells into a state that resembles functionally younger cells to allow cellular remodeling and adaptation of the organism to environmental change. This cellular adaptation program targets several process classes that are heavily implicated in aging, such as mitochondrial metabolism, cell-cell communication, intracellular signaling and epigenetic information processing and leads to functional improvements in these areas. I reverse engineer these activity-dependent gene programs, identify critical molecular nexus points such as CREB, MEF2 and cFos and speculate as to how one might leverage them to prevent and attenuate human aging-related decline of body function, enhance human performance and restore more youthful levels of function and morphology. The findings presented here can serve as a basis for the study and development of effective longevity efforts as the underlying gene programs could be used as markers for treatment success and as targets for therapy development.
ARTICLE | doi:10.20944/preprints202203.0251.v1
Online: 17 March 2022 (10:59:09 CET)
Despite accumulating evidence for the pro-apoptotic role for X-linked inhibitor of apoptosis-associated factor 1 (XAF1), its involvement in endoplasmic reticulum (ER) stress response remains undefined. Here, we report that XAF1 enhances cell sensitivity to ER stress and acts as a switch in unfolded protein response (UPR)-mediated cell-fate decisions favoring apoptosis over adaptive autophagy. XAF1 interacts with and destabilizes ER stress sensor GRP78 through the assembly of zinc finger protein 313-mediated destruction complex. Moreover, XAF1 gene transcription is activated by ER stress through PERK-Nrf2 signaling to direct an adaptive to apoptotic switch of stress response by blocking C-terminus of Hsc70-interacting protein (CHIP)-mediated K63-linked ubiquitination and subsequent phosphorylation of inositol-required enzyme-1α (IRE1α). In tumor xenograft assays, XAF1-/- tumors display substantially lower regression compared to XAF1+/+ tumors in response to cytotoxic dose of ER stress inducer. XAF1 and GRP78 expression show an inverse correlation in human cancer cell lines and primary breast carcinomas. Collectively this study uncovers an important role for XAF1 as a linchpin to govern the sensitivity to ER stress and the outcomes of UPR signaling, illuminating the mechanistic consequence of XAF1 inactivation in tumorigenesis.
REVIEW | doi:10.20944/preprints202203.0170.v2
Subject: Life Sciences, Molecular Biology Keywords: cancer; DNA informational entropy; cell compartmentation; evolutionary Biology; lactate dehydrogenase (LDH); lactic acid; metabolism; thermodynamic entropy; Warburg effect
Online: 17 March 2022 (03:37:53 CET)
Attempts to find and quantify the supposed low entropy of organisms and its preservation are revised. Absolute entropy of the mixed components of non-living biomass (around -1.6 x 103 J K-1 L-1) is the reference to which other entropy decreases would be ascribed to life. Compartmentation of metabolites and departure from the equilibrium of metabolic reactions account for 1 and 40-50 J K-1 L-1, respectively, decreases of entropy and, though small, are distinctive features of living tissues. DNA and proteins do not supply significant decreases of thermodynamic entropy, but their low informational entropy is relevant for life and its evolution. No other living feature contributes significantly to the low entropy associated to life. The photosynthetic conversion of radiant energy to biomass energy accounts for the most of entropy (2.8 x 105 J K-1 carbon kg-1) produced by living beings. The comparative very low entropy produced in other processes (around 4.8 x102 J K-1 L-1 day-1 in human body) must be rapidly exported outside as heat to preserve the low entropy decreases due to compartmentation and non-equilibrium metabolism. Enzymes and genes are described whose control minimize the rate of production of entropy and could explain selective pressures in biological evolution and the rapid proliferation of cancer cells.
ARTICLE | doi:10.20944/preprints202202.0357.v1
Subject: Life Sciences, Molecular Biology Keywords: granulosa cells; heat stress; apoptosis; oxidative stress; RNA-seq; transcriptomics; differentially expressed genes; signaling pathways
Online: 28 February 2022 (11:08:42 CET)
Heat stress affects the granulosa cells (GCs) and ovarian follicular microenvironment, causing poor oocyte developmental competence and fertility. This study aimed to investigate the physical responses and global transcriptomic changes in bovine GCs to acute heat stress (43 ℃ for 2 h) in-vitro and gave essential insights into the general interaction at cell–stress nexus. Heat-stressed GCs exhibited transient proliferation senescence, resumed proliferation at 48 h post-stress. While post-stress immediate culture-media change had a relatively positive effect on proliferation resumption. Increased accumulation of reactive oxygen species and apoptosis was observed in heat stress group. In spite of the upregulation of pro-apoptotic and caspase executioner genes, antioxidants and anti-apoptotic genes were also upregulated in heat-stressed GCs. Progesterone and Estrogen hormones along with steroidogenic genes expression, declined significantly, in spite of the upregulation of genes involved in cholesterol synthesis. Out of 12385 differentially expressed genes (DEGs), 330 significant DEGs (75 upregulated, 225 downregulated) were subjected to KEGG functional pathway annotation, gene ontology enrichment, and STRING network analyses. Based on the manual query of DEGs, pathway and enrichment analyses, a vast interplay observed among all major signaling pathways strongly evidence the repression of cellular transcriptional and proliferation activity, averting the effects of heat stress through remodeling of cellular structural proteins and energetic-homeostasis. This study presents detailed responses of acute heat-stressed GCs at physical, transcriptional, and pathway levels and presents interesting insights into future studies regarding GCs adaptation and their interaction with oocyte and reproductive system at ovarian level.
ARTICLE | doi:10.20944/preprints202202.0249.v1
Subject: Life Sciences, Molecular Biology Keywords: HIV Nef; neurotoxicity; inflammatory cytokines; kynurenine metabolite
Online: 21 February 2022 (10:00:10 CET)
HIV-1 Nef is a multifunctional protein with well-known lethal properties. HIV infects various cells from the brain compartment and expressed nef is responsible for developing neuropathogenic potential. HIV-infected glial cells express nefvirotoxinand stimulate the cascade of various pathways to activate uninfected cells to release neurotoxic elements damaging cells themselves. A lot of genetic variabilities of this protein have been reported from patients with HIV-associated neurocognitive disorders. To determine the neurotoxic potential of subtype-specific nef plasmids and nef plasmids of clinical samples with and without HAND were transfected in normal human astrocytes (NHA) and monocyte-derived macrophages (MDM) using nef-pCMV-HA plasmid constructs. Supernatants from subtype-specific Nef plasmids indicated the upregulation of proinflammatory cytokines. The induced expression might be due to the nef genetic variability or variations in the transfection efficiency and expression levels of nef.The mRNA expression of IL-6, IP-10, and TNF-α indicated upregulation of 5.0-fold in NHA and 3-fold in MDM with respect to empty vector control transfection. Further, the kynurenine metabolites were also assessed from culture supernatants of NHA and MDM indicating the upregulation of IDO and KYNU in NHA by 3.0-fold and 3.2-fold in MDM.The expression levels of nef and cytokines at the translational level were confirmed by western blotting and bio-plex Pro cytokine estimation assay respectively along with controls expressing green fluorescent protein (GFP).The oxidative stress was also found to be elevated as compared to control cells as determined by the estimation of nitric oxide from the culture supernatant to confirm the neurotoxic potential of HIV nef plasmids. The downregulation in the levels of cytokines, as well as kynurenine metabolites, was observed in culture supernatants after blocking the expression of nef using HIV nef siRNA. Phylogenetic analysis of Nef sequences indicated subtype C predominance except one sequence showing the partial sequence of HIV-1 subtype B sequence forming BC recombinantThe upregulation in the cytokine and pathway-specific metabolites might be linked with the neurotoxic potential of HIV-1 Nef leading to neuropathogenesis. In conclusion, the variation in the transfection efficiency, nef expression levels, and the genetic variability of Nef might be responsible for upregulating the expression levels of cytokines and kynurenine metabolites in astrocytes and MDM.
ARTICLE | doi:10.20944/preprints202202.0149.v1
Subject: Life Sciences, Molecular Biology Keywords: immune response; fatty acid; lipid metabolism; RNA-Seq; transcriptome
Online: 10 February 2022 (10:57:03 CET)
The objective of this study was to identify key transcription factors involved in lipid metabolism and immune response related to the differentially expressed genes (DEG) from the liver samples of 35 pig model for metabolic diseases fed diets containing either 1.5 or 3.0% soybean oil (SOY1.5 or SOY3.0). A total of 281 DEG between SOY1.5 and SOY3.0 diets (log2fold-change ≥ 1 or ≤ −1; FDR-corrected p-value < 0.1) were identified, in which 129 were down-regulated and 152 were up-regulated in SOY1.5 group. The functional annotation analysis detected transcription factors linked to lipid homeostasis and immune response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key transcription factors related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive the food technology and science.
ARTICLE | doi:10.20944/preprints202202.0103.v1
Subject: Life Sciences, Molecular Biology Keywords: heart disease; atrial fibrillation; atrial fibrosis; transcriptome; microRNA; RNA sequencing; syndecan-1; miR-302
Online: 7 February 2022 (19:01:55 CET)
Atrial fibrillation (AF) is a form of sustained cardiac arrhythmia and microRNAs (miRs) play crucial roles in pathophysiology of AF. To identify novel miR-mRNA pairs, we performed RNAseq from atrial biopsies of AF and non-AF patients. Differentially expressed miRs (11-down and 9-up) and mRNAs (95-up and 82-down) were identified and hierarchically clustered in a heat-map. Subsequently, GO, KEGG, and GSEA analyses were run to identify deregulated pathways. Then, miR targets were predicted in miRDB database, and a regulatory network of negatively correlated miR-mRNA pairs was constructed using Cytoscape. To select potential candidate genes from GSEA analysis, top-50 enriched genes in GSEA were overlaid with predicted targets of differentially deregulated miRs. Besides, protein-protein-interaction (PPI) network of enriched genes in GSEA was constructed, and subsequently GO and canonical pathway analyses were run for genes in PPI network. Our analyses showed that TNF-α, p53, EMT, and SYDECAN1 signaling were among the highly affected pathways in AF samples. SDC-1 (syndecan-1) was the top-enriched gene in p53, EMT, and SYDECAN1 signaling. Consistently, SDC-1 mRNA and protein levels were significantly higher in atrial samples of AF patients. Among negatively correlated miRs, miR-302b-3p was experimentally validated to suppress SDC-1 transcript levels. Overall, our results suggested that miR-302b-3p/SDC-1 axis may involve in pathogenesis of AF.
ARTICLE | doi:10.20944/preprints202202.0084.v1
Subject: Life Sciences, Molecular Biology Keywords: ribonucleoproteins; spliceosome; centrosome; CEP250
Online: 7 February 2022 (12:12:18 CET)
Ribonucleoproteins (RNP) condensates often contain intrinsically disordered proteins (IDPs) able to confer an exceptional multifunctionality necessary for gene expression, a process that defines cell types and enables cellular adaptation in metazoans. Centosomes, the microtubule-organizing centers of animal cells, are particularly enriched in disordered proteins but the role of RNPs surrounding the centrosome and the ciliary basal body remains largely unknown. By refining and integrating the existing protein-protein interaction network, spatial proteomics and transcriptomic data, we here report the subcellular and genomic proximity between the spliceosome, a huge nuclear RNP complex that removes introns from a transcribed pre-mRNA, and centrosome/cilia components. We present a comprehensive map of pre-RNA processing factors and other RNA-binding proteins playing a role in the regulation of splicing but localized to the centrosome and cilia. Protein-protein interactions studies reveal that a large number of spliceosome components interact with both centrosome linker and centriolar satellites elements, necessary for cellular division and ciliogenesis. RNAseq data from mouse Embryonic Stem Cells (mESC) and human tissues revealed a co-transcriptional coordination program of splicing and centrosome-related genes with relevance to tissue-specific neurosensory disorders and cancer types. Additionally, we found that centrosome and spliceosome genes form linearly and spatially colocalized genomic loci (CEP250, RBBM39, DHX35, and CTNNBL1) conserved in human and mouse genome, then explaining similarities in co-modification and subcellular distribution. Our results suggest that centrosome and cilia constitute cytoplasmic sites for the exchange of molecular machinery with nucleus, storage of RNA splicing and spliceosome condensates previously unrecognized. These complexes in response to external signals, could play an integral part in ciliogenesis and nuclear division to establish and maintain cellular identity in metazoans.
ARTICLE | doi:10.20944/preprints202201.0425.v1
Subject: Life Sciences, Molecular Biology Keywords: transposon; order; triplet frequency; tRNA; clustering; taxonomy; symmetry; photosystem
Online: 27 January 2022 (17:40:07 CET)
A comprehensive presentation of a variety of biologically sounding properties of genomes is present; chloroplast genomes are used as a biological matter. Triplet frequency composition is the general issue standing behind the properties. Besides, the new alignment-free error-tolerant method of sequences comparison highly efficient for in/del mismatches is present, for transposons search. Triplet frequency dictionaries determined for a genome, or for a part of that latter were studied through various clustering techniques. The interplay between triplet composition and function reveals on tRNA genes unambiguously shows the prevalence of the function encoded in tRNA gene over the phylogeny: the genes gather into the clusters comprising the genes encoding the same amino acid; more exactly, few gene families exhibit fine cluster pattern corresponding the synonymous codons of amino acid. Previously reported symmetry in chloroplast genomes is shown for a set of gymnosperm: that is mirror symmetry, rotational symmetry, and the second Chargaff's parity rule asymmetry. A family of transposons was found in gymnosperm chloroplast genomes. This family is revealed through the novel comparison method based on convolution calculation, for a set of DNA sequences.
ARTICLE | doi:10.20944/preprints202201.0324.v1
Subject: Life Sciences, Molecular Biology Keywords: UQCRB; mROS; Autophagy; Colorectal cancer; Lysosome
Online: 21 January 2022 (12:59:47 CET)
Human colon carcinomas, including HCT116 cells, often exhibit high basal autophagic flux under nutrient deprivation or hypoxic conditions. Mitochondrial ROS (mROS) is known as a “molecular switch”’ for regulating the autophagic pathway, which is critical for directing cancer cell survival or death. In early tumorigenesis, autophagy plays important roles in maintaining cellular homeostasis and contributes to tumor growth. However, the relationships between mROS and the autophagic capacities of HCT116 cells are poorly understood. Ubiquinol cytochrome c reductase binding protein (UQCRB) has been reported as a biomarker of colorectal cancer, but its role in tumor growth has not been clarified. Here, we showed that UQCRB was overexpressed in HCT116 cells compared to CCD18co cells, a normal colon fibroblast cell line. Pharmacological inhibition of UQCRB reduced mROS levels, autophagic flux, and the growth of HCT116 tumors in a xenograft mouse model. We further investigated mutant UQCRB-overexpressing cell lines to identify functional links in UQCRB-mROS-autophagy. Notably, an increasing level of mROS caused by UQCRB overexpression released Ca2+ by activation of lysosomal TRPML1 channels. This activation induced transcription factor EB nuclear translocation and lysosome biogenesis, leading to autophagy flux. Collectively, our study showed that increasing levels of mROS caused by overexpression of UQCRB in human colon carcinoma HCT116 cells could be linked to autophagy for cell survival.
ARTICLE | doi:10.20944/preprints202201.0321.v1
Subject: Life Sciences, Molecular Biology Keywords: Periodontitis; Tooth movement; Obesity; Palmitic Acid; Histone Modification; Inflammation; COX2/PGE2; IL10
Online: 21 January 2022 (12:50:31 CET)
The interrelationship between periodontal disease, obesity-related hyperlipidemia and mechanical forces as well as their modulating effects on the epigenetic profile of periodontal ligament (PdL) cells are assumed to be remarkably complex. The PdL serves as connective tissue between teeth and alveolar bone for pathogen defense and inflammatory response to mechanical stimuli occurring during tooth movement. Altered inflammatory signaling could promote root resorption and tooth loss. Hyperinflammatory COX2/PGE2 signaling was reported for human PdL fibroblasts (HPdLF) concomitantly stressed with P. gingivalis lipopolysaccharides and compressive force after exposure to palmitic acid (PA). The aim of this study was to investigate to what extent this is modulated by global and gene-specific changes in histone modifications. Quantitative expression of epigenetic key players and global H3Kac as well as H3K27me3 levels were evaluated in dual stressed HPdLF exposed to PA revealing a decreased force-related reduction in repressive H3K27me3. UNC1999-induced H3K27me3 inhibition reversed the hyperinflammatory response of dual-stressed PA-cultures characterized by COX2 expression, PGE2 secretion and THP1 adhesion. Reduced expression of the anti-inflammatory cytokine IL10 and increased association of H3K27me3 at its promoter-associated sites were reversed by inhibitor treatment. Thus, the data highlight an important epigenetic interplay between different stimuli to which the PdL is exposed.
ARTICLE | doi:10.20944/preprints202201.0225.v1
Subject: Life Sciences, Molecular Biology Keywords: Misdiagnosis; Random Amplification of Polymorphic DNA; 16S rRNA Sequencing; Loop-Mediated Isothermal Amplification; Antibiotic Resistance
Online: 17 January 2022 (12:35:53 CET)
Successful treatment against infectious agents depends on rapid and accurate detection of the causative organisms. Misdiagnosis can hamper such success while leading to improper advising of antibiotics. In Bangladesh, diagnostic centers detect and identify pathogens through culture and biochemical test-based methods and suggest antibiotics based solely on disk-diffusion methods. In this pilot study, we tried to validate the identity of the isolates characterized by diagnostic facilities near Dhaka. One hundred and twenty pre-characterized clinical isolates were collected and analyzed biochemically and genotypically. Random Amplification of Polymorphic DNA-PCR, rcsA, and phoA genes-based PCR and Loop-Mediated Isothermal Amplification (LAMP)-based identification of Klebsiella pneumoniae and Escherichia coli, respectively, followed by 16S rRNA sequencing confirmed misidentification of some clinical pathogens of other genera as Klebsiella spp. and E. coli. The Clinical and Laboratory Standards Institute (CLSI) provides different guidelines for each group of pathogens, where antibiotic choice, sensitivity pattern, and breakpoint measurement are other. The lack of adherence to proper standards resulting in misdiagnosis may facilitate antibiotic-resistant development. Henceforth, we have observed misidentification of clinical pathogens by the diagnostic centers and suggest that using rapid molecular techniques like LAMP may avoid misdiagnosis and subsequently circumvent antibiotic resistance development.
ARTICLE | doi:10.20944/preprints202201.0141.v1
Subject: Life Sciences, Molecular Biology Keywords: SAMHD1; NSCLC; breast cancer; ovarian cancer; solid tumors
Online: 11 January 2022 (13:05:00 CET)
SAMHD1 is a deoxynucleotide triphosphate (dNTP) triphosphohydrolase with important roles in the control of cell proliferation and apoptosis, either through the regulation of intracellular dNTPs levels or the modulation of the DNA damage response. However, SAMHD1 role in cancer evolution is still unknown. We performed the first in-depth study of SAMHD1 role in advanced solid tumors, by analyzing samples of 128 patients treated with chemotherapy agents based on platinum derivatives and/or antimetabolites and developing novel in vitro knock-out models to explore the mechanisms driving SAMHD1 function in cancer. Low or no expression of SAMHD1 was associated with a positive prognosis in breast, ovarian and non-small cell lung cancer (NSCLC) cancer patients. A predictive value was associated to low-SAMHD1 expression in NSCLC and ovarian patients treated with antimetabolites in combination with platinum derivatives. In vitro, SAMHD1 knock-out cells showed increased γ-H2AX and apoptosis suggesting that SAMHD1 depletion induces DNA damage leading to cell death. In vitro treatment with platinum-derived drugs significantly enhanced γ-H2AX and apoptotic markers expression in knock-out cells, indicating a synergic effect of SAMHD1 depletion and platinum-based treatment. SAMHD1 expression represents a new strong prognostic and predictive biomarker in solid tumors and thus, modulation of SAMHD1 function may constitute a promising target for the improvement of cancer therapy.
COMMUNICATION | doi:10.20944/preprints202201.0108.v1
Subject: Life Sciences, Molecular Biology Keywords: Acinetobacter baumannii; antimicrobial resistance; circular dichroism spectroscopy; efflux protein; efflux pump; foodborne pathogen; hospital-acquired infection; polyamine
Online: 10 January 2022 (12:19:07 CET)
The aim of this work was to test polyamines as potential natural substrates of the Acinetobacter baumannii chlorhexidine efflux protein AceI using near-UV synchrotron radiation circular dichroism (SRCD) spectroscopy. The Gram-negative bacterium A. Baumannii is a leading cause of hospital-acquired infections and an important foodborne pathogen. A. Baumannii strains are becoming increasingly resistant to antimicrobial agents, including the synthetic antiseptic chlorhexidine. AceI was the founding member of the recently recognised PACE family of bacterial multidrug efflux proteins. Using the plasmid construct pTTQ18-aceI(His6) containing the A. Baumannii aceI gene directly upstream from a His6-tag coding sequence, expression of AceI(His6) was amplified in E. coli BL21(DE3) cells. Near-UV (250-340 nm) SRCD measurements were performed on detergent-solubilised and purified AceI(His6) at 20 °C. Sample and SRCD experimental conditions were identified that detected binding of the triamine spermidine to AceI(His6). In a titration with spermidine (0-10 mM) this binding was saturable and fitting of the curve for the change in signal intensity produced an apparent binding affinity (KD) of 3.97 +/- 0.45 mM. These SRCD results were the first experimental evidence obtained for polyamines as natural substrates of PACE proteins.
REVIEW | doi:10.20944/preprints202201.0102.v1
Subject: Life Sciences, Molecular Biology Keywords: ChREBP; L-Myc; Max; Mga; Mlx; Mnt; MondoA; Mxd; N-Myc; tumor suppressor
Online: 10 January 2022 (12:01:35 CET)
Among the first discovered and most prominent cellular oncogenes is MYC, which encodes a bHLH-ZIP transcription factor (Myc) that both activates and suppresses numerous genes involved in proliferation, energy production, metabolism and translation. Myc belongs to a small group of bHLH-ZIP transcriptional regulators (the Myc Network) that includes its obligate heterodimerization partner Max and six “Mxd proteins” (Mxd1-4, Mnt and Mga) each of which heterodimerizes with Max and largely oppose Myc’s functions. More recently, a second group of bHLH-ZIP proteins (the Mlx Network) has emerged. It is comprised of the Myc-like factors ChREBP and MondoA, which, in association with the Max-like member Mlx, regulate smaller and more functionally restricted sets of target genes, some of which are shared with Myc. Opposing ChREBP and MondoA are heterodimers comprised of Mlx and Mxd1, Mxd4 and Mnt, which also structurally and operationally link the two Networks. We discuss here the functions of these “Extended Myc Network” members with particular emphasis on the roles played by Max, Mlx and Mxd proteins in suppressing normal and neoplastic growth. These roles are complex due to the temporally- and tissue-restricted expression of Extended Myc Network proteins in normal cells, their regulation of both common and unique target genes and, in some cases, their functional redundancy.
ARTICLE | doi:10.20944/preprints202112.0501.v1
Subject: Life Sciences, Molecular Biology Keywords: miRNA isoform; isomiR, miRNA editing; lung adenocarcinoma; race-disparities
Online: 31 December 2021 (10:41:04 CET)
Despite the development of targeted therapeutics, immunotherapy, and strategies for early detection, lung cancer carries a high mortality. Further, significant racial disparities in outcomes exist for which the molecular drivers have yet to be fully elucidated. The growing field of Epitranscriptomics has introduced a new layer of complexity to the molecular pathogenesis of cancer. RNA modifications can occur in coding and non-coding RNAs, such as miRNAs, possibly altering their gene regulatory function. The potential role for such modifications as clinically informative biomarkers remains largely unknown. Here, we concurrently profiled canonical miRNAs, shifted isomiRs (templated and non-templated), miRNAs with single-point modification events (RNA and DNA) in White American (W) and Black or African American (B/AA) lung adenocarcinoma (LUAD) patients. We found that while most deregulated miRNA isoforms were similar in W and B/AA LUAD tissues compared to normal adjacent tissues, there was a subgroup of isoforms with deregulation according to race. We specifically investigated an edited miRNA, miR-151a-3p with an A-to-I editing event at position 3, to determine how its altered expression may be associated with activation of divergent biological pathways between W and B/AA LUAD patients. Finally, we identified distinct race-specific miRNA isoforms that correlated with prognosis for both Ws and B/AAs. Our results suggest that concurrently profiling canonical and non-canonical miRNAs may have potential as a strategy for identifying additional distinct biological pathways and biomarkers in lung cancer.
ARTICLE | doi:10.20944/preprints202112.0290.v3
Subject: Life Sciences, Molecular Biology Keywords: crescentic glomerulonephritis; BET proteins; NOTCH; GREMLIN; Chronic kidney disease; Bromodomain
Online: 23 December 2021 (14:40:45 CET)
Crescentic glomerulonephritis is a devastating autoimmune disease that without early and properly treat-ment may rapidly progress to end-stage renal disease and death. Current immunosuppressive treatment provided limited efficacy and an important burden of adverse events. Epigenetic drugs are a source of novel therapeutic tools. Among them, bromodomain and extraterminal domain (BET) inhibitors (iBETs) block the interaction between bromodomains and acetylated proteins, including histones and transcription factors. iBETs have demonstrated protective effects on malignancy, inflammatory conditions and experi-mental kidney disease. Recently, Gremlin-1 was proposed as a urinary biomarker of disease progression in human anti-neutrophil cytoplasmic antibody (ANCA)-associated crescentic glomerulonephritis. We have now evaluated whether iBETs regulate Gremlin-1 in experimental anti-glomerular basement membrane nephritis induced by nephrotoxic serum (NTS) in mice, a model of human crescentic glomerulonephritis. In NTS-injected mice, the iBET JQ1 inhibited renal Gremlin-1 overexpression and diminished glomerular damage, including podocyte loss. Chromatin immunoprecipitation assay demonstrated BRD4 enrichment of the Grem-1 gene promoter in injured kidneys, consistent with Gremlin-1 epigenetic regulation. Moreover, JQ1 blocked BRD4 binding and inhibited Grem-1 gene transcription. The beneficial effect of iBETs was also mediated by targeting NOTCH signaling pathway. JQ1 inhibited the gene expression of the NOTCH effec-tors Hes-1 and Hey-1 in NTS-injured kidneys. Our results further support the role for epigenetic drugs, such as iBETs, in the treatment of rapidly progressive crescentic glomerulonephritis.
COMMUNICATION | doi:10.20944/preprints202112.0300.v1
Subject: Life Sciences, Molecular Biology Keywords: DNA adducts; nanopore; Oxford Nanopore Technology; mass spectrometry; adductomics; exposome
Online: 20 December 2021 (09:53:53 CET)
Abstract: Formation of DNA adducts is a key event for a genotoxic mode of action and its formation is often use as surrogate for mutation and cancer. Interest in DNA adducts are twofold, first, to demonstrate exposure, and second, to link DNA adduct location to subsequent mutations or altered gene regulation. High chemically specific mass spectrometry methods have been established for DNA adduct quantitation and elegant bio-analytic methods utilizing enzymes, various chemistries, and molecular biology methods to visualize the location of DNA adducts. Traditionally, these highly specific methods cannot be combined, and the results are incomparable. Initially developed for single-molecule DNA sequencing, nanopore-type technologies are expected to enable simultaneous quantitation and location of DNA adducts across the genome. We will briefly summarize the current methodologies for state-of-the-art quantitation of DNA adduct levels and mapping of DNA adducts and describe novel single-molecule DNA sequencing technology that is expected to achieve both measures simultaneously. Emerging technologies are expected to soon provide a comprehensive picture of the exposome and identify gene regions susceptible to DNA adduct formation.
REVIEW | doi:10.20944/preprints202111.0545.v1
Subject: Life Sciences, Molecular Biology Keywords: Rett syndrome; FOXG1; FOXG1 syndrome; Neurodevelopmental disorders; Disease modelling; hiPSCs; Brain development; Cerebral organoids
Online: 29 November 2021 (15:29:13 CET)
Development of the central nervous system (CNS) depends on accurate spatiotemporal control of signalling pathways and transcription programs. Forkhead Box G1 (FOXG1) is one of the master regulators that plays fundamental roles in forebrain development, from the timing of neurogenesis to the patterning of the cerebral cortex. Mutations in the FOXG1 gene cause a rare neurodevelopmental disorder called FOXG1 syndrome, also known as congenital form of Rett syndrome. Patients presenting with FOXG1 syndrome manifest a spectrum of phenotypes ranging from severe cognitive dysfunction and microcephaly to social withdrawal and communication deficits with varying severities. To develop and improve therapeutic interventions, there has been considerable progress towards unravelling the multi-faceted functions of FOXG1 in neurodevelopment and pathogenesis of FOXG1 syndrome. Moreover, recent advances in genome editing and stem cell technologies, as well as increased yield of information from high throughput omics opened promising and important new avenues in FOXG1 research. In this review, we provide a summary of clinical features and emerging molecular mechanisms underlying FOXG1 syndrome, and explore disease-modelling approaches in animals and human-based systems to highlight prospects of research and possible clinical interventions.
ARTICLE | doi:10.20944/preprints202111.0539.v1
Subject: Life Sciences, Molecular Biology Keywords: Replication fork trap; Tus-Ter; dif; ChIP-Seq; GC-skew; Enterobacterales
Online: 29 November 2021 (12:52:31 CET)
In Escherichia coli, DNA replication termination is orchestrated by two clusters of Ter sites forming a DNA replication fork trap when bound by Tus proteins. The formation of a ‘locked’ Tus-Ter complex is essential for halting incoming DNA replication forks. However, the absence of replication fork arrest at some Ter sites raised questions about their significance. In this study, we examined the genome-wide distribution of Tus and found that only the six innermost Ter sites (TerA-E and G) were significantly bound by Tus. We also found that a single ectopic insertion of TerB in its non-permissive orientation could not be achieved, advocating against a need for ‘back-up’ Ter sites. Finally, examination of the genomes of a variety of Enterobacterales revealed a new replication fork trap architecture mostly found outside the Enterobacteriaceae family. Taken together, our data enabled the delineation of a narrow ancestral Tus-dependent DNA replication fork trap consisting of only two Ter sites.
ARTICLE | doi:10.20944/preprints202111.0381.v1
Online: 22 November 2021 (11:08:58 CET)
Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation, that is, the target distribution function, the PMF potential energy is extracted, and then the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have gone through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.
REVIEW | doi:10.20944/preprints202111.0317.v1
Subject: Life Sciences, Molecular Biology Keywords: Non-Hodgkin lymphoma; Epigenetics; DNA methylation; HAT; HDAC; EZH2; bromodomain inhibitors; Drug combination; clinical testing
Online: 17 November 2021 (23:45:00 CET)
In a wide range of lymphoid neoplasms, the process of malignant transformation is associated to somatic mutations in B cells that affect the epigenetic machinery. Consequential alterations in histone modifications contribute to disease-specific changes in the transcriptional program. Affected genes commonly play important roles in cell cycle regulation, apoptosis-inducing signal transduction and DNA damage response, thus facilitating the emergence of malignant traits that impair immune surveillance and favor the emergence of different B-cell lymphoma subtypes. In the last two decades, the field has made a major effort to develop therapies that target these epigenetic alterations. In this review, we discuss which epigenetic alterations occur in non-Hodgkin B-cell lymphoma. Furthermore, we aim to present in close to comprehensive manner the current state-of-the-art in the preclinical and clinical development of epigenetic drugs. We focus on therapeutic strategies interfering with histone methylation and acetylation as these are most advanced in being deployed from the bench-to-bedside and have greatest potential to improve the prognosis of lymphoma patients.
REVIEW | doi:10.20944/preprints202111.0164.v1
Subject: Life Sciences, Molecular Biology Keywords: SETMAR; Metnase; H3K36me2; Hsmar1; non-homologous end joining repair; NHEJ; transposase; transposable elements; histone; methyltransferase
Online: 9 November 2021 (11:30:21 CET)
SETMAR is a protein lysine methyltransferase that is involved in several DNA processes, including DNA repair via the non-homologous end joining (NHEJ) pathway, regulation of gene expression, illegitimate DNA integration, and DNA decatenation. However, SETMAR is an atypical protein lysine methyltransferase since in anthropoid primates, the SET domain is fused to an inactive DNA transposase. The presence of the DNA transposase domain confers to SETMAR a DNA binding activity towards the remnants of its transposable element, which has resulted in the emergence of a gene regulatory function. Both the SET and the DNA transposase domains are involved in the different cellular roles of SETMAR, indicating the presence of novel and specific functions in anthropoid primates. In addition, SETMAR is dysregulated in different types of cancer, indicating a potential pathological role. While some light has been shed on SETMAR functions, more research and new tools are needed to better understand the cellular activities of SETMAR and to investigate the therapeutic potential of SETMAR.
ARTICLE | doi:10.20944/preprints202111.0107.v1
Subject: Life Sciences, Molecular Biology Keywords: Glycan structure; Knowledge representation; Pattern recognition; Ontology; Semantic web
Online: 5 November 2021 (08:34:05 CET)
The level of ambiguity in describing glycan structure has significantly increased with the upsurge of large scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as an appropriate solution for navigating this data. However, navigation is not sufficient and the model should also enable advanced search and comparison. A new ontology with a tree logical structure is introduced to represent glycan structures irrespective of the precision of molecular details. The model heavily relies on the GlycoCT encoding of glycan structures. Its implementation in the GlySTreeM knowledge base was validated with GlyConnect data and benchmarked with the Glycowork library. GlySTreeM is shown to be fast, consistent, reliable and more flexible than existing solutions for matching parts of or whole glycan structures. The model is also well suited to painless future expansion. Availability:https://glyconnect.expasy.org/glystreem/wiki
ARTICLE | doi:10.20944/preprints202111.0082.v1
Online: 3 November 2021 (14:08:46 CET)
PSD-95 (Dlg4) is an ionotropic glutamate receptor scaffolding protein essential in synapse stability and neurotransmission. PSD-95 levels are reduced during aging and in neurodegenerative diseases like Huntington’s disease (HD), and it is believed to contribute to synaptic dysfunction and behavioral deficits. However, the mechanism responsible for PSD-95 dysregulation under these conditions is unknown. The Heat Shock transcription Factor 1 (HSF1), canonically known for its role in protein homeostasis, is also depleted in both aging and HD. Synaptic protein levels, including PSD-95, are influenced by alterations in HSF1 levels and activity, but the direct regulatory relationship between PSD-95 and HSF1 has yet to be determined. Here, we showed that HSF1 chronic or acute depletion in cell lines and mice decreased PSD-95 expression. Furthermore, HSF1(+/-) mice had reduced PSD-95 synaptic puncta that paralleled a loss in thalamo-striatal excitatory synapses, an important circuit disrupted early in HD. We demonstrated that HSF1 binds to regulatory elements present in the PSD-95 gene and directly regulates PSD-95 expression. HSF1 DNA-binding on the PSD-95 gene was disrupted in an age-dependent manner in WT mice and worsened in HD cells and mice, leading to reduced PSD-95 levels. These results demonstrate a direct role of HSF1 in synaptic gene regulation that has important implications in synapse maintenance in basal and pathological conditions.
ARTICLE | doi:10.20944/preprints202111.0066.v1
Subject: Life Sciences, Molecular Biology Keywords: Leukodystrophy; Ataxia; Parkinson’s disease; HARS2, LARS2; TWNK; ERAL1; ClpB
Online: 3 November 2021 (08:40:03 CET)
Biallelic pathogenic variants in CLPP, encoding mitochondrial matrix peptidase ClpP cause a rare autosomal recessive condition, Perrault syndrome type 3 (PRLTS3). It is characterized by primary ovarian insufficiency and early sensorineural hearing loss, often associated with progressive neurological deficits. Mouse models showed that accumulations of (i) its main protein interactor, the substrate-selecting AAA+ ATPase ClpX, (ii) mitoribosomes, and (iii) mtDNA nucleoids are main cellular consequences of ClpP absence. However, the sequence of these events and their validity in human remain unclear. Here, we studied global proteome profiles to define ClpP substrates among mitochondrial ClpX interactors, which accumulated consistently in ClpP-null mouse embryonal fibroblasts and brain. Validation work included novel ClpP-mutant patient fibroblast proteomics. ClpX co-accumulated in mitochondria with POLDIP2 as nucleoid component, LRPPRC as mitochondrial poly(A) mRNA granule element, GFM1 (in mouse also GRSF1) as tRNA processing factors. Only in mouse, accumulated ClpX, GFM1 and GRSF1 appeared in nuclear fractions. Mitoribosomal accumulation was minor. Consistent accumulations in murine and human fibroblasts also affected multimerizing factors not known as ClpX interactors, namely OAT, ASS1, ACADVL, STOM, PRDX3, PC, MUT, ALDH2, PMPCB, UQCRC2 and ACADSB, but the impact on downstream metabolites was marginal. Our data demonstrate the primary impact of ClpXP on the assembly of proteins with nucleic acids, and show nucleoid enlargement in human as a key consequence.
ARTICLE | doi:10.20944/preprints202111.0049.v1
Subject: Life Sciences, Molecular Biology Keywords: Huntington’s disease; YAC128; HdhQ150; strain background; C57BL/6; synaptic pathology; extrasynaptic NMDAR
Online: 2 November 2021 (12:11:26 CET)
Mouse models are frequently used to study Huntington’s disease (HD). Onset and severity of neuronal and behavioral pathologies vary greatly between HD mouse models, which results from different huntingtin expression levels and different CAG repeat length. HD pathology appears to depend also on strain background of mouse models. Thus, behavioral deficits of HD mice are more severe in the FVB than in the C57BL/6 background. Alterations in medium spiny neuron (MSN) morphology and function has been well documented in young YAC128 mice in the FVB background. We here tested the relevance of strain background for mutant huntingtin (mHTT) toxicity on the cellular level by investigating HD pathologies in YAC128 mice in the C57BL/6 background (YAC128/BL6). Morphology, spine density, synapse function and membrane properties were not or only subtly altered in MSNs of 12-month-old YAC128/BL6 mice. Despite the mild cellular phenotype, YAC128/BL6 mice showed deficits in motor performance. More pronounced alterations in MSN function were found in the HdhQ150 mouse model in the C57BL/6 background (HdhQ150/BL6). Consistent with the differences in HD pathology, the number of inclusion bodies was considerably lower in YAC128/BL6 mice than HdhQ150/BL6 mice. This study highlights the relevance of strain background for mHTT toxicity in HD mouse models.
ARTICLE | doi:10.20944/preprints202111.0013.v1
Subject: Life Sciences, Molecular Biology Keywords: Nonsense-mediated mRNA Decay; UPF3B-knockout; RNA-Sequencing; Intellectual disability; Neuro-developmental disorders
Online: 1 November 2021 (12:17:15 CET)
UPF3B is a constituent of the classical nonsense-mediated mRNA decay (NMD) pathway that degrades both the aberrant transcripts and a set of physiological transcripts. In higher eukaryotes, UPF3B have significant biochemical functions in diverse cellular processes including NMD and translation. UPF3B plays a crucial role in neuronal development and differentiation. Next-generation sequencing technologies identified several loss-of-function mutations in the UPF3B gene that results in neuro-developmental disorders in humans. To uncover the mechanistic role of UPF3B in neuronal functions, we have generated the UPF3B-knockout mammalian cell line model system using CRISPR-Cas9 gene editing method. RNA-Sequencing Analysis of cellular transcriptome from UPF3B-KO cells identified specific genes involved in cell growth and neuronal functions. Altered expression of genes related to the axon guidance pathway delineated the UPF3B function to regulate the neuron-specific genes. Functional enrichment analysis identified the genes involved in the disorders related to mental health and intellectual disability. Our study has the potential to identify the direct players of intellectual disability and will have broader implications.
ARTICLE | doi:10.20944/preprints202110.0396.v1
Online: 26 October 2021 (17:31:55 CEST)
Cassava (Manihot esculenta Crantz), domesticated in the Amazonian region of South America, presents an important diversity in Ecuador, where it is a main staple food; however, only few Ecuadorian cassava accessions have been included in international molecular assessments. The purpose of this study was to apply suitable cassava mi-crosatellites to characterize the genetic variability of the Ecuadorian cassava collection composed mainly of local landraces from the Coast, Andes and Amazonia regions. The use of microsatellite markers allowed the determination of the genetic diversity of the collection. Seven selected SSR primers, permitted to identify homozygous and hetero-zygous materials within the cassava collection of 133 accessions. The loci presented an average genetic diversity value of 0.7 and an average PIC value of 0.67, which is con-sidered high. Low number of duplicates (8.8%) were identified in the Ecuadorian col-lection which is not fully duplicated at CIAT. Currently, a wide range of cassava diver-sity is still cultivated in multi-crop agro-ecosystem, mainly in the Coast and Amazo-nian regions. Especially in the Amazonian region, due to important cultural uses of cassava by local ethnic communities, more in depth studies in the region could unveil the genetic diversity present in situ today.
REVIEW | doi:10.20944/preprints202110.0344.v1
Subject: Life Sciences, Molecular Biology Keywords: Glycoprotein; gp120; HIV-1; conformation; immunity
Online: 25 October 2021 (11:50:08 CEST)
Infection by human immunodeficiency virus type I (HIV-1) requires virus particle binding to host cell-surface receptor CD4 via the viral envelope glycoprotein gp120. HIV-1 therapy and prevention efforts involve development of mimetic or recombinant gp120 vaccines or deployment of antiviral agents that target specific epitopes of gp120. The unliganded conformational state of gp120 is closed, whereas the CD4-bound state is open. However, in between, there exist dynamic conformational states, indicating intrinsically flexible region(s) of structural dynamics, imposing a structural challenge for developing drug or antibody targets. Known conformational states of gp120 were determined by X-ray crystallographic and cryo-electron microscopy, and neither method captures the population of gp120 species arising from conformational plasticity, motions, and transitions. gp120 plasticity brings up several important questions. How will differences in conformation affect receptor binding, antibody recognition, and neutralization? Which regions are crucial for gp120 structural plasticity? How could structural dynamics influence HIV-1 evasiveness against host immunity and drugs or vaccines, and facilitate the viral entry into its host? This review explores the structural constraints presented by conformational states of the glycoprotein to antibodies or drugs and how these conformational states provide structural avenues for the virus to escape neutralizing agents and evade host immunity.
REVIEW | doi:10.20944/preprints202110.0211.v1
Subject: Life Sciences, Molecular Biology Keywords: Extracellular Vesicles (EVs); Exosomes; Size Exclusion Chromatography (SEC); gradient Size Exclusion Chromatography (gSEC); Ion Exchange Chromatography; Hybrid Chromatography
Online: 14 October 2021 (10:23:28 CEST)
Extracellular vesicles (EVs) are cell-derived membranous particles secreted by all cell types into the extracellular milieu. EVs carry, protect, and transport a wide array of bioactive cargoes to recipient/target cells. EVs regulate physiological and pathophysiological processes in recipient cells and are important in therapeutics/drug delivery. Despite these great attributes of EVs, an efficient protocol for EV separation from biofluids is lacking. Numerous techniques have been adapted for the separation of EVs with size exclusion chromatography (SEC)-based methods being the most promising. Here, we review the SEC protocols used for EV separation, and discuss opportunities for significant improvements, such as the development of novel particle purification liquid chromatography (PPLC) system capable of tandem purification and characterization of biological and synthetic particles with near-single vesicle resolution. Finally, we identify future perspectives and current issues to make PPLC a tool capable of providing a unified, automated, adaptable, yet simple and affordable particle separation resource.
Subject: Life Sciences, Molecular Biology Keywords: G9a; EHMT2; glioblastoma; medulloblastoma; epigenetics; brain tumor
Online: 8 October 2021 (10:57:22 CEST)
Epigenetic mechanisms, including post-translational modifications of DNA and histones that influence chromatin structure, regulate gene expression during normal development, and are also involved in carcinogenesis and cancer progression. The histone methyltransferase G9a (euchromatic histone lysine methyltransferase 2, EHMT2), which mostly mediates mono- and dimethylation by histone H3 lysine 9 (H3K9), influences gene expression involved in embryonic development and tissue differentiation. Overexpression of G9a has been observed in several cancer types, and different classes of G9a inhibitors have been developed as potential anticancer agents. Here, we review the emerging evidence suggesting the involvement of changes in G9a activity in brain tumors, namely glioblastoma (GBM), the main type of primary malignant brain cancer in adults, and medulloblastoma (MB), the most common type of malignant brain cancer in children. We also discuss the role of G9a in neuroblastoma (NB) and the drug development of G9a inhibitors.
ARTICLE | doi:10.20944/preprints202110.0001.v1
Online: 1 October 2021 (08:18:18 CEST)
One of the hallmarks of the Alternative Lengthening of Telomeres (ALT) is the association with Promyelocytic Leukemia (PML) Nuclear Bodies, known as APBs. In the last years, APBs have been described as the main place where telomeric extension occurs in ALT positive cancer cell lines. A different set of proteins have been associated with APBs function, however, the molecular mechanisms behind their assembly, colocalization, and clustering of telomeres, among others, remain unclear. To improve the understanding of APBs in the ALT pathway, we integrated multi-omics analyses to evaluate genomic, transcriptomic and proteomic alterations, and functional interactions of 71 APBs-related genes/proteins in 32 PanCancer Atlas studies from The Cancer Genome Atlas Consortium (TCGA). As a result, we identified 13 key proteins which showed distinctive mutations, interactions, and functional enrichment patterns across all the cancer types and proposed this set of proteins as candidates for future ex vivo and in vivo analyses that will validate these proteins to improve the understanding of the ALT pathway, fill the current research gap about APBs function and their role in ALT, and be considered as potential therapeutic targets for the diagnosis and treatment of ALT positive cancers in the future.
ARTICLE | doi:10.20944/preprints202109.0454.v1
Subject: Life Sciences, Molecular Biology Keywords: CPA4; Bladder Urothelial Carcinoma; Immune cells; T cell exhaustion; checkpoint
Online: 27 September 2021 (16:02:31 CEST)
Carboxypeptidase A4 (CPA4) has shown the potential possibility as a biomarker in the early diagnosis for certain cancers. However, no previous research has linked CPA4 to therapeutic or prognostic significance in bladder cancer. Using data from The Cancer Genome Atlas (TCGA) database, we set out to determine the full extent of the link between CPA4 and BLCA. We further analyzed the interacting proteins of CPA4 and infiltrated immune cells via TIMER2，STRING and GEPIA2 databases. The expression of CPA4 in tumor and normal tissues was compared using the TCGA+GETx database. The connection between CPA44 expression and clinicopathologic characteristics and overall survival (OS) was investigated using multivariate methods and Kaplan-Meier survival curves. The potential functions and pathways were investigated via gene set enrichment analysis. Furthermore, we analyze the associations between CPA4 expression and infiltrated immune cells with their respective gene marker sets using the ssGSEA, TIMER2, and GEPIA2 databases. Compared to matching normal tissues, human CPA4 was found to be substantially expressed. We confirmed that overexpression of CPA4 is linked with shorter OS, DSF, PFI, and increased diagnostic potential using Kaplan-Meier and ROC analysis. The expression of CPA4 is related to T-bet, IL12RB2, CTLA4, and LAG3, among which T-bet and IL12RB2 are Th1 marker genes, while CTLA4 and LAG3 are related to T cell exhaustion, which may be used to guide the application of checkpoint blockade and the adoption of T cell transfer therapy.
ARTICLE | doi:10.20944/preprints202109.0401.v1
Subject: Life Sciences, Molecular Biology Keywords: AMPK; TOR Complex I; mitochondria; FMR1; Fragile X-associated Tremor/Ataxia Syndrome (FXTAS); CGG trinucleotide repeat
Online: 23 September 2021 (11:10:47 CEST)
The X-linked FMR1 gene contains a non-coding trinucleotide repeat in its 5’ region that in normal, healthy individuals contains 20-44 copies. Large expansions of this region (>200 copies) cause fragile X syndrome (FXS), but expansions of 55-199 copies (referred to as premutation alleles) predispose carriers to a neurodegenerative disease called fragile X-associated tremor/ataxia syndrome (FXTAS). The cytopathological mechanisms underlying FXTAS are poorly understood, but abnormalities in mitochondrial function are believed to play a role. We previously reported that lymphoblastoid cell lines (LCLs, or lymphoblasts) of premutation carriers have elevated mitochondrial respiratory activities. In the carriers, especially those not clinically affected with FXTAS, AMPK activity was shown to be elevated. In the FXTAS patients, however, it was negatively correlated with brain white matter lesions, suggesting a protective role in the molecular mechanisms. Here we report an enlarged and extended study of mitochondrial function and associated cellular stress-signalling pathways in lymphoblasts isolated from male and female premutation carriers, regardless of their clinical status, and healthy controls. The results confirmed the elevation of AMPK and mitochondrial respiratory activities and reduction of reactive O2 species (ROS) levels in premutation cells and revealed for the first time that TORC1 activities are reduced. Extensive correlation, multiple regression and Principal Components analysis revealed the best fitting statistical explanations of these changes in terms of the other variables measured. These suggested which variables might be the most “proximal” regulators of the others in the extensive network of known causal interactions amongst the measured parameters of mitochondrial function and cellular stress signalling. In the resulting model, the premutation alleles activate AMPK and inhibit both TORC1 and ROS production, the reduced TORC1 activity contributes to activation of AMPK activation and of nonmitochondrial metabolism, and the higher AMPK activity results in elevated catabolic metabolism, mitochondrial respiration and ATP steady state levels. In addition the results suggest a separate CGG repeat number-dependent elevation of TORC1 activity that is insufficient to overcome the inhibition of TORC1 in premutation cells, but may presage the previously reported activation of TORC1 in FXS cells.
REVIEW | doi:10.20944/preprints202109.0242.v1
Subject: Life Sciences, Molecular Biology Keywords: PDK1; breast cancer; survival; prognosis; targeted therapy
Online: 14 September 2021 (14:51:06 CEST)
Given that 3-Phosphoinositide-dependent kinase 1 (PDK1) plays a crucial role in malignant biological behaviors of a wide-range of cancers, we further review the influence of PDK1 in breast cancer (BC). First, we describe the power of PDK1 in cellular behaviors and extensively demonstrate the interacting networks of PDK1 via PI3K-dependent/ PI3K-independent pathway. Then we enlighten the roles of PDK1 in carcinogenesis, growth and survival, metastasis, and chemoresistance in BC cells. More important, we sort the current preclinical or clinical trials of PDK1 targeted therapy in BC and find that even though at present no selective PDK1 inhibitor is available for BC therapy, but the combination trials of PDK1 targeted therapy and other agents have demonstrated some benefit. Thus, there is increasing anticipations that PDK1 targeted therapy will have its space in future therapeutic concepts of BC, and we hope to feature PDK1 in BC to the clinic and bring the new promising to patients for targeted therapies.
REVIEW | doi:10.20944/preprints202109.0189.v1
Subject: Life Sciences, Molecular Biology Keywords: circadian clock; epigenetic clock; aging; senescence; reprogramming; methylome; DNA methylation; CpG-islands; induced pluripotent stem cells
Online: 10 September 2021 (15:13:04 CEST)
This review summarizes current understanding of the interaction between circadian rhythms of gene expression and epigenetic clocks characterized by the specific profile of DNA methylation in CpG-islands which mirror the chronological age of individual cells and the entire organism. Basic mechanisms of regulation for circadian genes CLOCK- BMAL1 as well as downstream clock-controlled genes (ССG) are also discussed here. It has been shown that circadian rhythms operate by finely tuned regulation of transcription and rely on various epigenetic mechanisms including activation of enhancers / suppressors, acetylation / deacetylation of histones and other proteins as well as DNA methylation. Overall, up to 20% of all genes expressed by the cell are subject to expression oscillations associated with circadian rhythms. Also included in the review is a brief list of genes involved in the regulation of circadian rhythms, along with genes important for metabolic control, aging, and oncogenesis. Knocking out some of them (for example, Sirt1) accelerates the aging process, while overexpression of Sirt1, on the contrary, protects against age-related changes. Circadian regulators control a number of genes that activate the cell cycle (Wee1, c-Myc, p20, p21, and Cyclin D1) and regulate histone modification and DNA methylation. Approaches for determining the epigenetic age from methylation profiles across CpG islands in individual cells are described. DNA methylation, which characterizes the function of the epigenetic clock, appears to link together such key biological processes as regeneration and functioning of stem cells, aging and malignant transformation. Finally, main features of adult stem cell aging in stem cell niches and current possibilities for modulating the epigenetic clock as part of antiaging therapy are discussed.
TECHNICAL NOTE | doi:10.20944/preprints202109.0183.v1
Online: 10 September 2021 (11:17:04 CEST)
Distinguishing circular RNA (circRNA) reads from reads derived from the linear host transcript is a challenging task because of sequence overlap. We developed a computational approach, CiLiQuant, that determines the relative circular and linear abundance of transcripts and gene loci using backsplice and forward splice junction reads generated by existing mapping and circRNA discovery tools.
REVIEW | doi:10.20944/preprints202109.0182.v1
Online: 10 September 2021 (11:07:13 CEST)
The biology of aging is focused on the identification of novel pathways that regulate the underlying processes of aging to develop interventions aimed at delaying the onset and progression of chronic diseases to extend lifespan. However, the research on the aging field has been conducted mainly in animal models, yeast, Caenorhabditis elegans and cell culture. Thus, it is unclear to what extent this knowledge is transferable to humans since they might not reflect the complexity of aging in people. Organoid culture is an in vitro 3D cell-culture technology that reproduces the physiological and cellular composition of the tissues and/or organs. This technology is being used in the cancer field to predict the response of a patient-derived tumor to a certain drug or treatment serving as patient stratification and drug-guidance approaches. Modeling aging with patient-derived organoids has a tremendous potential as a preclinical model tool to discover new biomarkers of aging, to predict adverse outcomes during aging and to design personalized approaches for prevention and treatment of aging-related diseases and geriatric syndromes. This could represent a novel approach to study chronological and/or biological aging paving the way to personalized interventions targeting the biology of aging.
REVIEW | doi:10.20944/preprints202109.0109.v1
Subject: Life Sciences, Molecular Biology Keywords: proteomics; transcriptomics; DNA methylation; mitochondria; metabolism; OXPHOS; ASD; neurogenesis; gliosis; neurodevelopment
Online: 6 September 2021 (17:14:37 CEST)
Abstract: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder with extensive genetic and aetiological heterogeneity. While the underlying molecular mechanisms involved remain unclear, significant progress has been facilitated by recent advances in high-throughput transcriptomic, epigenomic and proteomic technologies. Here, we review recently published ASD proteomic data and compare proteomic func-tional enrichment signatures to those of transcriptomic and epigenomic data. We iden-tify canonical pathways that are consistently implicated in ASD molecular data and find an enrichment of pathways involved in mitochondrial metabolism and neurogenesis. We identify a subset of differentially expressed proteins that are supported by ASD tran-scriptomic and DNA methylation data. Furthermore, these differentially expressed proteins are enriched for disease phenotype pathways associated with ASD aetiology. These proteins converge on protein-protein interaction networks that regulate cell pro-liferation and differentiation, metabolism and inflammation which demonstrates a link between canonical pathways, biological processes and the ASD phenotype. This review highlights how proteomics can uncover potential molecular mechanisms to explain a link between mitochondrial dysfunction and neurodevelopmental pathology.
REVIEW | doi:10.20944/preprints202109.0073.v1
Subject: Life Sciences, Molecular Biology Keywords: Mitochondrial dysfunction; Alzheimer's disease; Parkinson's disease; Neurodegeneration; Amyloid beta; Parkin
Online: 3 September 2021 (16:01:26 CEST)
Mitochondrial dysfunctions remained a pivotal mechanism in manifold neurodegenerative diseases. Mitochondrial homeostasis within the cell is an essential aspect of cell biology. Mitochondria which is also known as the power-generating set of the cell, have a dominant role in several processes associated with the genomic integrity and cellular equilibrium maintenance. They are involved in maintaining optimal cells functioning and guidance from possible DNA damage which could lead to mutations and onset of diseases. Conversely, system perturbations which could be due to environmental factors or senescence induce changes in the physiological balance and result in the mitochondrial functions impairment. The focal point of this review focuses on mitochondrial dysfunction as a significant condition in the onset of neuronal disintegration. We explain the pathways associated with the dysfunction of the mitochondria which are common amongst the most recurring neurodegenerative diseases including Alzheimers and Parkinsons disease. Do mitochondrial dysfunctions represent an early event in causing a shift towards neuropathological processes?
REVIEW | doi:10.20944/preprints202109.0041.v1
Subject: Life Sciences, Molecular Biology Keywords: connexin; gap junction; hemichannel; pannexin; peptide; cell signaling
Online: 2 September 2021 (13:38:54 CEST)
Gap junctions (GJ) and connexins play integral roles in cellular physiology and have been found to be involved in multiple pathophysiological states from cancer to cardiovascular disease. Studies over the last 60 years have demonstrated the utility of altering GJ signaling pathways in experimental models, which has led to them being attractive targets for therapeutic intervention. A number of different mechanisms have been proposed to regulate GJ signaling, including channel blocking, enhancing channel open state, and disrupting protein-protein interactions. The primary mechanism for this has been through the design of numerous peptides as therapeutics, that are either currently in early development or are in various stages of clinical trials. Despite over 25 years of research into connexin targeting peptides, the overall mechanisms of action are still poorly understood. In this overview, we discuss published connexin targeting peptides, their reported mechanisms of action and the potential for these molecules in the treatment of disease.
ARTICLE | doi:10.20944/preprints202109.0013.v1
Subject: Life Sciences, Molecular Biology Keywords: dextransucrases; GH70; lactic acid bacteria; sucrose-active enzymes; carbohydrate binding module; glucansucrase; cellulose binding domain; Leuconostoc
Online: 1 September 2021 (12:12:00 CEST)
The lactic acid bacteria (LAB) have great potential to produce homoexopolysaccharides (HoPS), have been the subject of extensive research efforts, given their health benefits and physicochemical properties. The HoPS functional properties are determined by structural characteristics of varied molecular weights, types of glycosidic linkages, degrees of branching and chemical composition. The dextransucrases (DSases) are responsible of the synthesis of a kind of HoPS (dextran polymers), which are among the first biopolymers produced at industrial scale with applications in medicine and biotechnology. The concept of glycodiversification opens additional applications for DSases. In that sense the design and characterization of new DSases is of prime importance. Previously, we described the isolation and characterization of a novel extracellular dextransucrase (DSR-F) encoding gene. In this study, from DSR-F, we design a novel chimeric dextransucrase DSR-F-∆SP-∆GBD-CBM2a, where DSR-F-∆SP-∆GBD is fused to the carbohydrate-binding module (CBM2a) of the β-1-4 exoglucanase/xylanase Cex (Xyn10A) of Cellulomonas fimi ATCC 484. This dextransucrase variant is active and without alteration in its specificity. The DSR-F-∆SP-∆GBD-CBM2a is purified by cellulose affinity chromatography for the very first time. Our results indicate that new hybrids and chimeric DSases with novel binding capacity to cellulose can be designed to obtain glyco-biocatalysts from renewable lignocellulosic materials.
REVIEW | doi:10.20944/preprints202108.0283.v1
Subject: Life Sciences, Molecular Biology Keywords: Type 1 diabetes; human leukocyte antigen; Kuwait Type 1 Diabetes Study; Islet autoantibodies; Insulin; prediction
Online: 13 August 2021 (08:19:26 CEST)
The incidence of Type 1 Diabetes (T1D) in the Arab world, particularly, oil and gas rich Gulf Cooperative Council (GCC) countries has more than doubled in the last twenty years. Therefore, there is a dire need for careful systematic familial cohort studies, especially in high-risk populations. Several immunogenetic factors affect the pathogenesis of the disease. Genes in the human leukocyte antigen (HLA) account for the major genetic susceptibility to the disease. The triggering agents initiate disease onset by destruction of pancreatic β-cells. The autoantibodies against glutamic acid decarboxylase (GADA), insulinoma antigen-2 (IA-2A), insulin (IAA), and zinc transporter-8 (ZnT-8A) comprise the most reliable biomarkers for T1D in both children and adults. Although three of the GCC countries, namely Kuwait, Saudi Arabia and Qatar are among the top 10 countries with high incidence rate of T1D, no proper diagnostic and prediction tools were applied in the region. Understanding the disease sequelae in a homogenous gene pool with high consanguinity in the GCC could help solve the challenges in understanding pathogenesis, as well as hasten the prevention of T1D. Arab states must incorporate T1D predictive and intervention policies on a war-footing basis to minimize the burden of this serious disease.
REVIEW | doi:10.20944/preprints202108.0058.v1
Subject: Life Sciences, Molecular Biology Keywords: SARS-CoV-2; COVID-19; Phylogenetic analysis; Next generation sequence analysis; Virus-Host interaction; Immunology; Antiviral agents; Vaccine; Virus diagnosis
Online: 2 August 2021 (16:17:24 CEST)
The global COVID-19 pandemic claiming global spread continues to evolve, now to the verge of a third wave of outbreak possibly caused by the novel variants of concern of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). The test positivity rate (TPR) and case fatal-ity rate (CFR) have increased steeply in the second wave of COVID-19 compared to the first. From the example of Kerala, a state in southern India, positivity increased from 1.33% at the peak of wave one in 10th June 2020 to 13.45% during 10th June 2021 in the second wave of pandemic. SARS-CoV-2 is an enveloped single-stranded RNA virus. Angiotensin-Converting Enzyme-2 (ACE-2) is a trans membrane surface protein present on multiple types of cells in the human body to which the viral spike protein attaches. Genetic variations in the SARS-CoV-2 and ACE2 receptor can affect the transmission, clinical manifestations, mortality and the efficacy of drugs and vaccines for COVID-19. Mutations are the primary cause of genetic variations. Given the high TPR and CFR, it is necessary to understand the variations of SARS-CoV-2 and cellular receptors of SARS-CoV-2 at the molecular level. In this review, we summarize the impact of genetic and ep-igenetic variations in determining COVID-19 pathogenesis and disease outcome.
REVIEW | doi:10.20944/preprints202106.0145.v1
Subject: Life Sciences, Molecular Biology Keywords: Repetitive element; Transposable element; Non-coding RNA; ncRNA; Functional element; Bioinformatics
Online: 4 June 2021 (15:33:17 CEST)
With a large number of annotated non-coding RNAs (ncRNAs), repetitive sequences are found to constitute functional components (termed as repetitive elements) in ncRNAs that perform specific biological functions. Bioinformatics analysis is a powerful tool for improving our understanding of the role of repetitive elements in ncRNAs. This chapter summarizes recent findings that reveal the role of repetitive elements in ncRNAs. Furthermore, relevant bioinformatics approaches are systematically reviewed, which promises to provide valuable resources for studying the functional impact of repetitive elements on ncRNAs.
REVIEW | doi:10.20944/preprints202105.0513.v1
Subject: Life Sciences, Molecular Biology Keywords: Cell penetrating peptides; protein transduction domains; tumor imaging; targeted therapies.
Online: 21 May 2021 (09:44:48 CEST)
Since their identification over twenty-five years ago, the plethora of cell penetrating peptides (CPP) and their applications has skyrocketed. These 5 to 30 amino acid long peptides have the unique property of breaching the cell membrane barrier while carrying cargoes larger then themselves into cells in an intact, functional form. CPPs can be conjugated to fluorophores, activatable probes, radioisotopes or contrast agents for imaging tissues, such as tumors. There is no singular mechanism for translocation of CPPs into a cell, and therefore, many CPPs are taken up by a multitude of cell types, creating the challenge of tumor specific translocation and hindering clinical effectiveness. Varying strategies have been developed to combat this issue and enhance their diagnostic potential by derivatizing CPPs for better targeting by constructing specific cell activated forms. These methods are currently being used to image integrin expressing tumors, breast cancer cells, human histiocytic lymphoma and protease secreting fibrosarcoma cells, to name a few. Additionally, identifying safe, effective therapeutics for malignant tumors has long been an active area of research. CPPs can circumvent many of the complications found in treating cancer with conventional therapeutics by targeted delivery of drugs into tumors, thereby decreasing off-target side effects, a feat not achievable by currently employed conventional chemotherapeutics. Myriad types of chemotherapeutics such as tyrosine kinase inhibitors, anti-tumor antibodies and nanoparticles can be functionally attached to these peptides leading to the possibility of delivering established and novel cancer therapeutics directly to tumor tissue. While much research is needed to overcome potential issues with these peptides, they offer a significant advancement over current mechanisms to treat cancer. In this review, we present a brief overview of the research leading to identification of CPPs with a comprehensive state of the art review on the role of these novel peptides in both cancer diagnostics as well as therapeutics.
REVIEW | doi:10.20944/preprints202105.0033.v1
Subject: Life Sciences, Molecular Biology Keywords: Campylobacter; Antimicrobial Resistance; Foodborne Pathogen; Animal Source
Online: 5 May 2021 (11:05:37 CEST)
Campylobacter is one of the major foodborne pathogens of concern in its growing trend of antimicrobial resistance. C. jejuni and C. coli are the major causative agents, with C. jejuni contributing to most of the cases in approximately 90% in the world. Infection is transmitted to humans due to consumption of contaminated food and water. Campylobacteriosis caused by C. jejuni is commonly presented with severe diarrhoea, abdominal pain, fever, headache, nausea, and vomiting with some extreme cases resulting in Guillain–Barré syndrome (GBS) and acute flaccid paralysis. Symptoms are severe in cases of children below 5 years, elderly and individuals who are immunocompromised. The infection is usually sporadic, and self-limiting and thus does not require antibiotics for treatment. Still, the antimicrobial resistance in Campylobacter is a major concern because of the transmission of resistance from animal sources to humans. This review highlights the recent epidemiology, geographical impact, resistance mechanisms, spread of Campylobacter spp. and the strategies to control the transmission of Campylobacter from veterinary sources and its antimicrobial resistance.
ARTICLE | doi:10.20944/preprints202102.0332.v1
Subject: Life Sciences, Molecular Biology Keywords: Angiogenesis; Pulmonary hypertension; Endothelium; PHD2 Deficiency; Hypoxia
Online: 16 February 2021 (13:43:56 CET)
Endothelial autocrine signaling is essential to maintain vascular hemostasis. There is limited in-formation about the role of endothelial autocrine signaling in regulating severe pulmonary vas-cular remodeling during the onset of pulmonary arterial hypertension (PAH). In this study, we employed the first severe PAH mouse model, Egln1Tie2Cre (Tie2Cre-mediated disruption of Egln1) mice, to identify the novel autocrine signaling mediating the pulmonary vascular endothelial cells (PVECs) hyperproliferation and the pathogenesis of PAH. PVECs isolated from Egln1Tie2Cre lung expressed upregulation of many growth factors or angiocrine factors such as CXCL12, and exhib-ited hyperproliferative phenotype in coincident with upregulation of proliferation specific tran-scriptional factor FoxM1. Treatment of CXCL12 on PVECs increased FoxM1 expression, which was blocked by CXCL12 receptor CXCR4 antagonist AMD3100 in culture human PVECs. Endo-thelial specific deletion of Cxcl12 (Egln1/Cxcl12Tie2 Cre) or AMD3100 treatment in Egln1Tie2Cre mice downregulated FoxM1 expression in vivo. We then generated and characterized a novel mouse model with endothelial specific FoxM1 deletion in Egln1Tie2Cre mice (Egln1/Foxm1Tie2Cre), and found that endothelial FoxM1 deletion reduced pulmonary vascular remodeling and right ventricular systolic pressure. Together, our study identified a novel mechanism of endothelial autocrine sig-naling in regulating PVECs hyperproliferation and pulmonary vascular remodeling in PAH.
REVIEW | doi:10.20944/preprints202101.0521.v1
Subject: Life Sciences, Molecular Biology Keywords: Data integration; multi-omics; integration strategies; genomics
Online: 25 January 2021 (16:19:31 CET)
Metabolomics deals with multiple and complex chemical reactions within living organisms and how these are influenced by external or internal perturbations. It lies at the heart of omics profiling technologies not only as the underlying biochemical layer that reflects information expressed by the genome, the transcriptome and the proteome, but also as the closest layer to the phenome. The combination of metabolomics data with the information available from genomics, transcriptomics, and proteomics offers unprecedented possibilities to enhance current understanding of biological functions, elucidate their underlying mechanisms and uncover hidden associations between omics variables. As a result, a vast array of computational tools have been developed to assist with integrative analysis of metabolomics data with different omics. Here, we review and propose five criteria – hypothesis, data types, strategies, study design and study focus – to classify statistical multi-omics data integration approaches into state-of-the-art classes under which all existing statistical methods fall. The purpose of this review is to look at various aspects that lead the choice of the statistical integrative analysis pipeline in terms of the different classes. We will draw a particular attention to metabolomics and genomics data to assist those new to this field in the choice of the integrative analysis pipeline.
REVIEW | doi:10.20944/preprints202012.0659.v1
Online: 25 December 2020 (13:00:28 CET)
Pirin is an oxidative stress (OS) sensor belonging to the functionally diverse cupin superfamily of proteins. Pirin is a suggested quercetinase and transcriptional activator of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway. Its biological role in cancer development remains as a novel area of study. This review shows accumulating evidence on the contribution of Pirin in epithelial cancers, signaling pathways involved, and as a suggested therapeutic target. Finally, we propose a model in which Pirin is upregulated by physical, chemical or biological factors involved in OS and cancer development.
TECHNICAL NOTE | doi:10.20944/preprints202012.0641.v1
Subject: Life Sciences, Molecular Biology Keywords: Neurodegeneration; dopamine; L-DOPA; dopaminergic; DBA; Western; IR; TH; Parkinson disease
Online: 25 December 2020 (07:10:33 CET)
We present a robust, fresh-frozen approach to immunohistochemistry (IHC), without committing the tissue to IHC via fixation and cryopreservation while maintaining long-term storage, using LiCor-based infrared (IR) quantification for sensitive assessment of TH in immunoreacted mid-brain sections for quantitative comparison across studies. In fresh-frozen tissue stored up to 1 year prior to IHC reaction, we found our method to be highly sensitive to rotenone treatment in 3-month-old Sprague-Dawley rats, and correlated with a significant decline in rotarod laten-cy-to-fall measurement by approximately 2.5 fold. The measured midbrain region revealed a 31% lower TH signal when compared to control (p<0.01 by t test, n=5). Bivariate analysis of in-tegrated TH counts versus rotarod latency-to-fall indicates a positive slope and modest but sig-nificant correlation of R2=0.68 (p<0.05, n=10). These results indicate this rapid, instrument-based quantification method by IR detection successfully quantifies TH levels in rat brain tissue, while taking only 5 days from euthanasia to data output. This approach also allows for the identifica-tion of multiple targets by IHC with the simultaneous performance of downstream molecular analysis within the same animal tissue, allowing for the use of fewer animals per study.