REVIEW | doi:10.20944/preprints202101.0220.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: RAS oncogene; RAS signaling networks; RAS in human cancer; targeting RAS; computational modeling; personalized therapies
Online: 12 January 2021 (12:29:58 CET)
RAS oncogenes are amongst the most commonly mutated proteins in human cancers. They regulate a wide range of effector pathways that control cell proliferation, survival, differentiation, migration and metabolic status. Including aberrations in these pathways, RAS dependent signaling is altered in more than half of human cancers. Targeting mutant RAS proteins and their downstream oncogenic signaling pathways has been elusive. However, recent results comprising detailed molecular studies, large scale omics studies and computational modeling have painted a new and more comprehensive portrait of RAS signaling that helps us to understand the intricacies of RAS, how its physiological and pathophysiological functions are regulated, and how we can target them. Here, we review these efforts particularly trying to relate the detailed mechanistic studies with global functional studies. We highlight the importance of computational modeling and data integration to derive an actionable understanding of RAS signaling that will allow us to design new mechanism based therapies for RAS mutated cancers.
ARTICLE | doi:10.20944/preprints202210.0296.v2
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Pancreatic Ductal Adenocarcinoma; K-Ras; N-Ras; G2 cyclins
Online: 16 February 2023 (03:22:47 CET)
Development of K-Ras independence may explain failure of targeted therapy for pancreatic cancer (PC). In this paper active N as well as K-Ras was shown in all human cell lines tested. In a cell line dependent on mutant K-Ras, it was shown that depleting K-Ras reduced total Ras activity, while cell lines described as independent had no significant decline in total Ras activity. Knockdown of N-Ras showed it had an important role in controlling the relative level of oxidative metabolism but only K-Ras depletion caused a decrease in G2 cyclins, proteasome inhibition reversed this and other targets of APC/c were also decreased by K-Ras depletion. K-Ras depletion did not cause an increase in ubiquitinated G2 cyclins but instead caused exit from G2 phase to slow relative to completion of S-phase, suggesting mutant K-Ras may inhibit APC/c prior to anaphase but stabilizes G2 cyclins independently of this. We propose that during tumorigenesis, cancer cells expressing wild type N-Ras protein are selected because the protein protects cancer cells from the deleterious effects of cell cycle independent induction of cyclins by mutant K-Ras. Mutation independence results when N-Ras activity becomes adequate to drive cell division even in cells where K-Ras is inhibited. Keywords: Pancreatic Ductal Adenocarcinoma, K-Ras, N-Ras, G2 cyclins.
REVIEW | doi:10.20944/preprints202010.0310.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Ras; nanocluster; Raf; dimerization; Ras orientation; membrane; HVR; structure
Online: 14 October 2020 (14:22:52 CEST)
Ras is the most frequently mutated oncogene and recent drug development efforts have spurred significant new research interest. Here we will review progress toward understanding how Ras functions in nanoscale, proteo-lipid signaling complexes on the plasma membrane, called nanocluster. We will discuss how G-domain reorientation is plausibly linked to Ras-nanoclustering and -dimerization. We will then look at how these mechanistic features could cooperate in the engagement and activation of RAF by Ras. Moreover, we will show how this structural information can be integrated with microscopy data that provide nanoscale resolution in cell biological experiments. Synthesizing the available data, we propose to distinguish between two types of Ras nanoclusters, an active, immobile RAF-dependent type and an inactive/ neutral membrane anchor-dependent. We conclude that it is possible that Ras reorientation enables dynamic Ras dimerization, while the whole Ras/ RAF complex transits into an active state. These transient di/oligomer interfaces of Ras may be amenable to pharmacological intervention. We close by highlighting a number of open questions including, whether all effectors form active nanoclusters and whether there is an isoform specific composition of Ras nanocluster.
ARTICLE | doi:10.20944/preprints202309.1034.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: papillary thyroid carcinoma; BRAF-like; RAS-like; BRAFV600E; RAS mutation; prediction model
Online: 15 September 2023 (10:54:29 CEST)
The Cancer Genome Atlas (TCGA) has classified papillary thyroid carcinoma (PTC) into indolent RAS-like and aggressive BRAF-like based on its distinct driver gene mutations. This study aimed to assess clinicopathology and pERK1/2 expression variations between BRAF-like and RAS-like PTCs and establish predictive models for BRAFV600E and RAS-mutated PTCs. A total of 222 PTCs underwent immunohistochemistry staining to assess pERK1/2 expression and Sanger sequencing to analyze the BRAF and RAS genes. Multivariate logistic regression was employed to develop prediction model. Independent predictors for the BRAFV600E mutation include a nuclear score of 3, the absence of capsules, an aggressive histology variant, and pERK1/2 levels exceeding 10% (X2=0.128, P>0.05, AUC=0.734, P<0.001). RAS mutation predictive model includes follicular histology variant and pERK1/2 expression >10% (X2=0.174, P>0.05, AUC=0.8, P<0.001). We proposed using the prediction model concurrently with four potential combination group outcomes. PTC cases included in combination of low BRAFV600E-scoring group and high RAS-scoring group are categorized as RAS-like (adjOR=4.857, P=0.01, 95% CI=1.470-16.049). PTCs included in combination of high BRAFV600E-scoring group and low RAS-scoring group are categorized as BRAF-like PTCs (adjOR=3.091, P=0.001, 95% CI=1.594-5.995). The different prediction models indicate variations in biological behaviour between BRAF-like and RAS-like PTCs, necessitating adjustments in treatment approaches.
ARTICLE | doi:10.20944/preprints202307.0502.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: oncogenic Ras, overgrowth, tensins, Drosophila
Online: 10 July 2023 (04:01:14 CEST)
Oncogenic mutations in the small GTPase Ras contributes to ~30% of human cancers. However, tissue growth induced by oncogenic Ras is restrained by induction of cellular senescence and additional mutations are required to induce tumor progression. Therefore, it is paramount to identify cooperating cancer genes. Recently, the tensin family of focal adhesion proteins, TNS1-4, have emerged as regulators of carcinogenesis, yet their role in cancer appears somewhat controversial. Around 90% of human cancers are of epithelial origin. We have used the Drosophila wing imaginal disc epithelium as model system to gain insight into the roles of two orthologs of human TNS2 and 4, blistery (by) and PVRAP, in epithelial cancer progression. We have generated null mutations in PVRAP and found that, as it is the case for by and mammalian tensins, PVRAP mutants are viable. We have also found that elimination of either PVRAP or by potentiates RasV12-mediated wing disc hyperplasia. Furthermore, our results have unravelled a mechanism by which tensins may limit Ras oncogenic capacity, the regulation of cell shape and growth. These results demonstrate that Drosophila tensins behave as suppressors of Ras-driven tissue hyperplasia, suggesting that the roles of tensins as modulators of cancer progression might be evolutionary conserved.
REVIEW | doi:10.20944/preprints202102.0107.v1
Online: 3 February 2021 (10:09:39 CET)
Pancreatic cancer is a fatal disease with mortality rate of 5% and a with a limited survival rate of 5 years. Despite of the extensive efforts that has been made to cure the disease it still has been considered as ‘undruggable’. It is characterized by epithelial to dense stromal tumor formation however due to lack of diagnosis options and treatment test available to detect the disease to the point at which resection of the tumor is possible, it makes it the fourth leading cause of cancer related death. The unavailable information regarding the early detection of biological markers along with the increased invasive tumor, the inherit chemoresistance against medication radiation and chemotherapy stubbornly fail the therapeutic options available. These associated problems made the scientists to reevaluate the approaches that are currently in practice and take a step back to fully understand the basic biological pathways that are involved in the pancreatic cancer, the heterogeneity of the tumor itself along with expression and a number of mutations that are observed at different locations. Clinical trial along with new approaches are nowadays focus of research to treat this tumor. The review paper describes the basic cellular pathways involved in pancreatic cancer, the gene mutations and their expression having effect on the pathology of the diseases along with treatment options that are available to treat the tumor. These efforts will help with the expansion of our knowledge to undergo the clinical trial and the synthesis of novel medicines for the prognosis of the disease.
ARTICLE | doi:10.20944/preprints202311.1406.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: lipidomics; hepatocellular carcinoma; ras oncogene; sex disparity
Online: 22 November 2023 (08:48:05 CET)
Lipid dysregulation is critically involved in hepatocellular carcinoma (HCC). Further, male predi-lection and Ras pathway hyperactivation are distinct characteristics of HCC. However, mecha-nisms underlying their connections remain unknown. The aim of the present study was to perform a comprehensive lipidomics analysis of a Hras12V transgenic mice (Ras-Tg) model of HCC induced by hepatocyte-specific Ras pathway activation and characterized by male predilection and a dis-rupted lipid metabolism. A total of 3437 lipids were identified in HCC (T) and peri-tumor tissues (P) of Ras-Tg mice and liver tissues of wild-type mice (W) of both sexes. Longitudinal comparisons of W, P, and T yielded 359 differentially expressed lipids (DELs) in male mice and 306 DELs in female mice. Generally, glycerolipid accumulation, glycerophospholipid reduction and monounsaturated fatty acid synthesis improvement were more frequent in T compared to P. The expression change pattern analysis revealed common and characteristic DELs positively/negatively associated with HCC or the Ras oncogene. Further lipid metabolism pathway investigations revealed that disordered lipid and fatty acid biosynthesis contributed to glycerolipid accumulation and glycerophospholipid re-duction in T. Comparisons between P and W suggests that different responses to the Ras oncogene in mice of different sexes, as well as higher amounts of aberrantly regulated lipids in males, may contribute to male-biased hepatocarcinogenesis. However, lateral comparisons between sexes showed a converging trend during hepatocarcinogenesis, explaining the poor efficacy for gen-der-specific therapies. In conclusion, the common and characteristic DELs and lipid metabolism pathways in HCC initiated by the Ras oncogene from sexually dimorphic hepatocytes provide novel insights into the clinical diagnosis and management of HCC.
ARTICLE | doi:10.20944/preprints202305.0364.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: K-Ras; centrin; calmodulin; mitosis; centrosome; BRET
Online: 5 May 2023 (11:41:23 CEST)
Recent data suggest that K-Ras4B (hereafter K-Ras) can drive cancer cell stemness via calmodulin (CaM)-dependent, non-canonical Wnt-signalling. Here we examined whether another Ca2+-binding protein, the CaM-related centrin1, binds to K-Ras and could mediate some K-Ras functions that were previously ascribed to CaM. While CaM and centrin1 appear to distinguish between peptides that were derived from their classical targets, they both bind to K-Ras in cells. Cellular BRET-data suggest that CaM engages more with K-Ras than centrin1 and that the interaction with the C-terminal membrane anchor of K-Ras is sufficient for this. Surprisingly, binding of neither K-Ras nor its membrane anchor alone to CaM or centrin1 is sensitive to inhibition of prenylation. In support of an involvement of the G-domain of K-Ras in cellular complexes with these Ca2+-binding proteins, we find that oncogenic K-RasG12V displays increased engagement with both CaM and centrin1. This is abrogated by addition of the D38A effector-site mutation, suggesting that K-RasG12V is held together with CaM or centrin1 in complexes with effectors. When treated with CaM-inhibitors the BRET-interaction of K-RasG12V with centrin1 was also disrupted in the low micromolar range, comparable to that with CaM. While CaM predominates in regulating functional membrane anchorage of K-Ras, it has a very similar co-distribution with centrin1 on mitotic organelles. Given these results, a significant overlap of the CaM- and centrin1-dependent functions of K-Ras is suggested.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: K-Ras; Hsp90; Cdc37; nanoclustering; cancer; drug development
Online: 31 March 2021 (15:30:27 CEST)
The natural product elaiophylin is a macrodiolide with broad biological activities. However, no direct target of elaiophylin in eukaryotes has been described so far, which hinders a systematic explanation of its astonishing activity range. We recently showed that the related conglobatin A, a protein-protein interface inhibitor of the interaction between the N-terminus of Hsp90 and its cochaperone Cdc37, blocks cancer stem cell properties by selectively inhibiting K-Ras4B but not H-Ras. Here we elaborate that elaiophylin likewise disrupts the Hsp90/ Cdc37 interaction, without affecting the ATP-pocket of Hsp90. Similar to conglobatin A, elaiophylin decreased expression levels of the Hsp90 client HIF1⍺, a transcription factor with various downstream targets, including galectin-3. Galectin-3 is a nanocluster scaffold of K-Ras, which explains the K-Ras selectivity of Hsp90 inhibitors. In agreement with this K-Ras targeting and the potent effect on other Hsp90 clients, we observed with elaiophylin treatment a submicromolar IC50 for MDA-MB-231 3D spheroid formation. Finally, a strong inhibition of the same cells grown in the chorioallantoic membrane (CAM) microtumor model was determined. These results suggest that several other macrodiolides may have the Hsp90/ Cdc37 interface as a target site.
ARTICLE | doi:10.20944/preprints201811.0170.v1
Subject: Medicine And Pharmacology, Clinical Medicine Keywords: CKD, ESKD, Death, anti-RAS, hyperkalemia, competing risk
Online: 7 November 2018 (14:48:30 CET)
Hyperkalemia burden in non-dialysis CKD under nephrology care is undefined. We prospectively followed 2443 patients with two visits (referral and control with 12-month interval) in 46 nephrology clinics. Patients were stratified in four categories of hyperkalemia (sK≥5.0 mEq/L) by sK at visit 1 and 2: Absent (no-no), Resolving (yes-no), New Onset (no-yes), Persistent (yes-yes). We assessed competing risks of ESKD and death after visit 2. Age was 65±15 y, eGFR 35±17 mL/min/1.73 m2, proteinuria 0.40 (0.14-1.21) g/24h. In the two visits sK was 4.8±0.6 and levels ≥6 mEq/L were observed in 4%. Hyperkalemia was absent in 46%, resolving 17%, new onset 15% and persistent 22%. Renin-angiotensin-system inhibitors (RASI) were prescribed in 79% patients. During 3.6-year follow-up, 567 patients reached ESKD and 349 died. Multivariable competing risk analysis [sub-hazard ratio-sHR, 95%Confidence Interval-CI] evidenced that new onset [sHR 1.34, 95%CI 1.05-1.72] and persistent [sHR 1.27, 95%CI 1.02-1.58] hyperkalemia predicted higher ESKD risk versus absent, independently from main determinants of outcome including eGFR change. Conversely, no effect on mortality was observed. Results were confirmed by testing sK as continuous variable. Therefore, in CKD under nephrology care, mild-to-moderate hyperkalemia status is common (37%) and predicts per se higher ESKD risk but not mortality.
ARTICLE | doi:10.20944/preprints201810.0066.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: nucleotide triphosphate, label-free, K-Ras, apyrase, terbium
Online: 3 October 2018 (17:32:44 CEST)
A new label-free molecular probe for luminescent nucleotide detection in neutral aqueous solution is presented. Phosphate-containing molecules such as nucleotides possess vital role in cell metabolism, energy economy, and signaling. Thus the monitoring of nucleotide concentration and nucleotide related enzymatic reactions is of high importance. Two component lanthanide complex formed from Tb(III) ion carrier and light harvesting antenna, readily distinguishes nucleotides containing different number of phosphates and enable direct detection of enzymatic reactions converting nucleotide triphosphate (NTP) to nucleotide di/monophosphate or the opposite. Developed sensor enables the detection of enzymatic activity with a low nanomolar sensitivity, as highlighted with K-Ras and apyrase enzymes in there hydrolysis assays performed in high throughput screening compatible 384-well plate format.
REVIEW | doi:10.20944/preprints202107.0642.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: SARS-CoV-2; RAS; acute kidney injury; immune response
Online: 29 July 2021 (10:20:36 CEST)
Coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To contain the virus, numerous preventive measures have been taken including isolation of patients, careful infection control, social distancing, and taking vaccine. So far, new confirmed and death cases are still increasing. SARS-CoV-2 invades cells by using the angiotensin converting enzyme 2 (ACE2). ACE2 is an essential enzyme of the renin-angiotensin system (RAS) which converts angiotensin II (Ang II) to angiotensin (1-7). ACE2 is expressed in different organs, including lung, heart, and kidney. A high number of COVID-19 patients developed kidney injury has been reported. Renal impairment and acute injury are associated with mortality of COVID-19, which is 14-16 times higher than other general patients. Acute Kidney Injury has been occured in 2.9 up to 43% of intensive care unit patients. The increasing evidence show that the components of RAS can activate the complement cascade, and cytokines production. Kidney injury caused by SARS-CoV-2 is related mainly to systemic and local inflammation. Moreover, the uncontrolled immune responses mediated by SARS-CoV-2 including hypercytokinaemia, secondary hemophagocytic lymphohistiocytosis, antibody dependent enhancement, complement system, and phagocytic cells activation can contribute in the virus pathogenesis leading to associated renal dysfunction. However, the role and crosstalk between of RAS components and immune response in mediating kidney injury remain undefined. In this review, we focus on the recent studies to provide the pathogenesis of SARS-CoV-2 interacting with RAS and immune responses to mediate kidney injury.
TECHNICAL NOTE | doi:10.20944/preprints202209.0410.v1
Subject: Engineering, Civil Engineering Keywords: 2D floodplain modeling; HEC-RAS; River Renaturation; finite difference approximation
Online: 27 September 2022 (03:53:09 CEST)
River renaturation can be an effective management method for restoring the floodplain's natural capacity and minimizing the effects during high flow periods. A 1D-2D HEC-RAS model, in which the flood plain was considered as 2D and the main channel as 1D, was used to simulate flooding in the restored reach of the Spree River. When computing in this model, finite volume and finite difference approximations using the Preissmann approach are used for the 1D and 2D models, respectively. To comprehend the sensitivity of the parameters and model, several scenarios were simulated using different time steps and grid sizes. Additionally, dykes, dredging, and changes to the vegetation pattern have been used to simulate flood mitigation measures. The model predicted that flooding would occur mostly in the downstream portion of the channel in the majority of the scenarios without mitigation measures, whereas with mitigation measures, flooding in the floodplain would be greatly reduced. By preserving the natural balance on the channel's floodplain, the restored area needs to be kept in good condition. Therefore, mitigating measures that balance the area's economic and environmental aspects must be considered in light of the potential for floods.
ARTICLE | doi:10.20944/preprints202010.0092.v1
Subject: Engineering, Automotive Engineering Keywords: ANOVA; Asphalt Binder Extraction; Quality Assurance; Quality Control; RAP; RAS
Online: 5 October 2020 (14:06:31 CEST)
Asphalt binder requires more investigation to be accurately and precisely extracted since it is a significant procedure for quality control quality assurance (QC/QA) and subsequent binder characterization. In this research, the authors provided a hands-on experience with binder extraction to deliver recommendations concerning the sensitive steps that may affect the outcomes (extracted binder content, Pbe%). Based on the extraction by the centrifuge method, two mineral matter determination methods (ashing and centrifuge) were addressed. Field cores were investigated with comparing the Pbe% to the actual binder content, Pba%. Analysis of variance (ANOVA) and Tukey Post-Hoc statistical analyses, in addition to linear least square regression analysis, were used to show the significance of difference according to 38 variant cores randomly obtained from the field segments (in-service roads) via the first two weeks from the construction date. Such cores involved reclaimed asphalt pavement (RAP), reclaimed asphalt shingles (RAS), and a wide range of additives. The two extraction methods were compared with concluding that the centrifuge method was highly recommended based on a quantitative evaluation, which delivered the same average Pba% based on the 38 cores. Furthermore, the centrifuge method provided much saving in the experimental time (almost half the time required for the ashing method). It was found that the ashing outcomes were equal to the centrifuge outcomes with disregarding the ammonium carbonate addition. Thus, it could be recommended to reassess the ammonium carbonate addition as it might excessively compensate for fake minerals that have not been lost by the ignition oven.
REVIEW | doi:10.20944/preprints201812.0006.v1
Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: oncology; ectopic RAS cancer cells; epigenetic stimulation PAC in oncology
Online: 3 December 2018 (04:27:03 CET)
Analyzed the literature devoted to the changes in the expression of the RAS proteins of cancer cells. A brief review of protein expression dynamics PAC in malignant tumors and the possible role of epigenetic mechanisms in these processes. Through research epigenetic mechanisms state for cancer have been developed principally new techniques for their correction, based on the use of selective regulators systems covalent modification-histone proteins (for example, deacetylase inhibitor) and microRNA synthesis technologies. Literature data show promising pharmacological correction epigenetic modification of chromatin in the treatment of cancer.
ARTICLE | doi:10.20944/preprints202005.0364.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: COVID-19; gender; transcriptomics; RAS; hydrolase activity; sex-based immunological differences
Online: 23 May 2020 (06:03:25 CEST)
Since the outbreak of the novel coronavirus disease (COVID-19) at the end of 2019, the clinical presentation of the disease showed a great heterogeneity with a diverse impact between different subpopulations. Emerging evidence from different parts of the world showed significantly poor outcome among males compared to female patients. A better understanding of the molecular mechanisms behind this difference might be a fundamental step for a more effective and targeted response to the outbreak. For that reason, here we try to investigate the molecular basis of the gender variations in mortality rates related to COVID-19 infection. To achieve this, we used our in-house pipeline to process publicly available lung transcriptomic data from 141 females compared to 286 males. After excluding Y specific genes, our results showed a shortlist of 73 genes that are differentially expressed between the two groups. Our results showed downregulation of a group of genes that are involved in the regulation of hydrolase activity including (AGTR1, CHM, DDX3X, FGFR3, SFRP2, and NLRP2), which is also believed to be essential for lung immune response and antimicrobial activity in the lung tissues in males compared to females. In contrast, our results showed an upregulation of angiotensin II receptor type 1 (AGTR1), a member of the renin-angiotensin system (RAS) that plays a role in angiotensin-converting enzyme 2 (ACE2) activity modulation. Interestingly, recent reports and experimental animal models highlight an important role of this receptor in SARS-Coronavirus lung damage as well as pulmonary edema, suggesting a possible role of its blockers like losartan and olmesartan as potential therapeutic options for COVID-19 infection. Finally, our results also showed a differential expression of different genes that are involved in the immune response including the NLRP2 and PTGDR2, further supporting the notion of the sex-based immunological differences. Taken together, our results provide an initial evidence of the molecular mechanisms that might be involved in the differential outcomes observed between both genders during the COVID-19 outbreak. This might be essential for the discovery of new targets and more precise therapeutic options to treat COVID-19 patients from different clinical and epidemiological characteristics with the aim of improving their outcome.
ARTICLE | doi:10.20944/preprints202210.0041.v1
Subject: Engineering, Architecture, Building And Construction Keywords: Food security; Urban farming; Fish protein; RAS; Land; Water; Sub-Sahara Africa
Online: 5 October 2022 (12:30:37 CEST)
The urban population in developing countries, especially sub-Saharan Africa, is rapidly increas-ing. As towns and cities grow, so does the demand for fish protein. While flow-through aqua-culture can provide fresh, healthy and nutritious fish protein, it is plagued by extensive land re-quirement as well as effluent discharge, thus, unsuitable for city regions. Alternatively, small-scale Recirculating Aquaculture System (RAS) could improve food and nutritional security (FNS), livelihoods as well as reduce environmental degradation in urban areas despite land and water constraints. The question however remains - what are the key technical, business and managerial issues, surrounding small-scale RAS in urban farming? This study reviews the RAS prototype of the Sustainable Aquaponics for Nutritional and Food Security in Urban Sub-Saharan Africa (SANFU) II project based on mass balance and stock density, relevant for fish survival and/or availability as well as net cash-flow analyses. The results suggest that small-scale RAS are technically and financially viable only with family labor having proper aquaculture monitoring and management skills. Furthermore, access to adequate equipment and inputs as well as electricity for the recirculating system are crucial. Urban innovation actors will adopt RAS if operations are profitable given that family labor is employed.
ARTICLE | doi:10.20944/preprints202203.0154.v1
Subject: Medicine And Pharmacology, Gastroenterology And Hepatology Keywords: Colorectal cancer; Cancer stem cell; Neural progenitor cell; Wnt/β-catenin; K-Ras
Online: 10 March 2022 (14:26:20 CET)
Cancer stem cells (CSCs) are a tumor cell subpopulation that drives tumor progression and metastasis, leading to poor overall survival of patients. In colorectal cancer (CRC), hyper-activation of Wnt/β-catenin signaling by mutation of both Adenomatous polyposis coli (APC) and K-Ras increases the size of the CSC population. We previously showed that the CPD0857 inactivates Wnt/β-catenin signaling by promoting ubiquitin-dependent proteasomal degradation of β-catenin and Ras proteins, thereby decreasing proliferation and increasing apoptosis of CRC lines. CPD0857 also decreased growth and invasiveness of CRC cells harboring mutant K-Ras resistant to EGFR mAb therapy. Here, we show that CPD0857 treatment decreases proliferation and increases neuronal differentiation of neural progenitor cells (NPCs). CDP0857 effectively reduced expression of CSC markers and suppressed self-renewal capacity. CPD0857 treatment also inhibited proliferation and expression of CSC markers in D-K-Ras MT cells carrying K-Ras, APC and PI3K mutations, indicating inhibition of PI3K/AKT signaling. Moreover, CPD0857-treated xenograft mice showed regression of tumor growth and decreased numbers of CSCs in tumors. We conclude that CPD0857 could serve as the basis of a drug development strategy targeting CSCs activated through Wnt/β-catenin-Ras MAPK-PI3K/AKT signaling in CRCs.
REVIEW | doi:10.20944/preprints202103.0510.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: RAF kinase independent; RAS; MST2; ASK; PLK; RHO-α; apoptosis; cell cycle; cancer therapy
Online: 22 March 2021 (10:29:37 CET)
Abstract: Oncogenic RAS mutations drive more than half of human cancers, and RAS inhibition is the holy grail of oncology. Thirty years of relentless efforts and harsh disappointments have taught us about the intricacies of oncogenic RAS signalling that allow us to now get a pharmacological grip on this elusive protein. The inhibition of effector pathways, such as the RAF-MEK-ERK pathway, has largely proven disappointing. So far, most of these efforts were aimed at blocking the activation of ERK. Here, we discuss RAF dependent pathways that are regulated through RAF functions independent of catalytic activity and their potential role as targets to block oncogenic RAS signalling. We focus on the now well documented roles of RAF kinase independent functions in apoptosis, cell cycle progression and cell migration.
ARTICLE | doi:10.20944/preprints201810.0650.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: TRMM; HEC-HMS; HEC-RAS; GIS; hydrological model; hydraulic model; flood; Chitral River Basin
Online: 29 October 2018 (04:28:08 CET)
Flash flooding, a hazard which is triggered by heavy rainfall is a major concern in many regions of the world often with devastating results in mountainous elevated regions. We adapted remote sensing modelling methods to analyse one flood in July 2015, and believe the process can be applicable to other regions in the world. The isolated thunderstorm rainfall occurred in the Chitral River Basin (CRB), which is fed by melting glaciers and snow from the highly elevated Hindu Kush Mountains (Tirick Mir peak’s elevation is 7708 m). The devastating cascade, or domino effect, resulted in a flash flood which destroyed many houses, roads, and bridges and washed out agricultural land. CRB had experienced devastating flood events in the past, but there was no hydraulic modelling and mapping zones available for the entire CRB region. That is why modelling analyses and predictions are important for disaster mitigation activities. For this flash flood event, we developed an integrated methodology for a regional scale flood model that integrates the Tropical Rainfall Measuring Mission (TRMM) satellite, Geographic Information System (GIS), hydrological (HEC-HMS) and hydraulic (HEC-RAS) modelling tools. We collected and use driver discharge and flood depth observation data for five river sub-stream areas, which were acquired in cooperation with the Aga Khan Rural Support Program (AKRSP) organization. This data was used for the model’s calibration and verification. This modelling methodology is applicable for other regional studies especially for rough mountainous areas which lack local observations and river discharge gauges. The results of flood modelling are useful for the development of a regional early flood warning system and flood mitigation in hazardous flood risk areas. The flood simulations and prepared connected video visualization can be used for local communities. This approach is applicable for flood mitigation strategies in other regions.
ARTICLE | doi:10.20944/preprints202304.0112.v1
Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: HEC-RAS model; Red River; LiDAR data; Flood mapping; Manning’s n-coefficient; Contraction Scour Depth
Online: 7 April 2023 (04:54:08 CEST)
This research is focused on two key areas. The first is mapping the 2022 flood in the Red River of the North near Grafton, North Dakota, US, and the second is evaluating the scour potential of the Grafton Bridge. Local scour of bridge piers can cause hydraulic structures such as bridge piers and abutments to fail during floods, making it a crucial area of investigation. To collect bathymetry and discharge data during low and high flow conditions, including a flood event with a 16.5-year return period in 2022, an Autonomous Surface Vehicle (ASV) incorporated with LiDAR DEM (Digital Elevation Model) data obtained from the US Geological Survey (USGS) National Map was used. Flood mapping and evaluation of local scour around the bridge pier were conducted using the HEC-RAS 6.0.0 software, which utilizes the Colorado State University method as a default equation. This research demonstrates the potential of ASVs in collecting critical data and LiDAR DEM data is an efficient method for flood mapping and determining scour potential, as it integrates bathymetry, flow velocity, and flood prediction.
ARTICLE | doi:10.20944/preprints202105.0784.v1
Subject: Chemistry And Materials Science, Analytical Chemistry Keywords: Quinoline; Isoquinoline; G-Quadruplex ligands; k-RAS; c-MYC; telomere; SAR; pyri-dine-dicarboxamide; molecular dynamics
Online: 31 May 2021 (14:03:28 CEST)
Quadruplex-interactive small molecules have a wide potential application, not only as drugs but also as sensors of quadruplexes structures. The purpose of this work is the synthesis of analogues of the bis-methylquinolinium-pyridine-2,6-dicarboxamide G4 ligand 360A, to identify relevant structure-activity relationships to apply to the design of other G4-interactive small molecules bearing bis-quinoline or bis-isoquinoline moieties. Thermal denaturation experiments revealed that non-methylated derivatives with a relative 1,4 position between the amide linker and the nitrogen of the quinoline ring are moderate G4 stabilizers, with a preference for the hybrid h-Telo G4. Insertion of a positive charge upon methylation of quinoline/isoquinoline nitrogen increases compounds capacity to selectively stabilize G4s compared to duplex DNA, with a preference for parallel structures. Among these, compounds having a relative 1,3-position between the charged methylquinolinium/isoquinolinium nitrogen and the amide linker are the best G4 stabilizers. More interestingly, these ligands showed different capacities to selectively block DNA polymer-ization in a PCR-stop assay and to induce G4 conformation switches of hybrid h-Telo G4. Mo-lecular dynamic simulations with the parallel k-RAS G4 structure showed that the relative spatial orientation of the two methylated quinoline/isoquinoline rings determines the ligands mode and strength of binding to G4s.
ARTICLE | doi:10.20944/preprints202309.1417.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: R-RAS2; RAS; GTPases; chronic lymphocytic leukemia; B-CLL; mouse model; ibrutinib; venetoclax; new therapies; cancer treatment
Online: 21 September 2023 (12:04:56 CEST)
B-cell chronic lymphocytic leukemia (B-CLL) is the most common type of leukemia in the Western world. Mutations in different genes, such as TP53 and ATM, and deletions in specific chromosomal regions, including 11q or 17p, have been associated with a worse prognosis for the disease. Recent research from our group has demonstrated that, contrary to the usual cancer development process through missense mutations, B-CLL is driven by the overexpression of the small GTPase RRAS2 in its wild-type form, without activating mutations. While some mouse models of this disease have been developed to date and are commonly used in B-CLL research, they come with various disadvantages, such as a long waiting period until the leukemia fully develops, the need for cell engraftment, or, in some cases, a failure to replicate the alterations found in human patients. We have recently introduced Rosa26-RRAS2fl/flxmb1-Cre as a new mouse model of B-CLL with full disease penetrance. In this work, we have validated this mouse model as a novel tool for the development of new therapies for B-CLL by testing two of the most widely applied targeted agents: ibrutinib and venetoclax. This also paves the way for the development of new targeted agents against R-RAS2 itself, an approach that has not yet been explored in clinical practice.
COMMUNICATION | doi:10.20944/preprints202305.1298.v1
Subject: Biology And Life Sciences, Life Sciences Keywords: Mass spectrometry; RAS; ACE; ACE2; CPN; bradykinin; hypertension; cardiovascular disease; antihypertensiva; ACE inhibitors; angiotensin receptor blockers; bradykinin; neuropeptide re-porter assay
Online: 18 May 2023 (08:13:10 CEST)
(1) Background: Co-morbidities such as hypertension and cardiovascular disease are major risk factors for severe COVID-19. The renin-angiotensin-system (RAS) is critically involved in their pathophysiology and is counterbalanced by both angiotensin-converting enzyme 2 (ACE2), the functional receptor of SARS-CoV-2, and the kallikrein-kinin-system (KKS). Considerable research interest with respect to COVID-19 treatment is, thus, currently directed towards the components of these systems. In an earlier study, we noticed significantly reduced carboxypeptidase N (CPN, KKS member) activity and partially excessive angiotensin-converting enzyme (ACE, RAS member) activity in the sera of both hospitalized (HoP) COVID-19 patients and a sub-group of covalescent patients, while in the majority of the probands recovering from the disease these values had returned to normal. The data had been obtained using bradykinin (BK) as a reporter peptide, which is a target of both CPN and ACE, and they were supplemented by serum proteomics of the same patient cohort. We hypothesized that the data could be indicative of Long COVID, which had not been fully appreciated at the time of our study.; (2) Methods: The data were re-evaluated in the light of Long COVID. The recent literature on the RAS in COVID-19, antihypertensiva, and Long COVID was briefly reviewed.; (3) Results: While the levels of the BK serum degradation products should return to normal concentrations during convalescence, this was not true for some patients. This could be due to persisting liver problems, because CPN is synthesized there, but also to a dysregulated RAS. This was not reflected in the levels of selected RAS/KKS serum proteins like angiotensinogen (AGT), although AGT correlated with disease severity in HoP. However, standard tests in routine patient care in Long COVID often come back normal, and it may be that BK degradation is specific in some pathophysiologies. Moreover, the HoP group was sub-divided based on the serum protein profiles and COVID-19 severity.; (4) Conclusions: We point out two insights: 1) Sensitive technology such as omics methods might provide unexpected significant differences within the pre-defined patient groups of a clinical study. Those can only be explored, if the cohorts are large enough and properly matched with respect to the parameters known beforehand (e.g., age, gender, co-morbidities). 2) Results of the BK-reporter serum protease activity assay could be indicative of persisting liver problems and/or potentially of Long COVID. Clinical studies are required to test this hypothesis.
REVIEW | doi:10.20944/preprints202307.1284.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Cancer; tumourigenesis; drug resistance; signalling pathways; Wnt/β-catenin pathway; JAK/STAT pathway; PI3K/Akt/mTOR pathway; RAS/RAF/MAPK/ERK signalling
Online: 19 July 2023 (09:14:02 CEST)
One of the leading causes of death worldwide, in both man and woman, is cancer. Despite the significant development in therapeutic strategies, the inevitable emergence of drug resistance limits the success and impedes the curative outcome. Intrinsic and acquired resistance are common mechanisms responsible for cancer relapse. Several factors crucially regulate tumourigenesis and resistance, including physical barriers, tumour microenvironment (TME), heterogeneity, genetic and epigenetic alterations, the immune system, tumour burden, growth kinetics and undruggable targets. Moreover, transforming growth factor-beta (TGF-β), Notch, epidermal growth factor receptor (EGFR), integrin-extracellular matrix (ECM), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), phosphoinositol-3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR), wingless-related integration site (Wnt)/β-catenin), Janus kinase/signal transducers and activators of transcription (JAK/STAT) and RAS/RAF/mitogen-activated protein kinase (MAPK) signalling pathways are some of the key players that have a pivotal role in drug resistance mechanisms. To guide future cancer treatments and improve results, a deeper comprehension of drug resistance pathways is necessary. This review will cover both intrinsic and acquired resistance and give a comprehensive overview of recent research on mechanisms that enable cancer cells to bypass barriers put by treatments, and like “satellite navigation”, find alternative routes to carry on their “journey” to cancer progression.
REVIEW | doi:10.20944/preprints202004.0160.v2
Subject: Biology And Life Sciences, Virology Keywords: COVID-19; ACE; ACE2; Angiotensin II; Bradykinin; RAS inhibitors; ACE inhibitors; AT1 receptor blockers; Losartan; Bradykinin Antagonists; Ang II loading; Giapreza; Icatibant.
Online: 14 April 2020 (14:34:43 CEST)
As the world grapples with a pandemic with various and expanding epicenters, a flurry of medical and scientific activity has gained speed and momentum in a race to halt COVID-19. A controversial topic has been the connection between COVID-19 and the Renin-Angiotensin system (RAS). COVID-19, like Sars before it, enters by way of the Angiotensin Converting Enzyme 2 (ACE2). ACE2 is ubiquitously expressed in many tissues in the body serving as the doorway by which the virus can enter and spread causing inflammatory havoc. Demographic evidence coming out of China and other locations make it clear that the elderly and those suffering cardiovascular complications such as hypertension etc are most at risk. The connection to RAS and the demographic nature of the data coming out has led many to advance hypothesis, recommendations and even therapies based on existing RAS inhibitors and other components of the renin-Angiotensin system. It is pertinent to review the literature in the context of our understanding of the renin-angiotesnin system to allow better judgements to be made as well as lines of research initiated advancing a quick resolution to COVID-19. Covid-19 appears invincible as if dipped in the river Styx, but even Achilles had a vulnerable heel. Understanding the homeostatic balance that the coronavirus disrupts, we can discover the arrow in corona’s heel.
REVIEW | doi:10.20944/preprints202212.0032.v1
Subject: Medicine And Pharmacology, Pulmonary And Respiratory Medicine Keywords: ACE2; Ang II; angiotensin(1-7); AT1R; Cathepsin; cell entry; COVID-19; Endocytosis; ERK1/2; Furin; IL-1β; IL-6; MAPK; MasR; NF-κB; PLC; PKC; RAS; RBD; SARS-CoV2; S protein; TMPRSS2; TNF-α
Online: 2 December 2022 (02:19:48 CET)
Since the spread of the deadly virus SARS-CoV2 in late 2019, researchers have restlessly been seeking for unraveling how the virus factually enters the host cells. Some proteins on each side of the interaction between the virus and the host cells are involved as the major contributors to this process: 1- the nano-machine Spike protein on behalf of the virus, 2- angiotensin converting enzyme II, the mono-carboxypeptidase and the key component of renin angiotensin system on behalf of the host cell, 3- some host proteases and proteins exploited by SARS-CoV2, In this review, the complex process of SARS-CoV2 entrance into the host cells with the contribution of the involved host proteins as well as the sequential conformational changes in the Spike protein tending to increase the probability of complexification of the latter with angiotensin converting enzyme II, the receptor of the virus on the host cells, are discussed. Besides, the release of the catalytic ectodomain of angiotensin converting enzyme II as its soluble form in the extracellular space and its positive or negative impact on the infectivity of the virus are considered.
COMMUNICATION | doi:10.20944/preprints202011.0174.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: MZA, Manzamine A; CTKD, C-terminal kinase domain; ras-ERK1/2 (extracellular-signal-regulated kinase 1/2) pathway; RSK1, 90kDa ribosomal protein S6 kinase 1; RSK2, 90kDa ribosomal protein S6 kinase 2; NTKD, N-terminal kinase domain
Online: 4 November 2020 (08:27:07 CET)
Manzamines are complex polycyclic marine-derived β-carboline alkaloids with reported anticancer, immunostimulatory, anti-inflammatory, antibacterial, antiviral, antimalarial, neuritogenic, hyperlipidemia and atherosclerosis suppression bioactivities, putatively associated with inhibition of glycogen synthase kinase-3, cyclin-dependent kinase 5, and vacuolar ATPases. We hypothesized that additional and yet undiscovered molecular targets might be associated with Manzamine A (MZA) reported pharmacological properties. We report herein for the first time to our knowledge that MZA inhibited a 90kDa ribosomal protein kinase S6 (RSK1) when screened against a panel of 30 protein kinases. Furthermore in vitro RSK kinase assays demonstrated a 10-fold selectivity in potency of MZA against RSK1 versus RSK2. MZA’s differential binding and selectivity toward the two isoforms is also supported by computational docking experiments. Specifically, the RSK1-MZA (N- and C-termini) complexes appear to have stronger interactions and preferable energetics contrary to the RSK2-MZA ones. In addition, our computational strategy suggests that MZA binds to the N-terminal kinase domain of RSK1 rather than the C-terminal domain. RSK is a vertebrate family of cytosolic serine-threonine kinases that act downstream of the ras-ERK1/2 (extracellular-signal-regulated kinase 1/2) pathway, which phosphorylates substrates shown to regulate several cellular processes including growth, survival and proliferation. Consequently, our findings have lead us to hypothesize that MZA and the 80 currently known manzamine-type alkaloids isolated from several sponge genera, may have novel pharmacological properties.