Biology subjects

Glass, M.

Publications and source records attributed to Glass, M..

15 recordsLinked to original sources

bioRxiv2026

Multi-level Analysis of Codon Usage Patterns Reveals Systematic Optimization of Oncogenic Gene Expression in Pancreatic Cancer

BackgroundCodon usage bias, the non-random usage of synonymous codons in coding sequences, represents a fundamental feature of genomic organization that has been largely understudied in cancer biology. Pancreatic ductal adenocarcinoma (PDAC), the predominant subtype of pancreatic cancer, is characterized by aggressive disease progression and limited therapeutic options, necessitating novel approaches to understand its molecular pathogenesis. Leveraging publicly available single-cell RNA sequencing data, we performed comprehensive codon usage analyses across different cellular populations in PDAC. ResultsEmploying a variety of computational codon usage indices uncovered the connections between cancer-specific cellular state features and codon usage signatures. Our findings reveal that malignant pancreatic cells express genes with significantly higher GC content, demonstrate preferential usage of optimal codons through increased frequency of preferred synonymous codons, and exhibit a marked preference for more cost-effective amino acids. Analysis of transcript-level bulk RNA-seq data from PDAC tumors revealed that these codon optimization patterns extend to alternative isoform usage, with highly expressed isoforms displaying increased codon optimality and enhanced mRNA stability. ConclusionThese codon usage-dependent adaptations operating at both gene expression and transcript isoform levels may enable malignant cells to enhance gene expression rates, potentially leading to increased translational efficiency and protein production. These insights into the codon usage landscape of PDAC may provide potential biomarkers for disease monitoring and treatment response prediction.

cancer biology↗

bioRxiv2026

Chd8 haploinsufficiency leads to molecular layer heterotopias and age-dependent cortical expansion

Mutations in the chromatin remodeler CHD8 are associated with autism and macrocephaly. While mouse models of Chd8 haploinsufficiency recapitulate brain overgrowth, the specific cellular mechanisms and developmental timing that lead to these anatomical abnormalities remain poorly understood. Here, we conducted 3D imaging of Chd8V986*/+ mouse brains using magnetic resonance imaging followed by tissue clearing and cellular resolution light-sheet microscopy across embryonic and postnatal developmental stages. We found that brain overgrowth occurs postnatally, driven by an increase in non-neuronal cells prior to volumetric expansion. Unexpectedly, we identified prevalent molecular layer heterotopias (MLH) within the frontal cortex of Chd8V986*/+ mice composed of neurons breaking through the pial surface during embryonic development and persisting throughout life. Increased incidence of MLH, previously identified in individuals with idiopathic autism, was replicated across three independent Chd8+/- mouse models and present across multiple genomic backgrounds, establishing aberrant neuronal migration as a core feature of Chd8 haploinsufficiency.

neuroscience↗

bioRxiv2026

GM-CSF regulates ILC states and myeloid cell signaling during ulceration in Crohns disease

Macrophage (M-), granulocyte (G-), and granulocyte-macrophage (GM-) colony-stimulating factors (CSFs) regulate myeloid cell function, yet their relative roles during inflammation remain poorly defined. To uncover how CSFs shape spatial immune niches in Crohns disease, we performed Xenium single-cell spatial transcriptomics on ileal tissues, revealing cell-type-specific expression and source-target interactions for each CSF. GM-CSF, unlike M-CSF or G-CSF, was locally enriched in ulcerated regions where lymphocytes adjacent to macrophage aggregates signaled through STAT5 phosphorylation. To study functional consequences, we developed a csf2rb-/- zebrafish model of intestinal injury. Using this model, we found that loss of GM-CSF signaling exacerbated epithelial damage and inflammation, whereas recombinant human GM-CSF limited injury by restraining ILC1 expansion, sustaining ILC3 maintenance, and promoting IL-22 production. Cross-species single-cell analysis revealed conserved ILC gene modules and GM-CSF-dependent transcriptional networks linking lymphoid and myeloid populations. These findings establish GM-CSF as a critical spatial regulator of myeloid- lymphoid crosstalk and intestinal immune homeostasis in Crohns disease.

immunology↗

bioRxiv2025

A gene set collection of RBP target genes

RNA binding proteins (RBPs) are key post-transcriptional regulators controlling every aspect of the RNA life cycle from synthesis to decay. We extracted RBP target genes from publicly available enhanced cross-linking and immunoprecipitation followed by sequencing (eCLIP-seq) data of 168 RBPs and assembled a gene set collection that can be used to examine gene lists for enriched RBP targets via functional enrichment analysis methods like over-representation analysis (ORA), gene set enrichment analysis (GSEA) or gene set variation analysis (GSVA).

bioinformatics↗

bioRxiv2025

RNA-seq derived sequence variations are excellent features for cell line identification

1Cell lines are indispensable models for analyzing molecular mechanisms underlying human diseases. However, incorrect annotation and cross-contamination can introduce severe bias in respective studies. Accordingly, various publishers request authentication of cell lines before publication. Short tandem repeat profiling is commonly used to verify cell line identity and purity but does not guarantee that published results are based on the samples tested by this method. In this study, we demonstrate that RNA-seq-derived sequence variation information is eligible for unambiguous cell line-specific clustering. Based on this finding, we propose methods for reliable cell line identification from RNA-seq data using supervised machine learning methods. In addition, we demonstrate the ability to detect cross-contamination of human cell lines. The presented methods are insensitive to different data pre-processing steps and quality measures. The proposed TopFracCCLE algorithm for cell line identification and detection of cross-contamination is available as R-script at https://github.com/HuettelmaierLab/topFracCCLE.

genomics↗

bioRxiv2025

CENTRA: Knowledge-Based Gene Contexuality Graphs Reveal Functional Master Regulators by Centrality and Fractality

Deciphering gene function via context-aware approaches is limited by various means. Especially static gene sets used in enrichment analyses and the lack of single-gene resolution in such analyses restrains the flexible association of genes with specific context. Here, we introduce CENTRA (Centrality-based Exploration of Network Topologies from Regulatory Assemblies), a framework that models gene contextuality through topic-specific gene co-occurrence networks derived from curated gene sets and associated literature. Using Latent Dirichlet Allocation on 12,045 abstracts linked to MSigDB C2 gene sets, we uncovered 27 biological topics and constructed corresponding topic-specific networks that reflect distinct biological states, perturbation conditions, and disease-related regulatory programs. Graph-topological metrics, including centrality, local fractality, and perturbation sensitivity, were computed for each gene to capture structural relevance within these topic-specific contexts. We demonstrate that topological profiles distinguish well-characterized regulators, identify emerging functional candidates, and reveal context-specific roles. Thereby, our framework enables the prioritization of understudied genes by assessing the robustness of their topological signatures across topic-specific networks. To support exploration of these results, we developed a publicly accessible interactive browser application, CENTRA, which enables dynamic navigation of networks and their functional annotations. CENTRA provides an interpretable, scalable framework for investigating context-dependent gene function and hypothesis generation, offering a novel entry point beyond traditional enrichment approaches. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/662180v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@10e4eeorg.highwire.dtl.DTLVardef@125d5b4org.highwire.dtl.DTLVardef@f137aeorg.highwire.dtl.DTLVardef@7ea4e5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Insights into anterograde trafficking and pharmacological chaperoning of Cannabinoid Receptor 2 (CB2)

Cannabinoid Receptor 2 (CB2) is a promising therapeutic target for modulating inflammation. Canonical signalling responses to receptor ligands are critically dependent on cell surface receptor expression. However, it is also now appreciated that intracellular G protein-coupled receptors can contribute to signalling responses and influence functional outcomes. Therefore, understanding how the subcellular distribution of receptors is controlled is also highly pertinent. CB2 is observed to be expressed at the cell surface as well as having a considerable proportion expressed intracellularly. Despite this distribution being well established, little is known about the regulation of CB2 anterograde trafficking and subcellular distribution. We report that sustained treatment with a range of CB2 agonists and inverse agonists stimulates a distinct population of CB2 to be delivered to the cell surface, at various expression levels and despite agonists concurrently internalising cell surface CB2. We present evidence that this ligand-stimulated anterograde trafficking is a result of CB2 agonists, as well as inverse agonists, acting as pharmacological chaperones. We also report that a di-lysine (KK) motif in the CB2 C-terminal tail is required for basal delivery to the cell surface. Corroborating the hypothesis that CB2 ligands can act as pharmacological chaperones, sustained CB2 ligand stimulation induces cell surface expression of the mutated receptor and alters maturation states as measured by western blotting. Our finding that prolonged exposure to CB2 ligands can induce CB2 cell surface delivery via pharmacological chaperoning may well have important implications for optimal design of CB2-targeted therapeutics.

pharmacology and toxicology↗

bioRxiv2024

Essential Dynamics of CB1 Receptor-Agonist Complexes: Implications for Signalling Bias

The CB1 cannabinoid receptor is implicated in a broad range of physiological processes and disease states, however CB1-targeting drugs in clinical use remain based on tetrahydrocannabinol (THC). Ligands that exhibit functional selectivity for different intracellular signalling pathways are currently an area of rapid development, and hold significant potential as therapeutic agents. Improved understanding of the exact molecular mechanisms underpinning biased activation of intracellular effector proteins for CB1 is necessary to enable drug development of biased CB1 ligands into candidates for treatment of human disease. Using molecular dynamics, this study shows that CB1conformations resulting from activation by the orthosteric ligands CP55940, {Delta}9-THC or 5F-MDMB-PICA exhibit differences in the dynamic organisation of key residues and receptor substructures involved in coupling to G proteins and {beta}-arrestins, that leads to selective activation of downstream signalling pathways. The identification of conformationally distinct CB1-agonist complexes that demonstrate different functional profiles provides an important step in unravelling the molecular determinants for biased signalling, and lays a platform for future rational design of novel therapeutic leads.

neuroscience↗

bioRxiv2024

Mannose Supplementation Curbs Liver Steatosis and Fibrosis in Murine MASH by Inhibiting Fructose Metabolism

Metabolic dysfunction-associated steatohepatitis (MASH) can progress to cirrhosis and liver cancer. There are no approved medical therapies to prevent or reverse disease progression. Fructose and its metabolism in the liver play integral roles in MASH pathogenesis and progression. Here we focus on mannose, a simple sugar, which dampens hepatic stellate cell activation and mitigates alcoholic liver disease in vitro and in vivo. In the well-validated FAT-MASH murine model, oral mannose supplementation improved both liver steatosis and fibrosis at low and high doses, whether administered either at the onset of the model ("Prevention") or at week 6 of the 12-week MASH regimen ("Reversal"). Thein vivo anti-fibrotic effects of mannose supplementation were validated in a second model of carbon tetrachloride-induced liver fibrosis. In vitro human and mouse primary hepatocytes revealed that the anti-steatotic effects of mannose are dependent on the presence of fructose, which attenuates expression of ketohexokinase (KHK), the main enzyme in fructolysis. KHK is decreased with mannose supplementation in vivo and in vitro, and overexpression of KHK abrogated the anti-steatotic effects of mannose. Our study identifies mannose as a simple, novel therapeutic candidate for MASH that mitigates metabolic dysregulation and exerts anti-fibrotic effects.

cell biology↗

bioRxiv2023

RAVER1 interconnects lethal EMT and miR/RISC activity by the control of alternative splicing

The RAVER1 protein was proposed to serve as a co-factor in guiding the PTBP-dependent control of alternative splicing (AS). Whether RAVER1 solely acts in concert with PTBPs and how it affects cancer cell fate remained elusive. Here we provide the first comprehensive investigation of RAVER1-controlled AS in cancer cell models and reveal a pro-oncogenic role of RAVER1 in tumor growth. This unravels that RAVER1 guides AS in synergy with PTBPs but more prominently serves PTBP1-independent roles in splicing. In cancer cells, one major function of RAVER1 is the control of proliferation and apoptosis, which involves the modulation of AS events within the miR/RISC pathway. Associated with this regulatory role, RAVER1 antagonizes lethal, TGFB-driven epithelial-mesenchymal-transition (EMT) by limiting TGFB signaling. RAVER1-modulated splicing events affect the insertion of protein interaction modules in factors guiding miR/RISC-dependent gene silencing. Most prominently, in all three human TNRC6 proteins, RAVER1 controls AS of GW-enriched motifs, which are essential for AGO2-binding. Disturbance of RAVER1-guided AS events in TNRC6 proteins and other facilitators of miR/RISC activity compromise miR/RISC activity which is essential to restrict TGFB signaling and lethal EMT.

molecular biology↗

bioRxiv2022

Chronic IFNα treatment induces leukopoiesis, increased plasma succinate and immune cell metabolic rewiring

Although clinically effective, the actions of IFN, either produced endogenously or by therapeutic delivery, remain poorly understood. Emblematic of this research gap is the disparate array of notable side effects that occur in susceptible individuals, such as neuropsychiatric consequences, autoimmune phenomena, and infectious complications. We hypothesised that these complications are driven at least in part by dysregulated cellular metabolism. Male Wistar rats were treated with either 170,000 IU/kg human recombinant IFN-2a or BSA/saline (0.9% NaCl) three times per week for three weeks. Bone marrow (BM) immune cells were isolated from the excised femurs for glycolytic rate and mitochondrial function assessment using Agilent Seahorse Technology. Frequencies of immune cell populations were assessed by flow cytometry to determine whether leukopoietic changes had occurred in both blood and BM. Plasma levels of lactate and succinate were also determined. BMDMs were metabolically assessed as above, as well as their metabolic response to an antigenic stimulus (iH37Rv). We observed that BM immune cells from IFN-treated rats exhibit a hypermetabolic state (increased basal OCR/GlycoPER) with decreased mitochondrial metabolic respiration and increased non-mitochondrial OCR. Flow cytometry results indicated an increase in immature granulocytes (RP1-SSChi CD45lo) and classical monocytes (CD43lo RP1hi) in the blood, together with increased succinate levels in the plasma. BMDMs from IFN-treated rats retained the hypermetabolic phenotype after differentiation and failed to induce a step-up in glycolysis and mitochondrial respiration after bacterial stimulation. This work provides the first evidence of the effects of IFN treatment in inducing hypermetabolic immune features that are associated with markers of inflammation, leukopoiesis, and defective responses to bacterial stimulation.

immunology↗

bioRxiv2022

RUNX1 isoform disequilibrium in the development of trisomy 21 associated myeloid leukemia

Aneuploidy is a hallmark of cancer, but its complex nature limits our understanding of how it drives oncogenesis. Gain of chromosome 21 (Hsa21) is among the most frequent aneuploidies in leukemia and is associated with markedly increased leukemia risk. Here, we propose that disequilibrium of the RUNX1 isoforms is key to the pathogenesis of trisomy 21 (i.e. Down syndrome)-associated myeloid leukemia (ML-DS). Hsa21-focused CRISPR-Cas9 screens uncovered a strong and specific RUNX1 dependency in ML-DS. Mechanistic studies revealed that excess of RUNX1A isoform - as seen in ML-DS patients - synergized with the pathognomonic Gata1s mutation in leukemogenesis by displacing RUNX1C from its endogenous binding sites and inducing oncogenic programs in complex with the MYC cofactor MAX. These effects were reversed by restoring the RUNX1A:RUNX1C equilibrium or pharmacological interference with MYC:MAX dimerization. Our study highlights the importance of alternative splicing in leukemogenesis, even on a background of aneuploidies, and opens new avenues for developing specific and targeted therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/483334v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@16c5a95org.highwire.dtl.DTLVardef@af0ec7org.highwire.dtl.DTLVardef@f36bcborg.highwire.dtl.DTLVardef@129e832_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2020

IGF2BP1 is a targetable SRC/MAPK-dependent driver of invasive growth in ovarian cancer

Epithelial-to-mesenchymal transition (EMT) is a hallmark of aggressive, mesenchymal-like high-grade serous ovarian carcinoma (HG-SOC). The SRC kinase is a key driver of cancer-associated EMT promoting adherens junction (AJ) disassembly by phosphorylation-driven internalization and degradation of AJ proteins. Here we show, that the IGF2 mRNA binding protein 1 (IGF2BP1) is up-regulated in mesenchymal-like HG-SOC and promotes SRC activation by a previously unknown protein-ligand-induced, but RNA-independent mechanism. IGF2BP1-driven invasive growth of ovarian cancer cells essentially relies on the SRC-dependent disassembly of AJs. Concomitantly, IGF2BP1 enhances ERK2 expression in a RNA-binding dependent manner. Together this reveals a post-transcriptional mechanism of interconnected stimulation of SRC/ERK signaling in ovarian cancer cells. The IGF2BP1-SRC/ERK2 axis is targetable by the SRC-inhibitor saracatinib and MEK-inhibitor selumetinib. However, due to IGF2BP1-directed stimulation only combinatorial treatment effectively overcomes the IGF2BP1-promoted invasive growth in 3D culture conditions as well as intraperitoneal mouse models. In conclusion, we reveal an unexpected role of IGF2BP1 in enhancing SRC/MAPK-driven invasive growth of ovarian cancer cells. This provides a rational for the therapeutic benefit of combinatorial SRC/MEK inhibition in mesenchymal-like HG-SOC. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

cancer biology↗

bioRxiv2019

Cannabinoid Receptor 2 (CB2) Signals via G-alpha-s and Induces IL-6 and IL-10 Cytokine Secretion in Primary Human Leukocytes

Cannabinoid receptor 2 (CB2) is a promising therapeutic target for immunological modulation. There is, however, a deficit of knowledge regarding CB2 signaling and function in human primary immunocompetent cells. We applied an experimental paradigm which closely models the in situ state of human primary leukocytes (PBMC; peripheral blood mononuclear cells) to characterize activation of a number of signaling pathways in response to a CB2-selective ligand (HU308). We observed a \"lag\" phase of unchanged cAMP concentration prior to development of classically-expected Gi-mediated inhibition of cAMP synthesis. Application of G protein inhibitors revealed that this apparent lag was a result of counteraction of Gi effects by concurrent Gs activation. Monitoring downstream signaling events, activation of p38 was mediated by Gi whereas ERK1/2 and Akt phosphorylation were mediated by Gi-coupled {beta}{gamma}. Activation of CREB integrated multiple components; Gs and {beta}{gamma} mediated [~]85% of the response, while [~]15% was attributed to Gi. Responses to HU308 had an important functional outcome - secretion of interleukins 6 (IL-6) and 10 (IL-10). IL-2, IL-4, IL-12, IL-13, IL-17A, MIP-1, and TNF- were unaffected. IL-6/IL-10 induction had a similar G protein coupling profile to CREB activation. All response potencies were consistent with that expected for HU308 acting via CB2. Additionally, signaling and functional effects were completely blocked by a CB2-selective inverse agonist, giving additional evidence for CB2 involvement. This work expands the current paradigm regarding cannabinoid immunomodulation and reinforces the potential utility of CB2 ligands as immunomodulatory therapeutics.\n\nSignificance statementCannabinoid receptor 2 (CB2) is a G protein-coupled receptor which plays a complex role in immunomodulation and is a promising target in a range of disorders with immune system involvement. However, to date the majority of the studies in this field have been performed on cell lines, rodent models, or stimulated primary cells. Here we provide a detailed account of CB2-mediated signaling in primary human immune cells under conditions which closely mimic their in vivo state. We reveal a complex signaling system involving an unprecedented CB2 signaling pathway and leading to immunomodulatory functional outcomes. This work provides not only a critical foundation impacting CB2-targeted drug discovery, but reveals important wider considerations for GPCR signaling studies and model validity.\n\nTable of Contents Summary Figure\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC=\"FIGDIR/small/663831v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@599095org.highwire.dtl.DTLVardef@2331a9org.highwire.dtl.DTLVardef@917860org.highwire.dtl.DTLVardef@75e8f7_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2018

The chemistry and pharmacology of putative synthetic cannabinoid receptor agonist (SCRA) new psychoactive substances (NPS) 5F-PY-PICA, 5F-PY-PINACA, and their analogues

The structural diversity of synthetic cannabinoid receptor agonist (SCRA) new psychoactive substances (NPS) has increased since the first examples were reported a decade ago. 5F-PY-PICA and 5F-PY-PINACA were identified in 2015 as putative SCRA NPS, although nothing is known of their pharmacology. 5F-PY-PICA, 5F-PY-PINACA, and analogues intended to explore structure-activity relationships within this class of SCRAs were synthesized and characterized by nuclear magnetic resonance spectroscopy and liquid chromatography-quadrupole time-of-flight-mass spectrometry. Using competitive binding experiments and fluorescence-based plate reader membrane potential assays, the affinities and activities of all analogues at cannabinoid type 1 and type 2 receptors (CB1 and CB2) were evaluated. All ligands showed minimal affinity for CB1 (pKi < 5), although several demonstrated moderate CB2 binding (pKi = 5.45-6.99). At 10 M none of the compounds produced an effect > 50% of CP55,950 at CB1, while several compounds showed a slightly higher relative efficacy at CB2. Unlike other SCRA NPS, 5F-PYPICA and 5F-PY-PINACA did not produce cannabimimetic effects in mice at doses up to 10 mg/kg.

pharmacology and toxicology↗