Biology subjects

Mohamed, N.

Publications and source records attributed to Mohamed, N..

10 recordsLinked to original sources

bioRxiv2026

Biofilm dispersion in Enterococcus faecalis is mediated by nutrient step-change and intra-species signaling

Enterococcus faecalis is a Gram-positive intestinal commensal and opportunistic pathogen capable of causing serious infections, including urinary tract infections, endocarditis, and wound infections. A major contributor to its persistence during infection is the ability to form biofilms on host tissues and medical devices. Biofilm cells have higher phenotypic tolerance to antimicrobial treatment than planktonic bacteria. While mechanisms governing biofilm assembly in E. faecalis have been widely studied, the processes that regulate biofilm dispersion, the final stage of the biofilm life cycle, remain poorly understood. In this study, we found that dispersion is triggered by a tenfold step-change increase in nutrient availability and by cell free supernatant (CFS) of E. faecalis OG1RF cultures. Cells released from biofilms regain sensitivity to antibiotics similar to planktonic cells but maintain a high potential for adherence. We characterized the glycosyltransferase epaOX, which contributes to the structure of the enterococcal polysaccharide antigen as necessary for nutrient step-change induced dispersion, CFS induced dispersion, and adhesion of dispersed cells. Supplementation of epaOX mutant CFS with galactose and N-acetylgalactosamine was sufficient to restore CFS induced dispersion. Together these data suggest that dispersion in OG1RF occurs with fast kinetics, affects antibiotic sensitivity and is regulated in part by known virulence factors. ImportanceE. faecalis causes difficult to treat infections at numerous body sites in human patients. E. faecalis biofilms are adherent populations that require high levels of antibiotics for treatment. Biofilms undergo a disassembly process named dispersion that allows individual cells to leave the biofilm and colonize new locations. Dispersed cells in other species are killed by lower amounts of antibiotics than biofilm cells. Here we showed that dispersion occurs in E. faecalis and lowers the level of antibiotics needed to kill dispersed cells. Dispersion triggers could be used in the future to design treatments that increase the effectiveness of antibiotics.

microbiology↗

bioRxiv2026

Fabrication of the high-resistance patch-clamp pipettes for mitochondrial electrophysiological studies using optimized two step method

The patch-clamp experimental technique is widely used to study the electrical properties of ion channels in biological and artificial lipid membranes. The key to the high quality of the experiments is the manufacturing of glass pipettes that provide highly electrically resistant contact between the edge of the pipette tip and the lipid bilayer. Preparation of the pipettes is particularly challenging for studies of the mitochondrial membranes due to the need for very small pipette tip sizes. Here, we present a robust procedure for producing pipettes suitable for experiments with native mitochondrial membranes. This procedure involves a two-step approach: initial fabrication of relatively large glass micropipettes using a standard micropipette puller, followed by tip refinement using a microforger to achieve smooth glass surface and reduced opening size. Pipette tip diameters and surface structure were examined using field emission - scanning electron microscopy (FE-SEM) imaging to assess the effects of variable parameters on pipette geometry and size. The resulting pipettes were validated in patch-clamp recording of the mitochondrial inner membranes. This approach enables the reproducible production of optimized pipettes for mitochondrial patch-clamp experiments, improving the quality and throughput of electrophysiological recordings of the mitochondrial ion channels.

biophysics↗

bioRxiv2026

Isoform-Resolved Genetic Architecture of Epilepsy and SUDEP Reveals Divergent Brain and Heart Channelopathy Signatures

Sudden unexpected death in epilepsy (SUDEP) is the most devastating complication of epilepsy, yet the molecular features distinguishing individuals at risk remain poorly defined. Although epilepsy and SUDEP share substantial genetic overlap, fatal outcomes may arise when shared risk genes are differentially deployed across neuronal and cardiac systems. Here, we identify tissue- and isoform-level regulation as a key determinant of divergence between epilepsy and SUDEP risk. We performed a large-scale integrated analysis of genetic variants reported in epilepsy and SUDEP across 419 sequencing-based studies encompassing 35,659 individuals, and quantified gene-level burden using a Bayesian Poisson-Gamma rate ratio framework. This analysis revealed preferential enrichment of genes related to cardiac electrophysiology and contractile function in SUDEP, whereas epilepsy was dominated by genes involved in neuronal excitability and synaptic signaling. To determine how shared genetic loci are deployed across tissues, we integrated GTEx-based tissue expression profiles with long-read single-cell transcriptomic datasets from human heart and brain to resolve isoform-level expression patterns. These analyses revealed pronounced tissue-specific transcript architectures. Cardiac-associated genes, including HCN4, KCNH2, KCNE1, MYH6, MYO18B, and ATP1A2, showed heart-restricted isoform expression, whereas neuronal genes such as ADGRV1, CACNA1A, GRIN2B, HCN1, HCN2, KCNA1, SCN1A, SCN2A, and SCN8A. Importantly, several shared genes exhibited tissue-partitioned isoform expression, with distinct transcript repertoires in heart and brain, particularly across pathways related to ion transport, signaling, metabolism, and structural organization. Consistent patterns were observed in iPSC-derived cardiomyocytes and neurons, indicating that lineage-dependent deployment of shared genes is preserved in controlled systems. Together, these findings suggest that tissue-specific isoform regulation provides a mechanistic basis linking shared epilepsy genetics to SUDEP susceptibility, whereby the same genetic loci contribute to neuronal dysfunction in epilepsy and to cardiac vulnerability in SUDEP. This positions SUDEP as a neuro-cardiac interface disorder shaped by isoform-level regulatory divergence.

genetics↗

bioRxiv2026

AADAT-Driven Metabolic Control of Malate and CoQ10 Shapes Immune Evasion in Triple-Negative Breast Cancer

Compared to other subtypes of breast cancer, triple-negative breast cancers (TNBC) have fewer treatment options and exhibit a worse prognosis. Through integrated transcriptomic, metabolomic, immunohistochemical, spatial, and clinical analyses, we identify the mitochondrial enzyme, -aminoadipate aminotransferase (AADAT) as a previously unrecognized metabolic immune checkpoint in TNBC. AADAT mRNA and protein were significantly upregulated in human TNBC, and high AADAT expression was associated with reduced intra-tumoral CD8 T-cell density and inferior survival. Genetic silencing of AADAT in orthotopic murine TNBC models curtailed primary tumor growth and distant metastasis in a CD8 T-cell-dependent manner, enhanced effector T-cell activation, and sensitized tumors to dual PD-1/CTLA-4 blockade. Mechanistically, unbiased metabolomics showed increased malate levels after AADAT knockdown. Additionally, 4-hydroxyphenylpyruvate, an essential precursor for coenzyme Q10(CoQ10) biosynthesis, decreased following AADAT knockdown, suggesting an impaired mitochondrial electron transport chain. CoQ10 supplementation restored metabolic balance and reversed malate accumulation caused by AADAT knockdown, indicating that AADAT helps maintain CoQ10-supported redox homeostasis, thereby preventing malate buildup and export. Notably, malate addition directly boosted CD8 T-cell oxidative metabolism, increased the NAD/NADH ratio and reactive oxygen species, and augmented TNF- and IFN-{gamma} production. In vivo, malate supplementation in drinking water phenocopied AADAT knockdown, restored the response to paclitaxel plus anti-PD-1 therapy in multiple independent syngeneic TNBC models with de novo or acquired resistance to immunotherapy, reduced tumor burden, and prolonged survival. In patient cohorts, higher spatially clustered intra-tumoral malate is associated with co-localization of functional CD8 T cells, decreased exhausted T-cell neighborhoods, and superior post-chemotherapy outcomes. These data position AADAT as a central metabolic orchestrator of immune escape in TNBC and nominate oral malate as a readily translatable adjuvant to reverse chemo-immunotherapy resistance in TNBC. Statement of SignificanceAADAT defines a metabolic-immune axis driving immune evasion and therapy resistance in triple-negative breast cancer. Blocking AADAT or administering oral malate reactivates CD8 T-cell immunity and sensitizes chemo-immunotherapy-resistant tumors to these agents. These findings uncover a readily translatable metabolic vulnerability with potential to improve outcomes for patients with aggressive breast cancer subtypes.

cancer biology↗

bioRxiv2025

Genome-wide SNVs revealed reticulate evolutionary history of an Eurasia-African songbird radiation

Phylogenomics has the power to uncover complex evolutionary hypothesis across taxa, thereby allowing important glimpses into the evolutionary history, such as incomplete lineage sorting (ILS) and introgression among closely related species. The Saxicola torquatus complex comprises several widely distributed insectivorous bird species across the Palearctic and Afrotropical realms. Nevertheless, the evolutionary history within this complex remains contentious, and previous findings suggest complication caused by cytonuclear discordance. Here, we conducted a phylogenomic analysis of nearly complete taxa within the complex using genome-wide SNVs to investigate potential causes of phylogenetic discordance across genomic regions and elucidate its evolutionary history. We detected multiple reticulate events during their diversification, leading to extensive phylogenetic discordance across the genome. The mitochondrial genome and W chromosome exhibited a consistent gene tree that conflicted with the species tree, with introgression being the most plausible explanation among several hypotheses. The Z chromosome was less affected by ILS/introgression and exhibited relatively stable local phylogenies compared to autosomes. Furthermore, we found that strongly introgressed regions were predominantly concentrated at the ends of smaller chromosomes, and the strength of introgression among species pairs showed consistently positive correlations, likely attributed to shared recombination hotspots in these regions. These findings stress the heterogeneous genomic landscape influenced by intricate evolutionary processes that endorse a reticulate evolution model for global speciation in the S. torquatus complex.

evolutionary biology↗

bioRxiv2025

PanScan: A Tool for Tertiary Analysis of Human Pangenome Graphs

The genomic representation of populations across the globe is critical to ensuring a comprehensive and equitable human reference. Constructing a pangenome graph reference for different populations is the best approach to addressing local genomic diversities. Although major initiatives across continents are underway to construct pangenome graph references, the field lacks the necessary toolsets for tertiary analysis to characterize telomere-to-telomere (T2T) assemblies and the complexity of haplotypes. PanScan is a bioinformatics software package developed for human pangenome tertiary analysis. It includes multiple modules designed to detect duplicated gene sets from T2T assemblies, identify novel variants and sequences, as well as detect and visualize complex genomic regions through pangenome graph haplotype loops. We have used multiple pangenomes across different populations to assess the tertiary analysis and their accuracy. The tool is designed to streamline tertiary analysis and is compatible with multiple pangenome graph construction algorithms. PanScan is freely available on GitHub (https://github.com/CATG-Github/panscan), where users can provide human pangenome assemblies or VCF files as inputs for automated analyses through command-line operations on Linux systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/651685v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@16cc212org.highwire.dtl.DTLVardef@13961d0org.highwire.dtl.DTLVardef@44d194org.highwire.dtl.DTLVardef@1b72aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

A draft Arab pangenome reference

Pangenomes represent a significant shift from relying on a single reference sequence to a robust set of assemblies, Arab populations remain significantly underrepresented; hence, we present the first Arab Pangenome Reference (APR) utilizing 53 individuals of diverse Arab ethnicities. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads yielded contiguous haplotype-phased de novo assemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of novel euchromatic sequences absent from existing human pangenomes, the T2T-CHM13, GRCh38 reference human genomes, and other public datasets. We identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome. We detected 883 gene duplications including 15.06% associated with recessive diseases and 1,436 bp of novel mitochondrial pangenome sequence. Our study provides a valuable resource for future genomic medicine initiatives in Arab population and other global populations.

genomics↗

bioRxiv2024

Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC

Racial disparities in the clinical outcomes of triple-negative breast cancer (TNBC) have been well-documented, but the underlying biological mechanisms remain poorly understood. To investigate these disparities, we employed a multi-omic approach integrating imaging mass cytometry and spatial transcriptomics to characterize the tumor microenvironment (TME) in self-identified Black American (BA) and White American (WA) TNBC patients. Our analysis revealed that the TME in BA patients is marked by a network of endothelial cells, macrophages, and mesenchymal-like cells, which correlates with reduced patient survival. In contrast, the WA TNBC microenvironment is enriched in T-cells and neutrophils, indicative of T-cell exhaustion and suppressed immune responses. Ligand-receptor and pathway analyses further demonstrated that BA TNBC tumors exhibit a relatively "immune-cold" profile, while WA TNBC tumors display features of an "inflamed" TME, suggesting the evolution of a unique immunosuppressive mechanism. These findings provide insight into racially distinct tumor-promoting and immunosuppressive microenvironments, which may contribute to the observed differences in clinical outcomes among BA and WA TNBC patients. Statement of SignificanceThis study identifies distinct tumor microenvironment (TME) profiles in Black and White American TNBC patients, providing new insights into the biological mechanisms driving outcome disparities. Our findings highlight the role of the tumor-endothelial-macrophage niche in these disparities, offering a potential therapeutic target for race-inclusive strategies aimed at improving clinical outcomes. By revealing racial differences in treatment response profiles, this work underscores the necessity for tailored therapies in TNBC. These insights lay the groundwork for the development of inclusive, precision-driven treatment approaches that may help mitigate racial disparities and enhance patient outcomes.

cancer biology↗

bioRxiv2022

Divergent acute versus prolonged in vivo GLP-1R responses in β-arrestin 2-deleted primary beta cells

The glucagon-like peptide-1 receptor (GLP-1R) is a major therapeutic target in type 2 diabetes (T2D) and obesity. Following activation, GLP-1Rs are rapidly desensitised by {beta}-arrestins, scaffolding proteins that terminate G protein interactions but also act as independent signalling mediators. While GLP-1R interacts with {beta}-arrestins 1 and 2, expression of the latter is greatly enhanced in beta cells, making this the most relevant isoform. Here, we have assessed in vivo glycaemic responses to the pharmacological GLP-1R agonist exendin-4 in adult beta cell-selective {beta}-arrestin 2 knockout (KO) mice. Lean female and high-fat, high-sucrose-fed KO mice of both sexes displayed worse acute responses versus control littermates, an effect that was inverted 6 hours post-agonist injection, resulting in prolonged in vivo cell-cell connectivity in KO islets implanted in mouse eyes. Similar effects were observed for the clinically relevant semaglutide and tirzepatide but not with exendin-phe1, an agonist biased away from {beta}-arrestin recruitment. Ex vivo acute cAMP was impaired, but overnight desensitisation was reduced in KO islets. The acute signalling defect was attributed to enhanced {beta}-arrestin 1 and phosphodiesterase (PDE) 4 activity in the absence of {beta}-arrestin 2, while the reduced desensitisation correlated with altered GLP-1R trafficking, involving impaired recycling and lysosomal targeting and increased trans-Golgi network (TGN) localisation and signalling, as well as reduced GLP-1R ubiquitination by the E3 ubiquitin ligase NEDD4. This study has unveiled fundamental aspects of the role of {beta}-arrestin 2 in regulating pharmacological GLP-1R responses with direct application to the rational design of improved GLP-1R-targeting therapeutics.

cell biology↗

bioRxiv2021

Determining pathogenicity of variants of uncertain significance and identification of a founder variant in the epilepsy-associated gene, SZT2

Biallelic pathogenic variants in SZT2 result in a neurodevelopmental disorder with shared features, including early-onset epilepsy, developmental delay, macrocephaly, and corpus callosum abnormalities. SZT2 is as a critical scaffolding protein in the amino acid sensing arm of the mTOR signaling pathway. Due to its large size (3432 amino acids), lack of crystal structure, and absence of functional domains, it is difficult to determine the pathogenicity of SZT2 missense and in-frame deletions. We report a cohort of twelve individuals with biallelic SZT2 variants and phenotypes consistent with SZT2-related neurodevelopmental disorder. The majority of this cohort contained one or more SZT2 variants of uncertain significance (VUS). We developed a novel individualized platform to functionally characterize SZT2 VUSs. We identified a recurrent in-frame deletion (SZT2 p.Val1984del) which was determined to be a loss-of-function variant and therefore likely pathogenic. Haplotype analysis determined this single in-frame deletion is a founder variant in those of Ashkenazi Jewish ancestry. Overall, we present a FACS-based rapid assay to distinguish pathogenic variants from VUSs in SZT2, using an approach that is widely applicable to other mTORopathies including the most common causes of the focal genetic epilepsies, DEPDC5, TSC1/2, MTOR and NPRL2/3.

genetics↗