Biology subjects

Hassan, S. A.

Publications and source records attributed to Hassan, S. A..

9 recordsLinked to original sources

bioRxiv2026

Quantitative Modeling of TLR Signaling Reveals Missing Negative Feedback Guiding Identification of TANK-IKKε Checkpoint

Toll-like receptor (TLR) signaling must be activated rapidly and then terminated to support host defense without sustained inflammation. We developed a rule-based model of mouse macrophage TLR4 signaling at the molecular-interaction level using measured protein copy numbers, RNA-seq-based abundance estimates, literature- and structure-informed reaction rates, and 979 dynamic experimental constraints. The trained model reproduced much of the TLR4-induced NF-{kappa}B and MAP kinase response but consistently failed to capture deactivation of MyD88, TRAF6-associated species, and IKK/{beta}. The recurrent model failure conveyed important biological information, localizing missing regulation to the proximal MyD88-IRAK-TRAF6 module and guiding experimental evaluation of IKK{varepsilon} and its scaffold TANK. Loss of IKK{varepsilon} enhanced transcriptional, cytokine, MAP kinase, and NF-{kappa}B responses to MyD88-specific TLR ligands. TANK deficiency produced a similar cellular phenotype and abolished stimulus-induced IKK{varepsilon} phosphorylation. Deficiency of either protein increased IRAK1 and TRAF6 ubiquitination without increasing MyD88 ubiquitination, placing the inhibitory checkpoint at or immediately downstream of the IRAK1-TRAF6 ubiquitin-signaling node. Overlapping but non-identical in vivo phenotypes further supported a shared regulatory axis with additional protein-specific functions. Our study presents a model-experiment discovery cycle where quantitative pathway discordance identifies missing biology and reveals a TANK-dependent IKK{varepsilon} checkpoint that restrains MyD88-driven inflammation.

systems biology↗

bioRxiv2026

Minimal Computational Framework for Systematic Identification of Antimicrobial Targets

Systematic identification of antimicrobial targets remains a major challenge, as discovery still relies largely on empirical, resource-intensive approaches with limited efficiency. We present a method for identifying antimicrobial targets based on protein dynamics, enabling rational polypharmacology. The approach spans multiple biological scales, from taxa (genus and species) to biological networks, including network hubs and edges, their constituent proteins, protein binding sites, and their conformational states. It is grounded in the premise that coordinated intervention across multiple, optimally selected targets, using combinations of compounds at safe or submaximal doses, can achieve therapeutic effects while reducing toxicity and limiting mutational escape. A survey of known antimicrobials indicates that a small number of recurrent protein-level mechanisms account for most disruptions of microbial survival. We introduce metrics to detect these mechanisms across a pathogen proteome and describe a streamlined, modular workflow for target identification and prioritization that is optimized for ease of deployment and naturally interfaces with downstream applications such as molecular screening and de novo design.

bioinformatics↗

bioRxiv2026

Drosophila pseudoobscura third chromosome inversion arrangements have sex-specific effects on life history traits

Chromosomal inversions can create polymorphic "supergenes" consisting of many alleles in linkage disequilibrium that affect constellations of traits. The coadaptation hypothesis supposes that many alleles within an inversion haplotype have synergistic epistatic interactions, which are maintained by suppressed recombination in inversion heterozygotes, heterozygote advantage, and context-dependent fitness effects. The fitness benefits of chromosomal inversions frequently arise from effects on life history syndromes, including ecotypes and reproductive strategies. Life history syndromes can also be caused by individual pleiotropic alleles in ways that resemble the effects of chromosomal inversions. It is therefore possible that the fitness effects of chromosomal inversions arise because of pleiotropic alleles and not coadaptation. These two hypotheses can be distinguished because pleiotropy predicts greater genetic correlations of traits than coadaptation. To test the coadaptation and pleiotropy hypotheses, we measured three life history traits (lifespan, development time, and body size) in Drosophila pseudoobscura with six different chromosomal inversion genotypes. We assayed males and females raised at multiple temperatures in order to expose phenotype variation. Temperature affected lifespan and development more than any other factor, but we also observed differences in mortality rates and development times that depended on chromosomal inversions and sex. Despite these context-dependent effects on life history traits, we failed to identify genetic correlations that would be evidence for pleiotropic alleles. Our results therefore suggest that the coadaptation hypothesis is better supported.

evolutionary biology↗

bioRxiv2026

Kidney disease reprograms microbiome-host signaling to promote heart failure

BackgroundHeart failure is prevalent in chronic kidney disease (CKD) and linked to chronic inflammation. CKD-typical gut microbiome dysbiosis may stimulate inflammation, as bacterial aromatic metabolites are highly abundant and engage transcriptional programs through the aryl hydrocarbon receptor (AhR). Whether this axis drives cardiac remodeling and is therapeutically targetable remains unknown. MethodsWe used the subtotal nephrectomy model (STNx) and microbiome depletion by oral antibiotics. We investigated cardiac and renal function, AhR activity, metabolite profiles, and immunophenotypes by flow cytometry and transcriptomics. Candidate metabolite indoxyl sulfate (IxS) was tested in experimental HFpEF. In vivo and in vitro AhR inhibition (AhRi) was performed using a clinically tested compound. Mechanistic studies were performed in primary human and murine cardiac fibroblasts and T cells, as well as translational validation using UK Biobank data. ResultsMicrobiome depletion lowered bacterial metabolites and attenuated cardiac fibrosis and diastolic dysfunction in STNx, identifying AhR-driven expansion of interleukin-17A (IL-17A)-producing T helper cells (TH17) as key effector. Plasma IL-17A was stage-dependently elevated in CKD patients, particularly in HFpEF, and associated with all-cause mortality. Bacterial metabolite IxS promoted TH17 polarization and exacerbated cardiac dysfunction in HFpEF. AhRi using a small molecule inhibitor reduced TH17 abundance and attenuated cardiac fibrosis in STNx. Mechanistically, AhR and IL-17A signaling synergistically induced a conserved pro-fibrotic phenotype in human and murine cardiac fibroblasts, and AhR inhibition blocked ECM production in response to CKD patient serum. ConclusionA microbiome-AhR-IL-17A axis drives CKD-associated cardiac fibrosis. AhRi prevents remodeling, highlighting a potential therapeutic avenue to prevent cardiorenal multimorbidity.

immunology↗

bioRxiv2025

Evolution of a fuzzy ribonucleoprotein complex in viral assembly

Previously we showed that the genetic diversity of SARS-CoV-2 nucleocapsid (N) protein explores a wide range of biophysical properties facilitated by non-local impact of point mutations to its intrinsically disordered regions (Nguyen et al., 2024). This includes modulation of self-association, such as the creation of a de novo binding interface through the P13L mutation characteristic of Omicron variants. In the present work we focus on the key function of N condensing viral RNA into ribonucleoprotein particles (RNPs) for viral assembly. Lacking high-resolution structural information, biochemical and biophysical approaches have revealed architectural principles of RNPs, which involve cooperative interactions of several protein-protein and protein-RNA interfaces, initiated through oligomerization of conserved transient helices in the central disordered linker of N. Here we study the impact of defining N-protein mutations in variants of concern on RNP formation, using biophysical tools, a virus-like particle assay, and reverse genetics experiments. We find convergent evolution in repeated, independent introduction of amino acid substitutions strengthening existing binding interfaces, compensating for other substitutions that promote viral replication but decrease RNP stability. Furthermore, we show that the P13L mutation of Omicron variants enhances RNP assembly and increases viral fitness. Overall, our data reveal RNP complexes to be highly variable not only in sequence and conformations, but also in thermodynamic and kinetic stability, with its pleomorphism affecting basic architectural principles. We hypothesize that the formation of polydisperse, fuzzy N-RNA clusters with multiple distributed weak binding interfaces optimizes reversible RNA condensation, while supporting host adaptation and allowing for a large sequence space to be explored.

biophysics↗

bioRxiv2024

Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD

BackgroundMitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative anaerobes (eg. Proteobacteria) and restricts obligate anaerobes (eg. Firmicutes). Dysbiotic metabolites negatively affect host metabolism and immunity. Our novel compound (AuPhos) upregulates intestinal epithelial cell (IEC) mito function, attenuates colitis and corrects dysbiosis in humanized Il10-/- mice. We posit that AuPhos corrects IBD-associated dysbiotic metabolism. MethodsPrimary effect of AuPhos on mucosal Mito respiration and healing process was studied in ex vivo treated human colonic biopsies and piroxicam-accelerated (Px) Il10-/- mice. Secondary effect on microbiome was tested in DSS-colitis WT B6 and germ-free 129.SvEv WT or Il10-/- mice reconstituted with human IBD stool (Hu-Il10-/-). Mice were treated orally with AuPhos (10- or 25- mg/kg; q3d) or vehicle, stool samples collected for fecal lipocalin-2 (f-LCN2) assay and microbiome analyses using 16S rRNA sequencing. AuPhos effect on microbial metabolites was determined using untargeted global metabolomics. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 staining in sections from pimonidazole HCl-infused DSS-mice. Effect of AuPhos on enteric oxygenation was assessed by E. coli Nissle 1917 WT (aerobic respiration-proficient) and cytochrome oxidase (cydA) mutant (aerobic respiration-deficient). ResultsMetagenomic (16S) analysis revealed AuPhos reduced relative abundances of Proteobacteria and increased blooms of Firmicutes in uninflamed B6 WT, DSS-colitis, Hu-WT and Hu-Il10-/- mice. AuPhos also increased hypoxyprobe-1 staining in surface IECs suggesting enhanced O2 utilization. AuPhos-induced anaerobiosis was confirmed by a significant increase in cydA mutant compared to WT (O2-utlizing) E.coli. Ex vivo treatment of human biopsies with AuPhos showed significant increase in Mito mass, and complexes I and IV. Further, gene expression analysis of AuPhos-treated biopsies showed increase in stem cell markers (Lgr4, Lgr5, Lrig1), with concomitant decreases in pro-inflammatory markers (IL1{beta},MCP1, RankL). Histological investigation of AuPhos-fed Px-Il10-/- mice showed significantly decreased colitis score in AuPhos-treated Px-Il10-/- mice, with decrease in mRNA of pro-inflammatory cytokines and increase in Mito complexes (ND5, ATP6). AuPhos significantly altered microbial metabolites associated with SCFA synthesis, FAO, TCA cycle, tryptophan and polyamine biosynthesis pathways. AuPhos increased pyruvate, 4-hydroxybutyrate, 2-hydroxyglutarate and succinate, suggesting an upregulation of pyruvate and glutarate pathways of butyrate production. AuPhos reduced IBD-associated primary bile acids (BA) with concomitant increase in secondary BA (SBA). AuPhos treatment significantly decreased acylcarnitines and increased L-carnitine reflective of enhanced FAO. AuPhos increases TCA cycle intermediates and creatine, energy reservoir substrates indicating enhanced OxPHOS. Besides, AuPhos also upregulates tryptophan metabolism, decreases Kynurenine and its derivatives, and increases polyamine biosynthesis pathway (Putresceine and Spermine). ConclusionThese findings indicate that AuPhos-enhanced IEC mitochondrial function reduces enteric O2 delivery, which corrects disease-associated metabolomics by restoring short-chain fatty acids, SBA, AA and IEC energy metabolism. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/584471v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@41e437org.highwire.dtl.DTLVardef@1eddf37org.highwire.dtl.DTLVardef@1d9bff3org.highwire.dtl.DTLVardef@c925f0_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres

Centromeres are constricted chromosomal regions that are essential for cell division. In eukaryotes, centromeres display a remarkable architectural and genetic diversity. The basis of centromere accelerated evolution remains elusive. Here we focused on Pneumocystis species, a group of Mammalian-specific fungal pathogens that form a sister taxon with that of the Schizosaccharomyces pombe, an important genetic model for centromere biology research. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-ACnp1 of Schizosaccharomyces pombe. Using organisms from a short-term in vitro culture or infected animal models and ChIP-Seq, we identified CENP-A bound regions in two Pneumocystis species that diverged [~]35 million years ago. Each species has a unique short regional centromere (< 10kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. These features suggest an epigenetic specification of centromere function. Analysis of centromeric DNA across multiple Pneumocystis species suggest a vertical transmission at least 100 million years ago. Common ancestry of Pneumocystis and S. pombe centromeres is untraceable at the DNA level but the overall architectural similarity could be the result of functional constraint for successful chromosomal segregation. Significance StatementPneumocystis species offer a suitable genetic system to study centromere evolution in pathogens because of their phylogenetic proximity with the nonpathogenic yeast Schizosaccharomyces pombe, a popular model for cell biology. We used this system to explore how centromeres have evolved after divergence of the two clades [~]460 million years ago. To address this question, we established a protocol combining short-term culture and ChIP-Seq to characterize centromeres in multiple Pneumocystis species. We show that Pneumocystis have short epigenetic centromeres that function differently from those in S. pombe. One sentence summaryInsights into the formation of genic centromeres in fungal pathogens.

genomics↗

bioRxiv2022

Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein

Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by 3-4 different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced co-assembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.

biophysics↗

bioRxiv2020

The Conquering influence of the Nano extracts of pomegranate peels and pistachio leaves in amelioration of acute liver failure

ObjectiveAcute liver failure (ALF) is a clinical condition with an unclear history of pathophysiology, making it a challenging task for scientists to reverse the disease in its initial phase and to help the liver re-function as usual: this study was proposed to estimate the hepatoprotective effects of Punicagranatum peel and Pistaciaatlantica leaves as a multi-rich antioxidants ingredients either in their normal and/or in their nano forms against thioacetamide induced acute liver failure in a rodent model. MethodSixty male Wistar rats were divided into six equal groups, the first group employed as a control; the second group was given a dose of thioacetamide (TAA)-350 mg/bwip., from the third to the sixth group received TAA {square} 2ml of 100gm of aqueous extracts of PunicagranatumL and Pistaciaatlantica either in their normal and/or Nano forms consecutively along 2 weeks. Resultsrecorded significant elevation in liver enzymes, lipid profiles, LPO and NO with marked significant decrease in GSH and SOD accompanied by elevation in inflammatory cytokine (IL6,TNF- and AFP) in addition to a noticeable increase in HSP70 level & degradation in DNA respectively in TAA challenged group. However significant and subsequent amelioration of most of the impaired markers has been observed with ipnano treatment of both extracts. ConclusionThe current results highlighted the high performance of both plant nano extracts and their hepatoprotective impact and their possible therapeutic role in the amelioration of TAA induced acute liver failure in experimental animals.

pharmacology and toxicology↗