Biology subjects

Ghazi, A.

Publications and source records attributed to Ghazi, A..

12 recordsLinked to original sources

bioRxiv2026

A TCER-1-siRNA Regulatory Axis Suppresses Antibacterial Innate Immunity in C. elegans

Small interfering RNA (siRNA) are important regulators of gene expression with well-established roles in pathogen defense. Yet, their specific roles in antibacterial immunity are not well understood. Here, we identify an siRNA pathway involved in repressing antibacterial innate immunity in Caenorhabditis elegans. We show that genes required for the biogenesis or function of WAGO Argonaute-associated siRNAs, called 22G-RNAs, function in a common genetic pathway with the immune-suppressive transcription elongation and splicing factor TCER-1 to inhibit immunity. Loss of tcer-1 reduced levels of 22G-RNAs from a subset of WAGO targets, while mutations in several WAGO 22G-RNA pathway genes phenocopied the enhanced immunoresistance of tcer-1 mutants, suggesting a shared regulatory module. Integrative 22G-RNA-mRNA analyses and molecular genetic studied show that this module does not induce widespread gene silencing, but instead targets a restricted set of immune-relevant effectors, including scrm-4, encoding a phospholipid translocase that promotes host resistance. Together, our findings establish endogenous WAGO 22G-RNAs as repressors of antibacterial immunity and identify TCER-1 as a physiological regulator that promotes 22G-RNA biogenesis to constrain host defense. The results uncover a previously unrecognized small RNA-dependent mechanism linking transcription, metabolism, and antibacterial innate immunity.

immunology↗

bioRxiv2026

Caffeine extends lifespan by enhancing lysosomal lipolysis in Caenorhabditis elegans

Caffeine is a globally consumed stimulant that has beneficial effects on biological processes including metabolism and aging, but its causal role in physiology remains incompletely understood. By using the roundworm Caenorhabditis elegans, here we show that caffeine extends lifespan by eliciting transcriptional remodeling that enhances lysosomal lipolysis. We found that transcriptomes of aged, caffeine-fed animals shifted toward youthful states. By comparing with three longevity-promoting regimens, including reduced insulin/insulin-like growth factor 1 (IGF-1) signaling, mild reductions in mitochondrial function, and dietary restriction (DR), we showed that caffeine induced a DR-like transcriptional program. Comparison with eat-2 mutants (a genetic DR model) identified lysosomal lipases lipl-1 and lipl-2 as commonly upregulated genes. The induction of lipl-1 and lipl-2 was required for increased lifespan and reduced neutral lipid accumulation by caffeine intake. Together, these findings indicate that caffeine promotes longevity in a DR-like metabolic reprogramming by enhancing lysosome-driven lipolysis.

genetics↗

bioRxiv2025

Pharmacologic activation of HNF4α/γ restores epithelial barrier function in Crohn's disease.

Background & Aims: Ileal barrier dysfunction in Crohn,s disease (CD) can occur in macroscopically non-inflamed mucosa, persist despite clinical and endoscopic remission, and predict adverse outcomes. The epithelial mechanisms underlying this defect remain unclear. We investigated whether coordinated reduction of hepatocyte nuclear factor 4, (HNF4) and HNF4{gamma} defines an epithelial-intrinsic, barrier-defective state in ileal CD. Methods: Barrier-associated transcriptional programs were compared in small-intestinal and colonic epithelium from wild-type mice and mice with intestinal epithelial deletion of Hnf4, Hnf4{gamma}, or both paralogs. Paracellular permeability was assessed in wild-type and Hnf4/{gamma} double-knockout (Hnf4{gamma}DKO) small-intestinal organoids. HNF4, HNF4{gamma}, and the direct HNF4 transcriptional target claudin-15 (CLDN15) were evaluated in human ileal CD tissue, patient-derived organoids (PDOs) generated from macroscopically non-inflamed ileal mucosa, and ileal tissue and organoids from Tnf{delta}ARE/+ mice. The effects of HNF4 agonists N-trans-caffeoyltyramine (NCT) and N-trans-feruloyltyramine (NFT) were assessed in CD PDOs and Tnf{delta}ARE/+ organoids. Results: Combined, but not individual, loss of HNF4-paralog broadly disrupted small-intestinal transcriptional programs governing tight junction (TJ) organization, epithelial polarity, junctional-cytoskeletal coupling, and TJ repair, with limited effects in the colon. Hnf4{gamma}DKO organoids exhibited size-selective paracellular permeability in the absence of inflammatory and stromal cells, demonstrating that combined Hnf4{gamma} loss is sufficient to produce an epithelial-intrinsic barrier defect. HNF4, HNF4{gamma}, and CLDN15 were coordinately reduced in human ileal CD epithelium and this HNF4-low phenotype was retained in PDOs from macroscopically non-inflamed ileal mucosa. Chronic TNF-driven ileitis reproduced this HNF4-low state, which was retained ex vivo in organoids. HNF4 agonists restored HNF4, HNF4{gamma}, and CLDN15 expression and improved transepithelial electrical resistance (TEER) in CD PDOs. They also increased HNF4 and CLDN15 expression in Tnf{delta}ARE/+ organoids. Conclusions: Coordinated HNF4/{gamma} suppression defines an epithelial-intrinsic, barrier-defective state in ileal CD that is present in PDOs derived from macroscopically non-inflamed ileal mucosa and retained ex vivo without continued exposure to the inflammatory tissue environment. Its pharmacologic reversibility identifies incomplete restoration of the HNF4-dependent epithelial program as a potential mechanism of persistent ileal barrier dysfunction and supports further evaluation of HNF4-directed barrier-restorative strategies.

pathology↗

bioRxiv2025

Evolving Threats: Leveraging C. elegans to Decode the Virulence Profiles of Highly Related Environmental Salmonella Newport Isolates

Salmonella enterica subspecies enterica, particularly serovar Newport, remains a leading cause of foodborne illnesses in the United States, implicated in numerous outbreaks associated with a diverse array of food products. This study rigorously investigates the virulence of five distinct S. Newport isolates, characterized by varying patterns of pulse-field gel electrophoresis (PFGE) molecular-diagnostic subtyping, using the nematode Caenorhabditis elegans as a host model organism. We conducted viability assays on C. elegans to evaluate how these isolates affect nematode survival. The selected bacterial strains, rooted in historical foodborne outbreak significance but environmentally isolated, were previously sequenced to provide a comprehensive genomic framework. A notable focus of our research was on the nearly genetically identical PFGE types Newport-61 and the Newport-1015 isolates, which differ by a [~]1.7 Mb genomic inversion. C. elegans survival assays in response to pathogenic-strain infections revealed that one Newport-1015 and the Newport-61 were particularly more virulent compared to other strains tested. These findings enhance our understanding of the pathogenic potential of environmental S. Newport and highlight the need to understand the regulatory mechanisms that contribute to virulence capacity.

microbiology↗

bioRxiv2025

LIPL-1 and LIPL-2 are TCER-1-regulated Lysosomal Lipases with Distinct Roles in Immunity and Fertility

Reproduction and immunity are fundamental, energy intensive processes that often compete for resources, leading to trade-offs observed across diverse species. Lipid metabolism plays a crucial role in integrating these processes, particularly during stressful conditions such as pathogenic infections. Yet the molecular mechanisms governing this integration remain poorly understood. TCER-1, the C. elegans homolog of mammalian TCERG1, suppresses immunity and promotes fertility, especially upon maternal infection. Here, we show that TCER-1 regulates two conserved lysosomal lipases, lipl-1 and lipl-2, to balance reproduction, immunity and lifespan. Using transcriptomic, lipidomic, and molecular-genetic analyses, we demonstrate that while both lipl-1 and lipl-2 mediate infection-induced lipid remodeling, lipl-1 enhances immunity and catalyzes the accumulation of ceramide species linked to stress response and longevity, whereas, lipl-2 unexpectedly does not. Both lipases contribute towards fertility outcomes, but lipl-2 is especially critical for maintaining embryonic-eggshell integrity during maternal infection and aging. Strikingly, expression of human lysosomal acid lipase (LAL), the ortholog of lipl genes, rescues the immune defects triggered by lipl-l loss and enhances immune resilience. Together, these findings uncover functionally distinct roles for lipl-1 and lipl-2 in modulating lipid species that shape immune fitness, healthspan and reproductive health, and suggest a potentially conserved mechanism by which lipid metabolism links fertility and immunity.

genetics↗

bioRxiv2024

Germline loss diminishes somatic mitochondria but confers preservation of respiratory function during aging and hypothermia

Reproductive status influences metabolism and health across lifespan in diverse ways and mitochondrial function playing a critical role in mediating this relationship. Using the Caenorhabditis elegans germline ablation model, we investigated the impact of germline stem cell (GSC) loss on mitochondrial dynamics and respiratory function. Our results show that GSC loss reduces mitochondrial volume and respiratory function in young adulthood but preserves mitochondrial activity during aging and upon exposure to hypothermic stress, correlating with enhanced survival. We found that the transcription factor NHR-49/PPAR, but not DAF-16/FOXO3A, was essential for preserving mitochondrial function and hypothermia resistance in these long-lived mutants. Together, these findings reveal the impact of germline signals on somatic mitochondrial health and underscore the intricate relationship between reproductive fitness and organismal health.

genetics↗

bioRxiv2021

ANALYSIS OF CHD-7 DEFECTIVE DAUER NEMATODES IMPLICATES COLLAGEN MISREGULATION IN CHARGE SYNDROME FEATURES.

CHARGE syndrome is a complex developmental disorder caused by mutations in the chromodomain helicase DNA-binding protein7 (CHD7) and characterized by retarded growth and malformations in the heart and nervous system. Despite the public health relevance of this disorder, relevant targets of CHD7 that relate to disease pathology are still poorly understood. Here we report that chd-7, the nematode ortholog of Chd7, is required for dauer morphogenesis, lifespan determination, and stress response. Consistent with our discoveries, we found chd-7 to be allelic to scd-3, a previously identified dauer suppressor from the TGF-{beta} pathway. Notably, DAF-12 promoted chd-7 expression, which is necessary to repress daf-9 for execution of the dauer program. Transcriptomic analysis comparing chd-7-defective and normal dauers showed enrichment of collagen genes, consistent with a conserved role for the TGF-{beta} pathway in formation of the extracellular matrix. To validate a conserved function for chd-7 in vertebrates, we used Xenopus laevis embryos, an established model to study craniofacial development. Morpholino mediated knockdown of Chd7 led to a reduction in col2a1 mRNA levels. Both embryonic lethality and craniofacial defects in Chd7-depleted tadpoles were partially rescued by over-expression of col2a1 mRNA. We suggest that pathogenic features of CHARGE syndrome caused by Chd7 mutations, such as craniofacial malformations, result from the reduction of collagen levels, implying that the extracellular matrix might represent a critical target of Chd7 in CHARGE development. SIGNIFICANCE STATEMENTCHARGE Syndrome is a complex developmental disorder caused by mutations in the chromodomain helicase DNA-binding protein-7 (CHD7). Unfortunately, the cellular events that lead to CHARGE syndrome are still poorly understood. In C. elegans, we identified chd-7 in a screen for suppressors of dauer formation, an alternative larval stage that develops in response to sensory signals of a harsh environment. We found that chd-7 regulates expression of collagens, which constitute the worms cuticle, a specialized extracellular matrix. In frogs embryos, we show that Chd7 inhibition leads to poor Col2a1, which is necessary and sufficient to exhibit CHARGE features. These studies establish C. elegans as an amenable animal model to study the etiology of the developmental defects associated with pathogenic Chd7.

genetics↗

bioRxiv2021

Nuclear Hormone Receptor NHR-49 controls a HIF-1-independent hypoxia adaptation pathway in Caenorhabditis elegans

The response to insufficient oxygen (hypoxia) is orchestrated by the conserved Hypoxia-Inducible Factor (HIF). However, HIF-independent hypoxia response pathways exist that act in parallel to HIF to mediate the physiological hypoxia response. Here, we describe a HIF-independent hypoxia response pathway controlled by Caenorhabditis elegans Nuclear Hormone Receptor NHR-49, an orthologue of mammalian Peroxisome Proliferator-Activated Receptor alpha (PPAR). We show that nhr-49 is required for worm survival in hypoxia and is synthetic lethal with hif-1 in this context, demonstrating that these factors act independently. RNA-seq analysis shows that in hypoxia nhr-49 regulates a set of genes that are hif-1-independent, including autophagy genes that promote hypoxia survival. We further show that Nuclear Hormone Receptor nhr-67 is a negative regulator and Homeodomain-interacting Protein Kinase hpk-1 is a positive regulator of the NHR-49 pathway. Together, our experiments define a new, essential hypoxia response pathway that acts in parallel to the well-known HIF-mediated hypoxia response.

genetics↗

bioRxiv2020

NHR-49 acts in distinct tissues to promote longevity versus innate immunity

Aging and immunity are inextricably linked and many genes that extend lifespan also enhance immunoresistance. However, it remains unclear if longevity-enhancing factors modulate immunity and longevity by distinct or shared mechanisms. Here, we demonstrate that the Caenorhabditis elegans pro-longevity factor, NHR-49, also promotes resistance against Pseudomonas aeruginosa, but modulates immunity and longevity by spatially and mechanistically distinct mechanisms. Fenofibrate, an agonist of NHR-49s mammalian functional homolog, PPAR, enhanced worm immunoresistance in an NHR-49-dependent manner. NHR-49 expression is increased by germline ablation, an intervention that extends lifespan, but lowered by pathogen exposure. NHR-49 acted in multiple somatic tissues to promote longevity, whereas, its pro-immunity function was mediated by neuronal expression. The canonical NHR-49 target genes, acs-2 and fmo-2, were upregulated by germline loss, but infection triggered fmo-2 downregulation and acs-2 upregulation. Interestingly, neither gene conferred resistance against Gram-negative Pseudomonas, unlike their reported roles in immunity against Gram-positive pathogens. Thus, NHR-49 is differentially regulated by interventions that bring about long-term changes (lifespan extension) vs. short-term stress (pathogen exposure) and in response it orchestrates distinct outputs, including pathogen-specific transcriptional programs. Overall, our study demonstrates the independent control of immunity and longevity by a conserved regulatory protein.

molecular biology↗

bioRxiv2020

NHR-49/PPAR-α and HLH-30/TFEB promote C. elegans host defense via a flavin-containing monooxygenase

During bacterial infection, the host is confronted with multiple overlapping signals that are integrated at the organismal level to produce defensive host responses. How multiple infection signals are sensed by the host and how they elicit the transcription of host defense genes is much less understood at the whole-animal level than at the cellular level. The model organism Caenorhabditis elegans is known to mount transcriptional defense responses against intestinal bacterial infections that elicit overlapping starvation and infection responses, but the regulation of such responses is not well understood. Direct comparison of C. elegans that were starved or infected with Staphylococcus aureus revealed a large infection-specific transcriptional signature. This signature was almost completely abrogated by deletion of transcription factor hlh-30/TFEB, except for six genes including a flavin-containing monooxygenase (FMO) gene, fmo-2/FMO5. Deletion of fmo-2/FMO5 severely compromised infection survival, thus identifying the first FMO with innate immunity functions in animals. Moreover, the mechanism of fmo-2/FMO5 induction required the nuclear hormone receptor, NHR-49/PPAR-, which induced fmo-2/FMO5 and host defense cell non-autonomously. These findings for the first time reveal an infection-specific host response to S. aureus, identify HLH-30/TFEB as its main regulator, reveal that FMOs are important innate immunity effectors in animals, and identify the mechanism of FMO regulation through NHR-49/PPAR- in C. elegans, with important implications for innate host defense in higher organisms.

microbiology↗

bioRxiv2020

C. elegans processes sensory information to choose between freeloading and self-defense strategies

Hydrogen peroxide is the preeminent chemical weapon that organisms use for combat. Individual cells rely on conserved defenses to prevent and repair peroxide-induced damage, but whether similar defenses might be coordinated across cells in animals remains poorly understood. Here, we identify a neuronal circuit in the nematode Caenorhabditis elegans that processes information perceived by two sensory neurons to control the induction of hydrogen-peroxide defenses in the organism. We found that catalases produced by Escherichia coli, the nematodes food source, can deplete hydrogen peroxide from the local environment and thereby protect the nematodes. In the presence of E. coli, the nematodes neurons signal via TGF{beta}-insulin/IGF1 relay to target tissues to repress expression of catalases and other hydrogen-peroxide defenses. This adaptive strategy is the first example of a multicellular organism modulating its defenses when it expects to freeload from the protection provided by molecularly orthologous defenses from another species.

neuroscience↗

bioRxiv2019

Identification of functional variants for platelet CD36 expression by Massively Parallel Reporter Assay.

CD36 is a platelet membrane glycoprotein whose engagement with oxidized low-density lipoprotein (oxLDL) results in platelet activation. The CD36 gene has been associated with platelet count, platelet volume, as well as lipid levels and CVD risk by genome-wide association studies. Platelet CD36 expression levels have been shown to be associated with both the platelet oxLDL response and an elevated risk of thrombo-embolism. Several genomic variants have been identified as associated with platelet CD36 levels, however none have been conclusively demonstrated to be causative. We screened 81 expression quantitative trait loci (eQTL) single nucleotide polymorphisms (SNPs) associated with platelet CD36 expression by a Massively Parallel Reporter Assay (MPRA) and analyzed the results with a novel Bayesian statistical method. Ten eQTLs located in a 35kb region upstream of the CD36 transcriptional start site demonstrated significant transcription shifts between their minor and major allele in the MPRA assay. Of these, rs2366739 and rs1194196, separated by only 20bp, were confirmed by luciferase assay to alter transcriptional regulation. In addition, electromobility shift assays demonstrated differential DNA:protein complex formation between the two alleles of this locus. Furthermore, deletion of the genomic locus by CRISPR/Cas9 in K562 cells results in upregulation of CD36 transcription. These data indicate that we have identified a variant that regulates expression of CD36, which in turn affects platelet function. To assess the clinical relevance of our findings we used the PhenoScanner tool, which aggregates large scale GWAS findings; the results reinforce the clinical relevance of our variants and the utility of the MPRA assay. The study demonstrates a generalizable paradigm for functional testing of genetic variants to inform mechanistic studies, support patient management and develop precision therapies. Author SummaryPlatelets are anucleate cells that are best known as regulators of vascular hemostasis and thrombosis but also play important roles in cancer, angiogenesis, and inflammation. CD36 is a platelet surface marker that can activate platelet in response to oxidized low density lipoprotein (oxLDL). CD36 has been associated with numerous cardiovascular traits in human including blood lipid levels, platelet count, and cardiovascular disease prevalence in human genetic studies. Human variability in platelet CD36 levels are associated with the platelet response to oxLDL. However, the genetic mechanisms responsible for the variability of CD36 levels are unknown. We examined 81 genetic variants associated with CD36 levels for functionality using a high-throughput assay. Of the ten variants that were identified in that assay, one doublet, rs2366739 and rs1194196, were confirmed using additional molecular and cellular assays. Deletion of the genomic region containing rs2366739 and rs1194196 resulted in overexpression of CD36 in a cell culture system. This finding indicates a control locus which can serve as a potential target in modulating CD36 expression and altering platelet function in cardiovascular disease.

genomics↗