Biology subjects

Ali, S. M.

Publications and source records attributed to Ali, S. M..

9 recordsLinked to original sources

bioRxiv2026

Ratiometric Fluorescent Protein Biosensors Reveal Citrate Dynamics and Cellular Heterogeneity

Citrate is a central intermediate metabolite linking the tricarboxylic acid cycle and lipid biosynthesis. Tools for monitoring of spatiotemporal citrate dynamics are critical for getting a better understanding of cellular metabolism. Here, we develope genetically encoded excitation ratiometric biosensors for citrate, based on our previous intensiometric green fluorescence protein-based citrate biosensor, Citron1. We find that a single mutation in the Citron1 chromophore-forming tripeptide provided an excitation ratiometric response. Further rounds of directed evolution yield highly responsive variants, exhibiting citrate-dependent fluorescence changes between two excitation peaks. When expressed in mammalian cells, these biosensors enable citrate dynamics to be monitored in both the cytosol and mitochondria. Comparative analysis across multiple human breast cancer cell lines uncovers cell line-specific differences in citrate levels and their heterogeneity, which could be linked to their malignancy. Furthermore, flow cytometry-based measurements in mouse embryonic stem cells demonstrate the proteomics signatures underlying the population-level variability in citrate concentrations and citrate rewiring during stem cell differentiation. Together, these results show that these excitation ratiometric citrate biosensors enable quantitative, compartment-resolved, and population-scale analysis of cellular metabolism.

molecular biology↗

bioRxiv2025

Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells

Pluripotent stem cells (SCs) rely on metabolic rewiring to regulate self-renewal and differentiation. The hexosamine biosynthetic pathway (HBP) integrates multiple metabolic inputs to produce uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc), a central substrate for protein and lipid glycoconjugates. While UDP-GlcNAc levels influence pluripotency, the broader metabolic roles of the HBP in stem cell maintenance and differentiation remain largely unexplored. Using proteomic and metabolomic analyses, we uncovered extensive enzymatic remodelling of the HBP during early mouse embryonic stem cell (mESC) differentiation, including a significant decrease in N-acetylglucosamine-6-phosphate (GlcNAc6P) levels, despite stable UDP-GlcNAc levels. Isotope labelling experiments revealed that pluripotent stem cells maintain UDP-GlcNAc biosynthesis through a combination of glucose-driven de novo synthesis and the N-Acetylglucosamine (GlcNAc) salvage pathway, both of which are downregulated during differentiation. Functionally, we identified GlcNAc6P--a point of convergence of the de novo synthesis and the salvage pathways--as a pivotal metabolite of stem cell fate. Preventing GlcNAc6Ps deacetylation by deleting or depleting AMDHD2 impaired mESC differentiation. Mechanistically, we demonstrated that GlcNAc6P catabolism is essential for sustaining cytosolic acetate and in turn acetyl-CoA levels, which are critical for lipid synthesis and histone modifications required for pluripotency exit. These findings establish AMDHD2 as a key supplier of cellular acetate and reveal an essential metabolic link between HBP activity and acetyl-CoA homeostasis. By expanding the role of the HBP beyond UDP-GlcNAc production, this study reveals an unrecognised metabolic vulnerability that can be exploited to manipulate stem cell identity.

molecular biology↗

bioRxiv2025

Excess prenatal folic acid supplementation alters cortical gene expression networks and electrophysiology

Folate is crucial for various biological processes, with deficiencies during pregnancy being linked to increased risk for neural tube defects and neurodevelopmental disorders. As a proactive measure, folic acid fortification in foods has been mandated in many countries, in addition to dietary supplementation recommendations during pregnancy. However, the risks of excess prenatal folic acid supply have yet to be fully understood. To better appreciate in utero molecular changes in mouse brain exposed to 5-fold folic acid excess over normal supplementation, we investigated the transcriptome and methylome for alterations in gene networks. RNA-seq analysis of cerebral cortex collected at birth, revealed significant expression differences in 646 genes with major roles in protein translation. Whole genome bisulfite sequencing revealed 910 significantly differentially methylated regions with functions enriched in glutamatergic synapse and glutathione pathways. To explore the physiological consequences of excess prenatal folic acid exposure, we applied high-density microelectrode arrays to record network-level firing patterns of dissociated cortical neurons. Folic acid excess-derived cortical neurons exhibited significantly altered network activity, characterized by reduced burst amplitude and increased burst frequency, indicating compromised network synchronization. These functional deficits align with the observed molecular alterations in glutamatergic synapse pathways, underscoring the potential for excess prenatal folic acid exposure to disrupt developing metabolic and neurological pathways.

neuroscience↗

bioRxiv2025

Profound taxonomic and functional gut microbiota alterations associated with trichuriasis: cross-country and country-specific patterns

BackgroundThe human gastrointestinal microbiota plays a crucial role in immune modulation, metabolism, and pathogen resistance. Soil-transmitted helminth (STH) infections, including Trichuris trichiura (whipworm), significantly alter gut microbial composition, yet the extent and functional consequences of these changes remain underexplored across different geographical regions. This study investigates the taxonomic and functional impacts of T. trichiura on gut microbiota in three endemic regions - Cote dIvoire, Laos, and Tanzania - using a unified high-resolution metagenomic sequencing approach. ResultsThis study reveals extensive gut microbiota disruptions linked to T. trichiura infection, with both regional and cross-country patterns. A core signature found across all study sites includes depletion of Faecalibacterium prausnitzii and Eubacterium rectale (Short-chain fatty acids (SCFA) producers) and enrichment of mucin-degrading bacteria (Ruminococcus, Bacteroides), alongside increased host-derived carbohydrate metabolism. Infection destabilized microbial networks, characterized by reduced connectivity and clustering, with opportunistic taxa such as Segatella copri emerging as network hubs across regions, indicating a shared ecological response. Both taxonomic and functional disruptions exhibited a combination of conserved and region-specific patterns; for example, whereas certain taxa, such as Prevotella and Streptococcus, showed notable geographic variability, specific functional changes, such as SCFA depletion and mucin degradation, were consistently observed across sites. These conserved functional changes suggest that T. trichiura imposes similar metabolic pressures on the gut microbiome across populations, potentially affecting host nutrient availability and immune responses in a predictable manner. Discussion and ConclusionThis study provides robust evidence that T. trichiura infection induces significant and consistent microbiome alterations across diverse populations. The depletion of SCFA-producing bacteria and the enrichment of mucin-degrading taxa, along with corresponding metabolic pathways, imply compromised gut barrier integrity, providing insights into the complex inflammatory processes associated with this helminth infection. Additionally, these microbiome differences could play a critical role in facilitating parasite persistence and reinfection, which remain major challenges limiting the efficacy of global control strategies. Our findings highlight the potential of microbiome-targeted interventions, such as probiotic supplementation or dietary modifications, to mitigate the health impacts of T. trichiura infections by restoring microbial homeostasis.

microbiology↗

bioRxiv2024

Discovery of a novel albendazole-ivermectin refractory Trichuris species, T. hominis, in C&ocircte d'Ivoire patients through fecal DNA metabarcoding

Albendazole-ivermectin combination therapy is a promising alternative to benzimidazole monotherapy for Trichuris trichiura control. We used fecal DNA metabarcoding to genetically characterize Trichuris populations in patients from a clinical trial showing lower albendazole-ivermectin efficacy in Cote dIvoire (ERR below 70%) than in Lao PDR and Tanzania (ERR above 98%). ITS-1 and ITS-2 rDNA metabarcoding revealed the entire Cote dIvoire Trichuris population was phylogenetically distinct from T. trichiura in Lao PDR and Tanzania, and more closely related to the porcine parasite Trichuris suis. Complete mitogenomes of eight adult Trichuris from Cote dIvoire confirmed their species-level differentiation. Corresponding Trichuris ITS-1 and ITS-2 sequences in NCBI from individual human patients in Cameroon and Uganda and three captive non-human primates suggest this newly recognized species, T. incognita, is distributed beyond Cote dIvoire and has zoonotic potential. Further work is needed to assess the impact of this Trichuris species on soil transmitted helminth control programs.

genomics↗

bioRxiv2023

Fluvoxamine maleate ameliorates Alzheimer disease pathology by mitigating amyloid-beta load and neuroinflammation in 5XFAD mice

BackgroundAlzheimer pathology (AD) is accompanied by the deposition of amyloid beta (A{beta}) and chronic neuroinflammation, where NLRP3 inflammasome is particularly involved. In this study, we found that the OCD drug fluvoxamine maleate (FXN) can potently ameliorate AD pathology in 5XFAD mice by autophagy-mediated clearance of A{beta} and inhibition of NLRP3 inflammasome. MethodsWe used mice primary astrocytes to establish the mechanism of action of FXN against NLRP3 inflammasome by using various techniques like ELISA, Western blotting, confocal microscopy, Immunofluorescence, etc. The validation of the anti-AD activity of FXN was done in transgenic 5XFAD mice after two months of treatment followed by behavior analysis and studying inflammatory and autophagy proteins along with immunohistochemistry analysis for A{beta} load in the hippocampi. ResultsOur data showed that FXN induces autophagy to inhibit NF-{kappa}B and NLRP3 inflammasome at a low concentration of 78 nM apart from directly inhibiting NLRP3 inflammasome in primary astrocytes. FXN activated the PRKAA2 pathway through CAMKK2 signaling, which led to the induction of autophagy in primary astrocytes. FXN inhibited the ATP-mediated NLRP3 inflammasome through autophagic degradation of NF-{kappa}B and thus caused the downregulation of pro-IL-1{beta} and NLRP3. The anti-NLRP3 inflammasome effect of FXN was reversed when autophagy was inhibited either by genetic knockdown of the PRKAA2 pathway or by bafilomycin A1. Furthermore, FXN treatment led to improved AD pathology in 5XFAD mice, which displayed a significant improvement in multiple behavior parameters like working memory and neuromuscular coordination and they behaved more like wild-type animals. We found that FXN improved behavior in 5XFAD mice by clearing the A{beta} deposits from the hippocampi along with a significant reduction in multiple inflammatory proteins, including NF-{kappa}B, GFAP, IBA1, IL-1{beta}, TNF-, and IL-6 associated with NF-{kappa}B and NLRP3 inflammasome in the brain. Moreover, these changes were accompanied by increased expression of autophagic proteins. ConclusionOur data suggest that to ameliorate AD pathology, FXN simultaneously targets two key pathological features of AD that is A{beta} deposits and neuroinflammation. Being an approved drug, FXN can be pushed as a potential drug candidate for human studies against AD.

neuroscience↗

bioRxiv2022

Mutations in TIC100 impair and repair chloroplast protein import and impact retrograde signalling

Chloroplast biogenesis requires synthesis of proteins in the nucleocytoplasm and the chloroplast itself. Nucleus-encoded chloroplast proteins are imported via multiprotein translocons in the organelles envelope membranes. Controversy exists around whether a 1 MDa complex comprising TIC20, TIC100 and other proteins constitutes the inner membrane TIC translocon. The Arabidopsis cue8 virescent mutant is broadly defective in plastid development. We identify CUE8 as TIC100. The tic100cue8 mutant accumulates reduced levels of 1 MDa complex components and exhibits reduced import of two nucleus-encoded chloroplast proteins of different import profiles. A search for suppressors of tic100cue8 identified a second mutation within the same gene, tic100soh1, which rescues the visible, 1 MDa complex-subunit abundance, and chloroplast protein import phenotypes. tic100soh1 retains but rapidly exits virescence, and rescues the synthetic lethality of tic100cue8 when retrograde signalling is impaired by the gun1 mutation. Alongside the strong virescence, changes in RNA editing and the presence of unimported precursor proteins show that a strong signalling response is triggered when TIC100 function is altered. Our results are consistent with a role for TIC100, and by extension the 1 MDa complex, in the chloroplast import of photosynthetic and non-photosynthetic proteins, a process which initiates retrograde signalling. One sentence summaryComplementary mutations in TIC100 of the chloroplast inner envelope membrane cause reductions or corrective improvements in chloroplast protein import, and highlight a signalling role.

plant biology↗

bioRxiv2019

Protective functions of ZO-2/Tjp2 expressed in hepatocytes and cholangiocytes against liver injury and cholestasis

BACKGROUND & AIMSTight junctions (TJs) establish tissue barriers that maintain osmotic homeostasis and, in the liver, isolate bile flow from the blood circulation. ZO-2/Tjp2 is a scaffold protein that tethers TJ transmembrane proteins to the actin cytoskeleton. Missense mutations in Tjp2 have recently been shown to cause progressive cholestatic liver disease in humans. However, the underlying mechanisms still remain elusive. To study the role of Tjp2 in cholestatic liver disease, we generated and characterized mice lacking Tjp2 in hepatocytes, cholangiocytes, or both. METHODSTjp2 was inactivated in the mouse liver (both in hepatocytes and cholangiocytes) or hepatocytes or cholangiocytes only. Liver function tests were carried out by biochemical analysis of plasma and liver samples and liver tissue was evaluated by immunohistochemistry and histology. The mice were also subjected to cholic acid (CA) diet to assess their susceptibility to liver insults. RESULTSDeletion of Tjp2 in the mouse liver did not result in apparent changes in TJ structure and composition, but lead to progressive cholestasis with lower expression levels of the bile acid (BA) transporter ABCB11/Bsep and the detoxification enzyme Cyp2b10. Feeding a CA diet that is well tolerated by control mice caused severe cholestasis and necrotic liver injury in mice lacking hepatic Tjp2. Administration of a CAR agonist, TCPOBOP, protected these mice from CA induced injury by enhancing the expression of the detoxifying enzyme Cyp2b10 in hepatocytes. Mice lacking Tjp2 in only hepatocytes or in only cholangiocytes showed less severe CA diet induced liver injury. CONCLUSIONLoss of Tjp2 from hepatocytes and cholangiocytes both contribute to progressive cholestatic liver disease and higher susceptibility to liver injury. In hepatocytes, Tjp2 exerts a protective role by regulating expression levels of BA transporters and detoxification enzymes. The mice may provide a new animal model for cholestatic liver disease linked to Tjp2 mutations in humans.

physiology↗

bioRxiv2019

Cellular Fitness Phenotype of Cancer Target Genes in Repurposing Cancer Therapeutics

To define the growing significance of cellular targets of cancer drugs, we examined the fitness dependency of cellular targets or effectors of cancer drug targets across human cancer cells from 19 cancer types. We observed that the deletion of 35 out of 47 cellular mediators or targets of oncology drugs did not result in the expected loss of cell fitness in appropriate cancer types for which drugs targeting or utilizing these molecules were approved. Additionally, our analysis recognized 43 cellular targets as fitness genes in several cancer types in which these drugs were not approved, and thus, providing clues repurposing approved oncology drugs in cancer types. For example, we found the widespread upregulation and fitness dependency of the components of the mevalonate and purine biosynthesis pathways (currently targeted by bisphosphonates, statins, and pemetrexed in certain cancers) and an association between the overexpression of these targets and reduction in the overall survival duration of patients with breast and other hard-to-treat cancers, for which such drugs are not approved. In brief, the present analysis raised cautions about off-target and undesirable effects of certain oncology drugs in a subset of cancers where the in-tended cellular effectors of drug might not be fitness genes and offers a potential rationale for repurposing certain approved oncology drugs for targeted therapeutics in additional cancer types.

cancer biology↗