Biology subjects

Fazal, S.

Publications and source records attributed to Fazal, S..

10 recordsLinked to original sources

bioRxiv2025

PIWIL4 regulates gene expression and piRNA levels in RSV-infected airway epithelial cells

Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections with significant morbidity and mortality in young children, the elderly and immunocompromised hosts. Despite its clinical burden, no effective RSV vaccine or therapy exists for infants, only prophylactic treatment. Small non-coding RNAs have emerged as important regulators of host-pathogen interactions. PIWI-interacting RNAs (piRNAs) are a distinct class of small non-coding RNAs known for maintaining the genome complexity and integrity in gonadal cells. However, there is growing evidence of their role in controlling gene expression in somatic cells. The biogenesis and function of piRNAs is associated with P-element Induced Wimpy testis (Piwi) proteins, whose function in the respiratory epithelium in response to infections remains largely unexplored. Here, we characterize the expression and function of the Piwi-like protein PIWIL4 in the context of RSV infection. We found that PIWIL4 is expressed in both primary and immortalized small airway epithelial cells and is significantly induced at the mRNA and protein levels following RSV infection or poly I:C stimulation, a proxy of viral infection. Immunofluorescence microscopy revealed that PIWIL4 was primarily nuclear in uninfected cells but translocated to the cytoplasm upon RSV exposure. While siRNA-mediated knockdown of PIWIL4 did not significantly affect RSV replication, it led to decreased secretion of several cytokines, chemokines and growth factors, indicating a role in modulating host innate immune responses. Transcriptomic analysis of PIWIL4-silenced iSAE cells showed significant changes in gene expression both in basal conditions and upon RSV infection. Ingenuity Pathway analysis of differentially expressed genes underscored the role of PIWIL4 in modulation of interferon signaling, cytokine production, stress and metabolic responses, as well as airway remodeling pathways. Silencing of PIWIL4 also resulted in global alteration of piRNA expression both in uninfected and infected cells. However, the predicted targets of the differentially expressed piRNAs had limited overlap with the differentially expressed genes identified by transcriptomics, suggesting a function of PIWIL4 in regulating airway epithelial cell responses at least in part independent of piRNAs. Taken together, our study uncovers an important role for PIWIL4 in somatic cells and position it as a key regulator of airway epithelial innate immunity. A better understanding of the mechanisms by which PIWIL4 affects host cells responses following a pathogen exposure may identify novel therapeutic strategies for RSV, as well as other viral respiratory infections.

microbiology↗

bioRxiv2025

A dNmnat-sensitized in vivo platform for unbiased discovery of regulators of neurodegeneration

Axon degeneration drives nervous system dysfunction in diverse neurological diseases and injuries. While key regulators of injury-induced Wallerian degeneration have been identified, approaches have largely relied on axotomy, a particularly extreme injury for a neuron. Here, we developed a forward genetic screening platform in the adult Drosophila wing that sensitizes neurons to degeneration through depletion of nicotinamide mononucleotide adenylyltransferase (dNmnat), the essential NAD+ biosynthetic enzyme. We screened 9,393 mutagenized chromosomes and recovered 59 mutations that suppress neurodegeneration induced by dNmant depletion, including the known pro-degenerative molecule dSarm, thereby validating our approach. We show loss of CG4098, the Drosophila homolog of the mammalian enzyme NUDT9, robustly preserved axons and induced widespread remodeling of NAD+-related metabolites, which provides a new link between cADP-ribose hydrolase activity and neuronal survival. We further show mutations in the transcription factor Abrupt resulted in elevated dNmnat protein levels and blocked axon degeneration, suggesting Abrupt normally tunes dNmnat levels and neuronal NAD+ homeostasis. dNmnat depletion is thus a versatile approach for unbiased discovery of axon death pathway components, each of which may provide new entry points for therapeutic strategies to preserve axons in neurodegenerative diseases.

neuroscience↗

bioRxiv2025

A molecular atlas of cell-type specific signatures in the parkinsonian striatum.

The progressive degeneration of dopaminergic projections to the striatum is a key disease mechanism in Parkinsons disease (PD). To define the cellular landscape in the parkinsonian striatum, we mapped the cell-type specific transcriptional landscape in early and progressive PD mouse models and in human PD stages. Our analyses revealed substantial transcriptomic changes across both neuronal and glial populations, with astrocytes and oligodendrocytes exhibiting distinct disease-associated gene expression profiles. Notably, progressive dopamine depletion uncovered differential neuronal vulnerability, identifying eccentric striatal projection neurons (SPNs) and Chst9-expressing direct-pathway SPNs as among the most resilient subtypes in both species. This cross-species resource establishes a comprehensive framework for investigating cell-state dynamics in the parkinsonian striatum and uncovers selectively vulnerable and resistant cell types that can inspire new therapeutic strategies.

neuroscience↗

bioRxiv2025

Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity

Short tandem repeat (STR) instability is a major cause of disease association, yet their full length-distributions and sequence content have been difficult to resolve with short-read sequencing. By analyzing long-read sequencing genomes from 2,645 participants of the All of Us Research Program, we establish a comprehensive STR resource of 23 billion alleles covering a catalog of 4.4 million loci. We find that known disease-associated STR loci exhibit markedly elevated allelic variability relative to genome-wide distributions, which is most pronounced when based on the length of uninterrupted, pure repeat motifs (Odds Ratio: 244, p=1.62e-29). We establish the Pure Length Variability Index (PLVI) as a measure of this instability, which is robust across ancestries and replicated in 500 samples from the 1000 Genomes Project (Odds Ratio: 84, p=2.72e-28). To illustrate, we identify 55 unstable coding CAG and 5-UTR CGG STR loci with this metric, 60% of which have not been associated with disease. From this set, we document potential pathogenic repeat expansions for FAM193B and EP400 by integrating PLVI with single-genome length outlier analysis. These data establish a population-scale framework for STR discovery in rare and common diseases using long-read sequencing cohorts.

genomics↗

bioRxiv2023

RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci

Tandem repeats (TRs) are polymorphic sequences of DNA that are composed of repeating units of motifs, whose lengths can vary depending on the type of TR. Expansions of TRs are responsible for approximately 50 monogenic diseases, compared to over 4,300 disease causing genes disrupted by single nucleotide variants and small indels. It appears thus reasonable to expect the discovery of additional pathogenic repeat expansions, which has the potential of significantly narrowing the current diagnostic gap in many diseases. Recently, short and long-read whole genome sequencing with the use of advanced bioinformatics tools, have identified a growing number of TR expansions in the human population. The majority of these loci are expanded in <1% of genomes. Categorizing and prioritizing such TR loci is a growing challenge to human genomic studies. We present a first-in-class machine learning tool, RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), which is designed to distinguish pathogenic from benign TR expansions. Leave-one-out cross validation results demonstrated that an ensemble approach comprised of support vector machines (SVM) and extreme gradient boosted decision tree (XGB) classify TRs with a precision of 92% and a recall of 90%. Further validation of RExPRT on unseen test data demonstrate a similar precision of 86%, and a recall of 60%. RExPRTs high precision in particular, will be of significant value to large-scale discovery studies, which require the prioritization of promising candidate loci for time-consuming and costly functional follow-up studies. Application of RExPRT to ~800,000 TRs in the reference genome identified ~30,000 TRs that would be likely pathogenic upon expansion. Thus, RExPRT establishes a foundation for the application of machine learning approaches to categorize the pathogenicity of tandem repeat loci.

bioinformatics↗

bioRxiv2021

REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats

BackgroundExpansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely-recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads. ResultsWe implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in STR research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically-relevant repeat interruptions by comparing visual assessment results of 44 FMR1 repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR. ConclusionsRead pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions.

bioinformatics↗

bioRxiv2020

An assessment of efficacy of Iodine complex (Renessans) against SARS-CoV-2 in non-human primates (Rhesus macaque)

Renessans is an iodine complex which has proven in vitro antiviral activity including Anti-SARS-CoV-2 activity. The present study was designed to determine its efficacy against SARS-CoV-2 in monkeys (Rhesus macaque). A total of 14 monkeys were divided into four groups: A) Prophylactic group (n=03), (B) Treatment group (n=03), (C) infection control group (n=04) and (D) negative control group (n=04) and were housed in BSL-3 Animal facility while group D was housed at another animal house. Group A was administered with Renessans @ 2.85 mg/7 kg from 5 days prior to the infection to 08 days post infections (DPI). Group B was administered with Renessans from 03-08 DPI @ 2.85 mg/7 kg. Group C was administered with WIF only. The infection @ 2 x 106 TCID of SARS-CoV-2 was given to all group monkeys through intranasal and oral route under anesthesia. Nasal swab samples (at different times) and fecal matter on daily basis were collected for the detection of SARS-CoV-2 through real-time quantitative PCR. Three monkeys (one from each of group A, B and C) were euthanized at 07 DPI to determine the gross pathological lesions and SARS-CoV-2 detection from internal tissues. Nasal swabs from all the monkeys from group A, B and C were positive for SARS-CoV-2 at 02 and 07 DPI (Day 05 of treatment). At 14 DPI, all (100%) nasal swabs from group A were negative for SARS-CoV-2 while 50% and 100% were positive from group B and C, respectively. At 21 DPI, monkeys from group B were negative and all in group C were still positive for SARS-CoV-2. Similarly, fecal matter of monkeys in group A and B was returned negative in significantly lesser time as compared to monkeys from infection control group. Based on these research findings it is concluded that the Renessans has in-vivo SARS-CoV-2 activity and may result in early clearance of SARS-CoV-2. Therefore, a clinical trial of the drug in COVID-19 patients may reveal its anti-COVID-19 potential.

microbiology↗

bioRxiv2020

An in vitro assessment of anti-SARS-CoV-2 activity of oral preparations of iodine complexes (RENESSANS)

Since the emergence of CoVID-19 pandemic in China in late 2019, scientists are striving hard to explore non-toxic, viable anti-SARS-CoV-2 compounds or medicines. We determined In Vitro anti-SARS-CoV-2 activity of oral formulations (syrup and capsule) of an Iodine-complex (Renessans). A monolayer of vero cells were exposed to SARS-CoV-2 in the presence and absence of different concentrations (equivalent to 50, 05 and 0.5 g/ml of I2) of Renessans. Anti-SARS-CoV-2 activity of each of the formulation was assessed in the form of cell survival, SARS-CoV-2-specific cytopathic effect (CPE) and genome quantization. With varying concentrations of syrup and capsule, a varying rate of inhibition of CPE, cells survival and virus replication was observed. Compared to 0.5 g/ml concentration of Renessans syrup, 5 and 50 g/ml showed comparable results where there was a 100% cell survival, no CPEs and a negligible viral replication ({Delta}CT= 0.11 and 0.13, respectively). This study indicates that Renessans, containing iodine, may have potential activity against SARS-CoV-2 which needs to be further investigated in human clinical trials.

microbiology↗

bioRxiv2020

Mendelian randomization identifies folliculin expression as a mediator of diabetic retinopathy.

The goal of the study was to identify genes whose aberrant expression can contribute to diabetic retinopathy. We determined differential gene expression in response to high glucose in lymphoblastoid cell lines derived from matched individuals with type 1 diabetes (T1D) with and without retinopathy. Those genes exhibiting the largest difference in glucose response between individuals with diabetes with and without retinopathy were assessed for association to diabetic retinopathy utilizing genotype data from a genome-wide association study meta-analysis. All genetic variants associated with gene expression (expression Quantitative Trait Loci, eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the eQTLs from the glucose response genes among small association p-values and identified folliculin (FLCN) as a susceptibility gene for diabetic retinopathy. We show that expression of FLCN in response to glucose was greater in individuals with diabetic retinopathy compared to individuals with diabetes without retinopathy. Three large, independent cohorts of individuals with diabetes revealed an association of FLCN eQTLs to diabetic retinopathy. Mendelian randomization further confirmed a direct positive effect of increased FLCN expression on retinopathy in individuals with diabetes. Together, our studies integrating genetic association and gene expression implicate FLCN as a disease gene for diabetic retinopathy.

genomics↗

bioRxiv2018

Computational Analysis of Dynamical Fluctuations of Oncoprotein E7 (HPV) for the Hot Spot Residue Identification Using Elastic Network Model

Virus proteins after invading human body alter host protein-protein interaction networks, resulting in the creation of new interactions, along with destroying or modifying other interactions or proteins. Topological features of new or modified networks compromise the host system causing increased production of viral particles. The molecular basis for this alteration of proteins interactivity is short linear peptide motifs similar in both virus and humans. These motifs are identified by modular domains, which are the subunits of a protein, in the human body, resulting in stabilization or moderation of these protein interactions Protein molecules can be modeled by elastic network models showing the fluctuations of residues when they are biologically active. We focused our computational study on the binding and competing interactions of the E7 protein of HPV with Rb protein. Our study was based on analysis of dynamic fluctuations of E7 in host cell and correlation analysis of specific residue found in motif of LxCxE, that is the key region in stabilizing interaction between E7 and Rb. Hot spot residue of E7 were also identified which could provide platform for drug prediction in future. Nevertheless, our study validates the role of linear binding motifs LxCxE of E7 of HPV in interacting with Rb as an important event in propagation of HPV in human cells and transformation of infection into cervical cancer.

bioinformatics↗