Biology subjects

Saad, M.

Publications and source records attributed to Saad, M..

13 recordsLinked to original sources

bioRxiv2026

Weaning imprints a hybrid cytotoxic-regulatory identity on intestinal CD4+ T lymphocytes

The intestinal immune system must adapt as the neonatal gut shifts from milk to solid food and becomes densely colonized. How the T cell compartment is established under these conditions remains unclear. Using fate-mapping to timestamp naive T cells, with imaging, transcriptomic, and repertoire analyses, we tracked them from suckling to adulthood. Intestinal T cell entry peaked at weaning, coinciding with relocation from crypts to villi guided by the tissue microenvironment and, partly, the microbiota. T cells timestamped at suckling persisted into adulthood and, at weaning, adopted a transient cytotoxic-regulatory state in the lamina propria, with granzyme B expression microbiota-dependent only in the ileum. Clonal expansions at weaning were restricted to the small intestinal lamina propria and absent in germ-free mice. Most expanded clones recognized early-life commensals. Weaning is a physiological window of transient inflammation imprinting a hybrid CD4 T cell compartment, suggesting that early-life commensals modulate T cell selection.

immunology↗

bioRxiv2026

Colorectal cancers with distinct metastatic potential trigger divergent early T cell responses

Colorectal cancer (CRC) remains a leading cause of cancer mortality, with most cases refractory to immunotherapy. Distinguishing tumor-induced from steady-state mucosal T cell responses has been a critical barrier to understanding antitumor immunity in CRC. Using orthotopic transplantation of CRC organoids with and without metastatic potential, combined with temporal T cell fate-mapping, we show that non-metastatic tumors elicit early recruitment of CD8{beta} and CD4 T cells that acquired cytotoxic and Th1-like programs, whereas pro-metastatic tumors induce a naive-like, hypoactivated state. Tumor-infiltrating CD4+ T cells underwent clonal expansion, including clones recognizing microbial and dietary antigens. T cells in physical contact with tumor cells, identified by uLIPSTIC, were enriched for expanded and cytotoxic clones. Fate-mapped T cells from non-metastatic tumors suppressed tumor growth in an IFN-{gamma}-dependent manner, whereas pro-metastatic tumor-derived T cells failed to do so. Mechanistically, pro-metastatic tumors downregulated MHCII, and Ciita targeting in non-metastatic organoids reduced CD4 clonal expansion and led to tumor progression. Together, these findings define divergent early T cell trajectories associated with CRC metastatic potential, indicating that ineffective local immune engagement precedes metastatic dissemination.

immunology↗

bioRxiv2026

Root endophyte sulfur metabolites enhance redox balance and drought tolerance in Arabidopsis

Drought is a major consequence of climate change and significantly limits crop productivity. Plant growth-promoting bacteria offer a promising solution to mitigate drought stress. The root endophyte Pseudomonas argentinensis SA190 has been shown to enhance plant performance under drought stress conditions, but the mechanistic basis of SA190s beneficial effects remained unclear. Given the pivotal role of sulfur-containing compounds in abiotic stress responses, we investigated multiple sulfur-related Arabidopsis mutants under drought stress. We found that SA190 enhances sulfate uptake and promotes glutathione (GSH) accumulation in shoots under stress conditions. SA190 treatment improved the GSH/GSSG ratio, indicating an enhanced redox balance under drought. Selective inhibition of Arabidopsis GSH biosynthesis using buthionine sulfoximine (BSO) confirmed the essential contribution of bacterial GSH to drought stress. In addition, by generation and use of bacterial mutants deficient in the GSH synthesis pathway, we show that the bacteria directly provide Arabidopsis with either GSH or its precursor {gamma}-EC. In summary, SA190 promotes drought tolerance by supplying the host plant with additional GSH thereby maintaining cellular redox homeostasis and enhancing drought stress resilience.

Plant Biology↗

bioRxiv2024

A mouse model to study glutathione limitation in vivo

Glutathione (GSH) is a highly abundant tripeptide thiol that performs diverse protective and biosynthetic functions in cells. While changes in GSH availability are linked to many diseases, including cancer and neurodegenerative disorders, determining the function of GSH in physiology and disease has been challenging due to its tight regulation. To address this, we generated cell and mouse models that express a bifunctional glutathione-synthesizing enzyme from Streptococcus Thermophilus (GshF). GshF expression allows efficient production of GSH in the cytosol and mitochondria and prevents cell death in response to GSH depletion, but not ferroptosis, indicating that GSH is not a limiting factor under lipid peroxidation. CRISPR screens using engineered enzymes revealed metabolic liabilities under compartmentalized GSH depletion. Finally, GshF expression in mice is embryonically lethal but sustains postnatal viability when restricted to adulthood. Overall, our work identifies a conditional mouse model to investigate the role of GSH availability in physiology and disease.

genetics↗

bioRxiv2023

Suppression of epithelial proliferation and tumorigenesis by immunoglobulin A

Immunoglobulin A (IgA) is the most abundant antibody isotype produced across mammals and plays a specialized role in mucosal homeostasis1. Constantly secreted into the lumen of the intestine, IgA binds commensal microbiota to regulate their colonization and function2,3 with unclear implications for health. IgA deficiency is common in humans but is difficult to study due to its complex aetiology and comorbidities4-8. Using genetically and environmentally controlled mice, here we show that IgA-deficient animals have increased susceptibility to endogenous colorectal tumours. Cellular and molecular analyses revealed that, in the absence of IgA, colonic epithelial cells induce antibacterial factors and accelerate cell cycling in response to the microbiota. Oral treatment with IgA was sufficient to both reduce steady-state proliferation and protect mice from tumours, but this function was due to antibody structure rather than binding specificity. In both organoid and monolayer culture systems, IgA directly suppressed epithelial growth. Co-immunoprecipitation mass spectrometry and a targeted CRISPR screen identified DMBT1 as an IgA-binding epithelial surface protein required for IgA-mediated suppression of proliferation. Together, IgA and DMBT1 regulate Notch signalling and tune the normal cycling of absorptive colonocyte progenitors. In mice, deleting the transmembrane and cytoplasmic signalling portions of DMBT1 or blocking Notch signalling was sufficient to reverse both the increased proliferation and tumour susceptibility of IgA knockouts. These experiments establish a homeostatic function for IgA in tempering physiological epithelial responses to microbiota to maintain mucosal health.

immunology↗

bioRxiv2023

Epigenetic Age Acceleration in Surviving versus Deceased COVID-19 Patients with Acute Respiratory Distress Syndrome following Hospitalization

Aging has been reported as a major risk factor for severe symptoms and higher mortality rates in COVID-19 patients. Molecular hallmarks such as epigenetic alterations and telomere attenuation reflect the biological process of aging. Epigenetic clocks have been shown to be valuable tools for measuring biological age in a variety of tissues and samples. As such, these epigenetic clocks can determine accelerated biological aging and time-to-mortality across various tissues. Previous reports have shown accelerated biological aging and telomere attrition acceleration following SARS-CoV-2 infection. However, the effect of accelerated epigenetic aging on outcome (death/recovery) in COVID-19 patients with Acute Respiratory Distress Syndrome (ARDS) has not been well investigated. In this study, we measured DNA methylation age and telomere attrition in 87 severe COVID-19 cases with ARDS under mechanical ventilation. Furthermore, we compared dynamic changes in epigenetic aging across multiples time-points until recovery or death. Epigenetic age was measured using the Horvath, Hannum, DNAm skin and blood, GrimAge, and PhenoAge clocks, whereas telomere length was calculated using the surrogate marker DNAmTL. Our analysis revealed significant accelerated epigenetic aging but no telomere attrition acceleration in severe COVID-19 cases. In addition, we observed epigenetic age deceleration at inclusion vs end of follow-up in recovered but not in deceased COVID-19 cases using certain clocks. When comparing dynamic changes in epigenetic age acceleration (EAA), we detected higher EAA using both the Horvath and PhenoAge clocks in deceased vs recovered patients. The DNAmTL measurements revealed telomere attrition acceleration in deceased COVID19 patients between inclusion and end of follow-up as well as a significant change in dynamic telomere attrition acceleration when comparing patients who recovered vs those who died. In conclusion, EAA and telomere attrition acceleration was associated with treatment outcome in hospitalized COVID-19 Patients with ARDS. A better understanding of the long-term effects of EAA in COVID19 patients and how they might contribute to Long COVID symptoms in recovered individuals is urgently needed.

genetics↗

bioRxiv2021

Longitudinal clonal dynamics of HIV-1 latent reservoirs measured by combination quadruplex polymerase chain reaction and sequencing

HIV-1 infection produces a long-lived reservoir of latently infected CD4+ T cells that represents the major barrier to HIV-1 cure. The reservoir contains both intact and defective proviruses, but only the proviruses that are intact can re-initiate infection upon cessation of antiretroviral therapy (ART). Here we combine 4 color quantitative polymerase chain reaction and next-generation sequencing (Q4PCR) to distinguish intact and defective proviruses and measure reservoir content longitudinally in 12 infected individuals. Q4PCR differs from other PCR based methods in that the amplified proviruses are sequence verified as intact or defective. Samples were collected systematically over the course of up to 10 years beginning shortly after the initiation of ART. The size of the defective reservoir was relatively stable with minimal decay during the 10-year observation period. In contrast, the intact proviral reservoir decayed with estimated half-life of 4.9 years. Nevertheless, both intact and defective proviral reservoirs are dynamic. As a result, the fraction of intact proviruses found in expanded clones of CD4+ T cells increases overtime with a concomitant decrease in overall reservoir complexity. Thus, reservoir decay measurements by Q4PCR are quantitatively similar to viral outgrowth (VOA) and intact proviral DNA PCR (IPDA) with the addition of sequence information that distinguishes intact and defective proviruses and informs reservoir dynamics. The data is consistent with the notion that intact and defective proviruses are under distinct selective pressure, and that the intact proviral reservoir is progressively enriched in expanded clones of CD4+ T cells resulting in diminishing complexity over time. SignificanceHIV-1 infection requires lifelong treatment with antiretroviral therapy (ART) due to viral rebound of a latent reservoir of intact, transcriptionally silent provirus found to persist in the genome of CD4+ T cells. One of the major challenges to understanding the nature of the latent reservoir is accurately characterizing the measuring the size of the reservoir. Herein, we use quadruplex polymerase chain reaction (Q4PCR) to assess the dynamics of the latent reservoir in HIV+ individuals who have been on long-term ART for up to 10 years. Our results show that Q4PCR can be used to accurately measure the latent reservoir, while providing the added benefit of assessing the genetic diversity of the reservoir to better understand changes to clonal dynamics overtime.

immunology↗

bioRxiv2020

Germline genetic contribution to the immune landscape of cancer

The role of germline genetics in shaping the tumor immune landscape is largely unknown. Using genotypes from >9,000 individuals in The Cancer Genome Atlas, we investigated the association of common and rare variants with 139 well-defined immune traits. Our analysis of common variants identified 10 immune traits with significant heritability estimates, and an additional 23 with suggestive heritability, including estimates of T-cell subset abundance and interferon signaling. We performed genome-wide association on the 33 heritable traits and identified 23 genome-wide significant loci associated with at least one immune trait, including SNPs in the IFIH1 locus previously associated with several autoimmune diseases. We also found significant associations between immune traits and pathogenic or likely-pathogenic rare variants in BRCA1 and in genes functionally linked to telomere stabilization, and Wnt/Beta-catenin signaling. We conclude that germline genetic variants significantly impact the composition and functional orientation of the tumor immune microenvironment.

immunology↗

bioRxiv2019

Identification of two aptamers binding to Legionella pneumophila with high affinity and specificity

Legionella pneumophila (Lp) is a water borne bacterium causing Legionnaires Disease (LD) in humans. Rapid detection of Lp in water system is essential to reduce the risk of LD outbreaks. The methods currently available require expert skills and are time intensive, thus delaying intervention. In situ detection of Lp by biosensor would allow rapid implementation of control strategies. To this end, a biorecognition element is required. Aptamers are considered promising biorecognition molecules for biosensing. Aptamers are short oligonucleotide sequence folding into a specific structure and are able to bind to specific molecules. Currently no aptamer and thus no aptamer-based technology exists for the detection of Lp. In this study, Systemic Evolution of Ligands through EXponential enrichment (SELEX) was used to identify aptamers binding specifically to Lp. Ten rounds of positive selection and two rounds of counter-selection against two Pseudomonas species were performed. Two aptamers binding strongly to Lp were identified with KD of 116 and 135 nM. Binding specificity of these two aptamers to Lp was confirmed by flow cytometry and fluorescence microscopy. Therefore, these two aptamers are promising biorecognition molecules for the detection of Lp in water systems.

microbiology↗

bioRxiv2019

Conditional activation of immune-related signatures and prognostic significance: a pan-cancer analysis

BackgroundIt is becoming clear that tumor immune T cell infiltration and its functional orientation have substantial effect on cancer progression, influencing both response to therapy and prognosis. In this pan-cancer study, the previously described Immunologic Constant of Rejection (ICR) signature is used to define opposing immune phenotypes (i.e., immuneactive and immune-silent) across 31 different histologies. We systematically analyze the interconnections between the genetic programming of neoplasms and their immune orientation across different histologies, and the prognostic impact of such interplay. Moreover, we investigated the predictive value of ICR classification across various public datasets of immune checkpoint inhibition therapy. MethodsRNA-seq data of samples from a total of 9,282 patient tumor samples representing 31 cancer types were obtained from The Cancer Genome Atlas (TCGA). We classified each cancer type based on the expression of the ICR gene signature. Oncogenic pathway gene set enrichment and mutational status were analyzed in relation to ICR phenotypes. To explore whether tumorintrinsic attributes associate with the prognostic value of ICR across cancers, we compared mutational load, oncogenic alterations and expression of oncogenic pathways between cancer types using an integrative bioinformatic pipeline. ResultsOur analyses identified a distinct prognostic connotation of ICR depending on cancer histology. We identified several oncogenic pathways whose enrichment inversely correlated with ICR in multiple tumor types. We found several cancer specific pathways that were differentially enriched between tumors in which ICR had a prognostic impact versus the ones in which ICR did not bear any prognostic connotation such as proliferation and TGF-beta signaling. Importantly, this conditional impact of ICR was also validated in the context of immune checkpoint inhibition treatment. ConclusionsWe identified tumor-intrinsic attributes that correlate with immune phenotypes and potentially influence their development. In addition, a relationship was observed between the enrichment of oncogenic pathways and the prognostic significance of the ICR and its predictive value for patients treated with anti-CTLA4 immune checkpoint inhibition. Such information can be used to prioritize potential candidates for therapies aimed at converting immune-silent into immuneactive tumors and to refine stratification algorithms.

cancer biology↗

bioRxiv2019

GIGI2: A Fast Approach for Parallel Genotype Imputation in Large Pedigrees

MotivationImputation of untyped SNPs has become important in Genome-wide Association Studies (GWAS). There has also been a trend towards analyzing rare variants, driven by the decrease of genome sequencing costs. Rare variants are enriched in pedigrees that have many cases or extreme phenotypes. This is especially the case for large pedigrees, which makes family-based designs ideal to detect rare variants associated with complex traits. The costs of performing relatively large family-based GWAS can be significantly reduced by fully sequencing only a fraction of the pedigree and performing imputation on the remaining subjects. The program GIGI can efficiently perform imputation in large pedigrees but can be time consuming. Here, we implement GIGIs imputation approach in a new program, GIGI2, which performs imputation with computational time reduced by at least 25x on one thread and 120x on eight threads. The memory usage of GIGI2 is reduced by at least 30x. This reduction is achieved by implementing better memory layout and a better algorithm for solving the Identity by Descent graphs, as well as with additional features, including multithreading. We also make GIGI2 available as a webserver based on the same framework as the Michigan Imputation Server. AvailabilityGIGI2 is freely available online at https://cse-git.qcri.org/eullah/GIGI2 and the websever is at https://imputation.qcri.org/ Contactmsaad@hbku.edu.qa

bioinformatics↗

bioRxiv2018

A hybrid mortality prediction model of patients with cavitary pulmonary carcinomas

To date, developing a reliable mortality prediction model remains challenging. Although clinical predictors like age, gender and laboratory results are of considerable predictive value, the accuracy often ranges only between 60-80%. In this study, we proposed prediction models built on the basis of clinical covariates with adjustment for additional variables that was radiographically induced. The proposed method exhibited a high degree of prediction accuracy of between 83-92%, as well as overall improvement of between 6-20% in all other metrics, such as ROC Area, False Positive Rates, Recall and Root Mean Square Error. We provide a proof of concept that there is an added value for incorporating the additional variables while predicting 24-month mortality in pulmonary carcinomas patients with cavitary lesions. It is hoped that the findings will be clinically useful to the medical community.

bioinformatics↗

bioRxiv2018

Quality Control and Integration of Genotypes from Two Calling Pipelines for Whole Genome Sequence Data in the Alzheimer’s Disease Sequencing Project

The Alzheimers Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed \"consensus calling,\" to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.\n\nAbbreviationsAD, Alzheimers disease; QC, Quality Control; LSSAC, Large-Scale Sequencing and Analysis Center; Broad, Broad Institute Genomics Service; Baylor, Baylor College of Medicine Human Genome Sequencing Center; WashU, Washington University-St. Louis McDonnell Genome Institute; WGS, whole genome sequencing; WES, whole exome sequencing; indel, insertion-deletion variants; VCF, variant control format; MI, Mendelian inconsistency; MC, Mendelian consistency; GWAS, genome-wide association study; VR, referent allele read depth; DP, overall read depth; MS, mapping score; GQ, genotype quality score; Ti/Tv, Transition/Transversion; CS, concordance code

genetics↗