Biology subjects

Bukhari, S.

Publications and source records attributed to Bukhari, S..

6 recordsLinked to original sources

bioRxiv2026

Somatic mutations reveal the ontogeny of human microglia

Microglia are the resident hematopoietic cells of the central nervous system1. In mice, microglia seed the brain during embryogenesis and can be maintained throughout life with minimal input from adult hematopoiesis2-4. The origins of human microglia are less clear, but recent evidence suggests that marrow-derived cells may be able to supplement the human microglial pool in certain individuals5,6. Here, to investigate the ontogeny of human microglia, we develop a method that uses the collection of accumulated somatic mutations which uniquely labels each clone of cells to track the infiltration of marrow-derived cells into the human brain. Applying this method to 20 aged individuals, we find evidence of an influx of marrow-derived cells into the brain in all examined individuals. Single cell analysis, including single cell lineage tracing using mitochondrial DNA variants, demonstrates that these infiltrating cells are nearly identical to microglia and can comprise a large fraction of the microglial pool. Analysis of large-scale sequencing cohorts demonstrates a protective association between most types of clonal hematopoiesis and Alzheimers disease. In sum, this work uncovers a widespread influx of myeloid cells into the healthy human brain which serves to reinforce the pool of human microglia and becomes common with aging.

immunology↗

bioRxiv2025

Metabolic and Redox Pathway Dysregulation in HIV-Associated Coronary Endothelial Dysfunction

BackgroundPeople with HIV (PWH), even with sustained viral suppression on antiretroviral therapy (ART), remain at increased risk for cardiovascular disease. Coronary endothelial dysfunction, a sensitive marker of early vascular injury and a potential target for intervention is common in this population, but its biological basis remains unknown. MethodsWe performed a cross-sectional study combining in vivo coronary MRI and high-throughput serum proteomics to investigate mechanisms of coronary endothelial dysfunction in treated HIV. Forty-five virally suppressed PWH and twenty-nine age- and sex-matched healthy controls underwent coronary MRI during isometric handgrip exercise to quantify coronary endothelial function, defined as the percentage change in coronary cross-sectional area (%CSA) from rest to stress. An increase in coronary CSA <2% indicated endothelial dysfunction. Parallel serum proteomic profiling was performed using the SomaScan 7K platform, and differential protein expression between groups was analyzed using linear modeling (LIMMA). ResultsCoronary endothelial dysfunction was more prevalent in PWH with suppressed viral load compared to controls (67% vs 10%, p<0.001). Pathway analysis of differentially expressed proteins between participants with and without endothelial dysfunction highlighted significant dysregulation of glutathione dependent detoxification, oxidative metabolism and fatty acid {beta}-oxidation pathways in individuals with endothelial dysfunction (adjusted p value <0.05). ConclusionsEndothelial dysfunction in PWH on ART is associated with metabolic and redox imbalance. These findings highlight glutathione and fatty acid oxidation related pathways as potential therapeutic targets for reducing cardiovascular risk in this patient population.

immunology↗

bioRxiv2023

PD-1 signaling uncovers a pathogenic subset of T cells in inflammatory arthritis

BackgroundPD-1 is an immune checkpoint on T cells and interventions to block this receptor result in T cell activation and enhanced immune response to tumors. Paired to that, and despite a decade of research, approaches to treat autoimmunity with PD-1 agonists still need to be more successful. To resolve this, new methods must be developed to augment PD-1 function beyond engaging the receptor. MethodsWe conducted a flow cytometry analysis of T cells isolated from the peripheral blood and synovial fluid of patients with rheumatoid arthritis. In addition, we performed a genome-wide CRISPR/Cas9 screen to identify genes associated with PD-1 signaling. We further analyzed genes involved in PD-1 signaling using publicly available bulk and single-cell RNA sequencing datasets. ResultsOur screen confirmed known regulators in proximal PD-1 signaling and, importantly, found an additional 1,112 unique genes related to PD-1 ability to inhibit T cell functions. These genes were strongly associated with the response of cancer patients to PD-1 blockades and with high tumor immune dysfunction and exclusion scores, confirming their role downstream of PD-1. Functional annotation revealed that more significant genes uncovered were those associated with known immune regulation processes. Remarkably, these genes were considerably downregulated in T cells isolated from patients with inflammatory arthritis, supporting their overall inhibitory functions. A study of rheumatoid arthritis single-cell RNA sequencing data demonstrated that five genes, KLRG1, CRTAM, SLAMF7, PTPN2, and KLRD1, were downregulated in activated and effector T cells isolated from synovial fluids. Back-gating these genes to canonical cytotoxic T cell signatures revealed PD-1+ HLA-DRHIGH KLRGLOW T cells as a novel inflammatory subset of T cells. ConclusionWe concluded that PD-1+ HLA-DRHIGH KLRGLOW T cells are a potential target for future PD-1 agonists to treat inflammatory diseases. Our study uncovers new genes associated with PD-1 downstream functions and, therefore, provides a comprehensive resource for additional studies that are much needed to characterize the role of PD-1 in the synovial subset of T cells.

immunology↗

bioRxiv2023

SAP expressing T peripheral helper cells identify systemic lupus erythematosus patients with lupus nephritis

IntroductionT follicular (TFH) and peripheral helper (TPH) cells have been increasingly recognized as a pathogenic subset of CD4 T cells in systemic lupus erythematosus (SLE). The SLAM Associated Protein (SAP) regulates TFH and TPH function by binding to the co -stimulatory signaling lymphocyte activation molecule family (SLAMF) receptors that mediate T cell - B cell interactions. SAP and SLAMF are critical for TPH dependent B cell maturation into autoantibody-producing plasma cells that characterize SLE pathogenesis. MethodsPeripheral blood mononuclear cells (PBMCs) were isolated using density gradient separation from whole blood. Cells were stained for cell surface markers, followed by permeabilization and staining of intracellular SAP for spectral flow cytometry analysis. Additionally, we analyzed SAP expression from renal infiltrating lupus nephritis (LN) T cells using the publicly available single-cell RNA sequencing (sc-RNA seq) Accelerated Medicines Partnership (AMP) in SLE dataset. ResultsPBMCs from 30 patients with SLE (34{+/-}10 years old, 83% female), including 10 patients with LN, were analyzed. We found an increase in total SAP-positive CD4 and CD8 T cells in SLE compared with controls (55.5{+/-}2.6 vs. 41.3{+/-}3.4, p=0.007 and 52.5{+/-}3.0 vs. 39.2{+/-}2.8, p=0.007 respectively). In CD4 T cells, the highest SAP expression was in the TPH subset. The frequency of SAP+TPH in circulation correlated with disease activity, SLE patients with renal disease had higher levels of circulating SAP+TPH that remained significant after adjusting for age, sex, race, low complements, and elevated anti-dsDNA (p=0.014). scRNA-seq data of renal infiltrating T cells identified increased SAP from LN compared with control kidney biopsy samples (p=0.03), including an expansion of SAP-positive TFH-like subsets in the LN kidneys. Increased SAP expression in LN was associated with the differential expression of SLAMF3 and SLAMF7 as well as granzyme K and EOMES. The existence of two predominant SAP-expressing subsets, the TFH-like CD4 T cells and granzyme K positive effector CD8 T cells, was verified using scRNA-seq data from a human transcriptomic atlas of fifteen major organs. ConclusionThe expansion of SAP expressing T helper cells was associated with lupus nephritis in our cohort and verified using scRNA-seq data of renal infiltrating T cells. Improved understanding of SLAM/SAP signaling can identify new therapeutic targets in LN.

immunology↗

bioRxiv2022

Single-cell Spatial Proteomic Imaging for Human Neuropathology

Neurodegenerative disorders are characterized by phenotypic changes and hallmark proteopathies. Quantifying these in archival human brain tissues remains indispensable for validating animal models and understanding disease mechanisms. We present a framework for nanometer-scale, spatial proteomics with multiplex ion beam imaging (MIBI) for capturing neuropathological features. MIBI facilitated simultaneous, quantitative imaging of 36 proteins on archival human hippocampus from individuals spanning cognitively normal to dementia. Customized analysis strategies identified cell types and proteopathies in the hippocampus across stages of Alzheimers disease (AD) neuropathologic change. We show microglia-pathologic tau interactions in hippocampal CA1 subfield, in AD dementia. Data driven, sample independent creation of spatial proteomic regions identified persistent neurons in pathologic tau neighborhoods expressing mitochondrial protein MFN2, regardless of cognitive status, suggesting a survival advantage. Our study revealed unique insights from multiplexed imaging and data-driven approaches for neuropathologic analysis and serves as a baseline for mechanistic and interventional understanding in human neurodegeneration.

systems biology↗

bioRxiv2019

Beyond Conventional Models: Recreating the Initiation, Evolution, and Genome of GBM

BackgroundImagining ways to prevent or treat glioblastoma (GBM) have been hindered by a lack of understanding of its pathogenesis. Although PDGF-AA overexpression may be an early event, critical details of the core biology are lacking. Existing PDGF-driven models replicate its microscopic appearance but not the genomic architecture characteristic of the human disease. Here we report a new model of GBM that overcomes this barrier to authenticity. MethodsUsing a method developed to study neural stem cells, we investigated the effects of PDGF-AA on subventricular zone (SVZ) cells, the putative cell of origin of GBM. We micro-dissected SVZ tissue from p53-null and wild-type adult mice, established primary cultures in media supplemented with PDGF-AA, and assessed cell viability, proliferation, genome stability, and tumour forming potential. ResultsCounterintuitive to its canonical role as a growth factor, we observed immediate and massive death of SVZ cells in PDGF-AA. Wild-type cells did not survive in PDGF-AA. However, a small fraction of null cells evaded apoptosis, displayed attenuated proliferation, gradually accumulated whole chromosome gains and losses, and, signalled by sudden rapid proliferation and growth factor independence, became tumorigenic in immune-competent syngeneic mice. Transformed cells had an OPC-like profile, were resistant to PDGFR- inhibition, and harboured highly abnormal karyotypes similar to those seen in human GBMs. ConclusionThis model associates genome instability in SVZ cells with chronic exposure to PDGF-AA; it is the first model to replicate the genomic landscape of GBM and first in which the earliest phases of GBM can be directly observed. IMPORTANCE OF STUDYWe have developed a mouse model in which the initiation, evolution and genomic landscape of GBM can be thoroughly studied thus paving the way for ideas about how this deadly brain cancer might be prevented, interrupted at an occult stage, or treated with very different therapies.

cancer biology↗