Biology subjects

Chandok, H.

Publications and source records attributed to Chandok, H..

4 recordsLinked to original sources

bioRxiv2026

Atlas of HIV cis-regulatory elements reveals extensive transcriptional variation across clades, isolates, and within individuals

Human immunodeficiency virus (HIV) replication, persistence, and reactivation depend on transcription from integrated proviruses. Despite extensive sequence variation, how viral genetic diversity influences transcriptional regulation remains poorly understood. Here, we generate a functional regulatory atlas of HIV-1 and HIV-2 by combining tiling and saturation mutagenesis massively parallel reporter assays (MPRAs) with comparative sequence analysis and predictive modeling. By profiling thousands of HIV isolates in Jurkat and human primary CD4+T cells, we reveal extensive variation in baseline and stimulus-induced long terminal repeat (LTR) activity across and within clades, driven by distinct transcription factor configurations. These activities frequently differ among proviruses from the same individual and shift over infection and transmission without consistent selection for activity. Beyond the LTR, we identify conserved intragenic cis-regulatory elements, revealing regulatory architectures that complement LTR activity. Finally, we develop sequence-based models that accurately predict transcriptional activity, enabling scalable functional annotation of viral diversity and evolution.

microbiology↗

bioRxiv2025

Global cis-regulatory landscape of double-stranded DNA viruses

Most double-stranded DNA (dsDNA) viruses use the host transcriptional machinery to express viral genes for replication and immune evasion. This is mediated by viral cis-regulatory elements (CREs) regulated by host and viral transcription factors (TFs). Although some viral CREs and their regulatory mechanisms have been determined, most remain unidentified. Here, we used massively parallel reporter assays to identify [~]2,000 CREs across 27 dsDNA viruses from the Adenovirus, Herpesvirus, Polyomavirus and Papillomavirus families. Viral genomes have a higher CRE density than the human genome, with most viral CREs having promoter-like features and overlapping protein coding sequences. Using saturation mutagenesis and machine learning models, we report viral CRE regulators, including SP, ETS, bZIPs, and TFs acting downstream of signal-activated pathways. Altogether, we present a comprehensive functional CRE map of human-infecting dsDNA viruses that serves as a blueprint for further studies in viral regulation, reactivation, evolution, and viral vector design.

genomics↗

bioRxiv2024

Linking candidate causal autoimmune variants to T cell networks using genetic and epigenetic screens in primary human T cells.

Genetic variants associated with autoimmune diseases are highly enriched within putative cis-regulatory regions of CD4+ T cells, suggesting that they alter disease risk via changes in gene regulation. However, very few genetic variants have been shown to affect T cell gene expression or function. We tested >18,000 autoimmune disease-associated variants for allele-specific expression using massively parallel reporter assays in primary human CD4+ T cells. The 545 expression-modulating variants (emVars) identified greatly enrich for likely causal variants. We provide evidence that many emVars are mediated by common upstream regulatory conduits, and that putative target genes of primary T cell emVars are highly enriched within a lymphocyte activation network. Using bulk and single-cell CRISPR-interference screens, we confirm that emVar-containing T cell cis-regulatory elements modulate both known and novel target genes that regulate T cell proliferation, providing plausible mechanisms by which these variants alter autoimmune disease risk.

genetics↗

bioRxiv2021

Specific BRCA and immune configurations determine optimal response to platinum-based chemotherapy in triple negative breast and ovarian carcinomas

Loss of homologous recombination repair (HRR) via germline and somatic BRCA1 or BRCA2 gene mutations and via BRCA1 promoter methylation has been associated with better response to platinum agents and PARP inhibitors, in both triple negative breast cancer (TNBC) and ovarian carcinoma (OvCa). A major conundrum arising from recent clinical studies is why cancers with BRCA1 promoter methylation (BRCA1meth) respond more poorly as compared to those bearing mutations in BRCA1 and BRCA2 (BRCAmut), given the biologically equivalent HRR deficiency in both states. We dissected this problem through detailed genomic analyses of primary TNBC and OvCa cohorts, as well as experimentation with patient-derived xenograft (PDX) models and genetically engineered cell lines. Using the precise genomic scar of the tandem duplicator phenotype as a precise genomic indicator of BRCA1 deficiency, we found that, in all cohorts, BRCA1mut and BRCA1meth cancers share an equivalent degree of BRCA1-linked genomic rearrangements. Nonetheless, we consistently found that patients with BRCAmut cancers, but not those with BRCA1meth cancers, had significantly better response outcomes when compared to those with BRCA proficient cancers. When fully promoter methylated BRCA1 PDX TNBCs were exposed to a single short course of platinum chemotherapy an unmethylated BRCA1 promoter allele emerged in resultant tumors associated with an increase in BRCA1 expression. A separate analysis of PDXs derived from treatment naive TNBCs featured complete methylation of the BRCA1 promoter, whereas those derived from post-chemotherapy TNBCs invariably had only partial methylation. PDXs with partial methylation were significantly associated with lower response rates to in vivo platinum-based therapy compared to those with complete promoter methylation. Using single cell clonal expansions from a partially BRCA1meth PDX, we confirmed that the reduced level of methylation was due to the demethylation of one of the BRCA1 promoter alleles and not to the outgrowth of a non-methylated clone. Clinically, analysis of primary OvCas confirmed that high levels of BRCA1 methylation were significantly associated with reduced BRCA1 gene expression whereas cancers with lower levels of BRCA1 methylation had expression levels approaching those found in BRCA1 proficient cancers. These data suggest that unlike BRCAmut cancers, where HRR deficiency is achieved via mutations that are genetically fixed, BRCA1meth cancers are highly adaptive to genotoxin exposure and more likely to recover BRCA1 expression, which may explain their poorer therapeutic response. We further found that an increased immune transcriptional signal, especially an elevated M1 macrophage signature, is associated with enhanced response to platinum-based chemotherapy only in patients with BRCA proficient cancers, in both TNBC and OvCa cohorts underscoring the importance of characterizing molecular heterogeneity to enhance predictive precision in assigning response probabilities in TNBC and OvCa.

cancer biology↗