Biology subjects

Koul, S.

Publications and source records attributed to Koul, S..

8 recordsLinked to original sources

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗

bioRxiv2025

Mapping the Subtype-Specific PARP1 ADP-ribosylated Proteome in Breast Cancer Cells

Breast cancers are molecularly heterogeneous, with subtype-specific differences in transcriptional programs, chromatin architecture, and therapeutic responses. While PARP1 has been extensively studied in the context of DNA repair, emerging evidence implicates its catalytic activity in a broader set of cellular processes, including the regulation of gene expression. Here, we employed an NAD analog-sensitive PARP1 (asPARP1) chemical genetics approach combined with mass spectrometry to map the ADP-ribosylated proteome across six human breast cancer cell lines representing luminal and basal/triple negative subtypes. We identified thousands of PARP1 substrates and hundreds of Glu/Asp ADPRylation sites, revealing both shared and subtype-specific modifications in cell lines maintained under basal growth conditions. Luminal-specific substrates were enriched in chromatin and transcriptional regulators, whereas basal-specific substrates were preferentially linked to translation and RNA processing, highlighting lineage-dependent PARP1 activity. Transcription factors emerged as major substrates, with TFAP2A serving as a proof-of-concept; it is selectively ADPRylated in luminal cells and inhibition of PARP1-mediated ADPRylation modulates its promoter occupancy in a subtype-specific manner. Our data provide a new resource for studying subtype-specific PARP1-mediated ADPRylation in breast cancer cells. Collectively, our findings expand the conceptual framework for PARP1 function beyond DNA repair, offering mechanistic insights into subtype-specific gene regulation and potential determinants of PARP inhibitor sensitivity in breast cancer.

cancer biology↗

bioRxiv2025

NAD+ Sensing by PARP7 Regulates the C/EBPβ-Dependent Transcription Program in Adipose Tissue In Vivo

We have identified PARP7, an NAD+-dependent mono(ADP-ribosyl) transferase, as a key regulator of the C/EBP{beta}-dependent proadipogenic transcription program. Moreover, PARP7 is required for efficient adipogenesis and downstream biological functions, including involution of the lactating mammary gland. PARP7 serves as a coregulator of C/EBP{beta}, and depletion of PARP7 causes a dramatic reduction in C/EBP{beta} binding across the genome. PARP7 functions as a sensor of nuclear NAD+ levels to control gene expression. At the relatively high nuclear NAD+ concentrations in undifferentiated preadipocytes, PARP7 is catalytically active for auto- mono(ADP-ribosyl)ation (autoMARylation). As nuclear NAD+ concentrations decline post- differentiation, autoMARylation decreases dramatically. AutoMARylation promotes instability of PARP7 through an E3 ligase-ubiquitin-proteasome pathway mediated by the ADP-ribose (ADPR)-binding ubiquitin E3 ligases DTX2 and RNF114. Genetic depletion of PARP7 in mice promotes a dramatic reduction in a wide array of lipids in the mammary gland fat pads and milk from lactating females, as well as a significant decrease in nicotinamide mononucleotide (NMN), a key nutrient in mothers milk. The latter is due to reduced expression of Nampt, the gene encoding NAMPT, the enzyme that produces NMN, which is a direct transcriptional target of PARP7 and C/EBP{beta}. Collectively, our results extend the biology of PARP7 to adipogenesis and perinatal health. Moreover, our results describe the molecular events that regulate these downstream biological functions.

cell biology↗

bioRxiv2025

X-Linked Cancer-Associated Polypeptide (XCP) from lncRNA1456 Cooperates with PHF8 to Regulate Gene Expression and Cellular Pathways in Breast Cancer

Recent studies have demonstrated that a subset of long "noncoding" RNAs (lncRNAs) produce functional polypeptides and proteins. In this study, we discovered a 132 amino acid protein in human breast cancer cells named XCP (X-linked Cancer-associated Polypeptide), which is encoded by lncRNA1456 (a.k.a. RHOXF1P3), a transcript previously thought to be noncoding. lncRNA1456 is a pancreas- and testis-specific RNA whose gene is located on chromosome X. We found that the expression of lncRNA1456 and XCP are highly upregulated in the luminal A, luminal B, and HER2 molecular subtypes of breast cancer. XCP modulates both estrogen-dependent and estrogen-independent growth of breast cancer cells by regulating cancer pathways, as shown in cell and xenograft models. XCP shares some homology with homeodomain-containing proteins and interacts with the histone demethylase plant homeodomain finger protein 8 (PHF8), which is also encoded by an X-linked gene. Mechanistically, XCP stimulates the histone demethylase activity of PHF8 to regulate gene expression in breast cancer cells. These findings identify XCP as a coregulator of transcription and emphasize the need to interrogate the potential functional roles of open reading frames originating from noncoding RNAs. Statement of SignificangeXCP, a polypeptide encoded by an X-linked lncRNA, regulates gene expression in breast cancer cells. XCP is a chromatin-associated protein that interacts with the histone demethylase PHF8 and modulates its demethylase activity to regulate gene expression. XCP drives cancer-specific phenotypes and serves as a potential biomarker and/or target for therapeutic intervention.

cancer biology↗

bioRxiv2025

A brainstem-thalamic circuitry for affective-motivational responses to cold pain

The medial thalamus is crucial for the sensory and affective-motivational responses to chronic pain. However, a mechanistic understanding of how the distinct subnuclei of the medial thalamus mediate behavioral responses to pain remains lacking. Taking advantage of intersectional viral genetics, chemogenetics, optogenetics, in-vivo imaging, and ex-vivo physiology, we reveal that the neurons in the parafascicular (PF) nuclei of the medial thalamus receive monosynaptic inputs from the lateral parabrachial nuclei (LPBN) in mice. LPBN is an essential nucleus in the ascending pain pathway, receiving projections from the dorsal horn of the spinal cord. The PF neurons downstream of LPBN (PFpost-LPBN) are nociceptive, sensitized by peripheral neuropathy, acutely aversive, and, when activated, drive both sensory and affective-motivational responses to cold pain. In contrast, the LPBN target neurons in the intralaminar centromedian thalamus (CMpost-LPBN), another nociceptive nucleus of the medial thalamus, are primarily involved in the affective-motivational aspects of pain. Together, we reveal that the LPBN, through two closely related thalamic nuclei, influences behavior in mice with cold hypersensitivity due to peripheral neuropathies.

neuroscience↗

bioRxiv2025

The E2F4 transcriptional repressor is a key mechanistic regulator of colon cancer resistance to irinotecan (CPT-11).

Background. Colorectal carcinomas (CRCs) are seldom eradicated by cytotoxic chemotherapy. Cancer cells with stem-like functional properties, often referred to as "cancer stem cells" (CSCs), display preferential resistance to several anti-tumor agents used in cancer chemotherapy, but the molecular mechanisms underpinning their selective survival remain only partially understood. Methods. In this study, we used Transcription Factor Target Genes (TFTG) enrichment analysis to identify transcriptional regulators (activators or repressors) that undergo preferential activation by chemotherapy in CRC cells with a "bottom-of-the-crypt" phenotype (EPCAM+/CD44+/CD166+; CSC-enriched) as compared to CRC cells with a "top-of-the-crypt" phenotype (EPCAM+/CD44neg/CD166neg; CSC-depleted). The two cell populations were purified in parallel by fluorescence-activated cell sorting (FACS) from a patient-derived xenograft (PDX) line representative of a moderately differentiated human CRC, following in vivo chemotherapy with irinotecan (CPT-11). The transcriptional regulators identified as differentially activated were tested for differential expression in normal vs. cancer tissues, and in cell populations enriched in stem/progenitor cell-types as compared to differentiated lineages (goblet cells, enterocytes) in the mouse colon epithelium. Finally, the top candidate was tested for mechanistic contribution to drug-resistance by selective down-regulation using short-hairpin RNAs (shRNAs). Results. Our analysis identified E2F4 and TFDP1, two core components of the DREAM transcriptional repression complex, as transcriptional modulators preferentially activated by irinotecan in EPCAM+/CD44+/CD166+ as compared to EPCAM+/CD44neg/CD166neg cancer cells. The expression levels of both genes (E2F4, TFDP1) were found up-regulated in CRCs as compared to human normal colon tissues, and in a sub-population of mouse colon epithelial cells enriched in stem/progenitor elements (Epcam+/Cd44+/Cd66alow/Kitneg) as compared to other sub-populations enriched in either goblet cells (Epcam+/Cd44+/Cd66alow/Kit+) or enterocytes (Epcam+/Cd44neg/Cd66ahigh). Most importantly, E2F4 down-regulation using shRNAs dramatically enhanced the sensitivity of human CRCs to in vivo treatment with irinotecan, across three independent PDX models. Conclusions. Our data identified E2F4 and the DREAM repressor complex as critical regulators of human CRC resistance to irinotecan, and as candidate targets for the development of chemo-sensitizing agents.

cancer biology↗

bioRxiv2024

RBN-2397, a PARP7 Inhibitor, Synergizes with Paclitaxel to Inhibit Proliferation and Migration of Ovarian Cancer Cells

ObjectivesMono(ADP-ribosyl)ation (MARylation), a post translational modification of proteins, is emerging as an important regulator of the biology of cancer cells. PARP7 (TiPARP), a mono (ADP-ribosyl) transferase (MART), MARylates its substrate -tubulin in ovarian cancer cells, promoting destabilization of microtubules, cell growth, and migration. Recent development of RBN-2397, a potent inhibitor that selectively acts on PARP7, has provided a new tool for exploring the role of PARP7 catalytic activity in biological processes. In this study, we investigated the role of PARP7 catalytic activity in the regulation of ovarian cancer cell biology via MARylation of -tubulin. MethodsOvarian cancer cell lines (OVCAR4, OVCAR3) were treated with RBN-2397 and paclitaxel, both separately and in combination. Western blotting and immunoprecipitation confirmed the effects of RBN-2397 on -tubulin MARylation and stabilization. Cell proliferation and migration were assessed, and -tubulin stabilization was quantified using immunofluorescent imaging. RNA-sequencing was performed to assess the effects on gene expression changes. ResultsRBN-2397 inhibited PARP7 activity, decreasing -tubulin MARylation, leading to its stabilization, and reducing cancer cell proliferation and migration. The addition of paclitaxel further enhanced these effects, highlighting a synergistic interaction between the two drugs. Mutating the site of PARP7-mediated MARylation on -tubulin similarly resulted in microtubule stabilization and decreased cell migration in the presence of paclitaxel. ConclusionsThis study demonstrates that targeting PARP7 with RBN-2397, particularly in combination with paclitaxel, offers an effective strategy for inhibiting aggressive ovarian cancer cell phenotypes. Our findings underscore the potential of combining PARP7 inhibitors with established chemotherapeutics to enhance treatment efficacy in ovarian cancer.

cancer biology↗

bioRxiv2021

Small molecule allosteric inhibitors of RORγt block Th17-dependent inflammation and associated gene expression in vivo.

Retinoic acid receptor-related orphan nuclear receptor (ROR) {gamma}t is a member of the RORC nuclear hormone receptor family of transcription factors. ROR{gamma}t functions as a critical regulator of thymopoiesis and immune responses. ROR{gamma}t is expressed in multiple immune cell populations including Th17 cells, where its primary function is regulation of immune responses to bacteria and fungi through IL-17A production. However, excessive IL-17A production has been linked to numerous autoimmune diseases. Moreover, Th17 cells have been shown to elicit both pro- and anti-tumor effects. Thus, modulation of the ROR{gamma}t/IL-17A axis may represent an attractive therapeutic target for the treatment of autoimmune disorders and some cancers. Herein we report the design, synthesis and characterization of three selective allosteric ROR{gamma}t inhibitors in preclinical models of inflammation and tumor growth. We demonstrate that these compounds can inhibit Th17 differentiation and maintenance in vitro and Th17-dependent inflammation and associated gene expression in vivo, in a dose-dependent manner. Finally, ROR{gamma}t inhibitors were shown to inhibit tumor formation in pancreatic ductal adenocarcinoma (PDAC) organoids.

immunology↗