Biology subjects

Sampat, K.

Publications and source records attributed to Sampat, K..

4 recordsLinked to original sources

bioRxiv2026

BET BD2 inhibition facilitates SPOP-mediated degradation of chromatin-associated BRD4/BRD4-NUT, a therapeutic vulnerability in NUT carcinoma

BET bromodomain inhibitors block binding of BET family bromodomains 1 and 2 (BD1, BD2) to chromatin and have demonstrated clinical activity in NUT carcinoma (NC), a BRD-NUT fusion-driven cancer, but toxicity from BD1 inhibition has limited their effectiveness. We investigated whether selective inhibition of BRD4 bromodomain 2 (BD2) could retain antitumor activity while reducing toxicity. NC cells were uniquely sensitive to the novel BRD4-BD2 inhibitor DC-9476 and other BD2-selective inhibitors, which induced differentiation and growth arrest. A CRISPR knockout screen identified the BRD4-targeting E3 ligase SPOP as the top resistance hit. BD2 inhibition, but not BD1-selective or pan-BET inhibition, triggered SPOP-dependent proteasomal degradation of BRD4 and BRD4-NUT; SPOP loss prevented degradation and largely rescued BD2 inhibitor-induced differentiation and growth arrest. Unexpectedly, BRD4 and BRD4-NUT remained chromatin-associated during BD2 inhibition, whereas BD1 or pan-BET inhibition displaced them. Together with evidence that ectopic BRD4-NUT expression sensitizes BRD4 to degradation, these findings support a model in which BRD4-NUT megadomains create a high-density, degradation-competent SPOP substrate pool of BRD4 and BRD4-NUT upon BD2 inhibition, whereas pan-BET inhibition disperses this substrate and limits efficient degradation. In preclinical NC models, BD2-selective inhibition achieved greater tumor growth inhibition and survival benefit than pan-BET inhibition, revealing a therapeutic vulnerability.

cancer biology↗

bioRxiv2026

NSD3 stabilizes nuclear compartmentalization and promotes megabase-scale chromatin interactions

Identifying biomolecules that shape nuclear organization is essential for understanding gene regulation in health and disease. Oncogenic fusion proteins rewire chromosome folding and generate biomolecular condensates, but the cofactors of oncoprotein-driven chromatin regulation remain poorly defined, and whether such factors have analogous functions in fusion-naive cells is unknown. We find that NSD3 mediates chromosome folding in fusion-positive and fusion-negative cells. NSD3 stabilizes the BRD4-NUT fusion oncoprotein on chromatin, promotes histone H3K36me2, and supports oncogene expression while maintaining BRD4-NUT nuclear condensates. NSD3 loss attenuates distant chromatin interactions between BRD4-NUT megadomains both within and between chromosomes. In cells lacking BRD4-NUT, the short, catalytically inactive isoform of NSD3, NSD3short, promotes chromatin contacts separated by multiple megabases. The ability of NSD3short to promote long-range chromatin contacts requires its PWWP domain. By combining chromatin structural analyses in fusion-positive and fusion-negative cells, we show that interrogating fusion oncoprotein-driven chromosome misfolding reveals the multicomponent basis of nuclear compartmentalization and uncovers an adaptor protein that promotes chromatin contacts independent of enzymatic activity.

molecular biology↗

bioRxiv2025

Biological insights and methodological challenges learned from working with a diverse heterotrophic marine bacterial library

BackgroundOrganized collections of bacterial strains can help bridge the gap between studying model organisms and communities, through comparative experiments between genetically and phenotypically diverse strains. We describe the establishment and initial characterization of a library of 62 marine heterotrophic bacteria, selected to represent a significant fraction of the genome-encoded functional diversity and a wide range of known phytoplankton-bacteria interactions. We focus on important but often undiscussed aspects of collecting and maintaining such a library, verifying strain identity, and applying classical microbiological methods across diverse strains. ResultsCultured strains contain up to hundreds of mutations compared with the reference genomes, with non-synonymous mutations in rpoB and/or rpoC genes observed in [~]15% of the cultures. Most strains grow well at 25{degrees}C, but the dependence of growth rate on temperature and the width of the temperature niche vary between strains in a systematic manner. We describe steps towards designing a universal, defined, minimal media for marine bacteria, revealing that growth inhibition on amino acids and peptides by carbohydrates is widespread. Cell counts obtained from flow cytometry and colony plating differ systematically, as do different methods to assess motility. Finally, we discuss traits potentially related to microbial interactions such as hemolysis, biofilm formation, and antibiotic resistance. Gammaproteobacteria such as Alteromonas, Pseudoalteromonas, and Vibrio reveal consistently robust growth, and activity, perhaps explaining why these clades are well-explored. ConclusionExplicitly discussing the insights and challenges of working with strain libraries will pave the way to robust, reproducible, and generalizable mapping of bacterial traits across diversity.

microbiology↗

bioRxiv2018

CDK inhibitors reduce cell proliferation and reverse hypoxia-induced metastasis of neuroblastoma tumours in a chick embryo model

Neuroblastoma is a paediatric cancer with a poor prognosis. This is in part due to the widespread metastasis at time of presentation, which is refractory to current treatment modalities. New therapeutic agents that can control not only tumour growth but also metastasis are urgently needed.\n\nOne current therapeutic option used in the clinic is differentiation therapy with retinoic acid, where the terminal differentiation of the neuroblastoma cells reduces tumour growth in the primary tumour as well as at metastatic sites. However, retinoic acid only works in a subset of patients.\n\nWe investigated the potential of CDK inhibitors on neuroblastoma cell differentiation, tumour progression and metastasis by utilising a 3R compliant cost effective preclinical chick embryo model. In both SK-N-AS and BE(2)C cell lines, when engrafted on the chorioallantoic membrane of chick embryos, we observed a reduction of tumour cell proliferation as well as a reduction in hypoxia preconditioning-driven metastasis by 60%. In addition, the expression of a panel of genes with known roles in metastasis, which increased upon hypoxia-preconditioning, was largely reduced by a CDK1 inhibitor. These results provide a promising alternative to currently existing therapies and might aid the development of new treatment protocols for retinoic acid-resistant patients.

cancer biology↗