Deciphering the phenotypic heterogeneity and drug response in cancer cells using genome-wide activity and interaction of chromatin domains.

Pandey, N.; Sharma, M.; Mathur, A.; Nzelu, G. A.; Hakimullah, M.; Jha, I. P.; Chandra, O.; Mishra, S.; Sharma, A.; Foo, R.; Mandoli, A.; DasGupta, R.; KUMAR, V.

doi:10.1101/2023.01.15.524115

bioRxiv · 10.1101/2023.01.15.524115

Deciphering the phenotypic heterogeneity and drug response in cancer cells using genome-wide activity and interaction of chromatin domains.

Pandey, N.·Sharma, M.·Mathur, A.·Nzelu, G. A.·Hakimullah, M.·Jha, I. P.·Chandra, O.·Mishra, S.·Sharma, A.·Foo, R.·Mandoli, A.·DasGupta, R.·KUMAR, V.

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Abstract

The effect of co-localization of genes in the topologically associated domains (TADs) and their activity as a regulatory unit in cancer samples and cells, together with drug-response, needs comprehensive analysis. Here, we analyzed the activity of TADs using cancer-cell transcriptomes along with chromatin-interaction and epigenome profiles to understand their relationship with drug-response. Our analysis of 819 cancer cell-line transcriptomes revealed that their response to multiple drugs was more correlated with the activity of individual TADs than genes. Applying our approach to 9014 cancer patients data (20 different cancer types) also revealed a higher association between survival and the activity of thousands of individual TADs in comparison to their genes. CRISPR-mediated knock-out of regulatory sites inside a TAD associated with cisplatin-response of oral cancer cells and discovery of primate-specific gain of synteny of genes within a TAD containing EGFR gene and its contribution towards cancer malignancy demonstrate greater utility of TAD-activity based analysis.

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Pandey, N., Sharma, M., Mathur, A., Nzelu, G. A., Hakimullah, M., Jha, I. P., Chandra, O., Mishra, S., Sharma, A., Foo, R., Mandoli, A., DasGupta, R., KUMAR, V.. 2023-01-18. Deciphering the phenotypic heterogeneity and drug response in cancer cells using genome-wide activity and interaction of chromatin domains.. https://doi.org/10.1101/2023.01.15.524115

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