Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer Cells

Abstract

Precision medicine depends critically on developing treatment strategies that can selectively target cancer cells with minimal adverse effects. Identifying unique transcriptional regulators of oncogenic signaling, and targeting cancer-cell-specific enhancers that may be active only in specific tumor cell lineages, could provide the necessary high specificity, but a scarcity of functionally validated enhancers in cancer cells presents a significant hurdle to this strategy. We address this limitation by carrying out large-scale functional screens for pro-growth enhancers using highly multiplexed CRISPR-based perturbation and sequencing in multiple cancer cell lines. We used this strategy to identify 488 pro-growth enhancers in a colorectal cancer cell line and 22 functional enhancers for the MYC and MYB key oncogenes in an additional nine cancer cell lines. The majority of pro-growth enhancers are accessible and presumably active only in cancer cells but not in normal tissues, and are enriched for elements associated with poor prognosis in colorectal cancer. We further identify master transcriptional regulators and demonstrate that the cancer pro-growth enhancers are modulated by lineage-specific transcription factors acting downstream of growth signaling pathways. Our results uncover context-specific, potentially actionable pro-growth enhancers from cancer cells, yielding insight into altered oncogenic transcription and revealing potential therapeutic targets for cancer treatment.

Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells

“…PLAC-seq library generation and data processing. PLAC-seq libraries were generated and processed as previously described 4 . The promoter interacting sequences (PINS) were identified by MAPS 5 with default parameters and the input data of PLAC-seq and H3K4me3 ChIP-seq (doi:10.17989/ENCSR443YAS for H1, ENCSR813CFB for HFF, and ENCFF699EUP for K562).…”

“…After initial debates 1 , chromatin-associated RNA (caRNA) has been recognized as a "widespread component of interphase chromosomes" rather than artificial degradation products [1][2][3][4][5][6] . Growing evidence confirms that caRNA regulates gene transcription [7][8][9][10][11][12][13][14][15][16] and post-transcriptional RNA processing and localization 17,18 .…”

Oncogenic reactivation of young L1s is a hallmark of colon cancer

“…Here we show that the oncogenic L1 establishes a novel interaction with INSIG2 (Fig. 3g), a gene reported to have prognostic capacity for colon cancer survivorship; its overexpression in cancer cells results in numerous cell phenotypes related to growth, invasion and apoptosis, appearing to suppress the efficacy of chemotherapy 15,16 . Overall, these findings indicate that reactivated young L1s can act as enhancers, altering gene expression.…”

“…A pro-growth enhancer identified from a CRISPRi screen in colon cancer cells 15 overlapped a recurrent L1 active in patient 28. Here we show that the oncogenic L1 establishes a novel interaction with INSIG2 (Fig.…”

Oncoproteins E6/E7 of the Human Papillomavirus Types 16 & 18 Cooperate in Modulating Oncogenes and Tumor Suppressor Proteins in Colorectal Cancer

“…While KRAS is an established oncogene (9)(10)(11)(12)(13)(14), TP53 is a well-known tumor suppressor gene (15)(16)(17)(18)(19)(20). Similarly, numerous other oncogenes and tumor suppressor proteins are known to be differentially modulated in CRC (21,22,31,(23)(24)(25)(26)(27)(28)(29)(30). Evidently, the mutational heterogeneity of CRC is indeed diverse, demanding an assortment of therapeutic strategies to treat the disease.…”