Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition

Abstract

Chemoresistance is the norm in pancreatic ductal adenocarcinoma (PDAC) leading to an abysmal five-year survival rate of less than 10%. We performed genome-wide CRISPR activation (CRISPRa) and CRISPR knock out (CRISPRko) screens to identify mechanisms of resistance to four cytotoxic chemotherapies (gemcitabine, 5-fluorouracil, irinotecan, and oxaliplatin) used to treat PDAC patients in two PDAC cell lines. Mirroring patient treatment outcomes, we found that multi-drug resistance genes were more likely to be associated with patient survival. We identified activation of ABCG2, a well-described efflux pump, as the most consistent resistance gene in four drugs and two cell lines. Small molecule inhibitors of ABCG2 restored sensitivity to chemotherapy. Our screen demonstrated that activation of members of the hemidesmisome complex and transcriptional repressor complexes conferred resistance to multiple drugs. Finally, we describe an approach for applying our results to predict drug sensitivity in PDAC tumors and cell lines based on gene expression.

Genomic analysis reveals HDAC1 regulates clinically relevant transcriptional programs in pancreatic cancer

“…Increased expression of CD44 , a cell surface protein important for cell adhesion and migration, is associated with a more mesenchymal-like phenotype which is characteristic of EMT 19 . This is in agreement with our finding that CD44 transcript and protein are more abundant in cells with HDAC1 overexpression and our past work showing that HDAC1 OE leads to increased migration 9 .…”

“…HDAC1 expression has been previously linked to increased cellular resistance to cytotoxic chemotherapeutic drugs 9 . To further evaluate the effects of HDAC1 overexpression on chemotherapeutic resistance, we used CRISPRa 17 to generate a stable MIA PaCa-2 cell line (MP2_HDAC1_OE) expressing HDAC1 at ~3 times the levels of the levels of the control line (MP2_NTC) which expresses a non-targeting control guide ( Extended Data Fig.…”

“…We previously demonstrated that overexpression of HDAC1 contributes to multidrug resistance in pancreatic cancer cells 9 . HDAC1 participates in several remodeling complexes including Sin3A, NuRD, and CoREST 10 .…”

ABI2‐mediated MEOX2/KLF4‐NANOG axis promotes liver cancer stem cell and drives tumour recurrence

“…CRISPR screening uncovered that ABI2 is a key determinant of multiple drug resistance in pancreatic cancer cells. 17 Kyoung Lim's research demonstrated that the Doxo-induced HCC cell senescence can be attenuated by TIS21 through inhibiting linear actin nucleation, which is regulated by Nox4-ROS-ABI2-DRF signal cascade. 18 These studies indicated that ABI2 might play a crucial role in drug resistance and relapse of tumour.…”