Identification of super-enhancer-driven peptidyl arginine deiminases as potential biomarkers and therapeutic targets for osimertinib-resistant non-small cell lung cancer

Abstract

Resistance to targeted drugs is now a challenging clinical problem in the treatment of non-small cell lung cancer (NSCLC). So far, there are no approved targeted therapeutic drugs for patients with disease progression after the third-generation epidermal growth factor receptor-tyrosine kinase inhibitor osimertinib resistance (OR). Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive gene expression. In this study, we aimed to explore the potential pathogenic SEs and their driven genes in OR NSCLC. OR cell line was established by exposure of H1975 cells to incremental dosing of osimertinib. RNA-sequencing and H3K27ac ChIP-sequencing were used to identify the differential expressed genes (DEGs) and SEs in parental and resistant cells. Gene ontology analysis for the OR-specific SEs-associated genes showed that histone citrullination, protein citrullination, and peptidyl-arginine modification are the top three biological processes, and the DEGs involved in these biological processes, including peptidyl arginine deiminase 1 (PADI1), PADI2, and PADI3. Realtime-PCR and western blot detections confirmed these genes were highly expressed in OR cells. SE inhibitor decreases their expression, ensuring that SEs regulate their transcriptional expressions. The PADI inhibitor inhibited OR cells’ proliferation, invasion, and colony formation. This study demonstrates that SE-driven PADI family genes are potential biomarkers and targets for OR NSCLC.

Peptidylarginine Deiminase 3 Modulates Response to Neratinib in HER2 Positive Breast Cancer

“…On the other hand, gain of function experiments carried out by overexpressing PADI3 in BT474 cells resulted in resistance to the antitumoral action of neratinib, supporting the concept that increased levels of PADI3 may provoke resistance to the drug. Other authors have demonstrated resensitization of NSCLC cells to osimertinib, a TKI against EGFR, after inhibiting PADI1, 2 and 3 with Cl-amidine (27). However, we are not aware of any studies that have demonstrated the involvement of these enzymes in the acquisition of resistance to any drug used in the therapy of HER2 + breast cancer.…”

“…Peptidylarginine deiminases (PADs) are a group of calcium-dependent enzymes that catalyze the post-translational conversion of arginine to citrulline, leading to changes in protein structure and function (22)(23)(24). Several studies have already demonstrated their involvement in the process of tumorigenesis or tumor progression (25)(26)(27). The 5 family members (PADI1, 2, 3, 4 and 6) have distinct substrate a nities and tissue-speci c expression patterns (28).…”

“…Although the role of PADI3 in tumorigenesis is still not entirely clear (26), different studies have shown its involvement in several processes that could justify its function as an oncogene (24,27,29). These actions include (i) activation of glycolysis through PKM2 citrullination, favoring cancer cell proliferation, (ii) epigenetic modi cations due to citrullination of histones that regulate chromatin status, and (iii) direct regulation of enzymes involved in the transcription of genes related to cell migration, invasion, and survival.…”