A four-tier classification system for studying homologous recombination repair gene reversion mutations as a mechanism of resistance to PARP inhibitors and platinum chemotherapy.

Abstract

3140 Background: Pathogenic mutations in homologous recombination repair (HRR) genes are highly associated with the oncogenesis of multiple cancers and represent favorable biomarkers for platinum (Pt)-based chemotherapy and poly ADP ribose polymerase inhibitors (PARPi). While the development of drug resistance by restoring protein function via secondary mutation is commonly observed, a thorough analysis of the landscape of HRR gene reversion mutation is lacking. Methods: A real-world database with ~13,000 pan-cancer patients who underwent targeted next-generation sequencing and contained a primary germline or somatic pathogenic mutation of 25 pre-defined HRR genes, including ATM, ATR, BARD1, BLM, BRCA1, BRCA2, BRIP1, CDK12, CHEK1, CHEK2, ERCC3, FANCA, FANCC, FANCD2, FANCI, FANCL, MRE11A, NBN, PALB2, RAD51, RAD51C, RAD51B, RAD51D, RAD54L, and WRN, was used to identify HRR secondary mutations, which were further classified into four tiers by mutation type and intended reversion mechanism. Patient’s clinical data and treatment history were retrospectively reviewed. Results: The potential mechanism of HRR gene reversion was categorized into four tiers, including Tier 1 (single nucleotide variation, SNV), Tier 2 (frameshift), Tier 3 (deletion), and Tier 4 of other mutation types that were not further discussed in this study. A total of 42 patients were identified with Tier 1/2/3 secondary HRR gene mutations in the presence of a primary pathogenic germline (N = 32) or somatic (N = 10) mutation. BRCA1 (15/42, 35.7%) and BRCA2 (23/42, 54.8%) were most frequently observed in this cohort with significant enrichment of exon 11 aberrations of both genes. The other HRR genes identified of Tier 1/2/3 reversion mutations included PALB2 (N = 3, Tier 3) and RAD51D (N = 1, Tier 1). More specifically, a majority of BRCA1 reversion mutations (8/15) were Tier 1 SNV, while the most prevalent reversion mechanism for BRCA2 was Tier 3 deletion, which accounted for 60.9% (14/23) of all BRCA2 cases with a median deleted length of 1164 bp (range: 153 – 6745 bp). Furthermore, we reported the treatment history data of three cancer patients (pancreatic, prostate, and lung, respectively) demonstrated the acquisition of BRCA2 reversion mutations (Tier 2 and Tier 3) at post-Pt/Olaparib in the presence of a primary germline BRCA2 pathogenic mutation, strongly suggestive of the role of reversion mutations in driving resistance to Olaparib or Pt-chemotherapy. Conclusions: Owing to a large-scale real-world dataset, we retrospectively investigated the landscape of the reversion mechanism of HRR genes and established a four-tier classification system for secondary HRR mutations in the presence of primary germline/somatic pathogenic HRR mutations. This study is of great clinical value in studying mechanisms of drug resistance to Pt-chemotherapy and PARPi.