Pan-sarcoma analysis of DNA damage response pathway alterations and deficiency.
Authors: Bialick Steven , Statz-Geary Kurt , Elliott Andrew , Abraham Jim , Walker Phillip , Espejo-Freire Andrea P. , Barreto Coelho Priscila , Costa Philippos Apolinario , Leu Kirsten , von Mehren Margaret , D'Amato Gina Z. , Jonczak Emily , Trent Jonathan C. , Rosenberg Andrew , Dhir Aditi 
Published: June 2022

11548

Background: Alterations in DNA damage response (DDR) pathways contribute to genomic instability and malignant progression and have been shown to be of clinical significance in several carcinomas and solid tumors. While some studies have identified ostensibly pathogenic variations in known and novel cancer genes with implications for sarcoma risk and treatment opportunities, there is limited information regarding the role of DDR pathway alterations in sarcoma. We identified a gene alteration in ERCC2, a gene that codes for a DNA helicase in the nucleotide excision repair pathway, in a patient with multiply relapsed epithelioid sarcoma (ES), prompting an investigation of DDR pathway alterations in sarcoma samples using a global next-generation sequencing (NGS) platform. Methods: Sarcoma patient samples (N = 5310), representing 38 pediatric and adult histologic subtypes, underwent NGS of DNA (592 gene panel or whole exome) and RNA (whole transcriptome sequencing, N = 3612) at a CLIA-certified laboratory (Caris Life Sciences, Phoenix, AZ). A threshold of 10 mut/Mb was used to identify high tumor mutational burden (TMB-H). IHC was performed for PD-L1 (SP142; 2+|5% = positive). Homologous recombination deficiency (HRD) scores were calculated as a composite of loss of heterozygosity, telomeric allelic imbalance, and large-scale transitions, using a positive threshold of 42 (N = 2138). HRD score association with biomarker status was evaluated overall and in sarcoma subtypes. Results: A pathogenic DDR pathway mutation was noted in 842 (15.9%) of the total samples. ATRX was by far the most commonly altered DDR gene (10% of all samples), with mutations observed across 25 sarcoma subtypes (11 subtypes with > 10% mutation rate: leiomyosarcoma [LMS], perivascular epithelioid cell tumor [PEComa], pleomorphic sarcoma [PLSARC], uterine sarcoma [OUSARC], osteosarcoma, spindle cell sarcoma, angiosarcoma, mesenchymal chondrosarcoma, sarcoma NOS, fibrosarcoma and ES). CHEK2, ATM, and MUTYH mutations were observed in 1-2% of sarcoma samples. More than 20 histologic subtypes showed distinct gene signatures with mutations occurring in > 3% of the samples investigated. ERCC2 was mutated in 3% of ES and 6.5% in PEComa. Median HRD scores ranged between 20-58 across sarcoma subtypes. High rates of deficient HRD (HRDd ≥ 42) were observed in PLSARC (83.2%), OUSARC (73.7%), and dedifferentiated chondrosarcoma (71.4%), while low rates of HRDd were observed in Ewing sarcoma (0%) and clear cell sarcoma (10%). In the overall cohort, ERCC2, ATRX and BRCA2 were significantly associated with increased HRD scores (p = 0.01). Conclusions:DDR pathway alterations are present in numerous histologic subtypes of sarcoma. A more comprehensive analysis of individual histologic subtypes is in progress. Further research will evaluate the clinical implications of these known and novel mutations to guide risk stratification and potential therapeutic options.