Genomic landscape and immune phenotype of malignant pleural mesothelioma.

Abstract

9056 Background: Malignant pleural mesothelioma (MPM) is a relatively uncommon malignancy with poor prognosis and no major therapeutic breakthroughs over the past decade. Better understanding of the genomic landscape and distribution of immune biomarkers in this disease has the potential to enable development of novel therapies. Methods: We analyzed molecular profiles of 222 MPM tumors using next-generation sequencing of 592 genes utilizing Caris Life Sciences platform. Genes were grouped into pathways: DNA damage repair (DDR) ( ATM, BRCA2, BRIP1, BAP1, CHEK2, ERCC2, FANCA/D2/E/L, MLH1, MSH6, MUTYH, NBN, PMS2, RAD50/51B, WRN), cell cycle regulation including TP53 ( RB1,CCNE1, CDKN2A, CCND1, CCND3, CDKN1B), chromatin remodeling (CR) ( ARID2, ASXL1, DNMT3A, EP300, EZH2, KDM6A, KMT2C, KMT2D, NSD3, PBRM1, SMARCB1/A4, SETD2), RAS/MAPK ( KRAS, MAP2K1, NF1, NF2), and PI3K/AKT ( AKT, PIK3CA, PIK3R1/R2, PTEN, RICTOR, TSC1, TSC2, ZNF703). Tumor mutational burden (TMB), PD-L1 expression (SP142 IHC, tumor staining), and MSI/MMR were analyzed. Seventy-two cases also had whole transcriptome sequencing data. Differences in alterations were compared for age, gender, and pathways. Results: Median age of patients (pts) was 72 yr (range, 37-90), 73% were male. Gene pathway alterations were seen in 81% of cases. DDR, specifically homologous recombination (HR), was the most commonly mutated pathway (36.9%), followed by RAS (25.2%) and CR (18.9%). Genes mutated in ≥5% of cases included BAP1 (26.3%), NF2 (23.5%), TP53 (15.5%), SETD2 (10.2%). PD-L1 was high (≥50% tumor cells positive) in 11.4% (n = 24), intermediate (1-49%) in 31.4% (n = 66), and negative ( < 1%) in 57.1% (n = 120) pts. TMB was high (≥10 mutations/Mb) in 9.6% of tumors (n = 20). None of the tumors were dMMR/MSI-H. HR gene BAP1 and CR gene SETD2 mutations trended to be more prevalent in pts ≥70 yo (p = 0.02). CR trended to be more commonly mutated in females (p = 0.02). No other significant differences were found in specific gene/pathway alterations, PD-L1 expression, or TMB in the context of age and gender. Distribution of PD-L1 expression was not different among various pathways. No highly recurrent, targetable fusion isoforms were seen among the 85 identified (mean 1.1 fusions/tumor), which have not yet been characterized for pathogenicity. Conclusions: The majority of MPM tumors harbor alteration in one of the key cellular pathways. HR pathway mutations are the most common. The majority of tumors were PD-L1 negative and carry low TMB indicating low immunogenicity. No age and gender specific differences exist except for BAP1 and SETD2 mutations.