Picking needles in a haystack: Exploring rare variants of a pan-cancer target in the RET landscape from 229,453 adult cancer patients.

Abstract

3150 Background: Advances in precision oncology have led to the approval of tumor-agnostic therapies, and RET, due to its role as a driver of oncogenesis across multiple tumor types, is increasingly recognized as a pan-cancer target. RET alterations, including mutations and fusions, are relatively rare events, however, potent and selective RET inhibitors such as selpercatinib and pralsetinib have demonstrated remarkable efficacy and changed clinical practice in RET-driven NSCLC, thyroid cancer and other cancers. Here, we present a comprehensive analysis of RET alterations in pan-cancer adult malignancies. Methods: 229,453 samples from 196,244 patients available from AACR Project GENIE v.17 database were analyzed for the prevalence of RET mutations, fusions and copy number alterations in a range of cancer types. Results: A total of 7011 separate RET alterations were identified in 6690 separate pts (3%), including 660 fusions (9.4%), 5553 missense mutations (79.2%), 373 splice site mutations (5.3%), 339 truncating mutations (4.8%), 86 in-frame mutations (1.2%). Most frequent tumor types included NSCLC, colorectal cancer, melanoma, thyroid cancer, endometrial cancer and glioma (23%, 12.2%, 9.5%, 6.6%, 6.4%, 5.3% identified RET alterations, respectively). RET fusions were observed in 0.3% of tumor samples, most identified in NSCLC, thyroid and colorectal cancer (53%, 24% and 4% of identified RET fusions). Most fusions were considered driver events using OncoKB database (632, 96%);frequent fusion gene partners included KIF5B, CCDC6, NCOA4 , and intragenic events (34%, 25%, 9.7%, 8% of 660 fusion samples). Of the 5553 missense mutations, most (89%) were considered variants of uncertain significance; 605 (11%) were considered oncogenic or likely oncogenic. Oncogenic missense mutations occurred across codons, most frequently involving codon 918 (n = 215, 36%; M918M/K/T/V), 648 (n = 41, 6.8%; V648I/A), 886 (n = 28, 4.6%; R886W/Q/L), 630 (n = 21, 3.5%; C630G/R/S/F/Y/W), 891 (n = 31, 5%, S891A/L/W). Documented on-target drivers of multi-kinase RET inhibitor resistance gatekeeper mutations (V804M/L), and selective RET inhibitor resistance mutations were noted in 61 samples, including G810C/S substitutions, solvent-front mutations K809R/N, activation loop mutations Y806C/N (33%, 53%, 3%, 3% of identified samples); most were classified as oncogenic or likely oncogenic (85%). Conclusions: RET fusions are rare events across cancers; however, most are characterized as oncogenic. RET missense mutations occur in 2.4% of malignancies, and while most RET missense variants are described as variants of uncertain significance, oncogenic RET variants are diverse, occurring across codons. We confirm multiple documented oncogenic drivers of on-target resistance, and their distinct and diverse mechanisms underline the urgent need to develop next generation RET inhibitors.