Abstract 2927: Proteogenomic heterogeneity in metastatic lung adenocarcinoma revealed from rapid/warm autopsy

Abstract

Abstract Introduction: Intratumor heterogeneity has been characterized among multiple cancer types. However, in lung adenocarcinoma, recent work has been limited to early stage primary tumors and intertumor heterogeneity has not been well-studied. Most importantly, an integrated tumor heterogeneity analysis at the level of somatic variants, copy number, transcript and protein expression, and the phosphoproteome is outstanding. Methods: In order to characterize both intra-tumor and inter-tumor heterogeneity of metastatic lung adenocarcinoma, we applied whole exome sequencing, RNA-seq, CNV-seq and mass spectrometry-based proteomic analyses on 33 tumor regions from metastatic sites including lung, liver and kidney, obtained by rapid/warm autopsy from 4 patients with Stage IV lung adenocarcinoma. The autopsy procedure was initiated between 2-4 hours of death. Results: We found considerable intertumor heterogeneity with organ-specific, branched evolution that was consistent across DNA, RNA and protein analyses. Intratumor heterogeneity differed depending on oncogene-status: oncogene-negative tumors (without RTK/RAS/RAF mutations or known fusion gene) had significantly higher genomic intratumor heterogeneity than oncogene positive tumors. The degree of heterogeneity at the genomic and proteomic level was patient-specific. The proteomic analysis complemented genomic variants-based clonal evolution analysis. High-confidence driver mutations (KRAS, EGFR, TP53, CTNNB1) uniformly occurred early in the evolution of metastatic lung adenocarcinoma consistent with the concept of these mutations as likely ‘founders’. In contrast, other known driver mutations occurred more often in later stages among specific organ branches. Notably, oncogene-negative tumors carried significantly more driver mutations than oncogene-positive tumors suggesting that genomic alterations may have a larger role in the metastatic process versus the early evolution of lung adenocarcinoma in oncogene-negative vs. oncogene-positive tumors. Among all patients, lung cancer specific focal copy number alterations frequently occurred within metastatic branch points. Single metastatic site biopsies would therefore be unlikely to capture all significant driver mutations and copy number alterations, particularly among oncogene-negative tumors. Conclusion: Metastatic lung adenocarcinoma evolves through a branched, organ-specific, process with acquisition of significant driver mutations and copy number changes, particularly among oncogene-negative tumors. The branched evolution is ultimately influenced by proteomic and phosphoproteomic alterations affecting key signaling pathways that may not be always a result of genomic changes. Citation Format: Nitin Roper, Tapan K. Maity, James Gao, Abhilash Venugopalan, Xu Zhang, Romi Biswas, Constance Cultraro, David Kleiner, Stephen Hewitt, Javed Khan, Guha Udayan. Proteogenomic heterogeneity in metastatic lung adenocarcinoma revealed from rapid/warm autopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2927. doi:10.1158/1538-7445.AM2017-2927