Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues
Jennifer G. Abelin, Erik J. Bergstrom, Keith Rivera, Hannah B. Taylor, Susan Klaeger, Charles Xu, Eva K. Verzani, C. Jackson White, Hilina Woldemichael, Maya Virshup, Meagan E. Olive, Myranda Maynard, Stephanie Vartany, Joseph D. Allen, Kshiti Meera Phulphagar, M. Harry Kane, Suzanna Rachimi, D.R. Mani, Michael A. Gillette, Shankha Satpathy, Karl R. Clauser, Namrata D. Udeshi, Steven A. Carr
Abstract
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each 'ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.