Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues

Jennifer G. Abelin (), Erik J. Bergstrom, Keith D. Rivera, Hannah B. Taylor, Susan Klaeger, Charles Xu, Eva K. Verzani, C. Jackson White, Hilina B. Woldemichael, Maya Virshup, Meagan E. Olive, Myranda Maynard, Stephanie A. Vartany, Joseph D. Allen, Kshiti Phulphagar, M. Harry Kane, Suzanna Rachimi, D. R. Mani, Michael A. Gillette, Shankha Satpathy, Karl R. Clauser, Namrata D. Udeshi () and Steven A. Carr ()
Additional contact information
Jennifer G. Abelin: Broad Institute of Massachusetts Institute of Technology and Harvard
Erik J. Bergstrom: Broad Institute of Massachusetts Institute of Technology and Harvard
Keith D. Rivera: Broad Institute of Massachusetts Institute of Technology and Harvard
Hannah B. Taylor: Broad Institute of Massachusetts Institute of Technology and Harvard
Susan Klaeger: Broad Institute of Massachusetts Institute of Technology and Harvard
Charles Xu: Broad Institute of Massachusetts Institute of Technology and Harvard
Eva K. Verzani: Broad Institute of Massachusetts Institute of Technology and Harvard
C. Jackson White: Broad Institute of Massachusetts Institute of Technology and Harvard
Hilina B. Woldemichael: Broad Institute of Massachusetts Institute of Technology and Harvard
Maya Virshup: Broad Institute of Massachusetts Institute of Technology and Harvard
Meagan E. Olive: Broad Institute of Massachusetts Institute of Technology and Harvard
Myranda Maynard: Broad Institute of Massachusetts Institute of Technology and Harvard
Stephanie A. Vartany: Broad Institute of Massachusetts Institute of Technology and Harvard
Joseph D. Allen: Broad Institute of Massachusetts Institute of Technology and Harvard
Kshiti Phulphagar: Broad Institute of Massachusetts Institute of Technology and Harvard
M. Harry Kane: Broad Institute of Massachusetts Institute of Technology and Harvard
Suzanna Rachimi: Broad Institute of Massachusetts Institute of Technology and Harvard
D. R. Mani: Broad Institute of Massachusetts Institute of Technology and Harvard
Michael A. Gillette: Broad Institute of Massachusetts Institute of Technology and Harvard
Shankha Satpathy: Broad Institute of Massachusetts Institute of Technology and Harvard
Karl R. Clauser: Broad Institute of Massachusetts Institute of Technology and Harvard
Namrata D. Udeshi: Broad Institute of Massachusetts Institute of Technology and Harvard
Steven A. Carr: Broad Institute of Massachusetts Institute of Technology and Harvard

Nature Communications, 2023, vol. 14, issue 1, 1-22

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-37547-0

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