Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens

• Published in: Frontiers in immunology Vol. 12; p. 765898
• Main Authors: Whiteaker, Jeffrey R., Lundeen, Rachel A., Zhao, Lei, Schoenherr, Regine M., Burian, Aura, Huang, Dongqing, Voytovich, Ulianna, Wang, Tao, Kennedy, Jacob J., Ivey, Richard G., Lin, Chenwei, Murillo, Oscar D., Lorentzen, Travis D., Thiagarajan, Mathangi, Colantonio, Simona, Caceres, Tessa W., Roberts, Rhonda R., Knotts, Joseph G., Reading, Joshua J., Kaczmarczyk, Jan A., Richardson, Christopher W., Garcia-Buntley, Sandra S., Bocik, William, Hewitt, Stephen M., Murray, Karen E., Do, Nhan, Brophy, Mary, Wilz, Stephen W., Yu, Hongbo, Ajjarapu, Samuel, Boja, Emily, Hiltke, Tara, Rodriguez, Henry, Paulovich, Amanda G.
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 11.11.2021
• Subjects: Antibodies - analysis; Antibodies - immunology; Blotting, Western; cancer; Cell Line, Tumor; Chromatography, Liquid - methods; correlative biomarkers; HeLa Cells; Humans; immuno-MRM; Immunology; immunotherapy; Jurkat Cells; mass spectrometry; Mass Spectrometry - methods; MCF-7 Cells; Peptides - analysis; Peptides - blood; Peptides - immunology; Proteome - analysis; Proteome - genetics; Proteome - immunology; Proteomics - methods; Reproducibility of Results; RNA-Seq - methods; Specimen Handling - methods; mass spectrometry; cancer; immuno-MRM; correlative biomarkers; immunotherapy
• ISSN: 1664-3224; 1664-3224
• DOI: 10.3389/fimmu.2021.765898

Immunotherapies are revolutionizing cancer care, producing durable responses and potentially cures in a subset of patients. However, response rates are low for most tumors, grade 3/4 toxicities are not uncommon, and our current understanding of tumor immunobiology is incomplete. While hundreds of immunomodulatory proteins in the tumor microenvironment shape the anti-tumor response, few of them can be reliably quantified. To address this need, we developed a multiplex panel of targeted proteomic assays targeting 52 peptides representing 46 proteins using peptide immunoaffinity enrichment coupled to multiple reaction monitoring-mass spectrometry. We validated the assays in tissue and plasma matrices, where performance figures of merit showed over 3 orders of dynamic range and median inter-day CVs of 5.2% (tissue) and 21% (plasma). A feasibility study in clinical biospecimens showed detection of 48/52 peptides in frozen tissue and 38/52 peptides in plasma. The assays are publicly available as a resource for the research community.