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Tables S6-S9 from Improvement of Tumor Neoantigen Detection by High-Field Asymmetric Waveform Ion Mobility Mass Spectrometry

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posted on 2024-08-01, 07:23 authored by Wei Meng, Yoshiko Takeuchi, Jeffrey P. Ward, Hussein Sultan, Cora D. Arthur, Elaine R. Mardis, Maxim N. Artyomov, Cheryl F. Lichti, Robert D. Schreiber

Table S6: Identification of mLama4 from ICT-naive T3 tumors. Table S7: Identification of mLama4 from ICT-treated T3 tumors. Table S8: Identification of mItgb1 from sorted CD45+ T3 TILs. Table S9: Identification of I-Ab bound peptides from ICT-treated T3 tumors.

Funding

Parker Institute for Cancer Immunotherapy (PICI)

National Cancer Institute (NCI)

United States Department of Health and Human Services

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ARTICLE ABSTRACT

Cancer neoantigens have been shown to elicit cancer-specific T-cell responses and have garnered much attention for their roles in both spontaneous and therapeutically induced antitumor responses. Mass spectrometry (MS) profiling of tumor immunopeptidomes has been used, in part, to identify MHC-bound mutant neoantigen ligands. However, under standard conditions, MS-based detection of such rare but clinically relevant neoantigens is relatively insensitive, requiring 300 million cells or more. Here, to quantitatively define the minimum detectable amounts of therapeutically relevant MHC-I and MHC-II neoantigen peptides, we analyzed different dilutions of immunopeptidomes isolated from the well-characterized T3 mouse methylcholanthrene (MCA)-induced cell line by MS. Using either data-dependent acquisition or parallel reaction monitoring (PRM), we established the minimum amount of material required to detect the major T3 neoantigens in the presence or absence of high field asymmetric waveform ion mobility spectrometry (FAIMS). This analysis yielded a 14-fold enhancement of sensitivity in detecting the major T3 MHC-I neoantigen (mLama4) with FAIMS-PRM compared with PRM without FAIMS, allowing ex vivo detection of this neoantigen from an individual 100 mg T3 tumor. These findings were then extended to two other independent MCA-sarcoma lines (1956 and F244). This study demonstrates that FAIMS substantially increases the sensitivity of MS-based characterization of validated neoantigens from tumors.

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Keywords

Immunology Tumor antigens/neoantigens Immunotherapy Cancer vaccines Checkpoint blockade

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