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Volume 14
Issue 5
10.3390/cancers14051243
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Article

Valid-NEO: A Multi-Omics Platform for Neoantigen Detection and Quantification from Limited Clinical Samples

by
Yuri Laguna Terai
1,
Chun Huang
2,
Baoli Wang
3,
Xiaonan Kang
4,
Jing Han
5,
Jacqueline Douglass
6,
Emily Han-Chung Hsiue
6,†,
Ming Zhang
6,
Raj Purohit
1,
Taylor deSilva
1 and
Qing Wang
1,*
1
Complete Omics Inc., Baltimore, MD 21227, USA
2
Department of Lung Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
3
Institute of Endocrinology, Tianjin Medical University Chu Hsien-I Memorial Hospital and Tianjin Institute of Endocrinology, Tianjin 300134, China
4
Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
5
Tianjin Hospital of ITCWM Nankai Hospital, Tianjin 300100, China
6
Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
*
Author to whom correspondence should be addressed.
†
Current address: Novartis Institutes for BioMedical Research, 250 Massachusetts Ave, Cambridge, MA 02139, USA.
Academic Editor: Samuel C. Mok
Cancers 2022, 14(5), 1243; https://doi.org/10.3390/cancers14051243
Received: 29 January 2022 / Revised: 25 February 2022 / Accepted: 25 February 2022 / Published: 28 February 2022
(This article belongs to the Special Issue Advances in Cancer Vaccines)
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Simple Summary

Neoantigens have emerged as highly personalized cancer therapeutic targets in recent years. Numerous studies have reported phenomenal therapeutic efficacy through treatments targeting cancer patient-specific neoantigens. Despite the growing interests, to identify druggable neoantigens is still largely dependent on genomic sequencing and AI algorithm-based prediction, which have been proven to be error-prone. Numerous reported mass spectrometry-based neoantigen assays utilized multi-gram levels of the tumor tissues, required invasive procedures, and were not practically feasible for most cancer patients, particularly patients that were non-operable or with early diseases, who may benefit most from immunotherapeutic approaches. Here we reported an integrated pipeline that can detect and quantify patient-specific neoantigens from a very limited amount of patient samples through a variety of innovative designs and optimizations. It may enable neoantigen-based therapeutics to benefit a broader spectrum of cancer and non-cancer patients.

Abstract

The presentation of neoantigens on the cell membrane is the foundation for most cancer immunotherapies. Due to their extremely low abundance, analyzing neoantigens in clinical samples is technically difficult, hindering the development of neoantigen-based therapeutics for more general use in the treatment of diverse cancers worldwide. Here, we describe an integrated system, “Valid-NEO”, which reveals patient-specific cancer neoantigen therapeutic targets from minute amounts of clinical samples through direct observation, without computer-based prediction, in a sensitive, rapid, and reproducible manner. The overall four-hour procedure involves mass spectrometry analysis of neoantigens purified from tumor samples through recovery of HLA molecules with HLA antibodies. Valid-NEO could be applicable to the identification and quantification of presented neoantigens in cancer patients, particularly when only limited amounts of sample are available. View Full-Text
Keywords: neoantigen; companion diagnostics; mass spectrometry; multi-omics assay; personalized cancer treatment neoantigen; companion diagnostics; mass spectrometry; multi-omics assay; personalized cancer treatment
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MDPI and ACS Style

Terai, Y.L.; Huang, C.; Wang, B.; Kang, X.; Han, J.; Douglass, J.; Hsiue, E.H.-C.; Zhang, M.; Purohit, R.; deSilva, T.; Wang, Q. Valid-NEO: A Multi-Omics Platform for Neoantigen Detection and Quantification from Limited Clinical Samples. Cancers 2022, 14, 1243. https://doi.org/10.3390/cancers14051243

AMA Style

Terai YL, Huang C, Wang B, Kang X, Han J, Douglass J, Hsiue EH-C, Zhang M, Purohit R, deSilva T, Wang Q. Valid-NEO: A Multi-Omics Platform for Neoantigen Detection and Quantification from Limited Clinical Samples. Cancers. 2022; 14(5):1243. https://doi.org/10.3390/cancers14051243

Chicago/Turabian Style

Terai, Yuri L., Chun Huang, Baoli Wang, Xiaonan Kang, Jing Han, Jacqueline Douglass, Emily H.-C. Hsiue, Ming Zhang, Raj Purohit, Taylor deSilva, and Qing Wang. 2022. "Valid-NEO: A Multi-Omics Platform for Neoantigen Detection and Quantification from Limited Clinical Samples" Cancers 14, no. 5: 1243. https://doi.org/10.3390/cancers14051243

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