Neoantigen-reactive T cells exhibit effective anti-tumor activity against colorectal cancer

ABSTRACT

Neoantigens play a crucial role in cancer immunotherapy. However, the effectiveness and safety of neoantigen-based immunotherapies in patients with colorectal cancer (CRC), particularly in the Chinese population, have not been well studied. This study explored the feasibility and effectiveness of neoantigens in the treatment of CRC. Whole-exome sequencing (WES) and transcriptome sequencing were used to identify somatic mutations, RNA expression, and human leukocyte antigen (HLA) alleles. Neoantigen candidates were predicted, and immunogenicity was assessed. The neoantigens TSHZ3-L523P, RARA-R83H, TP53-R248W, EYA2-V333I, and NRAS-G12D from Patient 4 (PW4); TASP1-P161L, RAP1GAP-S215R, MOSPD1-V63I, and NAV2-D1973N from Patient 10 (PW10); and HAVCR2-F39V, SEC11A-R11L, SMPDL3B-T452M, LRFN3-R118Q, and ULK1-S248L from Patient 11 (HLA-A0201⁺PW11) induced a heightened neoantigen-reactive T cell (NRT) response as compared with the controls in peripheral blood lymphocytes (PBLs) isolated from patients with CRC. In addition, we identified neoantigen-containing peptides SEC11A-R11L and ULK1-S248L from HLA-A0201⁺PW11, which more effectively elicited specific CTL responses than the corresponding native peptides in PBLs isolated from HLA-A0201⁺PW11 as well as in HLA-A2.1/K^b transgenic mice. Importantly, adoptive transfer of NRTs induced by vaccination with two mutant peptides could effectively inhibit tumor growth in tumor-bearing mouse models. These data indicate that neoantigen-containing peptides with high immunogenicity represent promising candidates for peptide-mediated personalized therapy.

Abbreviations: CRC: colorectal cancer; DCs: dendritic cells; ELISPOT: enzyme-linked immunosorbent spot; E:T: effector:target; HLA: human leukocyte antigen; MHC: major histocompatibility complex; Mut: mutant type; NGS: next-generation sequencing; NRTs: neoantigen-reactive T cells; PBMCs: peripheral blood mononuclear cells; STR: short tandem repeat; PBLs: peripheral blood lymphocytes; PBS: phosphate-buffered saline; PD-1: programmed cell death protein 1; TILs: tumor-infiltrating lymphocytes; RNA-seq: RNA sequencing; Tg: transgenic; TMGs: tandem minigenes; WES: whole-exome sequencing; WT: wild-type.

KEYWORDS:

• Colorectal cancer
• immunotherapy
• neoantigens
• tumor
• cancer vaccine

Acknowledgments

The authors thank the members of our laboratories for their contributions and helpful discussions. The authors also thank for the analysis of neoantigens by P&PMed (www.pnp-med.com).

Availability of data and materials

The dataset(s) supporting the findings of this study are included in the manuscript.

Consent for publication

Written informed consent for publication was obtained from all participants.

Code availability

Not applicable.

Cell line authentication

Cell lines were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA).

Data availability Statement

This article title (DOI: 10.21203/rs.3.rs-22032/v1) is present as a pre-print on the Research Square website and can be accessed on https://www.researchsquare.com/article/rs-22032/v1.

Disclosure statement

The authors declare that they have no conflicts of interest.

Ethical statement

In this study, all investigations and experiments have obtained patients’ consent and been approved by the Medical Ethics Committee of the Second Affiliated Hospital, Wenzhou Medical University (MEC numbers: LCKY2018–67). This study was conducted in accordance with the Declaration of Helsinki. Informed consent was obtained from all participants included in the study.

Supplementary material

Supplemental data for this article can be accessed on the publisher’s website at https://doi.org/10.1080/21645515.2021.1891814.

Additional information

Funding

The authors disclosed the receipt of the following financial support for the research, authorship, and/or publication of this manuscript. This work was supported by the National Natural Science Foundation of China (Grant no. 3197080252); Qingdao Science and Technology Project (for benefiting the people, 19–6–1–27-nsh); Qingdao Outstanding Health Professional Development Fund; the Wenzhou Major Science and Technology Special Project (2018ZY004) from Wenzhou Science and Technology Bureau; the Public Benefit Technology Research Project of Zhejiang Science and Technology Department (LGF20H160019); and the Research Foundation of Academician Helin Workstation (item no. 19331103).