The Diminished Neoantigens with Copy Number Aberrations and Diverse TCR Repertoire Shorten the Recurrence-Free Survival Period in Colorectal Cancer Cases

Background: We previously disclosed the evolutionary principle shaping intratumor heterogeneity shifts from Darwinian to neutral evolution in primary colorectal cancer (CRC) progression. Here, we focused on the role of copy number aberrations (CNAs) in impairment of the host tumor immune response, which is characterized by the level of neoantigen (NAG) and diversity of the T-cell receptor (TCR) repertoire, and in fostering postoperative recurrence. Methods: We compared single nucleotide variants (SNVs), NAG, and CNAs between primary tumors from eight cases of early CRC with postoperative recurrence (CRCR) and from eight cases of precancerous CRC lesions without recurrence (PCRC) by whole-exome sequencing. Then, we compared tumor immune response-related factors, such as NAG, cytolytic activity (CYT), and TCR repertoire diversity, between eight primary and 12 metastatic sites from eight CRCR cases. Findings: In comparison of 10 primary CRC tumors with recurrence (CRCR) and eight precancerous tumors of CRC (PCRC), neoantigens were fewer in CRCR than in PCRC, and CNAs at the arm level were significantly more frequent in CRCR than in PCRC. SNVs and copy numbers (CNs) were inversely associated. In TCGA analysis, cytotoxic T lymphocyte-related genes CD8A, CD4G, and PD-1 in 48 primary tumors with recurrence were downregulated relative to those in 242 tumors without recurrence. In CRCR cases, the frequency of CNAs and mutated driver genes with clonality in primary sites were equal to those in recurrent sites; however, the recurrence-free period was significantly extended under low NAG level and diverse TCR repertoire in metastatic but not primary sites. Interpretation: During the evolution of CRC toward recurrence, CNAs determine the metastatic capability with diminished levels of NAG in primary tumors, and impaired NAG and diminished TCR repertoire diversity predominantly determine the recurrence-free survival period. Funding Statement: This project was supported by Japan Society for the Promotion of Science KAKENHI (16K19107, 15H05707), Grant-in-Aid for Scientific Research on Innovative Areas (15H0912), and Priority Issue on Post-K computer (hp170227, hp160219) and partially supported by the Project for Cancer Research and Therapeutic Evolution (P-CREATE) and Practical Research for Innovative Cancer Control from Japan Agency for Medical Research and Development, AMED. The Takamatsunomiya Cancer Research Funding. This research used the supercomputing resource provided by the Human Genome Center, Institute of Medical Science, University of Tokyo. Declaration of Interests: There are no conflicts of interest to declare. Ethics Approval Statement: The study design was approved by the institutional review boards and ethics committees of the hospitals to which the patients were admitted (Kyushu University Hospital Institutional Review Board: protocol number 486–01; Cancer Institute Hospital Institutional Review Board: protocol number 12–27). The study was conducted according to the principles expressed in the Declaration of Helsinki. We obtained written informed consent from all participants in this study.