Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4

Abstract

BackgroundThe efficacy of checkpoint blockade immunotherapies in colorectal cancer is currently restricted to a minority of patients diagnosed with mismatch repair-deficient tumors having high mutation burden. However, this observation does not exclude the existence of neoantigen-specific T cells in colorectal cancers with low mutation burden and the exploitation of their anti-cancer potential for immunotherapy. Therefore, we investigated whether autologous neoantigen-specific T cell responses could also be observed in patients diagnosed with mismatch repair-proficient colorectal cancers.MethodsWhole-exome and transcriptome sequencing were performed on cancer and normal tissues from seven colorectal cancer patients diagnosed with mismatch repair-proficient tumors to detect putative neoantigens. Corresponding neo-epitopes were synthesized and tested for recognition by in vitro expanded T cells that were isolated from tumor tissues (tumor-infiltrating lymphocytes) and from peripheral mononuclear blood cells stimulated with tumor material.ResultsNeoantigen-specific T cell reactivity was detected to several neo-epitopes in the tumor-infiltrating lymphocytes of three patients while their respective cancers expressed 15, 21, and 30 non-synonymous variants. Cell sorting of tumor-infiltrating lymphocytes based on the co-expression of CD39 and CD103 pinpointed the presence of neoantigen-specific T cells in the CD39+CD103+ T cell subset. Strikingly, the tumors containing neoantigen-reactive TIL were classified as consensus molecular subtype 4 (CMS4), which is associated with TGF-β pathway activation and worse clinical outcome.ConclusionsWe have detected neoantigen-targeted reactivity by autologous T cells in mismatch repair-proficient colorectal cancers of the CMS4 subtype. These findings warrant the development of specific immunotherapeutic strategies that selectively boost the activity of neoantigen-specific T cells and target the TGF-β pathway to reinforce T cell reactivity in this patient group.

Neoadjuvant anti-OX40 (MEDI6469) therapy in patients with head and neck squamous cell carcinoma activates and expands antigen-specific tumor-infiltrating T cells

“…7b ) within the DP TIL fraction in HPV− patients are most likely tumor antigen-specific, but were not detected as such using our mutated short peptide/MHC I binding algorithm approach. In collaboration with a group in the Netherlands, we showed that in colon cancer patients, reactivity to neoantigens was confined to the CD103+ CD39+ CD8+ TIL 45 . Recent studies have highlighted limitations in current mutated antigen pipelines suggesting that intronic regions could contribute to the neoantigen pool 46 and some of the T-cell responses could be directed to overexpressed self-antigens.…”

Therapeutic targeting of TGF-β in cancer: hacking a master switch of immune suppression

“…This subtype is also associated with worst clinical prognosis [119,121,122]. Patients diagnosed with CMS4 colorectal cancers were shown to carry neoantigen-reactive T cells despite the fact that these patients do not benefit from checkpoint blockade in an advanced setting [123,124]. In addition, these tumours display some hallmarks of ongoing anti-tumour immunity and inflammatory processes, indicating a certain degree of immunogenicity that might be counterbalanced by TGF-β [123].…”

“…Patients diagnosed with CMS4 colorectal cancers were shown to carry neoantigen-reactive T cells despite the fact that these patients do not benefit from checkpoint blockade in an advanced setting [123,124]. In addition, these tumours display some hallmarks of ongoing anti-tumour immunity and inflammatory processes, indicating a certain degree of immunogenicity that might be counterbalanced by TGF-β [123]. In mice models that recapitulate the CMS4 molecular subtype, exclusion of CD4 + and CD8 + T cells could be explained by the presence of high Tgf-β levels that were produced by CAFs and other cells of the TME.…”

The Tumor Microenvironment and Immunotherapy of Oropharyngeal Squamous Cell Carcinoma

“…Viral HNSCC display only half of the mutations rate observed in non-viral HNSCC (125,126). CD8+ T cells responding to such mutations have been detected in a few patients with non-OPSCC either spontaneously induced (127) or following a complete response after pembrolizumab treatment (128). Notably, such neoantigen specific T cells can also be detected in low TMB tumors (129), suggesting that they may also be present in OPSCC.…”