The common neoantigens in colorectal cancer are predicted and validated to be presented or immunogenic

Abstract

23Colorectal cancer (CRC) is a malignant cancer with high incidence and mortality in the 24 world, as the result of the traditional treatments. Immunotherapy targeting neoantigens 25 can induce durable tumor regression in cancer patients, but is almost limited to 26 individual treatment, resulting from the unique neoantigens. Many shared oncogenic 27 mutations are detected, but whether the common neoantigens can be identified in CRC 28 is unknown. Using the somatic mutations data from 321 CRC patients combined with 29 a filter standard and 7 predicted algorithms, we screened and obtained 25 HLA-30 A*11:01 restricted common neoantigens with high binding affinity (IC50<50 nM) and 31 presentation score (EPIC>0.9). Except the positive epitope KRAS_G12V8-16, 11 out of 32 25 common neoantigens were proved to be naturally processed and presented on 33 constructed K562 cell surface by mass spectroscopy (MS), and 11 out of 25 common 34 neoantigens specifically induced in vitro pre-stimulated cytotoxic lymphocyte (CTL) 35 to secrete IFN-. However, only 2 out of 25 common neoantigens were simultaneously 36 presented and immunogenic. Moreover, using cell-sorting technology combined with 37 single-cell RNA sequencing, the immune repertoire profiles of C1orf170_S418G413-421 38 and KRAS_G12V8-16-specific CTL were clarified. Therefore, common neoantigens 39 with presentation and immunogenicity could be found in CRC, which would be 40 developed as the universal targets for CRC immunotherapy. 41 42 43 44 45 46 Colorectal cancer (CRC) is the third commonest diagnosed malignant cancer and 47 the second leading cause of cancer death in the world [1]. In 2018, more than 1.8 48 million new cases of CRC and almost 881 thousand cases of CRC-interrelated death 49 occurred in the world [1], and the global burden of CRC is estimated to reach over 2.2 50 million new cases and 1.1 million cancer deaths by 2030 [2]. Traditionally surgical 51 resection can cure the early stage of CRC, but about 50% of patients ultimately die of 52 distant metastases. While chemotherapy, radiation therapy and targeted therapy can 53 extend overall survival, less than 15% of patients with metastatic CRC survive 54 beyond 5 years [3]. Therefore, the novel and more effective therapeutic approaches 55 for CRC are necessary to develop. 56 In the recent years, based on a better knowledge of the complex interactions 57 between the immune system and the tumor microenvironment, immunotherapy has 58 become a novel effective and promising therapeutic strategy for cancer, and its 59 efficacy was widely tested by CRC model. The vast majority of CRC patients with 60 deficient mismatch repair (dMMR) or highly microsatellite instable (MSI-H) benefit 61 from immune checkpoint inhibitors, which is not effective in other CRC patients with 62 proficient MMR (pMMR) or microsatellite stable (MSS) [4]. Patients with CRC do 63 not respond to autologous tumour lysate DC (ADC) and peptide vaccines [4]. T cells, 64 which are engineered to express an affinity-enhanced T-cell rece...

Recurrent Neoantigens in Colorectal Cancer as Potential Immunotherapy Targets

“…Mayakonda et al have reported the high frequency of KRAS G12D mutations in pancreatic cancer [23,25]. Liang et al also demonstrated by mass spectrometry in 2019 that KRAS G12V-mutated neoantigen can be presented by HLA-A11:01 cell lines [28]. And as far as we know, clinical trials for KRAS G12V mutations in patients with HLA-A11:01 are already under way (NCT03190941).…”

Recurrent Neoantigens in Colorectal Cancer as Potential Immunotherapy Targets

“…Both G12D and G12V are highly mutated in multiple metastatic cancers, including Endometrial, CRC, and non-small cell lung cancer (Figure 4a-b). Witkiewicz et al have reported the high frequency of KRAS G12D mutations in pancreatic cancer [23,25]. Liang et al also demonstrated by mass spectrometry in 2019 that KRAS G12V mutated neoantigen can be presented by HLA-A11:01 cell lines [25].…”

“…Witkiewicz et al have reported the high frequency of KRAS G12D mutations in pancreatic cancer [23,25]. Liang et al also demonstrated by mass spectrometry in 2019 that KRAS G12V mutated neoantigen can be presented by HLA-A11:01 cell lines [25]. And as far as we know, clinical trials for KRAS G12V mutations in patients with HLA-A11:01 cancer are already under way (NCT03190941).…”

A Comprehensive Survey of Mutations in Oesophageal Carcinoma Reveals Recurrent Neoantigens as Potential Immunotherapy Targets

“…KRAS Gly12 (including G12V, G12C, and G12D) is a classic cancer mutation in multiple cancers including endometrial, colorectal cancer, and non-small cell lung cancer [30]. We previously reported high frequency mutations and high frequency neoantigens of G12D/V in gastric and colorectal cancer [14,31], our research group also demonstrated by mass spectrometry recently that KRAS G12V mutated neoantigen can be presented by HLA-A11:01 cell lines [32]. Previous studies have shown that gastrointestinal tumors, including esophageal cancer, gastric cancer, colon cancer and rectal cancer, have some similarities in tumor tissue origin and molecular characteristics [33], which are also reflected in this study, and high-frequency neoantigens in esophageal cancer are also similar to gastric cancer and colorectal cancer, suggesting the universality of neoantigen-based immunotherapy in gastrointestinal tumors.…”