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Wang F, Zhang Z, Mao M, Yang Y, Xu P, Lu S. COSMIC-based mutation database enhances identification efficiency of HLA-I immunopeptidome. J Transl Med 2024; 22:144. [PMID: 38336780 PMCID: PMC10858511 DOI: 10.1186/s12967-023-04821-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Neoantigens have emerged as a promising area of focus in tumor immunotherapy, with several established strategies aiming to enhance their identification. Human leukocyte antigen class I molecules (HLA-I), which present intracellular immunopeptides to T cells, provide an ideal source for identifying neoantigens. However, solely relying on a mutation database generated through commonly used whole exome sequencing (WES) for the identification of HLA-I immunopeptides, may result in potential neoantigens being missed due to limitations in sequencing depth and sample quality. METHOD In this study, we constructed and evaluated an extended database for neoantigen identification, based on COSMIC mutation database. This study utilized mass spectrometry-based proteogenomic profiling to identify the HLA-I immunopeptidome enriched from HepG2 cell. HepG2 WES-based and the COSMIC-based mutation database were generated and utilized to identify HepG2-specific mutant immunopeptides. RESULT The results demonstrated that COSMIC-based database identified 5 immunopeptides compared to only 1 mutant peptide identified by HepG2 WES-based database, indicating its effectiveness in identifying mutant immunopeptides. Furthermore, HLA-I affinity of the mutant immunopeptides was evaluated through NetMHCpan and peptide-docking modeling to validate their binding to HLA-I molecules, demonstrating the potential of mutant peptides identified by the COSMIC-based database as neoantigens. CONCLUSION Utilizing the COSMIC-based mutation database is a more efficient strategy for identifying mutant peptides from HLA-I immunopeptidome without significantly increasing the false positive rate. HepG2 specific WES-based database may exclude certain mutant peptides due to WES sequencing depth or sample heterogeneity. The COSMIC-based database can effectively uncover potential neoantigens within the HLA-I immunopeptidomes.
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Affiliation(s)
- Fangzhou Wang
- Medical School of Chinese People's Liberation Army (PLA), Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepatobiliary Surgery PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
| | - Mingsong Mao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yudai Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China.
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- School of Medicine, Guizhou University, Guiyang, China.
| | - Shichun Lu
- Medical School of Chinese People's Liberation Army (PLA), Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepatobiliary Surgery PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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Li F, Wu H, Du X, Sun Y, Rausseo BN, Talukder A, Katailiha A, Elzohary L, Wang Y, Wang Z, Lizée G. Epidermal Growth Factor Receptor-Targeted Neoantigen Peptide Vaccination for the Treatment of Non-Small Cell Lung Cancer and Glioblastoma. Vaccines (Basel) 2023; 11:1460. [PMID: 37766136 PMCID: PMC10534925 DOI: 10.3390/vaccines11091460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) plays crucial roles in several important biological functions such as embryogenesis, epithelial tissue development, and cellular regeneration. However, in multiple solid tumor types overexpression and/or activating mutations of the EGFR gene frequently occur, thus hijacking the EGFR signaling pathway to promote tumorigenesis. Non-small cell lung cancer (NSCLC) tumors in particular often contain prevalent and shared EGFR mutations that provide an ideal source for public neoantigens (NeoAg). Studies in both humans and animal models have confirmed the immunogenicity of some of these NeoAg peptides, suggesting that they may constitute viable targets for cancer immunotherapies. Peptide vaccines targeting mutated EGFR have been tested in multiple clinical trials, demonstrating an excellent safety profile and encouraging clinical efficacy. For example, the CDX-110 (rindopepimut) NeoAg peptide vaccine derived from the EGFRvIII deletion mutant in combination with temozolomide and radiotherapy has shown efficacy in treating EGFRvIII-harboring glioblastoma multiforme (GBM) patients undergone surgery in multiple Phase I and II clinical trials. Furthermore, pilot clinical trials that have administered personalized NeoAg peptides for treating advanced-stage NSCLC patients have shown this approach to be a feasible and safe method to increase antitumor immune responses. Amongst the vaccine peptides administered, EGFR mutation-targeting NeoAgs induced the strongest T cell-mediated immune responses in patients and were also associated with objective clinical responses, implying a promising future for NeoAg peptide vaccines for treating NSCLC patients with selected EGFR mutations. The efficacy of NeoAg-targeting peptide vaccines may be further improved by combining with other modalities such as tyrosine kinase or immune checkpoint inhibitor (ICI) therapy, which are currently being tested in animal models and clinical trials. Herein, we review the most current basic and clinical research progress on EGFR-targeted peptide vaccination for the treatment of NSCLC and other solid tumor types.
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Affiliation(s)
- Fenge Li
- Core Laboratory, Tianjin Beichen Hospital, Tianjin 300400, China
- Department of Oncology, Tianjin Beichen Hospital, Tianjin 300400, China
| | - Huancheng Wu
- Department of Neurosurgery, Tianjin Beichen Hospital, Tianjin 300400, China
| | - Xueming Du
- Department of Oncology, Tianjin Beichen Hospital, Tianjin 300400, China
| | - Yimo Sun
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Barbara Nassif Rausseo
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Amjad Talukder
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Arjun Katailiha
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Lama Elzohary
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Yupeng Wang
- Department of Oncology, Tianjin Beichen Hospital, Tianjin 300400, China
| | - Zhiyu Wang
- Department of Immuno-Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
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HLA and tumour immunology: immune escape, immunotherapy and immune-related adverse events. J Cancer Res Clin Oncol 2023; 149:737-747. [PMID: 36662304 DOI: 10.1007/s00432-022-04493-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 11/22/2022] [Indexed: 01/21/2023]
Abstract
PURPOSE As molecules responsible for presenting antigens to T lymphocytes, leukocytes antigens (HLAs) play a vital role in cancer immunology. This review aims to provide current understanding of HLAs in tumour immunology. METHODS Perspectives on how HLA alterations may contribute to the immune escape of cancer cells and resistance to immunotherapy, and potential methods to overcome HLA defects were summarized. In addition, we discussed the potential association between HLA and immune-related adverse events (irAEs), which has not been reviewed elsewhere. RESULTS Downregulation, loss of heterogeneity and entire loss of HLAs are responsible for the immune escape of tumour cells. The strategies to overcome the HLA defects can be effective therapies of cancer. Compared with classical HLA-I, non-classical HLA-I molecules, such as HLA-E and HLA-G, appear to be more reliable predictors of prognosis, as they tend to play immunosuppressive roles in antitumor response. Relative diversified or high expression of classical HLA-I are potential predictors of favourable response of immunotherapy. Certain HLA types may be associated to enhanced affinity to self-antigen-mimicked tumour-antigens, thus may positively correlated to irAEs triggered by checkpoint inhibitors. CONCLUSIONS Further studies exploring the relationship between HLAs and cancer may not only lead to the development of novel therapies but also bring about better management of irAEs.
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Batool S, Bin-T-Abid D, Batool H, Shahid S, Saleem M, Khan AU, Hamid A, Mahmood MS, Ashraf NM. Development of multi-epitope vaccine constructs for non-small cell lung cancer (NSCLC) against USA human leukocyte antigen background: an immunoinformatic approach toward future vaccine designing. Expert Opin Biol Ther 2021; 21:1525-1533. [PMID: 34547976 DOI: 10.1080/14712598.2021.1981285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES The design of peptide-based vaccines for cancer is a promising immunotherapy that can induce a cancer-specific cytotoxic response in tumor cells. METHODS Herein, we used the immunoinformatic approach in designing a multi-epitope vaccine targeting G-protein coupled receptor 87 (GPCR-87), cystine/glutamate transporter (SLC7A11), Immunoglobulin binding protein 1 (IGBP1), and thioredoxin domain-containing protein 5 (TXNDC5), which can potentially contribute to NSCLC. The MHC-I and MHC-II epitopes selected for the fusion construct were evaluated for their antigenic and non-allergenic natures via VaxiJen and AllerTop. RESULTS A total of five epitopes, four class-I (FIFYLKNIV, CRYTSVLFY, RYLKVVKPF, and RQAKIQRYK), and one class-II (NQVRGYPTLLWFRDG), having combined USA population coverage of 100%, were used to make ten possible multi-epitope fusion constructs. In these constructs, PADRE, a universal T-helper epitope, and RSO9, a TLR4 agonist, were fused as adjuvants. The molecular docking analysis revealed that two constructs were showing significant binding affinities toward HLA-A*02:01, the most prevalent HLA allele in USA. Moreover, MD simulations marked one construct as a promising therapeutic candidate. CONCLUSION The multi-epitope vaccine constructs designed using immunogenic, and non-allergenic peptides of NSCLS tumor-associated proteins are likely to pose significant therapeutic efficacies in cancer immunotherapy due to their high binding affinities toward HLA molecules.
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Affiliation(s)
- Sana Batool
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.,School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Duaa Bin-T-Abid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Hina Batool
- Department of Life Science, School of Science, University of Management Technology, Lahore, Pakistan
| | - Saher Shahid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mahjabeen Saleem
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Azmat Ullah Khan
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat Pakistan
| | | | - Malik Siddique Mahmood
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan.,Department of Biochemistry, Nur International University, Lahore, Pakistan
| | - Naeem Mahmood Ashraf
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat Pakistan
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Lin C, Liu X, Zheng B, Ke R, Tzeng CM. Liquid Biopsy, ctDNA Diagnosis through NGS. Life (Basel) 2021; 11:life11090890. [PMID: 34575039 PMCID: PMC8468354 DOI: 10.3390/life11090890] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/08/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
Liquid biopsy with circulating tumor DNA (ctDNA) profiling by next-generation sequencing holds great promise to revolutionize clinical oncology. It relies on the basis that ctDNA represents the real-time status of the tumor genome which contains information of genetic alterations. Compared to tissue biopsy, liquid biopsy possesses great advantages such as a less demanding procedure, minimal invasion, ease of frequent sampling, and less sampling bias. Next-generation sequencing (NGS) methods have come to a point that both the cost and performance are suitable for clinical diagnosis. Thus, profiling ctDNA by NGS technologies is becoming more and more popular since it can be applied in the whole process of cancer diagnosis and management. Further developments of liquid biopsy ctDNA testing will be beneficial for cancer patients, paving the way for precision medicine. In conclusion, profiling ctDNA with NGS for cancer diagnosis is both biologically sound and technically convenient.
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Affiliation(s)
- Chen Lin
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
| | - Xuzhu Liu
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
| | - Bingyi Zheng
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China;
- Xiamen Key Laboratory of Cancer Cell Theranostics and Clinical Translation, Xiamen 361102, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Quanzhou 362021, China; (C.L.); (X.L.)
- Correspondence: (R.K.); (C.-M.T.)
| | - Chi-Meng Tzeng
- Translational Medicine Research Center, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China;
- Xiamen Key Laboratory of Cancer Cell Theranostics and Clinical Translation, Xiamen 361102, China
- Correspondence: (R.K.); (C.-M.T.)
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