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Machaca V, Goyzueta V, Cruz MG, Sejje E, Pilco LM, López J, Túpac Y. Transformers meets neoantigen detection: a systematic literature review. J Integr Bioinform 2024; 0:jib-2023-0043. [PMID: 38960869 DOI: 10.1515/jib-2023-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/20/2024] [Indexed: 07/05/2024] Open
Abstract
Cancer immunology offers a new alternative to traditional cancer treatments, such as radiotherapy and chemotherapy. One notable alternative is the development of personalized vaccines based on cancer neoantigens. Moreover, Transformers are considered a revolutionary development in artificial intelligence with a significant impact on natural language processing (NLP) tasks and have been utilized in proteomics studies in recent years. In this context, we conducted a systematic literature review to investigate how Transformers are applied in each stage of the neoantigen detection process. Additionally, we mapped current pipelines and examined the results of clinical trials involving cancer vaccines.
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Affiliation(s)
| | | | | | - Erika Sejje
- Universidad Nacional de San Agustín, Arequipa, Perú
| | | | | | - Yván Túpac
- 187038 Universidad Católica San Pablo , Arequipa, Perú
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Luo X, Bi Q, Huang D, Li Y, Yao C, Zhang J, Wei W, Li J, Li Z, Zhang J, Ji S, Wang Y, Guo DA. Characterization of natural peptides in Pheretima by integrating proteogenomics and label-free peptidomics. J Pharm Anal 2023; 13:1070-1079. [PMID: 37842652 PMCID: PMC10568111 DOI: 10.1016/j.jpha.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 10/17/2023] Open
Abstract
Pheretima, also called "earthworms", is a well-known animal-derived traditional Chinese medicine that is extensively used in over 50 Chinese patent medicines (CPMs) in Chinese Pharmacopoeia (2020 edition). However, its zoological origin is unclear, both in the herbal market and CPMs. In this study, a strategy for integrating in-house annotated protein databases constructed from close evolutionary relationship-sourced RNA sequencing data from public archival resources and various sequencing algorithms (restricted search, open search, and de novo) was developed to characterize the phenotype of natural peptides of three major commercial species of Pheretima, including Pheretima aspergillum (PA), Pheretima vulgaris (PV), and Metaphire magna (MM). We identified 10,477 natural peptides in the PA, 7,451 in PV, and 5,896 in MM samples. Five specific signature peptides were screened and then validated using synthetic peptides; these demonstrated robust specificity for the authentication of PA, PV, and MM. Finally, all marker peptides were successfully applied to identify the zoological origins of Brain Heart capsules and Xiaohuoluo pills, revealing the inconsistent Pheretima species used in these CPMs. In conclusion, our integrated strategy could be used for the in-depth characterization of natural peptides of other animal-derived traditional Chinese medicines, especially non-model species with poorly annotated protein databases.
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Affiliation(s)
- Xiaoxiao Luo
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Qirui Bi
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dongdong Huang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jianqing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wenlong Wei
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiayuan Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhenwei Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jingxian Zhang
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shen Ji
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yurong Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - De-an Guo
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Xiang H, Zhang L, Bu F, Guan X, Chen L, Zhang H, Zhao Y, Chen H, Zhang W, Li Y, Lee LJ, Mei Z, Rao Y, Gu Y, Hou Y, Mu F, Dong X. A Novel Proteogenomic Integration Strategy Expands the Breadth of Neo-Epitope Sources. Cancers (Basel) 2022; 14:cancers14123016. [PMID: 35740681 PMCID: PMC9220843 DOI: 10.3390/cancers14123016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Tumor-specific antigens can activate T cell-based antitumor immune responses and are ideal targets for cancer immunotherapy. However, their identification is still challenging. Although mass spectrometry can directly identify human leukocyte antigen (HLA) binding peptides in tumor cells, it focuses on tumor-specific antigens derived from annotated protein-coding regions constituting only 1.5% of the genome. We developed a novel proteogenomic integration strategy to expand the breadth of tumor-specific epitopes derived from all genomic regions. Using the colorectal cancer cell line HCT116 as a model, we accurately identified 10,737 HLA-presented peptides, 1293 of which were non-canonical peptides that traditional database searches could not identify. Moreover, we found eight tumor neo-epitopes derived from somatic mutations, four of which were not previously reported. Our findings suggest that this new proteogenomic approach holds great promise for increasing the number of tumor-specific antigen candidates, potentially enlarging the tumor target pool and improving cancer immunotherapy.
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Affiliation(s)
- Haitao Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (H.X.); (X.G.); (W.Z.); (Y.L.)
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Le Zhang
- BGI-GenoImmune, BGI-Shenzhen, Shenzhen 518083, China; (L.Z.); (L.J.L.)
| | - Fanyu Bu
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Xiangyu Guan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (H.X.); (X.G.); (W.Z.); (Y.L.)
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Lei Chen
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Haibo Zhang
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Yuntong Zhao
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Huanyi Chen
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Weicong Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (H.X.); (X.G.); (W.Z.); (Y.L.)
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
| | - Yijian Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (H.X.); (X.G.); (W.Z.); (Y.L.)
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen 518083, China
| | - Leo Jingyu Lee
- BGI-GenoImmune, BGI-Shenzhen, Shenzhen 518083, China; (L.Z.); (L.J.L.)
| | - Zhanlong Mei
- BGI, Shenzhen 518083, China; (Z.M.); (Y.R.); (Y.H.)
| | - Yuan Rao
- BGI, Shenzhen 518083, China; (Z.M.); (Y.R.); (Y.H.)
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | - Yong Hou
- BGI, Shenzhen 518083, China; (Z.M.); (Y.R.); (Y.H.)
| | - Feng Mu
- BGI, Shenzhen 518083, China; (Z.M.); (Y.R.); (Y.H.)
- Correspondence: (F.M.); (X.D.)
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518103, China; (F.B.); (L.C.); (H.Z.); (Y.Z.); (H.C.); (Y.G.)
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen 518083, China
- Correspondence: (F.M.); (X.D.)
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