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Lischer C, Eberhardt M, Flamann C, Berges J, Güse E, Wessely A, Weich A, Retzlaff J, Dörrie J, Schaft N, Wiesinger M, März J, Schuler-Thurner B, Knorr H, Gupta S, Singh KP, Schuler G, Heppt MV, Koch EAT, van Kleef ND, Freen-van Heeren JJ, Turksma AW, Wolkenhauer O, Hohberger B, Berking C, Bruns H, Vera J. Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy. J Immunother Cancer 2024; 12:e008104. [PMID: 38724462 PMCID: PMC11086525 DOI: 10.1136/jitc-2023-008104] [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] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Tumor-associated antigens and their derived peptides constitute an opportunity to design off-the-shelf mainline or adjuvant anti-cancer immunotherapies for a broad array of patients. A performant and rational antigen selection pipeline would lay the foundation for immunotherapy trials with the potential to enhance treatment, tremendously benefiting patients suffering from rare, understudied cancers. METHODS We present an experimentally validated, data-driven computational pipeline that selects and ranks antigens in a multipronged approach. In addition to minimizing the risk of immune-related adverse events by selecting antigens based on their expression profile in tumor biopsies and healthy tissues, we incorporated a network analysis-derived antigen indispensability index based on computational modeling results, and candidate immunogenicity predictions from a machine learning ensemble model relying on peptide physicochemical characteristics. RESULTS In a model study of uveal melanoma, Human Leukocyte Antigen (HLA) docking simulations and experimental quantification of the peptide-major histocompatibility complex binding affinities confirmed that our approach discriminates between high-binding and low-binding affinity peptides with a performance similar to that of established methodologies. Blinded validation experiments with autologous T-cells yielded peptide stimulation-induced interferon-γ secretion and cytotoxic activity despite high interdonor variability. Dissecting the score contribution of the tested antigens revealed that peptides with the potential to induce cytotoxicity but unsuitable due to potential tissue damage or instability of expression were properly discarded by the computational pipeline. CONCLUSIONS In this study, we demonstrate the feasibility of the de novo computational selection of antigens with the capacity to induce an anti-tumor immune response and a predicted low risk of tissue damage. On translation to the clinic, our pipeline supports fast turn-around validation, for example, for adoptive T-cell transfer preparations, in both generalized and personalized antigen-directed immunotherapy settings.
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Affiliation(s)
- Christopher Lischer
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Martin Eberhardt
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Cindy Flamann
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Berges
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Esther Güse
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Anja Wessely
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Adrian Weich
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Jimmy Retzlaff
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Jan Dörrie
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Niels Schaft
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Manuel Wiesinger
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Johannes März
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Beatrice Schuler-Thurner
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Harald Knorr
- Department of Ophthalmology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
- CCC Erlangen-EMN, Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Krishna Pal Singh
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Gerold Schuler
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Markus Vincent Heppt
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Elias Andreas Thomas Koch
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | | | | | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Bettina Hohberger
- Department of Ophthalmology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
- CCC Erlangen-EMN, Erlangen, Germany
| | - Carola Berking
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Department of Dermatology, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Heiko Bruns
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Julio Vera
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Department of Dermatology, FAU Erlangen-Nürnberg, Erlangen, Germany
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Wang Y, Han Y, Jin L, Ji L, Liu Y, Lin M, Zhou S, Yang R. A novel prognostic signature based on cancer stemness and metabolism-related genes for cervical squamous cell carcinoma and endocervical adenocarcinoma. Aging (Albany NY) 2024; 16:7293-7310. [PMID: 38656879 PMCID: PMC11087133 DOI: 10.18632/aging.205757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND CESC is the second most commonly diagnosed gynecological malignancy. Given the pivotal involvement of metabolism-related genes (MRGs) in the etiology of multiple tumors, our investigation aims to devise a prognostic risk signature rooted in cancer stemness and metabolism. METHODS The stemness index based on mRNA expression (mRNAsi) of samples from the TCGA dataset was computed using the One-class logistic regression (OCLR) algorithm. Furthermore, potential metabolism-related genes related to mRNAsi were identified through weighted gene co-expression network analysis (WGCNA). We construct a stemness-related metabolic gene signature through shrinkage estimation and univariate analysis, thereby calculating the corresponding risk scores. Moreover, we selected corresponding DEGs between groups with high- and low-risk score and conducted routine bioinformatic analyses. Furthermore, we validated the expression of four hub genes at the protein level through immunohistochemistry (IHC) in samples obtained from our patient cohort. RESULTS According to the findings, it was found that six genes-AKR1B10, GNA15, ALDH1B1, PLOD2, LPCAT1, and GPX8- were differentially expressed in both TCGA-CSEC and GEO datasets among 23 differentially expressed metabolism-related genes (DEMRGs). mRNAsi exhibited a notable association with the extent of key oncogene mutation. The results showed that the AUC values for forecasting survival at 1, 3, and 5 years are 0.715, 0.689, and 0.748, individually. We observed a notable association between the risk score and different immune cell populations, along with enrichment in crucial signaling pathways in CESC. Four genes differentially expressed between different risk score groups were validated by IHC to be highly expressed in the CESC samples at the protein level. CONCLUSION The current investigation indicated that a 3-gene signature based on stemness-related metabolic and 4 hub genes with differential expression between high and low-risk score subgroups may serve as valuable prognostic markers and potential therapeutic targets in CESC.
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Affiliation(s)
- Yaokai Wang
- Department of Gynecology and Obstetrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, Guangdong, China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, Yunnan, China
| | - Liangzi Jin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, Yunnan, China
| | - Lulu Ji
- Department of Gynecology and Obstetrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, Guangdong, China
| | - Yanxiang Liu
- Yantian District Maternal and Child Health Hospital, Shenzhen, Guangdong, China
| | - Min Lin
- Department of Gynecology and Obstetrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, Guangdong, China
| | - Sitong Zhou
- Department of Dermatology, The First People’s Hospital of Foshan, Foshan, Guangdong, China
| | - Ronghua Yang
- Department of Burn and Plastic Surgery, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, Guangdong, China
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lv Y, Yuan CH, Han LY, Huang GR, Ju LC, Chen LH, Han HY, Zhang C, Zeng LH. The Overexpression of SLC25A13 Predicts Poor Prognosis and Is Correlated with Immune Cell Infiltration in Patients with Skin Cutaneous Melanoma. DISEASE MARKERS 2022; 2022:4091978. [PMID: 35607442 PMCID: PMC9124094 DOI: 10.1155/2022/4091978] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 11/29/2022]
Abstract
Purpose Skin cutaneous melanoma (SKCM) is one of the most malignant and aggressive cancers with poor prognosis due to its rapid progression towards metastasis. Thus, finding clinically relevant biomarkers for early diagnosis, prognosis, and therapy prediction is essential. This study focused on the identification of SLC25A13 as a novel biomarker for SKCM and is aimed at investigating the biological functions of solute carrier family 25 member 13 (SLC25A13) in the development of SKCM. Methods GEPIA was used to analyze the diagnostic and prognostic values of SLC25A13 in SKCM using the TCGA dataset. PrognoScan was used to validate the prognostic value of SLC25A13 and its coexpressed genes in SKCM. TISIDB was established to reveal the relationship between the expression of SLC25A13 and immune infiltration in SKCM. The protein expression of SLC25A13 in SKCM was evaluated by the Human Protein Atlas. The signaling pathways and biological functions of SLC25A13 in SKCM were analyzed by LinkOmics. Metascape was applied to analyze the functional enrichment analysis of SLC25A13. Protein-protein interaction analysis of SLC25A13 was performed by GeneMANIA. Results The mRNA and protein levels of SLC25A13 in the SKCM were much higher than those in the normal tissue. Furthermore, the overexpression of SLC25A13 predicts worse outcomes of SKCM patients. Moreover, the SLC25A13 expression was negatively correlated with the immune infiltration level of SKCM. The overexpression of SLC25A13 coexpressed genes, such as ACLY and AFG3L2, and SCL25A13 interacting genes also predicted the unfavorable prognosis of SKCM patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of SLC25A13 coexpressed genes showed that these genes are enriched in ATPase activity, cell cycle, mTOR, and VEGFA-VEGFR2 signaling pathways, which were relevant to tumor development and angiogenesis. Gene set enrichment analysis (GSEA) demonstrated that the SLC25A13 expression was related to infiltrating immune cells in SKCM. Conclusion Our findings revealed that SLC25A13 might be a potential prognostic and therapeutic biomarker for SKCM.
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Affiliation(s)
- Yue lv
- Department of Nursing, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
| | - Chun-hui Yuan
- Department of Pharmacology, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
| | - Lu-yao Han
- Department of Nursing, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
| | - Gao-ru Huang
- Department of Nursing, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
| | - Ling-ce Ju
- Department of Nursing, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
| | - Ling-hui Chen
- Thyroid Surgery Department, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China 310003
| | - Hai-ying Han
- Department of Nursing, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
| | - Chong Zhang
- Department of Nursing, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
- Department of Pharmacology, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
| | - Ling-hui Zeng
- Department of Nursing, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
- Department of Pharmacology, School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang, China 310015
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