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Liang S, Dang B, Chen S, Mi H. Prognostic value and immunological role of cathepsin S gene in pan‑cancer. Oncol Lett 2024; 27:41. [PMID: 38108072 PMCID: PMC10722551 DOI: 10.3892/ol.2023.14175] [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: 07/11/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023] Open
Abstract
The cathepsin S (CTSS) gene encodes a lysine cysteine protease and serves an important role in the development of autoimmune diseases, inflammation and nervous system diseases. Furthermore, CTSS is implicated in tumor invasion and metastasis by the induction of tumor angiogenesis and the degradation of the tumor extracellular matrix. Nevertheless, the precise impact of CTSS on predicting pan-cancer prognosis and its influence on the tumor microenvironment and immune infiltration in human cancers remains unknown. This present study employed a comprehensive array of bioinformatic methods to evaluate the expression of CTSS and its associations with prognosis, clinicopathological characteristics, tumor microenvironment, tumor immune infiltration, tumor mutational burden and microsatellite instability across numerous cancer types. The current study demonstrated abnormal expression and distinct genomic alteration profiles of CTSS in many of the cancers tested. Furthermore, CTSS expression exhibited close associations with the prognosis of numerous cancers. High CTSS expression was significantly associated with better overall survival and disease-specific survival in bladder urothelial carcinoma (BLCA) and skin cutaneous melanoma (SKCM) but worse outcomes in brain lower grade glioma (LGG) and uveal melanoma (UVM). Moreover, CTSS demonstrated significant correlations with tumor mutational burden and microsatellite instability in 8 and 12 cancer types respectively, as well as different responses in immunotherapy sub-cohorts, especially in melanoma and bladder cancers. CTSS expression showed a positive correlation with stromal and immune cell scores in the four aforementioned cancers. Moreover, CTSS expression was correlated with the number of infiltrating CD8+ T cells, CD4+ T cells and macrophages. Conversely, CTSS was negatively associated with resting Mast cells, resting NK cells and resting memory CD4+ T cell infiltration in BLCA, SKCM and kidney renal clear cell carcinoma (KIRC). Furthermore, CTSS expression was correlated with immune-related gene expression, notably PDCD1, LAG3, PDCD1 and TIGIT in BLCA, KIRC, SKCM, LGG and UVM. Functional enrichment analysis suggested that CTSS could drive a dynamic adjustment of biological functions and pathways in BLCA, SKCM, LGG and UVM, including immune response regulating signaling pathways, regulation of lymphocyte activation and T cell receptor singling pathways. The current study suggested that CTSS could be an essential biomarker for prognosis and immune infiltration features in multiple cancers.
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Affiliation(s)
- Shengsheng Liang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Bowen Dang
- Department of Urology, The First People's Hospital of Yulin, Yulin, Guangxi Zhuang Autonomous Region 537000, P.R. China
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hua Mi
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun 2023; 14:2744. [PMID: 37173324 PMCID: PMC10182072 DOI: 10.1038/s41467-023-38271-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
With the continued promise of immunotherapy for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Here, we study 1084 eQTLs affecting the TIME found through analysis of The Cancer Genome Atlas and literature curation. These TIME eQTLs are enriched in areas of active transcription, and associate with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. Polygenic score models built with TIME eQTLs reproducibly stratify cancer risk, survival and immune checkpoint blockade (ICB) response across independent cohorts. To assess whether an eQTL-informed approach could reveal potential cancer immunotherapy targets, we inhibit CTSS, a gene implicated by cancer risk and ICB response-associated polygenic models; CTSS inhibition results in slowed tumor growth and extended survival in vivo. These results validate the potential of integrating germline variation and TIME characteristics for uncovering potential targets for immunotherapy.
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Affiliation(s)
- Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victoria H Wu
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | - Eva Pérez-Guijarro
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Hyo Kim
- Undergraduate Bioengineering Program, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrea Castro
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - James V Talwar
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Steven Cao
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Divya Kirani
- Undergraduate Biology and Bioinformatics Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jessica Au
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivier Harismendy
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, 92093, USA
| | - Sandip Pravin Patel
- Center for Personalized Cancer Therapy, Division of Hematology and Oncology, UC San Diego Moores Cancer Center, San Diego, CA, 92037, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jill P Mesirov
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- The Laboratory of Immunology and Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK, 74136, USA
- Department of Radiology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wesley K Thompson
- Division of Biostatistics, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - J Silvio Gutkind
- Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, CA, 92093, USA
| | | | - Hannah Carter
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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Zhang J, Huang C, Yang R, Wang X, Fang B, Mi J, Yuan H, Mo Z, Sun Y. Identification of Immune-Related Subtypes and Construction of a Novel Prognostic Model for Bladder Urothelial Cancer. Biomolecules 2022; 12:1670. [PMID: 36421685 PMCID: PMC9687876 DOI: 10.3390/biom12111670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/06/2022] [Accepted: 11/08/2022] [Indexed: 12/20/2023] Open
Abstract
The purpose of this study was to explore the relationship between bladder urothelial cancer (BLCA) and immunity, to screen prognosis-related immune genes (PIGs), and to construct an immune-related prognosis model (IRPM). We processed the relevant data of The Cancer Genome Atlas (TCGA-BLCA) and GSE13507 using R software and Perl. We divided BLCA into high-immunity and low-immunity subtypes. There were significant differences in the two subtypes. In addition, we identified 13 PIGs of BLCA by jointly analyzing the gene expression data and survival information of GSE13507 and TCGA-BLCA, and constructed IRPM through nine of them. The low-risk group had better survival outcome than the high-risk group. We also constructed a nomogram based on clinicopathological information and risk scores of the patients. Moreover, the prognosis of BLCA patients was significantly impacted by the expression of almost every gene used to calculate the risk score. The result of real-time fluorescence quantitative polymerase chain reaction revealed that all the genes used to calculate the risk score were differentially expressed between BLCA and adjacent normal tissues, except PDGFRA. Our research provided potential targets for the treatment of BLCA and a reference for judging the prognosis of BLCA.
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Affiliation(s)
- Jiange Zhang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, China
- Department of Urology, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, China
| | - Caisheng Huang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, China
- Department of Urology, The Nanning Second People’s Hospital, The Third Affiliated Hospital of Guangxi Medical University, Nanning 530031, China
| | - Rirong Yang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, China
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
- Collaborative Innovation Center of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, China
| | - Xiang Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, China
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Bo Fang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, China
- Collaborative Innovation Center of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, China
| | - Junhao Mi
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, China
- Collaborative Innovation Center of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, China
| | - Hao Yuan
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, China
- Department of Immunology, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, China
| | - Zengnan Mo
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning 530021, China
- Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning 530021, China
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Key Laboratory of Colleges and Universities, Nanning 530021, China
| | - Yihai Sun
- Department of Urology, The Nanning Second People’s Hospital, The Third Affiliated Hospital of Guangxi Medical University, Nanning 530031, China
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