1
|
Tong Q, Zhou J. Construction of a 12-gene prognostic model for colorectal cancer based on heat shock protein-related genes. Int J Hyperthermia 2024; 41:2290913. [PMID: 38191150 DOI: 10.1080/02656736.2023.2290913] [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: 09/25/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024] Open
Abstract
Some heat shock proteins (HSPs) have been shown to influence tumor prognosis, but their prognostic significance in colorectal cancer (CRC) remains unclear. This study explored the prognostic significance of HSP-related genes in CRC. Transcriptional data and clinical information of CRC patients were obtained from The Cancer Genome Atlas (TCGA) database, and a literature search was conducted to identify HSP-related genes. Using Least Absolute Selection and Shrinkage Operator (LASSO) regression and univariate/multivariate Cox regression analyses, 12 HSP-related genes demonstrating significant associations with CRC survival were successfully identified and employed to formulate a predictive risk score model. The efficacy and precision of this model were validated utilizing TCGA and Gene Expression Omnibus (GEO) datasets, demonstrating its reliability in CRC prognosis prediction. gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed significant disparities between high- and low-risk groups in chromatin remodeling biological functions and neutrophil extracellular trap formation pathways. Single sample gene set enrichment analysis (ssGSEA) further revealed differences in immune cell types and immune functional status between the two risk groups. Differential analysis showed higher expression of immune checkpoints within the low-risk group, while the high-risk group exhibited notably higher Tumor Immune Dysfunction and Exclusion (TIDE) scores. Additionally, we predicted the sensitivity of different prognosis risk patients to various drugs, providing potential drug choices for tailored treatment. Combined, our study successfully crafted a novel CRC prognostic model that can effectively predict patient survival, immune landscape, and treatment response, providing important support and guidance for CRC patient prognosis.
Collapse
Affiliation(s)
- Qin Tong
- Department of Gastrointestinal Surgery, Jinhua Guangfu Hospital, Jinhua, China
| | - Junchao Zhou
- Department of Gastrointestinal Surgery, Jinhua Guangfu Hospital, Jinhua, China
| |
Collapse
|
2
|
Bedran G, Gasser HC, Weke K, Wang T, Bedran D, Laird A, Battail C, Zanzotto FM, Pesquita C, Axelson H, Rajan A, Harrison DJ, Palkowski A, Pawlik M, Parys M, O'Neill JR, Brennan PM, Symeonides SN, Goodlett DR, Litchfield K, Fahraeus R, Hupp TR, Kote S, Alfaro JA. The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides. Cancer Immunol Res 2023; 11:747-762. [PMID: 36961404 PMCID: PMC10236148 DOI: 10.1158/2326-6066.cir-22-0621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/25/2022] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Tumor antigens can emerge through multiple mechanisms, including translation of noncoding genomic regions. This noncanonical category of tumor antigens has recently gained attention; however, our understanding of how they recur within and between cancer types is still in its infancy. Therefore, we developed a proteogenomic pipeline based on deep learning de novo mass spectrometry (MS) to enable the discovery of noncanonical MHC class I-associated peptides (ncMAP) from noncoding regions. Considering that the emergence of tumor antigens can also involve posttranslational modifications (PTM), we included an open search component in our pipeline. Leveraging the wealth of MS-based immunopeptidomics, we analyzed data from 26 MHC class I immunopeptidomic studies across 11 different cancer types. We validated the de novo identified ncMAPs, along with the most abundant PTMs, using spectral matching and controlled their FDR to 1%. The noncanonical presentation appeared to be 5 times enriched for the A03 HLA supertype, with a projected population coverage of 55%. The data reveal an atlas of 8,601 ncMAPs with varying levels of cancer selectivity and suggest 17 cancer-selective ncMAPs as attractive therapeutic targets according to a stringent cutoff. In summary, the combination of the open-source pipeline and the atlas of ncMAPs reported herein could facilitate the identification and screening of ncMAPs as targets for T-cell therapies or vaccine development.
Collapse
Affiliation(s)
- Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Kenneth Weke
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Tongjie Wang
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Dominika Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Alexander Laird
- Urology Department, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Christophe Battail
- CEA, Grenoble Alpes University, INSERM, IRIG, Biosciences and Bioengineering for Health Laboratory (BGE) - UA13 INSERM-CEA-UGA, Grenoble, France
| | | | - Catia Pesquita
- LASIGE, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ajitha Rajan
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - David J. Harrison
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Aleksander Palkowski
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Maciej Pawlik
- Academic Computer Centre CYFRONET, AGH University of Science and Technology, Cracow, Poland
| | - Maciej Parys
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - J. Robert O'Neill
- Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stefan N. Symeonides
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David R. Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
- University of Victoria Genome BC Proteome Centre, Victoria, Canada
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Paris, France
| | - Ted R. Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Javier A. Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| |
Collapse
|
3
|
Mukherjee AG, Wanjari UR, Namachivayam A, Murali R, Prabakaran DS, Ganesan R, Renu K, Dey A, Vellingiri B, Ramanathan G, Doss C. GP, Gopalakrishnan AV. Role of Immune Cells and Receptors in Cancer Treatment: An Immunotherapeutic Approach. Vaccines (Basel) 2022; 10:1493. [PMID: 36146572 PMCID: PMC9502517 DOI: 10.3390/vaccines10091493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 12/07/2022] Open
Abstract
Cancer immunotherapy moderates the immune system's ability to fight cancer. Due to its extreme complexity, scientists are working to put together all the puzzle pieces to get a clearer picture of the immune system. Shreds of available evidence show the connection between cancer and the immune system. Immune responses to tumors and lymphoid malignancies are influenced by B cells, γδT cells, NK cells, and dendritic cells (DCs). Cancer immunotherapy, which encompasses adoptive cancer therapy, monoclonal antibodies (mAbs), immune checkpoint therapy, and CART cells, has revolutionized contemporary cancer treatment. This article reviews recent developments in immune cell regulation and cancer immunotherapy. Various options are available to treat many diseases, particularly cancer, due to the progress in various immunotherapies, such as monoclonal antibodies, recombinant proteins, vaccinations (both preventative and curative), cellular immunotherapies, and cytokines.
Collapse
Affiliation(s)
- Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Arunraj Namachivayam
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Reshma Murali
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - D. S. Prabakaran
- Department of Radiation Oncology, College of Medicine, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju 28644, Korea
- Department of Biotechnology, Ayya Nadar Janaki Ammal College (Autonomous), Srivilliputhur Main Road, Sivakasi 626124, Tamil Nadu, India
| | - Raja Ganesan
- Institute for Liver and Digestive Diseases, Hallym University, Chuncheon 24252, Korea
| | - Kaviyarasi Renu
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata 700073, West Bengal, India
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Gnanasambandan Ramanathan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - George Priya Doss C.
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| |
Collapse
|
4
|
Nayak DA, Binder RJ. Agents of cancer immunosurveillance: HSPs and dsDNA. Trends Immunol 2022; 43:404-413. [PMID: 35382994 PMCID: PMC9058224 DOI: 10.1016/j.it.2022.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 10/18/2022]
Abstract
Tumor immunosurveillance requires tumor cell-derived molecules to initiate responses through corresponding receptors on antigen presenting cells (APCs) and a specific effector response designed to eliminate the emerging tumor cells. This is supported by evidence from immunodeficient individuals and experimental animals. Recent discoveries suggest that adjuvanticity of tumor-derived heat shock proteins (HSPs) and double-stranded DNA (dsDNA) are necessary for tumor-specific immunity. There is also the obligatory early transfer of tumor antigens to APCs. We argue that tumor-derived HSPs deliver sufficient chaperoned antigen for cross-priming within the quantitative limits set by nascent tumors. In contrast to late-stage tumors, we are only just beginning to understand the unique interactions of the immune system with precancerous/nascent neoplastic cells, which is important for improved cancer prevention measures.
Collapse
|
5
|
Bateman AC. Immune Checkpoint Inhibitor Therapy in Colorectal Cancer-The Role of Cellular Pathology. Int J Surg Pathol 2021; 29:584-591. [PMID: 34142908 DOI: 10.1177/10668969211025844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Colorectal cancer (CRC) is a common malignancy with a worldwide distribution. Despite bowel cancer screening programmes, the management of patients with metastatic disease is still an important and challenging problem. Immune checkpoint inhibitor (ICI) therapy is a well-established treatment in several cancers, eg, malignant melanoma and non-small cell lung carcinoma and is used in metastatic disease. The principle of this treatment is to use monoclonal antibodies to block the immune tolerance that commonly develops to tumor cells, therefore allowing host T-cell immunity to recognise and lyse cancer cells. The cellular receptors most commonly targeted by ICI therapy are cytotoxic T-lymphocyte-associated protein-4 and the programmed death 1/programmed death ligand 1 system. This review provides a scientific background to current ICI therapy and discusses the factors that predict response to this treatment. This is followed by a description of the emerging evidence for the use of ICI therapy in CRC and the utility of cellular pathology in stratifying patients for this treatment, especially when the systemic disease is present.
Collapse
Affiliation(s)
- Adrian C Bateman
- 7425University Hospitals Southampton NHS Foundation Trust, Southampton, UK
| |
Collapse
|
6
|
Li C, Du Y, Zhang Y, Ji N. Immunotherapy with heat shock protein 96 to treat gliomas. Chin Neurosurg J 2020; 6:31. [PMID: 32922959 PMCID: PMC7469332 DOI: 10.1186/s41016-020-00211-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 02/07/2023] Open
Abstract
Heat shock protein 96 (gp96) is a highly conserved protein in the endoplasmic reticulum. The functions of gp96 include promoting the oncogenesis and progression of glioma. In addition, tumor-derived gp96 can activate anti-tumor immune. Therefore, this protein was used to generate an anti-tumor vaccine and widely applied to glioma therapy. This review summarizes the mechanisms of gp96 in glioma oncogenesis and clinical trials of the gp96 tumor vaccine in glioma treatment.
Collapse
Affiliation(s)
- Chunzhao Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No.119 South 4th Ring West Road, Fengtai District, Beijing, 100070 China
| | - Yifei Du
- Beijing Shijitan Hospital, Capital Medical University, No.10 Yangfangdian Road, Fengtai District, Beijing, 100038 China
| | - Yang Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No.119 South 4th Ring West Road, Fengtai District, Beijing, 100070 China.,China National Clinical Research Center Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, No.119 South 4th Ring West Road, Fengtai District, Beijing, 100070 China.,Beijing Key Laboratory of Brian Tumor, Beijing Tiantan Hospital Capital Medical University, No.119 South 4th Ring West Road, Fengtai District, Beijing, 100070 China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No.119 South 4th Ring West Road, Fengtai District, Beijing, 100070 China.,China National Clinical Research Center Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, No.119 South 4th Ring West Road, Fengtai District, Beijing, 100070 China.,Beijing Key Laboratory of Brian Tumor, Beijing Tiantan Hospital Capital Medical University, No.119 South 4th Ring West Road, Fengtai District, Beijing, 100070 China
| |
Collapse
|
7
|
Heat Shock Proteins in Cancer Immunotherapy. JOURNAL OF ONCOLOGY 2019; 2019:3267207. [PMID: 31885572 PMCID: PMC6927063 DOI: 10.1155/2019/3267207] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 12/24/2022]
Abstract
Heat shock proteins (HSPs) are highly conserved molecular chaperones with divergent roles in various cellular processes. The HSPs are classified according to their molecular size as HSP27, HSP40, HSP60, HSP70, and HSP90. The HSPs prevent nonspecific cellular aggregation of proteins by maintaining their native folding energetics. The disruption of this vital cellular process, driven by the aberrant expression of HSPs, is implicated in the progression of several different carcinomas. Many HSPs are also actively involved in promoting the proliferation and differentiation of tumor cells, contributing to their metastatic phenotype. Upregulation of these HSPs is associated with the poor outcome of anticancer therapy in clinical settings. On the other hand, these highly expressed HSPs may be exploited as viable immunotherapeutic targets for different types of cancers. This review discusses recent advances and perspectives on the research of HSP-based cancer immunotherapy.
Collapse
|
8
|
Rapoport BL, Anderson R. Realizing the Clinical Potential of Immunogenic Cell Death in Cancer Chemotherapy and Radiotherapy. Int J Mol Sci 2019; 20:ijms20040959. [PMID: 30813267 PMCID: PMC6412296 DOI: 10.3390/ijms20040959] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 02/06/2023] Open
Abstract
Immunogenic cell death (ICD), which is triggered by exposure of tumor cells to a limited range of anticancer drugs, radiotherapy, and photodynamic therapy, represents a recent innovation in the revitalized and burgeoning field of oncoimmunnotherapy. ICD results in the cellular redistribution and extracellular release of damage-associated molecular patterns (DAMPs), which have the potential to activate and restore tumor-targeted immune responses. Although a convincing body of evidence exists with respect to the antitumor efficacy of ICD in various experimental systems, especially murine models of experimental anticancer immunotherapy, evidence for the existence of ICD in the clinical setting is less compelling. Following overviews of hallmark developments, which have sparked the revival of interest in the field of oncoimmunotherapy, types of tumor cell death and the various DAMPs most prominently involved in the activation of antitumor immune responses, the remainder of this review is focused on strategies which may potentiate ICD in the clinical setting. These include identification of tumor- and host-related factors predictive of the efficacy of ICD, the clinical utility of combinatorial immunotherapeutic strategies, novel small molecule inducers of ICD, novel and repurposed small molecule immunostimulants, as well as the critical requirement for validated biomarkers in predicting the efficacy of ICD.
Collapse
Affiliation(s)
- Bernardo L Rapoport
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa.
- The Medical Oncology Centre of Rosebank, Johannesburg 2196, South Africa.
| | - Ronald Anderson
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa.
- Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa.
| |
Collapse
|