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Wong LM, Li WT, Shende N, Tsai JC, Ma J, Chakladar J, Gnanasekar A, Qu Y, Dereschuk K, Wang-Rodriguez J, Ongkeko WM. Analysis of the immune landscape in virus-induced cancers using a novel integrative mechanism discovery approach. Comput Struct Biotechnol J 2021; 19:6240-6254. [PMID: 34900135 PMCID: PMC8636736 DOI: 10.1016/j.csbj.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/17/2022] Open
Abstract
Background The mechanisms of carcinogenesis from viral infections are extraordinarily complex and not well understood. Traditional methods of analyzing RNA-sequencing data may not be sufficient for unraveling complicated interactions between viruses and host cells. Using RNA and DNA-sequencing data from The Cancer Genome Atlas (TCGA), we aim to explore whether virus-induced tumors exhibit similar immune-associated (IA) dysregulations using a new algorithm we developed that focuses on the most important biological mechanisms involved in virus-induced cancers. Differential expression, survival correlation, and clinical variable correlations were used to identify the most clinically relevant IA genes dysregulated in 5 virus-induced cancers (HPV-induced head and neck squamous cell carcinoma, HPV-induced cervical cancer, EBV-induced stomach cancer, HBV-induced liver cancer, and HCV-induced liver cancer) after which a mechanistic approach was adopted to identify pathways implicated in IA gene dysregulation. Results Our results revealed that IA dysregulations vary with the cancer type and the virus type, but cytokine signaling pathways are dysregulated in all virus-induced cancers. Furthermore, we also found that important similarities exist between all 5 virus-induced cancers in dysregulated clinically relevant oncogenic signatures and IA pathways. Finally, we also discovered potential mechanisms for genomic alterations to induce IA gene dysregulations using our algorithm. Conclusions Our study offers a new approach to mechanism identification through integrating functional annotations and large-scale sequencing data, which may be invaluable to the discovery of new immunotherapy targets for virus-induced cancers.
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Key Words
- Algorithm
- C2, Canonical pathway
- C6, Oncogenic signature
- C7, Immunological signature
- CA, Cancer-associated
- CESC, Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma
- CNA, Copy number alteration
- Cervical squamous cell carcinoma and endocervical adenocarcinoma
- EBV, Epstein-Barr virus
- Epstein-Barr virus
- FDR, False discovery rate
- GSEA, Gene set enrichment analysis
- HBV, Hepatitis B virus
- HCV, Hepatitis C virus
- HNSCC, Head and Neck Squamous Cell Carcinoma
- HPV, Human papillomavirus
- Head and neck squamous cell carcinoma
- Hepatitis B
- Hepatitis C
- Human papillomavirus
- IA, Immune-associated
- LIHC, Liver Hepatocellular Carcinoma
- Liver hepatocellular carcinoma
- MSigDB, Molecular Signature Database
- STAD, Stomach Adenocarcinoma
- Stomach adenocarcinoma
- TCGA
- TCGA, The Cancer Genome Atlas
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Affiliation(s)
- Lindsay M. Wong
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Wei Tse Li
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Neil Shende
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Joseph C. Tsai
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jiayan Ma
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jaideep Chakladar
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Aditi Gnanasekar
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Yuanhao Qu
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Kypros Dereschuk
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jessica Wang-Rodriguez
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- Pathology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Weg M. Ongkeko
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, 92093, USA
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
- Corresponding author at: Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA 92093, USA.
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