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Gourmet L, Sottoriva A, Walker-Samuel S, Secrier M, Zapata L. Immune evasion impacts the landscape of driver genes during cancer evolution. Genome Biol 2024; 25:168. [PMID: 38926878 PMCID: PMC11210199 DOI: 10.1186/s13059-024-03302-x] [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] [Received: 02/05/2023] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Carcinogenesis is driven by interactions between genetic mutations and the local tumor microenvironment. Recent research has identified hundreds of cancer driver genes; however, these studies often include a mixture of different molecular subtypes and ecological niches and ignore the impact of the immune system. RESULTS In this study, we compare the landscape of driver genes in tumors that escaped the immune system (escape +) versus those that did not (escape -). We analyze 9896 primary tumors from The Cancer Genome Atlas using the ratio of non-synonymous to synonymous mutations (dN/dS) and find 85 driver genes, including 27 and 16 novel genes, in escape - and escape + tumors, respectively. The dN/dS of driver genes in immune escaped tumors is significantly lower and closer to neutrality than in non-escaped tumors, suggesting selection buffering in driver genes fueled by immune escape. Additionally, we find that immune evasion leads to more mutated sites, a diverse array of mutational signatures and is linked to tumor prognosis. CONCLUSIONS Our findings highlight the need for improved patient stratification to identify new therapeutic targets for cancer treatment.
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Affiliation(s)
- Lucie Gourmet
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK
- UCL Centre for Computational Medicine, University College London, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Simon Walker-Samuel
- UCL Centre for Computational Medicine, University College London, London, UK
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
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Yanan L, Hui L, Zhuo C, Longqing D, Ran S. Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma. Sci Rep 2023; 13:7480. [PMID: 37161060 PMCID: PMC10170109 DOI: 10.1038/s41598-023-34698-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/05/2023] [Indexed: 05/11/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common tumour type in otorhinolaryngology, and its occurrence is related to long-term exposure to tobacco and alcohol. Recently, HPV infection has become an increasingly important contributor to HNSCC, and HPV-associated HNSCC has a different clinical course and better prognosis than non-HPV-associated HNSCC. However, the exact molecular mechanism of HNSCC is unclear. Here, we obtained data from The Cancer Genome Atlas (TCGA) and gene expression omnibus (GEO) to analyse the mitophagy process and related influencing factors of HPV-associated HNSCC via the integration of bioinformatics analysis and experimental validation. We found that in HPV-associated HNSCC, process of mitophagy affects tumour development, immune cell infiltration and prognosis. In the mitophagy process of HPV-related HNSCC: NOS2, IL17REL, TMSB15A, TUBB4A and other hub genes showed significantly higher expression levels than in non-HPV-related HNSCC. Furthermore, this was also confirmed by quantitative real-time PCR (qRT‒PCR), which was used to detect the expression of differentially expressed genes in HNSCC tissues. Furthermore, we found that the unique immunological characteristics by expressing CD8+ T cell in a high level in HPV-related HNSCC, and the scores obtained from the score model affected the prognosis of patients. In conclusion, our study revealed the unique biomolecular signature of mitophagy in HPV-associated HNSCC, which may contribute to the development of precise treatment regimens for HPV-associated HNSCC patients.
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Affiliation(s)
- Li Yanan
- Department of Otorhinolaryngology, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250000, Shandong, China
| | - Liang Hui
- Department of Otorhinolaryngology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Ji'nan, 250014, Shandong, China.
| | - Cheng Zhuo
- Department of Otorhinolaryngology, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250000, Shandong, China
| | - Ding Longqing
- Department of Otorhinolaryngology, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250000, Shandong, China
| | - Sun Ran
- Department of Otorhinolaryngology, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250000, Shandong, China
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Khalil MI, Yang C, Vu L, Chadha S, Nabors H, Welbon C, James CD, Morgan IM, Spanos WC, Pyeon D. HPV upregulates MARCHF8 ubiquitin ligase and inhibits apoptosis by degrading the death receptors in head and neck cancer. PLoS Pathog 2023; 19:e1011171. [PMID: 36867660 PMCID: PMC10016708 DOI: 10.1371/journal.ppat.1011171] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/15/2023] [Accepted: 02/01/2023] [Indexed: 03/04/2023] Open
Abstract
The membrane-associated RING-CH-type finger ubiquitin ligase MARCHF8 is a human homolog of the viral ubiquitin ligases Kaposi's sarcoma herpesvirus K3 and K5 that promote host immune evasion. Previous studies have shown that MARCHF8 ubiquitinates several immune receptors, such as the major histocompatibility complex II and CD86. While human papillomavirus (HPV) does not encode any ubiquitin ligase, the viral oncoproteins E6 and E7 are known to regulate host ubiquitin ligases. Here, we report that MARCHF8 expression is upregulated in HPV-positive head and neck cancer (HNC) patients but not in HPV-negative HNC patients compared to normal individuals. The MARCHF8 promoter is highly activated by HPV oncoprotein E6-induced MYC/MAX transcriptional activation. The knockdown of MARCHF8 expression in human HPV-positive HNC cells restores cell surface expression of the tumor necrosis factor receptor superfamily (TNFRSF) death receptors, FAS, TRAIL-R1, and TRAIL-R2, and enhances apoptosis. MARCHF8 protein directly interacts with and ubiquitinates the TNFRSF death receptors. Further, MARCHF8 knockout in mouse oral cancer cells expressing HPV16 E6 and E7 augments cancer cell apoptosis and suppresses tumor growth in vivo. Our findings suggest that HPV inhibits host cell apoptosis by upregulating MARCHF8 and degrading TNFRSF death receptors in HPV-positive HNC cells.
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Affiliation(s)
- Mohamed I. Khalil
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Department of Molecular Biology, National Research Centre, El-Buhouth St., Cairo, Egypt
| | - Canchai Yang
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Lexi Vu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Smriti Chadha
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Harrison Nabors
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Craig Welbon
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, United States of America
| | - Claire D. James
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Iain M. Morgan
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - William C. Spanos
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, United States of America
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Zhang Y, Qin Y, Li D, Yang Y. A risk prediction model mediated by genes of APOD/APOC1/SQLE associates with prognosis in cervical cancer. BMC Womens Health 2022; 22:534. [PMID: 36536343 PMCID: PMC9764686 DOI: 10.1186/s12905-022-02083-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer is one of the most common gynecological malignancies. Due to the high heterogeneity of cervical cancer accelerating cancer progression, it is necessary to identify new prognostic markers and treatment regimens for cervical cancer to improve patients' survival rates. We purpose to construct and verify a risk prediction model for cervical cancer patients. Based on the analysis of data from the Gene Expression Omnibus database (GEO) and The Cancer Genome Atlas (TCGA), differences of genes in normal and cancer samples were analyzed and then used analysis of WGCNA along with consistent clustering to construct single-factor + multi-factor risk models. After regression analysis, the target genes were obtained as prognostic genes and prognostic risk models were constructed, and the validity of the risk model was confirmed using the receiver operating characteristic curve (ROC) and Kaplan-Meier curve. Subsequently, the above model was verified on the GSE44001 data validation followed by independent prognostic analysis. Enrichment analysis was conducted by grouping the high and low risks of the model. In addition, differences in immune analysis (immune infiltration, immunotherapy), drug sensitivity, and other levels were counted by the high and low risks groups. In our study, three prognostic genes including APOD, APOC1, and SQLE were obtained, and a risk model was constructed along with validation based on the above-mentioned analysis. According to the model, immune correlation and immunotherapy analyses were carried out, which will provide a theoretical basis and reference value for the exploration and treatment of cervical cancer.
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Affiliation(s)
- Ya Zhang
- grid.413458.f0000 0000 9330 9891Department of Obstetrics and Gynecology, Guizhou Medical University, No.9 Beijing Road, Yunyan District, Guizhou, 550000 Guizhou Province China
| | - Yuankun Qin
- grid.413458.f0000 0000 9330 9891Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, Guizhou, 550025 Guizhou Province, China
| | - Danqing Li
- grid.413458.f0000 0000 9330 9891Department of Obstetrics and Gynecology, Guizhou Medical University, No.9 Beijing Road, Yunyan District, Guizhou, 550000 Guizhou Province China
| | - Yingjie Yang
- grid.413458.f0000 0000 9330 9891Department of Obstetrics and Gynecology, Guizhou Medical University, No.9 Beijing Road, Yunyan District, Guizhou, 550000 Guizhou Province China ,grid.413458.f0000 0000 9330 9891Guizhou Medical University, No.9 Beijing Road, Yunyan District, Guiyang, 550001 China ,grid.413458.f0000 0000 9330 9891Tthe Affiliated Cancer Hospital of Guizhou Medical University, No.1 Beijing West Road, Guiyang, 550000 Guizhou Province China
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Zhang S, Wang H, Liu J, Tao T, Zeng Z, Wang M. RGS1 and related genes as potential targets for immunotherapy in cervical cancer: computational biology and experimental validation. J Transl Med 2022; 20:334. [PMID: 35879796 PMCID: PMC9310486 DOI: 10.1186/s12967-022-03526-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022] Open
Abstract
Background Effective treatment is needed for advanced, inoperable, or chemotherapy-resistant cervical cancer patients. Immunotherapy has become a new treatment modality for cervical cancer patients, and there is an urgent need to identify additional targets for cervical cancer immunotherapy. Methods In this study the core gene, RGS1, which affects immune status and the FIGO stage of cervical cancer patients was identified by WGCNA analysis and differential analysis using TCGA database. 10 related genes interacting with RGS1 were identified using PPI network, and the functional and immune correlations were analyzed. Based on the expression of RGS1 and related genes, the consensus clustering method was used to divide CESC patients into two groups (group 1, high expression of RGS1; group 2, low expression of RGS1). Then, the functional enrichment analysis was used to search for the functional differences in differentially expressed genes (DEGs) between group 1 and group 2. Immune infiltration analysis was performed using ESTIMATE, CIBERSORT, and ssGSEA, and the differences in expression of immune checkpoint inhibitors (ICIs) targets were assessed between the two groups. We investigated the effect of RGS1 on the clinical relevance of CESC patients, and experimentally verified the differences in RGS1 expression between cervical cancer patient tissues and normal cervical tissues, the role of RGS1 in cell function, and the effect on tumor growth in tumor-bearing mice. Results We found that RGS1 was associated with CD4, GNAI3, RGS2, GNAO1, GNAI2, RGS20, GNAZ, GNAI1, HLA-DRA and HLA-DRB1, especially CD4 and RGS2. Functional enrichment of DEGs was associated with T cell activation. Compared with group 2, group 1 had stronger immune infiltration and higher ICI target expression. RGS1 had higher expression in cervical cancer tissues than normal tissues, especially in HPV-E6 positive cancer tissues. In cervical cancer cell lines, knockdown of RGS1 can inhibited cell proliferation, migration, invasion, and tumor growth in nude mice and promoted apoptosis. Conclusions RGS1, as an oncogenic gene of cervical cancer, affects the immune microenvironment of patients with cervical cancer and may be a target of immunotherapy.
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