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Karihtala P, Kilpivaara O, Porvari K. Mutational signatures and their association with survival and gene expression in urological carcinomas. Neoplasia 2023; 44:100933. [PMID: 37678146 PMCID: PMC10495641 DOI: 10.1016/j.neo.2023.100933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023]
Abstract
Different sources of mutagenesis cause consistently identifiable patterns of mutations and mutational signatures that mirror the various carcinogenetic processes. We used publicly available data from the Cancer Genome Atlas to evaluate the associations between the activity of the mutational signatures and various survival endpoints in six types of urological cancers after adjusting for established prognostic factors. The predictive power of the signatures was evaluated with dynamic area under curve models. In addition, links between mutational signature activities and differences in gene expression patterns were analysed. APOBEC-related signature SBS2 was associated with improved overall survival (OS) and disease-specific survival (DSS) in bladder carcinomas in the multivariate analysis, while clock-like signature SBS1 predicted shortened DSS and progression-free interval (PFI) in clear cell renal cell carcinomas (ccRCC). In papillary renal cell carcinomas (pRCC), SBS45 was a predictor of improved outcomes, and APOBEC-related SBS13 was a predictor of worse outcomes. Gene expression analyses revealed various enriched pathways between the low- and high-signature groups. Interestingly, in both the ccRCC and pRCC cohorts, the genes of several members of the melanoma antigen (MAGE) family were highly upregulated in the signatures, which predicted poor outcomes, and downregulated in signatures, which were associated with improved survival. To summarize, SBS signatures provide substantial prognostic value compared with just the traditional prognostic factors in certain cancer types. APOBEC-related SBS2 and SBS13 seem to provide robust prognostic information for particular urological cancers, maybe driven by the expression of specific groups of genes, including the MAGE gene family.
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Affiliation(s)
- Peeter Karihtala
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center and University of Helsinki, Helsinki FI-00290, Finland.
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki FI-00014, Finland; Department of Medical and Clinical Genetics, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland; HUSLAB Laboratory of Genetics, HUS Diagnostic Center, Helsinki University Hospital, Helsinki FI-00014, Finland
| | - Katja Porvari
- Department of Pathology, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu FI-90220, Finland
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Shankar Tade R, Onkar Patil P. Fabrication of poly (aspartic) acid functionalized graphene quantum dots based FRET sensor for selective and sensitive detection of MAGE-A11 antigen. Microchem J 2022; 183:107971. [DOI: 10.1016/j.microc.2022.107971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Pan Y, Fan Y, Lu Y, Peng S, Lin H, Deng Q. Molecular characterization of matrix metalloproteinase gene family across primates. Aging (Albany NY) 2022; 14:3425-3445. [PMID: 35444067 PMCID: PMC9085222 DOI: 10.18632/aging.204021] [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: 10/12/2021] [Accepted: 04/12/2022] [Indexed: 11/25/2022]
Abstract
Deregulation of matrix metalloproteinases (MMPs) contributes considerably to cancers, psychiatric disorders, macular degeneration and bone diseases. The use of humans in the development of MMPs as prognostic biomarkers and therapeutic targets is complicated by many factors, while primate models can be useful alternatives for this purpose. Here, we performed genome-enabled identification of putative MMPs across primate species, and comprehensively investigated the genes. Phylogenetic topology of the MMP family showed each type formulates a distinct clade, and was further clustered to classes, largely agreeing with classification based on biochemical properties and domain organization. Across primates, the excess of candidate sites of positive selection was detected for MMP-19, in addition to 1-3 sites in MMP-8, MMP-10 and MMP-26. MMP-26 showed Ka/Ks value above 1 between human and chimpanzee copies. We observed two copies of MMP-19 in the old-world monkey genomes, suggesting gene duplication at the early stage of or prior to the emergence of the lineage. Furin-activatable MMPs demonstrate the most variable properties regarding Domain organization and gene structure. During human aging, MMP-11 showed gradually decreased expression in testis, so as MMP-2, MMP-14, MMP15 and MMP-28 in ovary, while MMP-7 and MMP-21 showed elevated expression, implying their distinct roles in different reproductive organs. Co-expression clusters were formed among human MMPs both within and across classes, and expression correlation was observed in MMP genes across primates. Our results illuminate the utilization of MMPs for the discovery of prognostic biomarkers and therapeutic targets for aging-related diseases and carry new messages on MMP classification.
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Affiliation(s)
- Yinglian Pan
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, People's Republic of China
| | - Yadan Fan
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, People's Republic of China
| | - Yanda Lu
- Department of Medical Oncology, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan, People's Republic of China
| | - Siyuan Peng
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, People's Republic of China
| | - Haixue Lin
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, People's Republic of China
| | - Qingchun Deng
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, Hainan, People's Republic of China
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Liu M, Li J, Wang Y, Ghaffar M, Yang Y, Wang M, Li C. MAGEA6 positively regulates MSMO1 and promotes the migration and invasion of oesophageal cancer cells. Exp Ther Med 2022; 23:204. [PMID: 35126707 PMCID: PMC8796618 DOI: 10.3892/etm.2022.11127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 08/02/2021] [Indexed: 11/20/2022] Open
Abstract
The melanoma antigen gene family A (MAGEA) family of proteins comprises of cancer-testis antigens that are highly expressed in a number of tumours but are minimally expressed in normal cells. Due to its expression characteristics, this protein family has become a popular target for anti-cancer drugs and immunotherapy research over recent years. Although, elevated expression levels of MAGEA6 has been found in different types of tumours, there remains to be insufficient information on the function of MAGEA6 and its associated gene regulation pathways. The present study used Transwell, Cell Counting Kit-8 and wound healing assays to analyse the effects of MAGEA6 on Eca109 cell invasion, migration and proliferation. The main functions and pathways involved in MAGEA6 were predicted by Illumina Hiseq screening for mutually regulated genes and core genes. Eca109 cell line with a high expression of MAGEA6 was a stable cell line obtained by transfection in the early stage, and this cell line was used in subsequent experiments. Transcriptome sequencing was performed on this cell line and the Eca109 cell line that normally expressed MAGEA6. It was revealed that a high expression of MAGEA6 conferred a significant stimulating effect on cell proliferation whilst also significantly increasing cell invasion and migration. Transcriptomic analysis identified 14 differentially expressed genes and 13 core regulatory genes closely associated with MAGEA6 expression regulation, such as methylsterol monooxygenase 1 (MSMO1). The present study suggest that MAGEA6 positively regulated MSMO1 expression, which may serve an oncogenic role in cells through this regulatory effect. Overall, this provided a novel route of investigation for an in-depth study of the regulatory function of MAGEA6.
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Affiliation(s)
- Manyu Liu
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, P.R. China
| | - Jintao Li
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, P.R. China
| | - Yangjunqi Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, P.R. China
| | - Maliha Ghaffar
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, P.R. China
| | - Yishu Yang
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, P.R. China
| | - Minglian Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, P.R. China
| | - Changshuo Li
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, P.R. China
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Florke Gee RR, Chen H, Lee AK, Daly CA, Wilander BA, Fon Tacer K, Potts PR. Emerging roles of the MAGE protein family in stress response pathways. J Biol Chem 2020; 295:16121-16155. [PMID: 32921631 PMCID: PMC7681028 DOI: 10.1074/jbc.rev120.008029] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
The melanoma antigen (MAGE) proteins all contain a MAGE homology domain. MAGE genes are conserved in all eukaryotes and have expanded from a single gene in lower eukaryotes to ∼40 genes in humans and mice. Whereas some MAGEs are ubiquitously expressed in tissues, others are expressed in only germ cells with aberrant reactivation in multiple cancers. Much of the initial research on MAGEs focused on exploiting their antigenicity and restricted expression pattern to target them with cancer immunotherapy. Beyond their potential clinical application and role in tumorigenesis, recent studies have shown that MAGE proteins regulate diverse cellular and developmental pathways, implicating them in many diseases besides cancer, including lung, renal, and neurodevelopmental disorders. At the molecular level, many MAGEs bind to E3 RING ubiquitin ligases and, thus, regulate their substrate specificity, ligase activity, and subcellular localization. On a broader scale, the MAGE genes likely expanded in eutherian mammals to protect the germline from environmental stress and aid in stress adaptation, and this stress tolerance may explain why many cancers aberrantly express MAGEs Here, we present an updated, comprehensive review on the MAGE family that highlights general characteristics, emphasizes recent comparative studies in mice, and describes the diverse functions exerted by individual MAGEs.
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Affiliation(s)
- Rebecca R Florke Gee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Helen Chen
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anna K Lee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christina A Daly
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Benjamin A Wilander
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Klementina Fon Tacer
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA.
| | - Patrick Ryan Potts
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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Jia S, Zhang M, Li Y, Zhang L, Dai W. MAGE-A11 Expression Predicts Patient Prognosis in Head and Neck Squamous Cell Carcinoma. Cancer Manag Res 2020; 12:1427-1435. [PMID: 32161495 PMCID: PMC7051897 DOI: 10.2147/cmar.s237867] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 11/08/2019] [Accepted: 02/11/2020] [Indexed: 11/23/2022] Open
Abstract
Background Head and neck squamous cell carcinomas (HNSCCs) are the sixth most common cancer worldwide. Growing evidence showed that Melanoma-associated antigen-A11 (MAGE-A11) was abnormally expressed in various malignancies, but MAGE-A11 expression and its biological roles in HNSCC had not been reported in detail. The aim of the study was to investigate the association between MAGE-A11 signatures and clinicopathological features of HNSCC patients and uncover its potential mechanisms in HNSCC patients. Methods In the present study, we analyzed the expression of MAGE-A11 gene and evaluated the impact of MAGE-A11 genes expression on clinical outcome from the Cancer Genome Atlas (TCGA) database. MAGE-A11 expression was assessed in a well-characterized series of HNSCC (N = 75) with long-term follow-up and 10 cases of adjacent non-cancerous tissues, which were diagnosed between 2013 and 2014, by using immunohistochemistry. The correlation between MAGE-A11 expression and clinicopathological factors was analyzed. Kaplan-Meier and Cox regression analyses were used to assess the prognostic significance of MAGE-A11 expression among HNSCC patients. Results The results showed that MAGE-A11 mRNA expression was increased in HNSCC tissues compared to "normal" tissues (P < 10-12). MAGE-A11 protein expression was not correlated with lymph node status, relapse, age, gender, histological grade, differentiation, clinical stage, tumor size, radiotherapy or chemotherapy. The patients with high MAGE-A11 expression had lower 5-year overall survival (OS) rates than those with low MAGE-A11 expression as determined using the Kaplan-Meier method. The univariate and multivariate analyses confirmed that elevated MAGE-A11 was an independent prognostic factor for the OS of HNSCC patients. Conclusion These findings indicate that MAGE-A11 may be a valuable diagnostic or prognostic marker as well as a potential molecular therapy target for HNSCC patients.
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Affiliation(s)
- Shiheng Jia
- Key Laboratory of Cell Biology, Ministry of Public Health, China Medical University, Liaoning, Shenyang 110122, People's Republic of China.,Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Liaoning, Shenyang 110122, People's Republic of China.,Department of Cell Biology, China Medical University, Liaoning, Shenyang 110122, People's Republic of China.,Department of Clinical Medicine, China Medical University, Liaoning, Shenyang 110122, People's Republic of China
| | - Minghui Zhang
- Key Laboratory of Cell Biology, Ministry of Public Health, China Medical University, Liaoning, Shenyang 110122, People's Republic of China.,Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Liaoning, Shenyang 110122, People's Republic of China.,Department of Cell Biology, China Medical University, Liaoning, Shenyang 110122, People's Republic of China.,Department of Clinical Medicine, China Medical University, Liaoning, Shenyang 110122, People's Republic of China
| | - Yanshu Li
- Key Laboratory of Cell Biology, Ministry of Public Health, China Medical University, Liaoning, Shenyang 110122, People's Republic of China.,Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Liaoning, Shenyang 110122, People's Republic of China.,Department of Cell Biology, China Medical University, Liaoning, Shenyang 110122, People's Republic of China
| | - Lan Zhang
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Liaoning, Shenyang 110002, People's Republic of China
| | - Wei Dai
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Liaoning, Shenyang 110002, People's Republic of China
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