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Li P, Xu Q, Liu K, Ye J. CRYL1 is a Potential Prognostic Biomarker of Clear Cell Renal Cell Carcinoma Correlated with Immune Infiltration and Cuproptosis. Technol Cancer Res Treat 2024; 23:15330338241237439. [PMID: 38497139 PMCID: PMC10946081 DOI: 10.1177/15330338241237439] [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: 10/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is a widespread urogenital neoplasm. However, the therapeutic efficacy of these methods is unsatisfactory. In-depth screening of biomarkers could aid early diagnosis and therapy and predict patient prognosis. METHODS The GEO datasets were selected with specific criteria. Differentially expressed gene (DEG), weighted gene coexpression network analysis (WGCNA), protein-protein interaction, LASSO, random forest, and Cox regression analyses were applied to identify the independent prognostic biomarkers. Survival analysis, correlation with clinical features, gene set enrichment analysis (GSEA), GO enrichment, immune infiltration analysis, and correlation with cuproptosis-related genes were carried out to determine the prognostic value and possible molecular mechanisms of the TSVR. Wound healing assays, transwell assays, cell colony formation experiments, flow cytometry, and immunohistochemistry (IHC) analysis were used to validate the functional attributes of CRYL1. RESULTS Four GEO datasets were included to screen for hub genes. DEG combined with WGCNA showed a key module with 300 genes having the strongest correlation with "survival state" (R2 = -0.24 and P = 7e-8); six genes were identified by LASSO, random forest, and Cytoscape. Finally, CRYL1 (hazard ratio (HR) = 2.01, P < 0.001) was selected as an independent prognostic biomarker. The higher CRYL1 expression group had better DFS and overall survival (OS). GSEA demonstrated that the CRYL1-related DEGs were enriched mainly in the metabolism of sugar, fat, and amino acids. CRYL1 is positively correlated with FDX1 and the LIAS pathway, which are important molecule involved in cuproptosis. CRYL1 affects the infiltration abundance of four immune cells and can predict a positive OS. Wound healing, transwell, cell colony formation, and flow cytometry assays demonstrated that CRYL1 silencing enhances migration and proliferation and leads to a decreased apoptotic ratio. IHC analysis suggested that CRYL1 was highly expressed in adjacent tissues. CONCLUSIONS CRYL1 is a robust predictive marker for clinicopathological characteristics and survival status in ccRCC patients.
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Affiliation(s)
- Peng Li
- The 6th affiliated hospital of wenzhou medical university, Lishui city people's hospital, Lishui, Zhejiang, China
- Lishui city people's hospital, The first affiliated hospital of Lishui University, Lishui, Zhejiang, China
| | - Qiangqiang Xu
- The 6th affiliated hospital of wenzhou medical university, Lishui city people's hospital, Lishui, Zhejiang, China
- Lishui city people's hospital, The first affiliated hospital of Lishui University, Lishui, Zhejiang, China
| | - Ken Liu
- The 6th affiliated hospital of wenzhou medical university, Lishui city people's hospital, Lishui, Zhejiang, China
- Lishui city people's hospital, The first affiliated hospital of Lishui University, Lishui, Zhejiang, China
| | - Junjie Ye
- The 6th affiliated hospital of wenzhou medical university, Lishui city people's hospital, Lishui, Zhejiang, China
- Lishui city people's hospital, The first affiliated hospital of Lishui University, Lishui, Zhejiang, China
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Chiang YT, Lin PH, Lo MY, Chen HL, Lee CY, Tsai CY, Lin YH, Tsai SF, Liu TC, Hsu CJ, Chen PL, Hsu JSJ, Wu CC. Genetic Factors Contribute to the Phenotypic Variability in GJB2-Related Hearing Impairment. J Mol Diagn 2023; 25:827-837. [PMID: 37683890 DOI: 10.1016/j.jmoldx.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 09/10/2023] Open
Abstract
Recessive variants in GJB2 are the most important genetic cause of sensorineural hearing impairment (SNHI) worldwide. Phenotypes vary significantly in GJB2-related SNHI, even in patients with identical variants. For instance, patients homozygous for the GJB2 p.V37I variant, which is highly prevalent in the Asian populations, usually present with mild-to-moderate SNHI; yet severe-to-profound SNHI is occasionally observed in approximately 10% of p.V37I homozygotes. To investigate the genomic underpinnings of the phenotypic variability, we performed next-generation sequencing of GJB2 and other deafness genes in 63 p.V37I homozygotes with extreme phenotypic severities. Additional pathogenic variants of other deafness genes were identified in five of the 35 patients with severe-to-profound SNHI. Furthermore, case-control association analyses were conducted for 30 unrelated p.V37I homozygotes with severe-to-profound SNHI against 28 p.V37I homozygotes with mild-to-moderate SNHI, and 120 population controls from the Taiwan Biobank. The severe-to-profound group exhibited a higher frequency of the crystallin lambda 1 (CRYL1) variant (rs14236), located upstream of GJB2, than the mild-to-moderate and Taiwan Biobank groups. Our results demonstrated that pathogenic variants in other deafness genes and a possible modifier, the CRYL1 rs14236 variant, may contribute to phenotypic variability in GJB2-realted SNHI, highlighting the importance of comprehensive genomic surveys to delineate the genotype-phenotype correlations.
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Affiliation(s)
- Yu-Ting Chiang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Hsuan Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Otolaryngology Head and Neck Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Yu Lo
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Lin Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Surgical Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Chen-Yu Lee
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Cheng-Yu Tsai
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yin-Hung Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Feng Tsai
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan; Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Tien-Chen Liu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chuan-Jen Hsu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Otolaryngology Head and Neck Surgery, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Jacob Shu-Jui Hsu
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Chen-Chi Wu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
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Feng L, Ding G, Zhou Y, Zhu H, Jiang H. Downregulation of Crystallin Lambda 1 is a New Independent Prognostic Marker in Clear Cell Renal Cell Carcinoma. Pharmgenomics Pers Med 2022; 15:857-866. [PMID: 36246497 PMCID: PMC9563328 DOI: 10.2147/pgpm.s382564] [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: 07/15/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC), the most prevalent kidney cancer subtype, has a high mortality rate. Crystallin lambda 1 (CRYL1) encodes an enzyme that catalyzes the dehydrogenation of L-gulonate into dehydro-L-gulonate in uronate cycle. CRYL1 dysregulation has been linked to the progression of several cancers. This research aimed to evaluate the prognostic significance of CRYL1 expression in ccRCC prognosis. Methods Clinical data and gene expression profiles on ccRCC were retrieved from the University of California Santa Cruz Xena platform. Differences (variations) in the expression profiles of CRYL1 in ccRCC and healthy tissues were found using RNA-sequencing data, and these findings were validated using qPCR with real-world samples. CRYL1 expression levels were also linked to clinicopathological characteristics, survival, and immune microenvironments. The potential pathway via which CRYL1 expression levels impact the prognosis of patients with ccRCC was investigated using gene set enrichment analysis (GSEA). Results In ccRCC tissues, CRYL1 expression levels were lower compared to healthy renal tissues in TCGA cohort (n = 535, P < 0.001), which was validated in another real-world cohort (n = 14, P < 0.001). Lower CRYL1 expression levels were linked to unfavorable clinicopathological characteristics and prognoses (P < 0.001). According to multivariate Cox regression analysis (P < 0.001), CRYL1 expression levels in patients with ccRCC could serve as an independent prognostic indicator. Furthermore, a strong link between CRYL1 expression levels and immune microenvironment was observed (P < 0.001). Finally, GSEA revealed that CRYL1 expression levels (P < 0.001) were associated with fatty acid metabolism, G2M checkpoint delays, and epithelial-mesenchymal transitions in ccRCC. Conclusion Our study found that lower levels of CRYL1 expression were linked to unfavorable clinicopathological characteristics and worse prognoses, and CRYL1 could serve as a new target for the treatment of ccRCC, which is useful for personalized medicine.
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Affiliation(s)
- Lingsong Feng
- Department of Urology, Meizhou People’s Hospital, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China
| | - Guodong Ding
- Department of Urology, Meizhou People’s Hospital, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China
| | - Yang Zhou
- Department of Urology, Meizhou People’s Hospital, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China
| | - Haiyuan Zhu
- Department of Urology, Meizhou People’s Hospital, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China
| | - Huiming Jiang
- Department of Urology, Meizhou People’s Hospital, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China,Correspondence: Huiming Jiang, Tel +86-13560990839, Email
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Osakunor DNM, Ishida K, Lamanna OK, Rossi M, Dwomoh L, Hsieh MH. Host tissue proteomics reveal insights into the molecular basis of Schistosoma haematobium-induced bladder pathology. PLoS Negl Trop Dis 2022; 16:e0010176. [PMID: 35167594 PMCID: PMC8846513 DOI: 10.1371/journal.pntd.0010176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/17/2022] [Indexed: 12/25/2022] Open
Abstract
Urogenital schistosomiasis remains a major public health concern worldwide. In response to egg deposition, the host bladder undergoes gross and molecular morphological changes relevant for disease manifestation. However, limited mechanistic studies to date imply that the molecular mechanisms underlying pathology are not well-defined. We leveraged a mouse model of urogenital schistosomiasis to perform for the first time, proteome profiling of the early molecular events that occur in the bladder after exposure to S. haematobium eggs, and to elucidate the protein pathways involved in urogenital schistosomiasis-induced pathology. Purified S. haematobium eggs or control vehicle were microinjected into the bladder walls of mice. Mice were sacrificed seven days post-injection and bladder proteins isolated and processed for proteome profiling using mass spectrometry. We demonstrate that biological processes including carcinogenesis, immune and inflammatory responses, increased protein translation or turnover, oxidative stress responses, reduced cell adhesion and epithelial barrier integrity, and increased glucose metabolism were significantly enriched in S. haematobium infection. S. haematobium egg deposition in the bladder results in significant changes in proteins and pathways that play a role in pathology. Our findings highlight the potential bladder protein indicators for host-parasite interplay and provide new insights into the complex dynamics of pathology and characteristic bladder tissue changes in urogenital schistosomiasis. The findings will be relevant for development of improved interventions for disease control.
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Affiliation(s)
- Derick N. M. Osakunor
- Division of Urology, Department of Surgery, Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, Washington, District of Columbia, United States of America
| | - Kenji Ishida
- Division of Urology, Department of Surgery, Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, Washington, District of Columbia, United States of America
| | - Olivia K. Lamanna
- Division of Urology, Department of Surgery, Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, Washington, District of Columbia, United States of America
| | - Mario Rossi
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Louis Dwomoh
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Michael H. Hsieh
- Division of Urology, Department of Surgery, Sheikh Zayed Institute for Pediatric Surgical Innovation, Children’s National Hospital, Washington, District of Columbia, United States of America
- Departments of Urology, Department of Pediatrics, and Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, District of Columbia, United States of America
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Uronic acid metabolic process-related gene expression-based signature predicts overall survival of glioma. Biosci Rep 2021; 41:227321. [PMID: 33324981 PMCID: PMC7791545 DOI: 10.1042/bsr20203051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 11/17/2022] Open
Abstract
Glioma is the most common and malignant cancer of the central nervous system, and the prognosis is poor. Metabolic reprogramming is a common phenomenon that plays an important role in tumor progression including gliomas. Searching the representative process among numerous metabolic processes to evaluate the prognosis aside from the glycolytic pathway may be of great significance. A novel prediction signature was constructed in the present study based on gene expression. A total of 1027 glioma samples with clinical and RNA-seq data were used in the present study. Lasso-Cox, gene set variation analysis, Kaplan-Meier survival curve analysis, Cox regression, receiver operating characteristic curve, and elastic net were performed for constructing and verifying predictive models. The R programming language was used as the main tool for statistical analysis and graphical work. This signature was found to be stable in prognostic prediction in the Chinese Glioma Genome Atlas Network and the Cancer Genome Atlas databases. The possible mechanism was also explored, revealing that the aforementioned signature was closely related to DNA replication and ATP binding. In summary, a prognosis prediction signature for patients with glioma based on five genes was constructed and showed great potential for clinical application.
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6
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Screening and identification of potential prognostic biomarkers in bladder urothelial carcinoma: Evidence from bioinformatics analysis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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7
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Huang Y, Zheng J, Chen D, Li F, Wu W, Huang X, Wu Y, Deng Y, Qiu F. Transcriptome profiling identifies a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma. Oncotarget 2018; 8:40693-40704. [PMID: 28489570 PMCID: PMC5522265 DOI: 10.18632/oncotarget.17244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 04/05/2017] [Indexed: 01/05/2023] Open
Abstract
We performed transcriptome sequencing for hepatocellular carcinoma (HCC) and adjacent non-tumorous tissues to investigate the molecular basis of HCC. Nine HCC patients were recruited and differentially expressed genes (DEGs) were identified. Candidate fusion transcripts were also identified. A total of 1943 DEGs were detected, including 690 up-regulated and 1253 down-regulated genes, and enriched in ten pathways including cell cycle, DNA replication, p53, complement and coagulation cascades, etc. Seven candidate fusion genes were detected and CRYL1-IFT88 was successfully validated in the discovery sequencing sample and another 5 tumor samples with the recurrent rate of about 9.52% (6/63). The full length of CRYL1-IFT88 was obtained by 3′ and 5′ RACE. The function of the fusion transcript is closed to CRYL1 because it contained most of domain of CRYL1. According to the bioinformatics analysis, IFT88, reported as a tumor suppressor, might be seriously depressed in the tumor cell with this fusion because the transcript structure of IFT88 was totally changed. The function depression of IFT88 caused by gene fusion CRYL1-IFT88 might be associated with tumorigenesis or development of HCC.
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Affiliation(s)
- Yi Huang
- Provincial Clinical College, Fujian Medical University, Fuzhou 350001, Fujian, China.,Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou 350001, Fujian, China
| | - Jiaying Zheng
- Provincial Clinical College, Fujian Medical University, Fuzhou 350001, Fujian, China.,Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou 350001, Fujian, China
| | - Dunyan Chen
- Provincial Clinical College, Fujian Medical University, Fuzhou 350001, Fujian, China.,Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou 350001, Fujian, China
| | - Feng Li
- Provincial Clinical College, Fujian Medical University, Fuzhou 350001, Fujian, China.,Department of Pathology, Fujian Provincial Hospital, Fuzhou 350001, Fujian, China
| | - Wenbing Wu
- Provincial Clinical College, Fujian Medical University, Fuzhou 350001, Fujian, China.,Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou 350001, Fujian, China
| | - Xiaoli Huang
- Provincial Clinical College, Fujian Medical University, Fuzhou 350001, Fujian, China.,Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou 350001, Fujian, China
| | - Yanan Wu
- Provincial Clinical College, Fujian Medical University, Fuzhou 350001, Fujian, China.,Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou 350001, Fujian, China
| | - Yangyang Deng
- Department of Bioinformatics, MyGene Diagnostics Co., Ltd, Guangzhou 510300, Guangdong, China
| | - Funan Qiu
- Provincial Clinical College, Fujian Medical University, Fuzhou 350001, Fujian, China.,Department of Hepatobiliary Surgery, Fujian Provincial Hospital, Fuzhou 350001, Fujian, China
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Tornesello ML, Buonaguro L, Izzo F, Buonaguro FM. Molecular alterations in hepatocellular carcinoma associated with hepatitis B and hepatitis C infections. Oncotarget 2018; 7:25087-102. [PMID: 26943571 PMCID: PMC5041890 DOI: 10.18632/oncotarget.7837] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/20/2016] [Indexed: 02/07/2023] Open
Abstract
Chronic infections with hepatitis B (HBV) and hepatitis C viruses (HCV) are the leading cause of cirrhosis and hepatocellular carcinoma (HCC) worldwide. Both viruses encode multifunctional regulatory proteins activating several oncogenic pathways, which induce accumulation of multiple genetic alterations in the infected hepatocytes. Gene mutations in HBV- and HCV-induced HCCs frequently impair the TP53, Wnt/b-catenin, RAS/RAF/MAPK kinase and AKT/mTOR pathways, which represent important anti-cancer targets. In this review, we highlight the molecular mechanisms underlying the pathogenesis of primary liver cancer, with particular emphasis on the host genetic variations identified by high-throughput technologies. In addition, we discuss the importance of genetic alterations, such as mutations in the telomerase reverse transcriptase (TERT) promoter, for the diagnosis, prognosis, and tumor stratification for development of more effective treatment approaches.
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Affiliation(s)
- Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Luigi Buonaguro
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Francesco Izzo
- Hepato-Biliary Surgery Department, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Franco M Buonaguro
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
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9
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Ramaker RC, Lasseigne BN, Hardigan AA, Palacio L, Gunther DS, Myers RM, Cooper SJ. RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature. Oncotarget 2017; 8:38668-38681. [PMID: 28454104 PMCID: PMC5503562 DOI: 10.18632/oncotarget.16961] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/29/2017] [Indexed: 02/06/2023] Open
Abstract
Despite advances in cancer diagnosis and treatment strategies, robust prognostic signatures remain elusive in most cancers. Cell proliferation has long been recognized as a prognostic marker in cancer, but the generation of comprehensive, publicly available datasets allows examination of the links between cell proliferation and cancer characteristics such as mutation rate, stage, and patient outcomes. Here we explore the role of cell proliferation across 19 cancers (n = 6,581 patients) by using tissue-based RNA sequencing data from The Cancer Genome Atlas Project and calculating a 'proliferative index' derived from gene expression associated with Proliferating Cell Nuclear Antigen (PCNA) levels. This proliferative index is significantly associated with patient survival (Cox, p-value < 0.05) in 7 of 19 cancers, which we have defined as "proliferation-informative cancers" (PICs). In PICs, the proliferative index is strongly correlated with tumor stage and nodal invasion. PICs demonstrate reduced baseline expression of proliferation machinery relative to non-PICs. Additionally, we find the proliferative index is significantly associated with gross somatic mutation burden (Spearman, p = 1.76 x 10-23) as well as with mutations in individual driver genes. This analysis provides a comprehensive characterization of tumor proliferation indices and their association with disease progression and prognosis in multiple cancer types and highlights specific cancers that may be particularly susceptible to improved targeting of this classic cancer hallmark.
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Affiliation(s)
- Ryne C. Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Andrew A. Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Laura Palacio
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
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10
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Retinoblastoma binding protein 6 and crystallin lambda 1 are cadmium-responsive genes in zebrafish embryos and adults retinae. C R Biol 2017; 340:197-203. [DOI: 10.1016/j.crvi.2017.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/08/2017] [Indexed: 12/21/2022]
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Oelsner KT, Guo Y, To SBC, Non AL, Barkin SL. Maternal BMI as a predictor of methylation of obesity-related genes in saliva samples from preschool-age Hispanic children at-risk for obesity. BMC Genomics 2017; 18:57. [PMID: 28068899 PMCID: PMC5223358 DOI: 10.1186/s12864-016-3473-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 12/26/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The study of epigenetic processes and mechanisms present a dynamic approach to assess complex individual variation in obesity susceptibility. However, few studies have examined epigenetic patterns in preschool-age children at-risk for obesity despite the relevance of this developmental stage to trajectories of weight gain. We hypothesized that salivary DNA methylation patterns of key obesogenic genes in Hispanic children would 1) correlate with maternal BMI and 2) allow for identification of pathways associated with children at-risk for obesity. RESULTS Genome-wide DNA methylation was conducted on 92 saliva samples collected from Hispanic preschool children using the Infinium Illumina HumanMethylation 450 K BeadChip (Illumina, San Diego, CA, USA), which interrogates >484,000 CpG sites associated with ~24,000 genes. The analysis was limited to 936 genes that have been associated with obesity in a prior GWAS Study. Child DNA methylation at 17 CpG sites was found to be significantly associated with maternal BMI, with increased methylation at 12 CpG sites and decreased methylation at 5 CpG sites. Pathway analysis revealed methylation at these sites related to homocysteine and methionine degradation as well as cysteine biosynthesis and circadian rhythm. Furthermore, eight of the 17 CpG sites reside in genes (FSTL1, SORCS2, NRF1, DLC1, PPARGC1B, CHN2, NXPH1) that have prior known associations with obesity, diabetes, and the insulin pathway. CONCLUSIONS Our study confirms that saliva is a practical human tissue to obtain in community settings and in pediatric populations. These salivary findings indicate potential epigenetic differences in Hispanic preschool children at risk for pediatric obesity. Identifying early biomarkers and understanding pathways that are epigenetically regulated during this critical stage of child development may present an opportunity for prevention or early intervention for addressing childhood obesity. TRIAL REGISTRATION The clinical trial protocol is available at ClinicalTrials.gov ( NCT01316653 ). Registered 3 March 2011.
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Affiliation(s)
- Kathryn Tully Oelsner
- College of Medicine, Medical University of South Carolina, 96 Jonathan Lucas St, Suite 601, MSC 617, Charleston, SC 29425 USA
| | - Yan Guo
- Center for Quantitative Research, School of Medicine, Vanderbilt University, 2220 Pierce Ave, 571 Preston Research Building, Nashville, TN USA
| | - Sophie Bao-Chieu To
- Department of Biological Sciences, Vanderbilt University, 1210 BSB, 465 21st Ave S, Nashville, TN USA
| | - Amy L. Non
- Department of Anthropology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Shari L. Barkin
- Department of Pediatrics, Vanderbilt University School of Medicine, 2200 Children’s Way, Doctor’s Office Tower 8232, Nashville, TN 37232-9225 USA
- Pediatric Obesity Research, Diabetes Research and Training Center, Vanderbilt University School of Medicine, 2200 Children’s Way, Doctor’s Office Tower 8232, Nashville, TN 37232-9225 USA
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12
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Zhang ZZ, Huang J, Wang YP, Cai B, Han ZG. NOXIN as a cofactor of DNA polymerase-primase complex could promote hepatocellular carcinoma. Int J Cancer 2015; 137:765-75. [PMID: 25612832 DOI: 10.1002/ijc.29451] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 12/23/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Zhuang-Zhuang Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital; Shanghai Jiao Tong University School of Medicine; Shanghai China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics; Chinese National Human Genome Center at Shanghai; Shanghai China
| | - Jian Huang
- Shanghai-MOST Key Laboratory for Disease and Health Genomics; Chinese National Human Genome Center at Shanghai; Shanghai China
| | - Yu-Ping Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital; Shanghai Jiao Tong University School of Medicine; Shanghai China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics; Chinese National Human Genome Center at Shanghai; Shanghai China
| | - Bing Cai
- Department of Hepatobiliary Surgery; Wuxi People's Hospital of Nanjing Medical University; Jiangsu China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital; Shanghai Jiao Tong University School of Medicine; Shanghai China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics; Chinese National Human Genome Center at Shanghai; Shanghai China
- Shanghai Center for Systems Biomedicine; Shanghai Jiao Tong University; Shanghai China
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Schifferli A, Hitzler J, Bartholdi D, Heinimann K, Hoeller S, Diesch T, Kühne T. Transient myeloproliferative disorder in neonates without Down syndrome: case report and review. Eur J Haematol 2014; 94:456-62. [DOI: 10.1111/ejh.12382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Alexandra Schifferli
- Department of haematology/oncology; University Children's Hospital Basel; Basel Switzerland
| | - Johann Hitzler
- Department of haematology/oncology; The Hospital for Sick Children; Toronto Canada
| | | | - Karl Heinimann
- Department of genetic; University Hospital Basel; Basel Switzerland
| | - Sylvia Hoeller
- Department of pathology; University Hospital Basel; Basel Switzerland
| | - Tamara Diesch
- Department of haematology/oncology; University Children's Hospital Basel; Basel Switzerland
| | - Thomas Kühne
- Department of haematology/oncology; University Children's Hospital Basel; Basel Switzerland
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14
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Chen J, Chan AWH, To KF, Chen W, Zhang Z, Ren J, Song C, Cheung YS, Lai PBS, Cheng SH, Ng MHL, Huang A, Ko BCB. SIRT2 overexpression in hepatocellular carcinoma mediates epithelial to mesenchymal transition by protein kinase B/glycogen synthase kinase-3β/β-catenin signaling. Hepatology 2013; 57:2287-98. [PMID: 23348706 DOI: 10.1002/hep.26278] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 12/09/2012] [Indexed: 12/15/2022]
Abstract
UNLABELLED Sirtuin 1 (SIRT1) has been implicated in telomere maintenance and the growth of hepatocellular carcinoma (HCC). Nevertheless, the role of other sirtuins in the pathogenesis of HCC remains elusive. We found that sirtuin 2 (SIRT2), another member of the sirtuin family, also contributes to cell motility and invasiveness of HCC. SIRT2 is up-regulated in HCC cell lines and in a subset of human HCC tissues (23/45). Up-regulations of SIRT2 in primary HCC tumors were significantly correlated with the presence of microscopic vascular invasion (P = 0.001), a more advanced tumor stage (P = 0.004), and shorter overall survival (P = 0.0499). Functional studies by short hairpin RNA-mediated suppression of SIRT2 expression in HCC cell lines revealed significant inhibition of motility and invasiveness. Depletion of SIRT2 also led to the regression of epithelial-mesenchymal transition (EMT) phenotypes, whereas the ectopic expression of SIRT2 in the immortalized hepatocyte cell line L02 promoted cell motility and invasiveness. Mechanistic studies revealed that SIRT2 regulates the deacetylation and activation of protein kinase B, which subsequently impinges on the glycogen synthase kinase-3β/β-catenin signaling pathway to regulate EMT. CONCLUSIONS Our findings have uncovered a novel role for SIRT2 in HCC metastasis, and provide a rationale to explore the use of sirtuin inhibitors in HCC therapy. (HEPATOLOGY 2013;).
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Affiliation(s)
- Juan Chen
- The Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
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15
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Masui O, White NMA, DeSouza LV, Krakovska O, Matta A, Metias S, Khalil B, Romaschin AD, Honey RJ, Stewart R, Pace K, Bjarnason GA, Siu KWM, Yousef GM. Quantitative proteomic analysis in metastatic renal cell carcinoma reveals a unique set of proteins with potential prognostic significance. Mol Cell Proteomics 2012; 12:132-44. [PMID: 23082029 DOI: 10.1074/mcp.m112.020701] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Metastatic renal cell carcinoma (RCC) is one of the most treatment-resistant malignancies, and patients have a dismal prognosis, with a <10% five-year survival rate. The identification of markers that can predict the potential for metastases will have a great effect in improving patient outcomes. In this study, we used differential proteomics with isobaric tags for relative and absolute quantitation (iTRAQ) labeling and LC-MS/MS analysis to identify proteins that are differentially expressed in metastatic and primary RCC. We identified 1256 non-redundant proteins, and 456 of these were quantified. Further analysis identified 29 proteins that were differentially expressed (12 overexpressed and 17 underexpressed) in metastatic and primary RCC. Dysregulated protein expressions of profilin-1 (Pfn1), 14-3-3 zeta/delta (14-3-3ζ), and galectin-1 (Gal-1) were verified on two independent sets of tissues by means of Western blot and immunohistochemical analysis. Hierarchical clustering analysis showed that the protein expression profile specific for metastatic RCC can distinguish between aggressive and non-aggressive RCC. Pathway analysis showed that dysregulated proteins are involved in cellular processes related to tumor progression and metastasis. Furthermore, preliminary analysis using a small set of tumors showed that increased expression of Pfn1 is associated with poor outcome and is a potential prognostic marker in RCC. In addition, 14-3-3ζ and Gal-1 also showed higher expression in tumors with poor prognosis than in those with good prognosis. Dysregulated proteins in metastatic RCC represent potential prognostic markers for kidney cancer patients, and a greater understanding of their involved biological pathways can serve as the foundation of the development of novel targeted therapies for metastatic RCC.
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Affiliation(s)
- Olena Masui
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada, M3J 1P3
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16
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Han ZG. Functional genomic studies: insights into the pathogenesis of liver cancer. Annu Rev Genomics Hum Genet 2012; 13:171-205. [PMID: 22703171 DOI: 10.1146/annurev-genom-090711-163752] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Liver cancer is the sixth-most-common cancer overall but the third-most-frequent cause of cancer death. Among primary liver cancers, hepatocellular carcinoma (HCC), the major histological subtype, is associated with multiple risk factors, including hepatitis B and C virus infection, alcohol consumption, obesity, and diet contamination. Although previous studies have revealed that certain genetic and epigenetic changes, such as TP53 and β-catenin mutations, occur in HCC cells, the pathogenesis of this cancer remains obscure. Functional genomic approaches-including genome-wide association studies, whole-genome and whole-exome sequencing, array-based comparative genomic hybridization, global DNA methylome mapping, and gene or noncoding RNA expression profiling-have recently been applied to HCC patients with different clinical features to uncover the genetic risk factors and underlying molecular mechanisms involved in this cancer's initiation and progression. The genome-wide analysis of germline and somatic genetic and epigenetic events facilitates understanding of the pathogenesis and molecular classification of liver cancer as well as the identification of novel diagnostic biomarkers and therapeutic targets for cancer.
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Affiliation(s)
- Ze-Guang Han
- National Human Genome Center of Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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17
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Chung KY, Cheng IKC, Ching AKK, Chu JH, Lai PBS, Wong N. Block of proliferation 1 (BOP1) plays an oncogenic role in hepatocellular carcinoma by promoting epithelial-to-mesenchymal transition. Hepatology 2011; 54:307-18. [PMID: 21520196 DOI: 10.1002/hep.24372] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
UNLABELLED Genomic amplification of regional chromosome 8q24 is a common event in human cancers. In hepatocellular carcinoma (HCC), a highly aggressive malignancy that is rapidly fatal, recurrent 8q24 gains can be detected in >50% of cases. In this study, attempts to resolve the 8q24 region by way of array comparative genomic hybridization for affected genes in HCC revealed distinctive gains of block of proliferation 1 (BOP1). Gene expression evaluation in an independent cohort of primary HCC (n = 65) revealed frequent BOP1 up-regulation in tumors compared with adjacent nontumoral liver (84.6%; P < 0.0001). Significant associations could also be drawn between increased expressions of BOP1 and advance HCC staging (P = 0.004), microvascular invasion (P = 0.006), and shorter disease-free survival of patients (P = 0.02). Examination of expression of C-MYC, a well-known oncogene located in proximity to BOP1, in the same series of primary HCC cases did not suggest strong clinicopathologic associations. Functional investigations by small interfering RNA-mediated suppression of BOP1 in HCC cell lines indicated significant inhibition on cell invasion (P < 0.005) and migration (P < 0.05). Overexpression of BOP1 in the immortalized hepatocyte cell line L02 showed increase cellular invasiveness and cell migratory rate (P < 0.0001). In both gene knockdown and ectopic expression assays, BOP1 did not exert an effect on cell viability and proliferation. Evident regression of the epithelial-mesenchymal transition (EMT) phenotype was readily identified in BOP1 knockdown cells, whereas up-regulation of epithelial markers (E-cadherin, cytokeratin 18, and γ-catenin) and down-regulation of mesenchymal markers (fibronectin and vimentin) were seen. A corresponding augmentation of EMT was indicated from the ectopic expression of BOP1 in L02. In addition, BOP1 could stimulate actin stress fiber assembly and RhoA activation. CONCLUSION Our findings underline an important role for BOP1 in HCC invasiveness and metastasis potentials through inducing EMT and promoting actin cytoskeleton remodeling.
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Affiliation(s)
- Kit-Ying Chung
- Department of Anatomical and Cellular Pathology, Li Ka-Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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18
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Bonnefont CMD, Toufeer M, Caubet C, Foulon E, Tasca C, Aurel MR, Bergonier D, Boullier S, Robert-Granié C, Foucras G, Rupp R. Transcriptomic analysis of milk somatic cells in mastitis resistant and susceptible sheep upon challenge with Staphylococcus epidermidis and Staphylococcus aureus. BMC Genomics 2011; 12:208. [PMID: 21527017 PMCID: PMC3096985 DOI: 10.1186/1471-2164-12-208] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 04/28/2011] [Indexed: 11/12/2022] Open
Abstract
Background The existence of a genetic basis for host responses to bacterial intramammary infections has been widely documented, but the underlying mechanisms and the genes are still largely unknown. Previously, two divergent lines of sheep selected for high/low milk somatic cell scores have been shown to be respectively susceptible and resistant to intramammary infections by Staphylococcus spp. Transcriptional profiling with an 15K ovine-specific microarray of the milk somatic cells of susceptible and resistant sheep infected successively by S. epidermidis and S. aureus was performed in order to enhance our understanding of the molecular and cellular events associated with mastitis resistance. Results The bacteriological titre was lower in the resistant than in the susceptible animals in the 48 hours following inoculation, although milk somatic cell concentration was similar. Gene expression was analysed in milk somatic cells, mainly represented by neutrophils, collected 12 hours post-challenge. A high number of differentially expressed genes between the two challenges indicated that more T cells are recruited upon inoculation by S. aureus than S. epidermidis. A total of 52 genes were significantly differentially expressed between the resistant and susceptible animals. Further Gene Ontology analysis indicated that differentially expressed genes were associated with immune and inflammatory responses, leukocyte adhesion, cell migration, and signal transduction. Close biological relationships could be established between most genes using gene network analysis. Furthermore, gene expression suggests that the cell turn-over, as a consequence of apoptosis/granulopoiesis, may be enhanced in the resistant line when compared to the susceptible line. Conclusions Gene profiling in resistant and susceptible lines has provided good candidates for mapping the biological pathways and genes underlying genetically determined resistance and susceptibility towards Staphylococcus infections, and opens new fields for further investigation.
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Chen J, Zhang B, Wong N, Lo AWI, To KF, Chan AWH, Ng MHL, Ho CYS, Cheng SH, Lai PBS, Yu J, Ng HK, Ling MT, Huang AL, Cai XF, Ko BCB. Sirtuin 1 is upregulated in a subset of hepatocellular carcinomas where it is essential for telomere maintenance and tumor cell growth. Cancer Res 2011; 71:4138-49. [PMID: 21527554 DOI: 10.1158/0008-5472.can-10-4274] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hepatocellular carcinoma (HCC) is a highly malignant tumor with a poor prognosis. Treatment of HCC is complicated by the fact that the disease is often diagnosed at an advanced stage when it is no longer amenable to curative surgery, and current systemic chemotherapeutics are mostly inefficacious. Sirtuin 1 (SIRT1) is a class III histone deacetylase that is implicated in gene regulations and stress resistance. In this study, we found that SIRT1 is essential for the tumorigenesis of HCC. We showed that although SIRT1 was expressed at very low levels in normal livers, it was overexpressed in HCC cell lines and in a subset of HCC. Tissue microarray analysis of HCC and adjacent nontumoral liver tissues revealed a positive correlation between the expression levels of SIRT1 and advancement in tumor grades. Downregulation of SIRT1 consistently suppressed the proliferation of HCC cells via the induction of cellular senescence or apoptosis. SIRT1 silencing also caused telomere dysfunction-induced foci and nuclear abnormality that were clearly associated with reduced expressions of telomerase reverse transcriptase (TERT), and PTOP, which is a member of the shelter in complex. Ectopic expression of either TERT or PTOP in SIRT1-depleted cells significantly restored cell proliferation. There was also a positive correlation between the level of induction of SIRT1 and TERT [corrected] in human HCC. Finally, SIRT1-silencing sensitized HCC cells to doxorubicin treatment. Together, our findings reveal a novel function for SIRT1 in telomere maintenance of HCC, and they rationalize the clinical exploration of SIRT1 inhibitors for HCC therapy.
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Affiliation(s)
- Juan Chen
- The State Key Laboratory in Oncology in South China, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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