1
|
Zhang J, Zhang Q, Hu W, Liang Y, Jiang D, Chen H. A transcriptome-wide association study identified susceptibility genes for hepatocellular carcinoma in East Asia. Gastroenterol Rep (Oxf) 2024; 12:goae057. [PMID: 38846986 PMCID: PMC11153834 DOI: 10.1093/gastro/goae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/07/2024] [Accepted: 04/30/2024] [Indexed: 06/09/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and is prevalent in East Asia. Although genome-wide association studies (GWASs) of HCC have identified 23 risk regions, the susceptibility genes underlying these associations largely remain unclear. To identify novel candidate genes for HCC, we conducted liver single-tissue and cross-tissue transcriptome-wide association studies (TWASs) in two populations of East Asia. Methods GWAS summary statistics of 2,514 subjects (1,161 HCC cases and 1,353 controls) from the Chinese Qidong cohort and 161,323 subjects (2,122 HCC cases and 159,201 controls) from the BioBank Japan project were used to conduct TWAS analysis. The single-tissue and cross-tissue TWAS approaches were both used to detect the association between susceptible genes and the risk of HCC. TWAS identified genes were further annotated by Metascape, UALCAN, GEPIA2, and DepMap. Results We identified 22 novel genes at 16 independent loci significantly associated with HCC risk after Bonferroni correction. Of these, 13 genes were located in novel regions. Besides, we found 83 genes overlapped in the Chinese and Japanese cohorts with P < 0.05, of which, three genes (NUAK2, HLA-DQA1, and ATP6V1G2) were discerned by both single-tissue and cross-tissue TWAS approaches. Among the genes identified through TWAS, a significant proportion of them exhibit a credible role in HCC biology, such as FAM96B, HSPA5, POLRMT, MPHOSPH10, and RABL2A. HLA-DQA1, NUAK2, and HSPA5 associated with the process of carcinogenesis in HCC as previously reported. Conclusions Our findings highlight the value of leveraging the gene expression data to identify new candidate genes beyond the GWAS associations and could further provide a genetic insight for the biology of HCC.
Collapse
Affiliation(s)
- Jingjing Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Qingrong Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Wenyan Hu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Yuxuan Liang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Deke Jiang
- Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Haitao Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| |
Collapse
|
2
|
Zaravinos A. Unveiling the Future of Oncology and Precision Medicine through Data Science. Int J Mol Sci 2024; 25:5797. [PMID: 38891982 PMCID: PMC11171842 DOI: 10.3390/ijms25115797] [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: 04/06/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Information generated via next-generation sequencing (NGS) technologies is often termed multi-omics data [...].
Collapse
Affiliation(s)
- Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus;
- Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
| |
Collapse
|
3
|
Wang Y, Liu X, Zuo X, Wang C, Zhang Z, Zhang H, Zeng T, Chen S, Liu M, Chen H, Song Q, Li Q, Yang C, Le Y, Xing J, Zhang H, An J, Jia W, Kang L, Zhang H, Xie H, Ye J, Wu T, He F, Zhang X, Li Y, Zhou G. NRDE2 deficiency impairs homologous recombination repair and sensitizes hepatocellular carcinoma to PARP inhibitors. CELL GENOMICS 2024; 4:100550. [PMID: 38697125 PMCID: PMC11099347 DOI: 10.1016/j.xgen.2024.100550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
To identify novel susceptibility genes for hepatocellular carcinoma (HCC), we performed a rare-variant association study in Chinese populations consisting of 2,750 cases and 4,153 controls. We identified four HCC-associated genes, including NRDE2, RANBP17, RTEL1, and STEAP3. Using NRDE2 (index rs199890497 [p.N377I], p = 1.19 × 10-9) as an exemplary candidate, we demonstrated that it promotes homologous recombination (HR) repair and suppresses HCC. Mechanistically, NRDE2 binds to the subunits of casein kinase 2 (CK2) and facilitates the assembly and activity of the CK2 holoenzyme. This NRDE2-mediated enhancement of CK2 activity increases the phosphorylation of MDC1 and then facilitates the HR repair. These functions are eliminated almost completely by the NRDE2-p.N377I variant, which sensitizes the HCC cells to poly(ADP-ribose) polymerase (PARP) inhibitors, especially when combined with chemotherapy. Collectively, our findings highlight the relevance of the rare variants to genetic susceptibility to HCC, which would be helpful for the precise treatment of this malignancy.
Collapse
Affiliation(s)
- Yahui Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Xinyi Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Xianbo Zuo
- Department of Dermatology, Department of Pharmacy, China-Japan Friendship Hospital, Beijing, P.R. China
| | - Cuiling Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Zheng Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Haitao Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Tao Zeng
- Faculty of Hepato-Biliary-Pancreatic Surgery, the First Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Shunqi Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Mengyu Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Hongxia Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Qingfeng Song
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning City, Guangxi Province, P.R. China
| | - Qi Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; Department of Neurosciences, School of Medicine, University of South China, Hengyang City, Hunan Province, P.R. China
| | - Chenning Yang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China
| | - Yi Le
- Department of Hepatobiliary Surgery, the 5th Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Experimental Teaching Center of Basic Medicine, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Hongxin Zhang
- Department of Pain Treatment, Tangdu Hospital, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Jiaze An
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Medical University, Xi'an City, Shaanxi Province, P.R. China
| | - Weihua Jia
- State Key Laboratory of Oncology in Southern China, Guangzhou City, Guangdong Province, P.R. China; Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou City, Guangdong Province, P.R. China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang City, Shaanxi Province, P.R. China
| | - Hongxing Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China
| | - Hui Xie
- Department of Interventional Oncology, the Fifth Medical Center of Chinese PLA General of Hospital, Beijing, P.R. China
| | - Jiazhou Ye
- Department of Hepatobiliary & Pancreatic Surgery, Guangxi Medical University Cancer Hospital, Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning City, Guangxi Province, P.R. China
| | - Tianzhun Wu
- Department of Hepatobiliary & Pancreatic Surgery, Guangxi Medical University Cancer Hospital, Guangxi Liver Cancer Diagnosis and Treatment Engineering and Technology Research Center, Nanning City, Guangxi Province, P.R. China
| | - Fuchu He
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, P.R. China.
| | - Xuejun Zhang
- Department of Dermatology and Institute of Dermatology, First Affiliated Hospital, Anhui Medical University, Hefei City, Anhui Province, P.R. China.
| | - Yuanfeng Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China.
| | - Gangqiao Zhou
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P.R. China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, P.R. China.
| |
Collapse
|
4
|
Fares S, Wehrle CJ, Hong H, Sun K, Jiao C, Zhang M, Gross A, Allkushi E, Uysal M, Kamath S, Ma WW, Modaresi Esfeh J, Linganna MW, Khalil M, Pita A, Kim J, Walsh RM, Miller C, Hashimoto K, Schlegel A, Kwon DCH, Aucejo F. Emerging and Clinically Accepted Biomarkers for Hepatocellular Carcinoma. Cancers (Basel) 2024; 16:1453. [PMID: 38672535 PMCID: PMC11047909 DOI: 10.3390/cancers16081453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death and the sixth most diagnosed malignancy worldwide. Serum alpha-fetoprotein (AFP) is the traditional, ubiquitous biomarker for HCC. However, there has been an increasing call for the use of multiple biomarkers to optimize care for these patients. AFP, AFP-L3, and prothrombin induced by vitamin K absence II (DCP) have described clinical utility for HCC, but unfortunately, they also have well established and significant limitations. Circulating tumor DNA (ctDNA), genomic glycosylation, and even totally non-invasive salivary metabolomics and/or micro-RNAS demonstrate great promise for early detection and long-term surveillance, but still require large-scale prospective validation to definitively validate their clinical validity. This review aims to provide an update on clinically available and emerging biomarkers for HCC, focusing on their respective clinical strengths and weaknesses.
Collapse
Affiliation(s)
- Sami Fares
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Chase J. Wehrle
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Hanna Hong
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Keyue Sun
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Chunbao Jiao
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Mingyi Zhang
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Abby Gross
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Erlind Allkushi
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Melis Uysal
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Suneel Kamath
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.K.); (W.W.M.)
| | - Wen Wee Ma
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.K.); (W.W.M.)
| | - Jamak Modaresi Esfeh
- Department of Gastroenterology, Hepatology, and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (J.M.E.); (M.W.L.)
| | - Maureen Whitsett Linganna
- Department of Gastroenterology, Hepatology, and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (J.M.E.); (M.W.L.)
| | - Mazhar Khalil
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Alejandro Pita
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Jaekeun Kim
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - R. Matthew Walsh
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Charles Miller
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Koji Hashimoto
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Andrea Schlegel
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - David Choon Hyuck Kwon
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| | - Federico Aucejo
- Department of Hepato-Pancreato-Biliary & Liver Transplant Surgery, Digestive Diseases and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA; (S.F.); (H.H.); (K.S.); (C.J.); (M.Z.); (A.G.); (E.A.); (M.U.); (M.K.); (A.P.); (J.K.); (R.M.W.); (K.H.); (A.S.); (D.C.H.K.)
| |
Collapse
|
5
|
Han L, Huo Y, Huang L, Zheng Y, Yu X, Zhang N, Yang M. Genome-wide functional integration identified MAZ-controlled RPS14 dysregulation in hepatocellular carcinoma. Arch Toxicol 2024; 98:985-997. [PMID: 38189915 DOI: 10.1007/s00204-023-03669-z] [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: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/09/2024]
Abstract
Chronic infection with Hepatitis B virus (HBV) significantly increases the risk of hepatocellular carcinoma (HCC), particularly in Eastern Asia. However, only a subset of individuals with chronic HBV infection develop HCC, suggesting the role for genetic factors in HCC etiology. Despite genome-wide association studies (GWASs) identifying multiple single nucleotide polymorphisms (SNPs) associated with HBV-related HCC susceptibility, the underlying mechanisms and causal genetic polymorphisms remain largely unclear. To address this, we developed The Updated Integrative Functional Genomics Approach (TUIFGA), an methodology that combines data from transcription factor (TF) cistromics, ATAC-seq, DNAase-seq, and the 1000 Genomes Project to identify cancer susceptibility SNPs within TF-binding sites across human genome. Using TUIFGA, we discovered SNP rs13170300 which located in the TF MAZ binding motif of RPS14. The RPS14 rs13170300 was significantly associated with HCC risk in two case-control sets, with the T allele as the protective allele (Shandong discovery set: TT OR = 0.60, 95% CI = 0.49-0.74, P = 1.0 × 10-6; CT OR = 0.69, 95% CI = 0.55-0.86, P = 0.001; Jiangsu validation set: TT OR = 0.70, 95% CI = 0.56-0.87, P = 0.001; CT OR = 0.65, 95% CI = 0.53-0.82, P = 1.6 × 10-4). SNP rs13170300 affected MAZ binding in the RPS14 promoter, resulting in allele-specific changes in gene expression. RPS14 functions as a novel oncogene in HCC, specifically via activating the AKT signaling. Our findings present important insights into the functional genetics underlying HBV-related HCC development and may contribute to personalized approaches for cancer prevention and novel therapeutics.
Collapse
Affiliation(s)
- Linyu Han
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong Province, China
| | - Yanfei Huo
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong Province, China
| | - Linying Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong Province, China
| | - Yanxiu Zheng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong Province, China
| | - Xinyuan Yu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong Province, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong Province, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu Province, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong Province, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu Province, China.
- Shandong University Cancer Center, Shandong Province, Jinan, 250117, China.
| |
Collapse
|
6
|
Soliman N, Saharia A, Abdelrahim M, Connor AA. Molecular profiling in the management of hepatocellular carcinoma. Curr Opin Organ Transplant 2024; 29:10-22. [PMID: 38038621 DOI: 10.1097/mot.0000000000001124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to both summarize the current knowledge of hepatocellular carcinoma molecular biology and to suggest a framework in which to prospectively translate this knowledge into patient care. This is timely as recent guidelines recommend increased use of these technologies to advance personalized liver cancer care. RECENT FINDINGS The main themes covered here address germline and somatic genetic alterations recently discovered in hepatocellular carcinoma, largely owing to next generation sequencing technologies, and nascent efforts to translate these into contemporary practice. SUMMARY Early efforts of translating molecular profiling to hepatocellular carcinoma care demonstrate a growing number of potentially actionable alterations. Still lacking are a consensus on what biomarkers and technologies to adopt, at what scale and cost, and how to integrate them most effectively into care.
Collapse
|
7
|
Chotiprasidhi P, Sato-Espinoza AK, Wangensteen KJ. Germline Genetic Associations for Hepatobiliary Cancers. Cell Mol Gastroenterol Hepatol 2023; 17:623-638. [PMID: 38163482 PMCID: PMC10899027 DOI: 10.1016/j.jcmgh.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Hepatobiliary cancers (HBCs) include hepatocellular carcinoma, cholangiocarcinoma, and gallbladder carcinoma, which originate from the liver, bile ducts, and gallbladder, respectively. They are responsible for a substantial burden of cancer-related deaths worldwide. Despite knowledge of risk factors and advancements in therapeutics and surgical interventions, the prognosis for most patients with HBC remains bleak. There is evidence from familial aggregation and case-control studies to suggest a familial risk component in HBC susceptibility. Recent progress in genomics research has led to the identification of germline variants including single nucleotide polymorphisms (SNPs) and pathogenic or likely pathogenic (P/LP) variants in cancer-associated genes associated with HBC risk. These findings emerged from genome-wide association studies and next-generation sequencing techniques such as whole-exome sequencing. Patients with other cancer types, including breast, colon, ovarian, prostate, and pancreatic cancer, are recommended by guidelines to undergo germline genetic testing, but similar recommendations are lagging in HBC. This prompts the question of whether multi-gene panel testing should be integrated into clinical guidelines for HBC management. Here, we review the hereditary genetics of HBC, explore studies investigating SNPs and P/LP variants in HBC patients, discuss the clinical implications and potential for personalized treatments and impact on patient's family members, and conclude that additional studies are needed to examine how genetic testing can be applied clinically.
Collapse
Affiliation(s)
- Perapa Chotiprasidhi
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Kirk J Wangensteen
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota.
| |
Collapse
|
8
|
Zhan S, Qiu M, Wei X, Wei J, Qin L, Jiang B, Wen Q, Chen P, Lin Q, Wei X, Zhou Z, Jiang Y, Liang X, Li R, Liu Y, Yu H. Potentially functional genetic variants in ferroptosis-related CREB3 and GALNT14 genes predict survival of hepatitis B virus-related hepatocellular carcinoma. Cancer Med 2023; 13:e6848. [PMID: 38151984 PMCID: PMC10807646 DOI: 10.1002/cam4.6848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Ferroptosis is a known crucial player in the development of cancers. However, the effect of single nucleotide polymorphisms (SNPs) in ferroptosis-related genes on survival in hepatitis B virus (HBV)-related hepatocellular carcinoma (HBV-HCC) patients remains unknown. METHODS We used two-stage multivariable Cox proportional hazards regression analyses to estimate the associations between 48,774 SNPs in 480 ferroptosis-related genes and overall survival (OS) of 866 HBV-HCC patients. RESULTS We identified that two potentially functional SNPs (CREB3 rs10814274 C > T and GALNT14 rs17010547 T > C) were significantly independently associated with the OS of HBV-HCC patients (CT + TT verse CC, hazards ratio (HR) = 0.77, 95% confidence interval (CI) = 0.67-0.89, p < 0.001 for rs10814274 and TC + CC verse TT, HR = 0.66, 95% CI = 0.53-0.82, p < 0.001 for rs17010547, respectively). Additional joint assessment of protective genotypes of these two SNPs showed that patients with 1-2 protective genotypes had a significantly better OS compared with those carrying 0 protective genotypes (HR = 0.56, 95% CI = 0.45-0.70, p < 0.001). Moreover, the expression quantitative trait loci (eQTL) analysis revealed that the survival-associated SNP rs10814274 T allele was significantly correlated with reduced CREB3 transcript levels in both normal liver tissues and whole blood cells, while the GALNT14 rs17010547 C allele had a significant correlation with increased GALNT14 transcript levels in whole blood cells. CONCLUSION These results suggest that genetic variants of CREB3 and GALNT14 may affect the survival of HBV-HCC patients, likely via transcriptional regulation of respective genes. However, further studies are required to confirm these findings.
Collapse
Affiliation(s)
- Shicheng Zhan
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Moqin Qiu
- Department of Respiratory OncologyGuangxi Medical University Cancer HospitalNanningChina
| | - Xueyan Wei
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Junjie Wei
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Liming Qin
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Department of Epidemiology and Health Statistics, School of Public HealthGuangxi Medical UniversityNanningChina
| | - Binbin Jiang
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Qiuping Wen
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Peiqin Chen
- Editorial Department of Chinese Journal of Oncology Prevention and TreatmentGuangxi Medical University Cancer HospitalNanningChina
| | - Qiuling Lin
- Department of Clinical ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Xiaoxia Wei
- Department of Clinical ResearchGuangxi Medical University Cancer HospitalNanningChina
| | - Zihan Zhou
- Department of Cancer Prevention and ControlGuangxi Medical University Cancer HospitalNanningChina
| | - Yanji Jiang
- Scientific Research DepartmentGuangxi Medical University Cancer HospitalNanningChina
| | - Xiumei Liang
- Department of Disease Process ManagementGuangxi Medical University Cancer HospitalNanningChina
| | - Runwei Li
- Department of Civil Engineering, College of EngineeringNew Mexico State UniversityLas CrucesNew MexicoUSA
| | - Yingchun Liu
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health CommissionGuangxi Medical University Cancer HospitalNanningChina
| | - Hongping Yu
- Department of Experimental ResearchGuangxi Medical University Cancer HospitalNanningChina
- Key Cultivated Laboratory of Cancer Molecular Medicine of Guangxi Health CommissionGuangxi Medical University Cancer HospitalNanningChina
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University)Ministry of EducationNanningChina
| |
Collapse
|
9
|
Liu TY, Liao CC, Chang YS, Chen YC, Chen HD, Lai IL, Peng CY, Chung CC, Chou YP, Tsai FJ, Jeng LB, Chang JG. Identification of 13 Novel Loci in a Genome-Wide Association Study on Taiwanese with Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:16417. [PMID: 38003606 PMCID: PMC10671380 DOI: 10.3390/ijms242216417] [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: 10/02/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Liver cancer is caused by complex interactions among genetic factors, viral infection, alcohol abuse, and metabolic diseases. We conducted a genome-wide association study and polygenic risk score (PRS) model in Taiwan, employing a nonspecific etiology approach, to identify genetic risk factors for hepatocellular carcinoma (HCC). Our analysis of 2836 HCC cases and 134,549 controls revealed 13 novel associated loci such as the FAM66C gene, noncoding genes, liver-fibrosis-related genes, metabolism-related genes, and HCC-related pathway genes. We incorporated the results from the UK Biobank and Japanese database into our study for meta-analysis to validate our findings. We also identified specific subtypes of the major histocompatibility complex that influence both viral infection and HCC progression. Using this data, we developed a PRS to predict HCC risk in the general population, patients with HCC, and HCC-affected families. The PRS demonstrated higher risk scores in families with multiple HCCs and other cancer cases. This study presents a novel approach to HCC risk analysis, identifies seven new genes associated with HCC development, and introduces a reproducible PRS model for risk assessment.
Collapse
Affiliation(s)
- Ting-Yuan Liu
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chi-Chou Liao
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Ya-Sian Chang
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Yu-Chia Chen
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
- Million-Person Precision Medicine Initiative, Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Hong-Da Chen
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - I-Lu Lai
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Cheng-Yuan Peng
- Department of Internal Medicine, Section of Hepatobiliary Tract, China Medical University Hospital, Taichung 40447, Taiwan;
| | - Chin-Chun Chung
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Yu-Pao Chou
- Center for Precision Medicine and Epigenome Research Center, China Medical University Hospital, Taichung 40447, Taiwan; (T.-Y.L.); (C.-C.L.); (Y.-S.C.); (Y.-C.C.); (H.-D.C.); (I.-L.L.); (C.-C.C.); (Y.-P.C.)
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
- Division of Pediatric Genetics, Children’s Hospital of China Medical University, Taichung 40447, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Long-Bin Jeng
- Department of Surgery, Section of Hepatobiliary Tract, China Medical University Hospital, Taichung 40447, Taiwan;
| | - Jan-Gowth Chang
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan
| |
Collapse
|
10
|
Haycock PC, Borges MC, Burrows K, Lemaitre RN, Harrison S, Burgess S, Chang X, Westra J, Khankari NK, Tsilidis KK, Gaunt T, Hemani G, Zheng J, Truong T, O’Mara TA, Spurdle AB, Law MH, Slager SL, Birmann BM, Saberi Hosnijeh F, Mariosa D, Amos CI, Hung RJ, Zheng W, Gunter MJ, Davey Smith G, Relton C, Martin RM. Design and quality control of large-scale two-sample Mendelian randomization studies. Int J Epidemiol 2023; 52:1498-1521. [PMID: 38587501 PMCID: PMC10555669 DOI: 10.1093/ije/dyad018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/10/2023] [Indexed: 03/27/2024] Open
Abstract
Background Mendelian randomization (MR) studies are susceptible to metadata errors (e.g. incorrect specification of the effect allele column) and other analytical issues that can introduce substantial bias into analyses. We developed a quality control (QC) pipeline for the Fatty Acids in Cancer Mendelian Randomization Collaboration (FAMRC) that can be used to identify and correct for such errors. Methods We collated summary association statistics from fatty acid and cancer genome-wide association studies (GWAS) and subjected the collated data to a comprehensive QC pipeline. We identified metadata errors through comparison of study-specific statistics to external reference data sets (the National Human Genome Research Institute-European Bioinformatics Institute GWAS catalogue and 1000 genome super populations) and other analytical issues through comparison of reported to expected genetic effect sizes. Comparisons were based on three sets of genetic variants: (i) GWAS hits for fatty acids, (ii) GWAS hits for cancer and (iii) a 1000 genomes reference set. Results We collated summary data from 6 fatty acid and 54 cancer GWAS. Metadata errors and analytical issues with the potential to introduce substantial bias were identified in seven studies (11.6%). After resolving metadata errors and analytical issues, we created a data set of 219 842 genetic associations with 90 cancer types, generated in analyses of 566 665 cancer cases and 1 622 374 controls. Conclusions In this large MR collaboration, 11.6% of included studies were affected by a substantial metadata error or analytical issue. By increasing the integrity of collated summary data prior to their analysis, our protocol can be used to increase the reliability of downstream MR analyses. Our pipeline is available to other researchers via the CheckSumStats package (https://github.com/MRCIEU/CheckSumStats).
Collapse
Affiliation(s)
- Philip C Haycock
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maria Carolina Borges
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Sean Harrison
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat—National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Jason Westra
- Department of Mathematics, Statistics, and Computer Science, Dordt College, Sioux Center, IA, USA
| | - Nikhil K Khankari
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Tom Gaunt
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Therese Truong
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, Team “Exposome, Heredity, Cancer and Health”, CESP, Villejuif, France
| | - Tracy A O’Mara
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, Australia
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Daniela Mariosa
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Christopher I Amos
- Dan L Duncan Comprehensive Cancer Center Baylor College of Medicine, Houston, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health and University of Toronto, Toronto, Canada
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC), Lyon, France
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
| |
Collapse
|
11
|
Hamilton EM, Rassam W, Yan Y, Singh A, Ng SYA, Zhang J, Lv J, Islam N, Malouf R, Yang L, Millwood IY, Chen Z. Correlates of chronic hepatitis B virus infection in the general adult population of China: Systematic review and meta-analysis. J Viral Hepat 2023; 30:470-488. [PMID: 36751939 DOI: 10.1111/jvh.13816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/19/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023]
Abstract
Chronic infection with hepatitis B virus (HBV) is a significant public health issue in China. Understanding factors associated with chronic HBV is important to enable targeted screening and education and to improve early diagnosis and prevention of disease progression. This systematic review and meta-analysis aimed to identify and describe correlates of chronic HBV among Chinese adults. Searches were conducted in MEDLINE, EMBASE and grey literature up to 25 June 2020. Eligible papers included observational studies in adults of the general population in China that reported factors associated with chronic HBV, measured by Hepatitis B surface antigen (HBsAg). Meta-analysis was performed using fixed-effect models of HBsAg prevalence among factors, and of adjusted odds ratios (ORs) for chronic HBV associated with each factor. Overall 39 articles were included, covering 22 factors, including a range of sociodemographic, behavioural and medical factors. In meta-analysis of eligible studies, a range of factors were significantly associated with higher HBsAg prevalence, including middle age, male sex, being married, rural residence, lower education, smoking, having a HBsAg positive household contact, family history of HBV, history of surgery or blood transfusion. The adjusted ORs varied, from 1.11 (95% CI 1.05-1.18) for smoking to 5.13 (95% CI 4.99-5.26) for having a HBsAg positive household contact. In Chinese adults, a range of factors are associated with chronic HBV infection, which may help inform targeted screening in the general population.
Collapse
Affiliation(s)
- Elizabeth Mova Hamilton
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Wadie Rassam
- Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Yan Yan
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Avjit Singh
- Department of Surgery, Townsville University Hospital, Townsville, Queensland, Australia
| | - Sarah Yoon Ai Ng
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jiabi Zhang
- Department of Nutrition and Integrative Physiology, College of Health, University of Utah, Salt Lake City, Utah, USA
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- Center for Public Health and Epidemic Preparedness & Response, Beijing, China
| | - Nazrul Islam
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
- National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- School of Primary Care, Population Sciences and Medical Education, University of Southampton, Southampton, UK
| | - Reem Malouf
- National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Ling Yang
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit (MRC PHRU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Iona Y Millwood
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit (MRC PHRU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Zhengming Chen
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| |
Collapse
|
12
|
Genetic Susceptibility to Hepatocellular Carcinoma in Patients with Chronic Hepatitis Virus Infection. Viruses 2023; 15:v15020559. [PMID: 36851773 PMCID: PMC9964813 DOI: 10.3390/v15020559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths globally. The risk factors for HCC include chronic hepatitis B and C virus infections, excessive alcohol consumption, obesity, metabolic disease, and aflatoxin exposure. In addition to these viral and environmental risk factors, individual genetic predisposition is a major determinant of HCC risk. Familial clustering of HCC has been observed, and a hereditary factor likely contributes to the risk of HCC development. The familial aggregation may depend on a shared environment and genetic background as well as the interactions of environmental and genetic factors. Genome-wide association studies (GWASs) are one of the most practical tools for mapping the patterns of inheritance for the most common form of genomic variation, single nucleotide polymorphisms. This approach is practical for investigating genetic variants across the human genome, which is affected by thousands of common genetic variants that do not follow Mendelian inheritance. This review article summarizes the academic knowledge of GWAS-identified genetic loci and their association with HCC. We summarize the GWASs in accordance with various chronic hepatitis virus infection statuses. This genetic profiling could be used to identify candidate biomarkers to refine HCC screening and management by enabling individual risk-based personalization and stratification. A more comprehensive understanding of the genetic mechanisms underlying individual predisposition to HCC may lead to improvements in the prevention and early diagnosis of HCC and the development of effective treatment strategies.
Collapse
|
13
|
Liu J, Peng W, Yu F, Shen Y, Yu W, Lu Y, Lin W, Zhou M, Huang Z, Luo X, You W, Ke C. Genomic selection applications can improve the environmental performance of aquatics: a case study on the heat tolerance of abalone. Evol Appl 2022; 15:992-1001. [PMID: 35782008 PMCID: PMC9234619 DOI: 10.1111/eva.13388] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/02/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022] Open
Abstract
Aquaculture is one of the world's fastest‐growing and most traded food industries, but it is under the threat of climate‐related risks represented by global warming, marine heatwave (MHW) events, ocean acidification, and deoxygenation. For the sustainable development of aquaculture, selective breeding may be a viable method to obtain aquatic economic species with greater tolerance to environmental stressors. In this study, we estimated the heritability of heat tolerance trait of Pacific abalone Haliotis discus hannai, performed genome‐wide association studies (GWAS) analysis for heat tolerance to detect single nucleotide polymorphisms (SNPs) and candidate genes, and assessed the potential of genomic selection (GS) in the breeding of abalone industry. A total of 1120 individuals were phenotyped for their heat tolerance and genotyped with 64,788 quality‐controlled SNPs. The heritability of heat tolerance was moderate (0.35–0.42) and the predictive accuracy estimated using BayesB (0.55 ± 0.05) was higher than that using GBLUP (0.40 ± 0.01). A total of 11 genome‐wide significant SNPs and 2 suggestive SNPs were associated with heat tolerance of abalone, and 13 candidate genes were identified, including got2,znfx1,l(2)efl, and lrp5. Based on GWAS results, the prediction accuracy using the top 5K SNPs was higher than that using randomly selected SNPs and higher than that using all SNPs. These results suggest that GS is an efficient approach for improving the heat tolerance of abalone and pave the way for abalone selecting breeding programs in rapidly changing oceans.
Collapse
Affiliation(s)
- Junyu Liu
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Feng Yu
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Yawei Shen
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Wenchao Yu
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Yisha Lu
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Weihong Lin
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Muzhi Zhou
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science College of Ocean and Earth Sciences Xiamen University Xiamen 361102 PR China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms Xiamen University Xiamen 361102 China
| |
Collapse
|
14
|
Shen T, Ni T, Chen J, Chen H, Ma X, Cao G, Wu T, Xie H, Zhou B, Wei G, Saiyin H, Shen S, Yu P, Xiao Q, Liu H, Gao Y, Long X, Yin J, Guo Y, Wu J, Wei GH, Hou J, Jiang DK. An enhancer variant at 16q22.1 predisposes to hepatocellular carcinoma via regulating PRMT7 expression. Nat Commun 2022; 13:1232. [PMID: 35264579 PMCID: PMC8907293 DOI: 10.1038/s41467-022-28861-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 02/16/2022] [Indexed: 12/24/2022] Open
Abstract
Most cancer causal variants are found in gene regulatory elements, e.g., enhancers. However, enhancer variants predisposing to hepatocellular carcinoma (HCC) remain unreported. Here we conduct a genome-wide survey of HCC-susceptible enhancer variants through a three-stage association study in 11,958 individuals and identify rs73613962 (T > G) within the intronic region of PRMT7 at 16q22.1 as a susceptibility locus of HCC (OR = 1.41, P = 6.02 × 10-10). An enhancer dual-luciferase assay indicates that the rs73613962-harboring region has allele-specific enhancer activity. CRISPR-Cas9/dCas9 experiments further support the enhancer activity of this region to regulate PRMT7 expression. Mechanistically, transcription factor HNF4A binds to this enhancer region, with preference to the risk allele G, to promote PRMT7 expression. PRMT7 upregulation contributes to in vitro, in vivo, and clinical HCC-associated phenotypes, possibly by affecting the p53 signaling pathway. This concept of HCC pathogenesis may open a promising window for HCC prevention/treatment.
Collapse
Affiliation(s)
- Ting Shen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China.,School of Life Sciences, Central South University, 510006, Changsha, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Jiaxuan Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Haitao Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China.,School of Public Health (Shenzhen), Sun Yat-sen University, 528406, Shenzhen, China
| | - Xiaopin Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Naval Medical University, 200433, Shanghai, China
| | - Tianzhi Wu
- Institute of Bioinformatics, School of Basic Medical Science, Southern Medical University, 510515, Guangzhou, China
| | - Haisheng Xie
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Suqin Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Peng Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Qianyi Xiao
- School of Public Health, Fudan University, 200032, Shanghai, China
| | - Hui Liu
- School of Basic Medical Sciences; The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's hospital, Guangzhou Medical University, 510182, Guangzhou, China
| | - Yuzheng Gao
- Department of Forensic Medicine, Medical College of Soochow University, 215123, Suzhou, Jiangsu Province, China
| | - Xidai Long
- Department of Pathology, Youjiang Medical College for Nationalities, 533000, Baise, Guangxi Province, China
| | - Jianhua Yin
- Department of Epidemiology, Naval Medical University, 200433, Shanghai, China
| | - Yanfang Guo
- Institute of Bioinformatics, School of Basic Medical Science, Southern Medical University, 510515, Guangzhou, China
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014, Oulu, Finland.,School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - De-Ke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China.
| |
Collapse
|
15
|
Rao R, Shah S, Bhattacharya D, Toukam DK, Cáceres R, Pomeranz Krummel DA, Sengupta S. Ligand-Gated Ion Channels as Targets for Treatment and Management of Cancers. Front Physiol 2022; 13:839437. [PMID: 35350689 PMCID: PMC8957973 DOI: 10.3389/fphys.2022.839437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 12/24/2022] Open
Abstract
Ligand-gated ion channels are an ionotropic receptor subtype characterized by the binding of an extracellular ligand, followed by the transient passage of ions through a transmembrane pore. Ligand-gated ion channels are commonly subcategorized into three superfamilies: purinoreceptors, glutamate receptors, and Cys-loop receptors. This classification is based on the differing topographical morphology of the receptors, which in turn confers functional differences. Ligand-gated ion channels have a diverse spatial and temporal expression which implicate them in key cellular processes. Given that the transcellular electrochemical gradient is finely tuned in eukaryotic cells, any disruption in this homeostasis can contribute to aberrancies, including altering the activity of pro-tumorigenic molecular pathways, such as the MAPK/ERK, RAS, and mTOR pathways. Ligand-gated ion channels therefore serve as a potential targetable system for cancer therapeutics. In this review, we analyze the role that each of the three ligand-gated ion channel superfamilies has concerning tumor proliferation and as a target for the treatment of cancer symptomatology.
Collapse
Affiliation(s)
| | | | | | | | | | - Daniel A. Pomeranz Krummel
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Soma Sengupta
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, Cincinnati, OH, United States
| |
Collapse
|
16
|
Metabolomics and the Multi-Omics View of Cancer. Metabolites 2022; 12:metabo12020154. [PMID: 35208228 PMCID: PMC8880085 DOI: 10.3390/metabo12020154] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cancer is widely regarded to be a genetic disease. Indeed, over the past five decades, the genomic perspective on cancer has come to almost completely dominate the field. However, this genome-only view is incomplete and tends to portray cancer as a disease that is highly heritable, driven by hundreds of complex genetic interactions and, consequently, difficult to prevent or treat. New evidence suggests that cancer is not as heritable or purely genetic as once thought and that it really is a multi-omics disease. As highlighted in this review, the genome, the exposome, and the metabolome all play roles in cancer’s development and manifestation. The data presented here show that >90% of cancers are initiated by environmental exposures (the exposome) which lead to cancer-inducing genetic changes. The resulting genetic changes are, then, propagated through the altered DNA of the proliferating cancer cells (the genome). Finally, the dividing cancer cells are nourished and sustained by genetically reprogrammed, cancer-specific metabolism (the metabolome). As shown in this review, all three “omes” play roles in initiating cancer. Likewise, all three “omes” interact closely, often providing feedback to each other to sustain or enhance tumor development. Thanks to metabolomics, these multi-omics feedback loops are now much more evident and their roles in explaining the hallmarks of cancer are much better understood. Importantly, this more holistic, multi-omics view portrays cancer as a disease that is much more preventable, easier to understand, and potentially, far more treatable.
Collapse
|
17
|
Ezzat R, Eltabbakh M, El Kassas M. Unique situation of hepatocellular carcinoma in Egypt: A review of epidemiology and control measures. World J Gastrointest Oncol 2021; 13:1919-1938. [PMID: 35070033 PMCID: PMC8713321 DOI: 10.4251/wjgo.v13.i12.1919] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/17/2021] [Accepted: 10/18/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common primary malignancy worldwide, and the third most common cause of death among cancers worldwide. HCC occurs in several pre-existing conditions, including hepatitis C, hepatitis B virus, and non-alcoholic cirrhosis. Egypt used to be the country with the heaviest hepatitis C virus (HCV) burden. The relationship between HCV and HCC is an important research area. In Egypt, HCC is a significant public health problem. A possible cause for the increasing rates of detection of HCC in Egypt is the mass screening program that was carried by the government for detecting and treating HCV. A multidisciplinary approach is now widely applied to HCC management in health centers all over Egypt. Different treatment modalities are available in Egypt, with success rates comparable to global rates. The Egyptian health authorities have made the elimination of HCV from Egypt a special priority, and this approach should lead to a decrease in number of HCC cases in the near future. In this article we review the current situation of HCC in Egypt, including epidemiological aspects, relevant risk factors for HCC development, strategies, and efforts established by health authorities for the screening and prevention of both HCV and HCC in Egypt. We highlight the different modalities for HCC treatment.
Collapse
Affiliation(s)
- Reem Ezzat
- Internal Medicine Department, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Mohamed Eltabbakh
- Tropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed El Kassas
- Endemic Medicine Department, Faculty of Medicine, Helwan University, Cairo 11795, Cairo, Egypt
| |
Collapse
|
18
|
Wang Z, Budhu AS, Shen Y, Wong LL, Hernandez BY, Tiirikainen M, Ma X, Irwin ML, Lu L, Zhao H, Lim JK, Taddei T, Mishra L, Pawlish K, Stroup A, Brown R, Nguyen MH, Koshiol J, Hernandez MO, Forgues M, Yang HI, Lee MH, Huang YH, Iwasaki M, Goto A, Suzuki S, Matsuda K, Tanikawa C, Kamatani Y, Mann D, Guarnera M, Shetty K, Thomas CE, Yuan JM, Khor CC, Koh WP, Risch H, Wang XW, Yu H. Genetic susceptibility to hepatocellular carcinoma in chromosome 22q13.31, findings of a genome-wide association study. JGH Open 2021; 5:1363-1372. [PMID: 34950780 PMCID: PMC8674550 DOI: 10.1002/jgh3.12682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIM Chronic hepatitis C virus (HCV) infection, long-term alcohol use, cigarette smoking, and obesity are the major risk factors for hepatocellular carcinoma (HCC) in the United States, but the disease risk varies substantially among individuals with these factors, suggesting host susceptibility to and gene-environment interactions in HCC. To address genetic susceptibility to HCC, we conducted a genome-wide association study (GWAS). METHODS Two case-control studies on HCC were conducted in the United States. DNA samples were genotyped using the Illumian microarray chip with over 710 000 single nucleotide polymorphisms (SNPs). We compared these SNPs between 705 HCC cases and 1455 population controls for their associations with HCC and verified our findings in additional studies. RESULTS In this GWAS, we found that two SNPs were associated with HCC at P < 5E-8 and six SNPs at P < 5E-6 after adjusting for age, sex, and the top three principal components (PCs). Five of the SNPs in chromosome 22q13.31, three in PNPLA3 (rs2281135, rs2896019, and rs4823173) and two in SAMM50 (rs3761472, rs3827385), were replicated in a small US case-control study and a cohort study in Singapore. The associations remained significant after adjusting for body mass index and HCV infection. Meta-analysis of multiple datasets indicated that these SNPs were significantly associated with HCC. CONCLUSIONS SNPs in PNPLA3 and SAMM50 are known risk loci for nonalcoholic fatty liver disease (NAFLD) and are suspected to be associated with HCC. Our GWAS demonstrated the associations of these SNPs with HCC in a US population. Biological mechanisms underlying the relationship remain to be elucidated.
Collapse
Affiliation(s)
- Zhanwei Wang
- University of Hawaii Cancer Center Honolulu Hawaii USA
| | - Anuradha S Budhu
- Laboratory of Human Carcinogenesis, Liver Cancer Program, Center for Cancer Research National Cancer Institute Bethesda Maryland USA
| | - Yi Shen
- University of Hawaii Cancer Center Honolulu Hawaii USA
| | | | | | | | - Xiaomei Ma
- Yale School of Public Health New Haven Connecticut USA
| | | | - Lingeng Lu
- Yale School of Public Health New Haven Connecticut USA
| | - Hongyu Zhao
- Yale School of Public Health New Haven Connecticut USA
| | - Joseph K Lim
- Yale School of Medicine New Haven Connecticut USA
| | - Tamar Taddei
- Yale School of Medicine New Haven Connecticut USA
| | - Lopa Mishra
- Center for Translational Medicine, Department of Surgery The George Washington University Washington District of Columbia USA
| | - Karen Pawlish
- New Jersey State Cancer Registry, New Jersey Department of Health Trenton New Jersey USA
| | - Antoinette Stroup
- Rutgers Cancer Institute, and Rutgers School of Public Health New Brunswick New Jersey USA
| | - Robert Brown
- Weill Cornell Medical College, and College of Physicians and Surgeons, Columbia University New York New York USA
| | - Mindie H Nguyen
- Division of Gastroenterology and Hepatology Stanford University Medical Center Palo Alto California USA
| | - Jill Koshiol
- Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda Maryland USA
| | - Maria O Hernandez
- Laboratory of Human Carcinogenesis Center for Cancer Research, National Cancer Institute Bethesda Maryland USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis Center for Cancer Research, National Cancer Institute Bethesda Maryland USA
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica Taipei Taiwan.,Institute of Clinical Medicine, National Yang Ming University Taipei Taiwan
| | - Mei-Hsuan Lee
- Institute of Clinical Medicine, National Yang Ming University Taipei Taiwan
| | - Yu-Han Huang
- Institute of Clinical Medicine, National Yang Ming University Taipei Taiwan
| | - Motoki Iwasaki
- Division of Epidemiology Center for Public Health Sciences, National Cancer Center Tokyo Japan
| | - Atsushi Goto
- Division of Epidemiology Center for Public Health Sciences, National Cancer Center Tokyo Japan
| | - Shiori Suzuki
- Division of Epidemiology Center for Public Health Sciences, National Cancer Center Tokyo Japan
| | - Koichi Matsuda
- Graduate School of Frontier Sciences, and Institute of Medical Science, University of Tokyo Tokyo Japan
| | - Chizu Tanikawa
- Graduate School of Frontier Sciences, and Institute of Medical Science, University of Tokyo Tokyo Japan
| | - Yoichiro Kamatani
- Graduate School of Frontier Sciences, and Institute of Medical Science, University of Tokyo Tokyo Japan
| | - Dean Mann
- Department of Pathology University of Maryland School of Medicine Baltimore Maryland USA
| | - Maria Guarnera
- Department of Pathology University of Maryland School of Medicine Baltimore Maryland USA
| | - Kirti Shetty
- Department of Gastroenterology and Hepatology University of Maryland School of Medicine Baltimore Maryland USA
| | - Claire E Thomas
- Division of Cancer Control and Population Sciences University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center Pittsburgh Pennsylvania USA.,Department of Epidemiology Graduate School of Public Health, University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center Pittsburgh Pennsylvania USA.,Department of Epidemiology Graduate School of Public Health, University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research Singapore Singapore.,Singapore Eye Research Institute Singapore Singapore
| | - Woon-Puay Koh
- Health Systems and Services Research, Duke-NUS Medical School Singapore Singapore Singapore.,Saw Swee Hock School of Public Health, National University of Singapore Singapore Singapore
| | - Harvey Risch
- Yale School of Public Health New Haven Connecticut USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Liver Cancer Program, Center for Cancer Research National Cancer Institute Bethesda Maryland USA
| | - Herbert Yu
- University of Hawaii Cancer Center Honolulu Hawaii USA
| |
Collapse
|
19
|
Tariq F, Khan W, Ahmad W, Riaz SK, Khan M, Sherwani S, Haque S, Malik MFA, Iftikhar MJ, Khan S, Haq F. Effect of MHC Linked 7-Gene Signature on Delayed Hepatocellular Carcinoma Recurrence. J Pers Med 2021; 11:jpm11111129. [PMID: 34834481 PMCID: PMC8625636 DOI: 10.3390/jpm11111129] [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: 09/18/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Dysregulated immune response significantly affects hepatocellular carcinoma's (HCC) prognosis. Human Leukocyte Antigens are key in devising immune responses against HCC. Here, we investigated how HLAs modulate HCC development at the transcriptomic level. RNA-seq data of 576 patients from two independent cohorts was retrieved. The clinicopathological relevance of all HLA genes was investigated using Fisher-Exact, correlation, and Kaplan-Meier and cox regression survival tests. Clustering of ~800 immune-related genes against HLAs was completed using a ward-agglomerative method. Networks were generated using 40 HLA associated unique genes and hub genes were investigated. HLAs including HLA-DMA, HLA-DMB, HLA-DOA and HLA-DRB6 were associated with delayed recurrence in both discovery (204 HCC cases) and validation (372 HCC cases) cohorts. Clustering analyses revealed 40 genes associated with these four HLAs in both cohorts. A set of seven genes (NCF4, TYROBP, LCP2, ZAP70, PTPRC, FYN and WAS) was found co-expressed at gene-gene interaction level in both cohorts. Furthermore, survival analysis revealed seven HLA-linked genes as predictors of delayed recurrence. Multivariate analysis also predicted that mean expression of 7-gene is an independent predictor of delayed recurrence in both cohorts. We conclude that the expression of 7-gene signature may lead to improved patient prognosis. Further studies are required for consideration in clinical practice.
Collapse
Affiliation(s)
- Fomaz Tariq
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
| | - Walizeb Khan
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
| | - Washaakh Ahmad
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
| | - Syeda Kiran Riaz
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan
- College of Medicine, Texas A&M University, College Station, TX 77840-77845, USA
| | - Mahvish Khan
- Department of Biology, College of Science, Ha’il University, Ha’il 55211, Saudi Arabia; (M.K.); (S.S.)
| | - Subuhi Sherwani
- Department of Biology, College of Science, Ha’il University, Ha’il 55211, Saudi Arabia; (M.K.); (S.S.)
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Faculty of Medicine, Görükle Campus, Bursa Uludağ University, Bursa 16059, Turkey
| | - Muhammad Faraz Arshad Malik
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
| | | | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha’il University, Ha’il 55211, Saudi Arabia
- Correspondence: (S.K.); (F.H.)
| | - Farhan Haq
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
- Correspondence: (S.K.); (F.H.)
| |
Collapse
|
20
|
Xu Y, Wang T, Zeng J, Wang B, Zhou L, Yang M, Zhang L, Zhang N. Integrative Functional Genomics Implicated the Key T-/B-Cell Deficiency Regulator RAG1 in Transarterial Chemoembolization of Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:720791. [PMID: 34646823 PMCID: PMC8502842 DOI: 10.3389/fcell.2021.720791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023] Open
Abstract
Transarterial chemoembolization (TACE) has significantly prolonged overall survival (OS) of unresectable hepatocellular carcinoma (HCC) patients. Unfortunately, there are still a portion of patients without therapeutic responses to TACE. Although genome-wide association studies identified multiple HCC susceptibility SNPs, it is still largely unclear how genome-wide identified functional SNPs impacting gene expression contribute to the prognosis of TACE-treated HCC patients. In this study, we developed an integrative functional genomics methodology to identify gene expression-related SNPs significantly contributing to prognosis of TACE-treated HCC patients across the whole genome. Employing integration of data from expression quantitative trait locus (eQTLs) analyses of The Cancer Genome Atlas (TCGA) liver hepatocellular carcinoma (LIHC) as well as the 1000 Genomes project, we successfully annotated 60 gene expression-related SNPs which are associated with OS of the TCGA patients. After genotyping these 60 SNPs in our TACE cohort, we identified four SNPs (rs12574873, rs12513391, rs34597395, and rs35624901) which are significantly associated with OS of HCC patients treated with TACE. For instance, multivariate Cox proportional hazards model indicated that the rs35624901 Deletion.Deletion (Del.Del) genotype carriers had markedly prolonged OS and a 55% decreased death risk compared with individuals with the GG genotype after TACE therapy (p = 8.3 × 10–5). In support of this, the rs35624901 Del.Del genotype is correlated to higher expression of RAG1, a key T-/B-cell deficiency regulator. Our findings reported the first evidence supporting the prognostic value of four eQTL SNPs in TACE-treated HCC patients. Importantly, our data implicated that antitumor immunity might contribute to TACE efficiency for unresectable HCC patients.
Collapse
Affiliation(s)
- Yeyang Xu
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Teng Wang
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiajia Zeng
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Bowen Wang
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Liqing Zhou
- Department of Radiation Oncology, Huaian No. 2 Hospital, Huaian, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Li Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| |
Collapse
|
21
|
Hsieh AR, Fann CSJ, Lin HC, Tai J, Hsieh SY, Tai DI. Hepatitis B virus persistent infection-related single nucleotide polymorphisms in HLA regions are associated with viral load in hepatoma families. World J Gastroenterol 2021; 27:6262-6276. [PMID: 34712031 PMCID: PMC8515798 DOI: 10.3748/wjg.v27.i37.6262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Genome-wide association studies from Asia indicate that HLA-DP and HLA-DQ loci are important in persistent hepatitis B virus (HBV) infections. One of the key elements for HBV-related carcinogenesis is persistent viral replication and inflammation.
AIM To examine genetic and nongenetic factors with persistent HBV infection and viral load in families with hepatocellular carcinoma (HCC).
METHODS The HCC families included 301 hepatitis B surface antigen (HBsAg) carriers and 424 noncarriers born before the nationwide vaccination program was initiated in 1984. Five HBV-related single nucleotide polymorphisms (SNPs) — rs477515, rs9272105, rs9276370, rs7756516, and rs9277535 — were genotyped. Factors associated with persistent HBV infection and viral load were analyzed by a generalized estimating equation.
RESULTS In the first-stage persistent HBV study, all SNPs except rs9272105 were associated with persistent infection. A significantly higher area under the reciprocal operating characteristic curve for nongenetic factors vs genetic factors (P < 0.001) suggests that the former play a major role in persistent HBV infection. In the second-stage viral load study, we added 8 HBsAg carriers born after 1984. The 309 HBsAg carriers were divided into low (n = 162) and high viral load (n = 147) groups with an HBV DNA cutoff of 105 cps/mL. Sex, relationship to the index case, rs477515, rs9272105, and rs7756516 were associated with viral load. Based on the receiver operating characteristic curve analysis, genetic and nongenetic factors affected viral load equally in the HCC family cohort (P = 0.3117).
CONCLUSION In these east Asian adults, the mechanism of persistent HBV infection-related SNPs was a prolonged viral replication phase.
Collapse
Affiliation(s)
- Ai-Ru Hsieh
- Department of Statistics, Tamkang University, New Taipei City 25137, Taiwan
| | - Cathy S J Fann
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Hung-Chun Lin
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan 33305, Taiwan
| | - Jennifer Tai
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan 33305, Taiwan
| | - Sen-Yung Hsieh
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan 33305, Taiwan
| | - Dar-In Tai
- Division of Hepatology, Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan 33305, Taiwan
| |
Collapse
|
22
|
Qi HX, Shen QD, Zhao HY, Qi GZ, Gao L. Network-based analysis revealed significant interactions between risk genes of severe COVID-19 and host genes interacted with SARS-CoV-2 proteins. Brief Bioinform 2021; 23:6372084. [PMID: 34535795 DOI: 10.1093/bib/bbab372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/04/2021] [Accepted: 08/20/2021] [Indexed: 12/15/2022] Open
Abstract
Whether risk genes of severe coronavirus disease 2019 (COVID-19) from genome-wide association study could play their regulatory roles by interacting with host genes that were interacted with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins was worthy of exploration. In this study, we implemented a network-based approach by developing a user-friendly software Network Calculator (https://github.com/Haoxiang-Qi/Network-Calculator.git). By using Network Calculator, we identified a network composed of 13 risk genes and 28 SARS-CoV-2 interacted host genes that had the highest network proximity with each other, with a hub gene HNRNPK identified. Among these genes, 14 of them were identified to be differentially expressed in RNA-seq data from severe COVID-19 cases. Besides, by expression enrichment analysis in single-cell RNA-seq data, compared with mild COVID-19, these genes were significantly enriched in macrophage, T cell and epithelial cell for severe COVID-19. Meanwhile, 74 pathways were significantly enriched. Our analysis provided insights for the underlying genetic etiology of severe COVID-19 from the perspective of network biology.
Collapse
Affiliation(s)
- Hao-Xiang Qi
- Department of Bioinformatics, School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an 271099, Shandong, China
| | - Qi-Dong Shen
- Department of Bioinformatics, School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an 271099, Shandong, China
| | - Hong-Yi Zhao
- Department of Bioinformatics, School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an 271099, Shandong, China
| | - Guo-Zhen Qi
- Department of Bioinformatics, School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an 271099, Shandong, China
| | - Lei Gao
- Department of Bioinformatics, School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an 271099, Shandong, China
| |
Collapse
|
23
|
Mai H, Xie H, Hou J, Chen H, Zhou B, Hou J, Jiang D. A Genetic Variant of PPP1CB Influences Risk of Hepatitis B Virus-Related Hepatocellular Carcinoma in Han Chinese: A Pathway Based Analysis. J Hepatocell Carcinoma 2021; 8:1055-1064. [PMID: 34513747 PMCID: PMC8422165 DOI: 10.2147/jhc.s321939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/18/2021] [Indexed: 01/10/2023] Open
Abstract
Purpose Activation of actin cytoskeleton remodeling is an important stage preceding cancer cell metastasis. Previous genome-wide association studies (GWAS) have identified multiple hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC)-associated risk loci. However, limited sample size or strict significance threshold of GWAS may cause HBV-related HCC risk-associated genetic loci to be undetected. We aimed to investigate the performance of the SNP rs13025377 in PPP1CB in HCC. Patients and Methods We performed a case-control study including 1161 cases and 1353 controls to evaluate associations between single nucleotide polymorphisms (SNPs) from 98 actin-cytoskeleton regulatory genes and risk of HBV-related HCC. The effects of SNPs on HBV-related HCC risk were assessed under logistic regression model and corrected by false discovery rate (FDR). Results We found that rs13025377 in PPP1CB was significantly associated with HBV-related HCC risk [odds ratio (OR) = 0.81, 95% confidence interval (CI) = 0.72~0.91, P = 4.88×10-4]. The risk allele A of rs13025377 increased PPP1CB expression levels in normal liver tissue. SNP rs4665434 was tagged by rs13025377 (r2 = 0.9) and its protective allele disrupted CTCF and Cohesin motifs. According to public datasets, PPP1CB, CTCF and Cohesin expression levels are increased in tumor tissues. Kaplan-Meier plots demonstrated that higher PPP1CB expression was significantly associated with shorter overall survival (OS). Moreover, we observed strong correlation between CTCF, Cohesin, and PPP1CB in various liver tissues. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis confirmed that PPP1CB plays a role in HCC through actin-cytoskeleton regulation. Conclusion Thus, these findings indicated that PPP1CB may be a key gene in actin-cytoskeleton regulation and rs13025377 contributes to the risk of HBV-related HCC by regulating PPP1CB expression.
Collapse
Affiliation(s)
- Haoming Mai
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Haisheng Xie
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Jia Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Haitao Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| | - Deke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, People's Republic of China
| |
Collapse
|
24
|
Zhang D, Guo S, Schrodi SJ. Mechanisms of DNA Methylation in Virus-Host Interaction in Hepatitis B Infection: Pathogenesis and Oncogenetic Properties. Int J Mol Sci 2021; 22:9858. [PMID: 34576022 PMCID: PMC8466338 DOI: 10.3390/ijms22189858] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/10/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV), the well-studied oncovirus that contributes to the majority of hepatocellular carcinomas (HCC) worldwide, can cause a severe inflammatory microenvironment leading to genetic and epigenetic changes in hepatocyte clones. HBV replication contributes to the regulation of DNA methyltransferase gene expression, particularly by X protein (HBx), and subsequent methylation changes may lead to abnormal transcription activation of adjacent genes and genomic instability. Undoubtedly, the altered expression of these genes has been known to cause diverse aspects of infected hepatocytes, including apoptosis, proliferation, reactive oxygen species (ROS) accumulation, and immune responses. Additionally, pollutant-induced DNA methylation changes and aberrant methylation of imprinted genes in hepatocytes also complicate the process of tumorigenesis. Meanwhile, hepatocytes also contribute to epigenetic modification of the viral genome to affect HBV replication or viral protein production. Meanwhile, methylation levels of HBV integrants and surrounding host regions also play crucial roles in their ability to produce viral proteins in affected hepatocytes. Both host and viral changes can provide novel insights into tumorigenesis, individualized responses to therapeutic intervention, disease progress, and early diagnosis. As such, DNA methylation-mediated epigenetic silencing of cancer-related genes and viral replication is a compelling therapeutic goal to reduce morbidity and mortality from liver cancer caused by chronic HBV infection. In this review, we summarize the most recent research on aberrant DNA methylation associated with HBV infection, which is involved in HCC development, and provide an outlook on the future direction of the research.
Collapse
Affiliation(s)
- Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Steven J. Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
25
|
Zhu M, Liang Z, Pan J, Zhang X, Xue R, Cao G, Hu X, Gong C. Hepatocellular carcinoma progression mediated by hepatitis B virus-encoded circRNA HBV_circ_1 through interaction with CDK1. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 25:668-682. [PMID: 34589285 PMCID: PMC8463320 DOI: 10.1016/j.omtn.2021.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) produces circular RNA (circRNA), whose functions have not yet been clearly elucidated. In this study, a novel circRNA HBV_circ_1 produced by HBV was identified in HBV-positive HepG2.2.15 cells and HBV-related hepatocellular carcinoma (HCC) tissue (HCCT). Microarray analysis of 68 HCCT samples showed that HBV_circ_1 abundance was significantly higher than that in paracancerous tissues. In addition, survival rate of HBV_circ_1-positive patients was significantly lower compared with HBV_circ_1-negative patients. Transient expression indicated that HBV_circ_1 enhanced cell proliferation, migration, and invasion and inhibited apoptosis in vitro. Furthermore, ectopical HBV_circ_1 expression increased tumor size in vivo. HBV_circ_1 was confirmed to interact with cyclin-dependent kinase 1 (CDK1) to regulate cell proliferation. These results suggest that HCC progression may be promoted by interaction of HBV_circ_1 with CDK1. Our data not only showed a novel clue to understand carcinogenesis and progress of HBV-related HCC but also provided a new target for the development of therapeutic drugs.
Collapse
Affiliation(s)
- Min Zhu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Zi Liang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Jun Pan
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Xing Zhang
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Renyu Xue
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Guangli Cao
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Xiaolong Hu
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Chengliang Gong
- School of Biology & Basic Medical Science, Soochow University, Suzhou 215123, China
| |
Collapse
|
26
|
Mai H, Chen J, Chen H, Liu Z, Huang G, Wang J, Xiao Q, Ren W, Zhou B, Hou J, Jiang D. Fine Mapping of the MHC Region Identifies Novel Variants Associated with HBV-Related Hepatocellular Carcinoma in Han Chinese. J Hepatocell Carcinoma 2021; 8:951-961. [PMID: 34430511 PMCID: PMC8378933 DOI: 10.2147/jhc.s321919] [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: 05/26/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction Genome-wide association studies identified susceptibility loci in the major histocompatibility complex region for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). However, the causal variants underlying HBV-related HCC pathogenesis remain elusive. Methods With a total of 1,161 HBV-related HCC cases and 1,353 chronic HBV carriers without HCC, we imputed human leukocyte antigen (HLA) variants based on a Chinese HLA reference panel and evaluated the associations of these variants with the risk of HBV-related HCC. Conditional analyses were used to identify independent signals associated with the risk of HBV-related HCC (P false-discovery rate (FDR) <0.20). A total of 14,930 variants within the MHC region were genotyped or imputed. Results We identified two variants, rs114401688 (P = 1.05 × 10−6, PFDR = 2.43 × 10−3) and rs115126566 (P = 9.04 × 10−5, PFDR = 1.77 × 10−1), that are independently associated with the risk of HBV-related HCC. Single nucleotide polymorphism (SNP) rs114401688 is in linkage disequilibrium with a previously reported SNP rs9275319. In the current study, we found that its association with HCC could be explained by HLA-DQB1*04 and HLA-DRB1*04. SNP rs115126566 is a novel risk variant and may function by regulating transcriptions of HLA-DPA1/DPB1 through enhancer-mediated mechanisms. HLA zygosity analysis showed that homozygosity at HLA-DQB1 gene is suggestively associated with a higher risk of HCC (P = 0.10) and the risk was more pronounced in the older age group (age ≥50, P = 0.03). Discussion Our findings further the understanding of the genetic basis for HBV-related HCC predisposition in chronic HBV carriers.
Collapse
Affiliation(s)
- Haoming Mai
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jiaxuan Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Haitao Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, People's Republic of China
| | - Zhiwei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Guanlin Huang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jialin Wang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Qianyi Xiao
- School of Public Health, Fudan University, Shanghai, 200032, People's Republic of China
| | - Weihua Ren
- Central Laboratory, First Affiliated Hospital, Henan University of Science and Technology, Luoyang, Henan Province, 471009, People's Republic of China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Deke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| |
Collapse
|
27
|
Song Y, Xing H, Zhou L, Zhang N, Yang M. LncRNA H19 modulated by miR-146b-3p/miR-1539-mediated allelic regulation in transarterial chemoembolization of hepatocellular carcinoma. Arch Toxicol 2021; 95:3063-3070. [PMID: 34251499 DOI: 10.1007/s00204-021-03119-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/07/2021] [Indexed: 12/19/2022]
Abstract
Transarterial chemoembolization (TACE) is an effective treatment for unresectable hepatocellular carcinoma (HCC) patients. Although overall survival (OS) of TACE-treated patients has been evidently prolonged, not all unresectable HCC patients can benefit from TACE. Genome-wide association studies identified multiple HCC susceptibility single nucleotide polymorphisms (SNPs). However, it is still unclear how lncRNAs and their functional SNPs impact therapeutic responses of TACE. In the study, we hypothesized that the functional lncRNA H19 SNP(s) might impact H19 expression and, thus, prognosis of TACE-treated HCC patients. We found that the H19 rs3741219 SNP was significantly associated with OS of HCC patients received TACE. Cox proportional hazards model demonstrated that the rs3741219 CC genotype was associated with longer OS and a 37% decreased death risk compared with the TT carriers after TACE therapy (P = 0.001). Interestingly, the rs3741219 T-to-C change led to allelic down-regulation of lncRNA H19 expression via creating the binding sites of miR-146b-3p and miR-1539. Luciferase reporter gene assays indicated that miR-146b-3p and miR-1539 could markedly silence the rs3741219 C-allelic H19 expression but not lncRNA H19 with the T allele. Consistently, there was significantly reduced expression of lncRNA H19 in HCC and normal tissues of the C allele carriers compared with the H19 levels in patients with the T allele. Knock-down of lncRNA H19 significantly promoted the anti-viability efficiency of oxaliplatin (the main chemotherapy drug used in TACE) to HCC cells. In view of these results, we assume that lncRNA H19 might be a potential therapeutic target for unresectable HCC patients.
Collapse
Affiliation(s)
- Yemei Song
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Huaixin Xing
- Department of Anesthesiology, Shandong Cancer Hospital and Institute, Shandong First Medical University, and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Liqing Zhou
- Department of Radiation Oncology, Huaian No. 2 Hospital, Huaian, Jiangsu Province, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China.
| |
Collapse
|
28
|
Liu Q, Liu G, Lin Z, Lin Z, Tian N, Lin X, Tan J, Huang B, Ji X, Pi L, Yu X, Liu L, Gao Y. The association of lncRNA SNPs and SNPs-environment interactions based on GWAS with HBV-related HCC risk and progression. Mol Genet Genomic Med 2021; 9:e1585. [PMID: 33432784 PMCID: PMC8077159 DOI: 10.1002/mgg3.1585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 11/30/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022] Open
Abstract
Background Long non‐coding RNA (lncRNA) plays an essential role in hepatitis B virus‐related hepatocellular carcinoma (HBV‐related HCC) occurrence and development. Single nucleotide polymorphism (SNP) may affect HBV‐related HCC susceptibility by altering the function of lncRNA. However, the relationship between lncRNA SNPs and HBV‐related HCC occurrence and development is still unclear. Methods In the present study, based on HBV‐related HCC genome‐wide association studies, eight potentially functional SNPs from two lncRNAs were predicted using a set of bioinformatics strategies. In 643 HBV‐related HCC patients, 549 CHB carriers, and 553 HBV natural clearance subjects from Southern Chinese, we evaluated associations between SNPs and HBV‐related HCC occurrence or development with odds ratio (OR) and 95% confidence interval (CI) under credible genetic models. Results In HBV‐related HCC patients, rs9908998 was found to significantly increase the risk of lymphatic metastasis under recessive model (Adjusted OR = 1.95, 95% CI = 1.20–3.17). Lnc‐RP11‐150O12.3 rs2275959, rs1008547, and rs11776545 with cancer family history may show significant multiplicative and additive interactions on HBV‐related HCC susceptibility (all pAdjusted < .05). The associations of rs2275959, rs1008547, and rs11776545 with distant metastasis of HBV‐related HCC patients were observed in additive model (Adjusted OR = 1.45, 95% CI = 1.06–1.97 for rs2275959; Adjusted OR = 1.45, 95% CI = 1.06–1.98 for rs1008547; Adjusted OR = 1.40, 95% CI = 1.03–1.91 for rs11776545). Conclusion Taken together, lnc‐ACACA‐1 rs9908998, lnc‐RP11‐150O12.3 rs2275959, rs1008547, and rs11776545 might be predictors for HBV‐related HCC risk or prognosis.
Collapse
Affiliation(s)
- Qing Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Guiyan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhifeng Lin
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ziqiang Lin
- Department of Psychiatry, New York University Langone School of Medicine, New York, NY, USA
| | - NaNa Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xinqi Lin
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jianyi Tan
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Baoying Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaohui Ji
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Lucheng Pi
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xinfa Yu
- Department of Oncology, Shunde Hospital of Southern Medical University, Foshan, China
| | - Li Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yanhui Gao
- Department of Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| |
Collapse
|
29
|
Wangensteen KJ, Chang KM. Multiple Roles for Hepatitis B and C Viruses and the Host in the Development of Hepatocellular Carcinoma. Hepatology 2021; 73 Suppl 1:27-37. [PMID: 32737895 PMCID: PMC7855312 DOI: 10.1002/hep.31481] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/21/2020] [Accepted: 07/02/2020] [Indexed: 02/06/2023]
Abstract
Chronic hepatitis B and C viral infections are major risk factors for hepatocellular carcinoma (HCC) in the United States and worldwide. Direct and indirect mechanisms of viral infection lead to the development of HCC. Chronic viral infection leads to inflammation and liver damage, culminating in cirrhosis, the penultimate step in the progression toward HCC. Host, viral, and environmental factors likely interact to promote oncogenesis. Clinical considerations include recommendations for screening for HCC in persons at risk, treatment with antivirals, and an emerging role for immunotherapy in HCC. We pose unanswered questions regarding HCC susceptibility and pathogenesis in the setting of chronic hepatitis B and C.
Collapse
Affiliation(s)
- Kirk J. Wangensteen
- Kirk Wangensteen, MD/PhD, Assistant Professor of Medicine and Genetics, Gastroenterology Division, University of Pennsylvania Perelman School of Medicine, 421 Curie BLVD, BRB 910, Philadelphia, PA 19104
| | - Kyong-Mi Chang
- Kyong-Mi Chang, MD, Associate Chief of Staff and Associate Dean for Research, The Corporal Michael J. Crescenz VAMC, Professor of Medicine in GI, University of Pennsylvania Perelman School of Medicine, 3900 Woodland Ave, Philadelphia PA 19104
| |
Collapse
|
30
|
McGlynn KA, Petrick JL, El-Serag HB. Epidemiology of Hepatocellular Carcinoma. Hepatology 2021; 73 Suppl 1:4-13. [PMID: 32319693 PMCID: PMC7577946 DOI: 10.1002/hep.31288] [Citation(s) in RCA: 976] [Impact Index Per Article: 325.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/22/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023]
Abstract
Liver cancer is a major contributor to the worldwide cancer burden. Incidence rates of this disease have increased in many countries in recent decades. As the principal histologic type of liver cancer, hepatocellular carcinoma (HCC) accounts for the great majority of liver cancer diagnoses and deaths. Hepatitis B virus (HBV) and hepatitis C virus (HCV) remain, at present, the most important global risk factors for HCC, but their importance will likely decline in the coming years. The effect of HBV vaccination of newborns, already seen in young adults in some countries, will be more notable as vaccinated cohorts age. In addition, effective treatments for chronic infections with both HBV and HCV should contribute to declines in the rates of viral-associated HCC. Unfortunately, the prevalence of metabolic risk factors for HCC, including metabolic syndrome, obesity, type II diabetes and non-alcoholic fatty liver disease (NAFLD) are increasing and may jointly become the major cause of HCC globally. Excessive alcohol consumption also remains an intractable risk factor, as does aflatoxin contamination of food crops in some parts of the world. While significant efforts in early diagnosis and better treatment are certainly needed for HCC, primary prevention efforts aimed at decreasing the prevalence of obesity and diabetes and controlling mycotoxin growth, are just as urgently required.
Collapse
Affiliation(s)
- Katherine A McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | | |
Collapse
|
31
|
Evaluation for the Genetic Association between Store-Operated Calcium Influx Pathway (STIM1 and ORAI1) and Human Hepatocellular Carcinoma in Patients with Chronic Hepatitis B Infection. BIOLOGY 2020; 9:biology9110388. [PMID: 33182378 PMCID: PMC7695319 DOI: 10.3390/biology9110388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/06/2020] [Indexed: 01/05/2023]
Abstract
Hepatocellular carcinoma (HCC) often develops from chronic hepatitis B (CHB) through replication of hepatitis B virus (HBV) infection. Calcium (Ca2+) signaling plays an essential role in HBV replication. Store-operated calcium (SOC) channels are a major pathway of Ca2+ entry into non-excitable cells such as immune cells and cancer cells. The basic components of SOC signaling include the STIM1 and ORAI1 genes. However, the roles of STIM1 and ORAI1 in HBV-mediated HCC are still unclear. Thus, long-term follow-up of HBV cohort was carried out in this study. This study recruited 3631 patients with chronic hepatitis (345 patients with HCC, 3286 patients without HCC) in a Taiwanese population. Genetic variants of the STIM1 and ORAI1 genes were detected using an Axiom CHB1 genome-wide array. Clinical associations of 40 polymorphisms were analyzed. Three of the STIM1 single-nucleotide polymorphisms (SNPs) (rs6578418, rs7116520, and rs11030472) and one SNP of ORAI1 (rs6486795) showed a trend of being associated with HCC disease (p < 0.05). However, after correction for multiple testing, none of the SNPs reached a significant level (q > 0.05); in contrast, neither STIM1 nor ORAI1 showed a significant association with HCC progression in CHB patients. Functional studies by both total internal reflection fluorescence images and transwell migration assay indicated the critical roles of SOC-mediated signaling in HCC migration. In conclusion, we reported a weak correlation between STIM1/ORAI1 polymorphisms and the risk of HCC progression in CHB patients.
Collapse
|
32
|
Gu S, Lv L, Lin X, Li X, Dai J, Zhang J, Kong R, Xie W, Li J. Using structural analysis to explore the role of hepatitis B virus mutations in immune escape from liver cancer in Chinese, European and American populations. J Biomol Struct Dyn 2020; 40:1586-1596. [PMID: 33030111 DOI: 10.1080/07391102.2020.1830852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hepatitis B virus (HBV) infection is an important problem threatening human health. After HBV virus invades human body, it may assemble a complete virus particle in the cytoplasm to trigger the immune reaction, especially the interaction between the HBV virus and the host that mediated by CD8+ T cell. We collected the sequences of HBV from the HBVdb database, then screened candidate mutation sites in Chinese, European and American populations based on conservation and physicochemical properties. After that we constructed the three-dimensional structure of Major histocompatibility complex class I (MHC I) -peptide complexes, performed molecular docking, run molecular dynamics to compare the binding free energy, stability, and affinity of MHC I-peptide complexes with the aim to estimate the effect of peptide mutation. The specific HBV virus subtypes of the Chinese, European and American population were studied and the candidate mutation sites were used to predict the mutant peptide antigen. Finally, based on physical and chemical properties and peptide antigen prediction scores, 21 HBV mutation sites were selected. Then combined with specific Human lymphocyte antigen (HLA) subtypes, 11 mutations were found to have a significant negative impact on affinity, stability and binding free energy. Overall, our work found important potential mutations, which provide an evaluation of HBV mutations and a clue of it in immunotherapy.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shuanglin Gu
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Li Lv
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Xue Lin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Xingyu Li
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Juncheng Dai
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Jianqiong Zhang
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Wei Xie
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, China
| | - Jian Li
- Key Laboratory of DGHD, MOE, Institute of Life Sciences, Southeast University, Nanjing, China
| |
Collapse
|
33
|
Han J, Chen C, Wang C, Qin N, Huang M, Ma Z, Zhu M, Dai J, Jiang Y, Ma H, Jin G, Shen H, Hu Z. Transcriptome-wide association study for persistent hepatitis B virus infection and related hepatocellular carcinoma. Liver Int 2020; 40:2117-2127. [PMID: 32574393 DOI: 10.1111/liv.14577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 06/01/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Previous genome-wide association studies (GWAS) have identified multiple susceptible variants associated with persistent hepatitis B virus (HBV) infection. However, most of these variants are located in the noncoding regions, which make it difficult to determine the effective genes underlying these associations. We performed a two-stage study, in the first stage we integrated RNA sequencing data of liver tissues and high-density genotyping data from the Genotype-Tissue Expression (GTEx) project with our previous GWAS data to conduct a transcriptome-wide association study (TWAS) on HBV infection. Firstly, the cis-heritable genes were screened by a genetic relatedness matrix of genome-wide complex trait analysis (GCTA) from GTEx data. Then, the genetic expression of 2587 cis-heritable genes was predicted by restricted maximum likelihood (REML) of genome-wide efficient mixed-model association (GEMMA) in our GWAS data with 951 HBV carrier cases and 937 HBV cleared controls. Next, we investigated the associations between predictive expression levels and persistent HBV infection risk. Gene set enrichment analysis (GSEA) was applied to infer the function of the identified genes. To identify the causal single nucleotide polymorphisms (SNPs) of HBV infection risk, we conducted the expression quantitative trait loci (eQTL)-based stepwise logistic regression analysis in the regions around 1 Mb of these genes and validated the association between 994 health controls and 994 HBV-persistent infection cases by genotyping experiment. In the second stage, 1538 HBV-related hepatocellular carcinoma (HCC) cases and 1465 persistent HBV infection controls were collected to determine the effect of these variants on HBV-related HCC as well, which were examined by the additive model in logistic regression analysis. We identified seven genes associated with HBV infection. In the classic human leukocyte antigen (HLA) region, three novel genes BAK1, HLA-DOB and C4A (Z range from -3.95 to -3.64, P range from 7.84 × 10-5 to 2.00 × 10-4 ), as well as two genes (HLA-DPA1 and HLA-DPB1) were reported by previous GWAS. In the non-HLA region, immune related at newly identified loci, PARP9 (Z = 3.69, P = 2.20 × 10-4 ) at 3q21.1. At 22q11.21, we identified TMEM191A (Z = 3.55, P = 3.80 × 10-4 ) as a target gene in addition to the reported non-cis-heritable gene UBE2L3. After further stepwise logistic regression analysis and validation, we identified eight variants independently associated with persistent HBV infection. Among those variants, the additive model showed that two SNPs associated with HBV-related HCC risk (rs9272714 and rs9394194, OR range from 1.20 to 1.25, P range from 1.19 × 10-4 to 3.97 × 10-4 ). By integrating transcriptome data, our study not only identified new susceptibility loci of persistent HBV infection but also determined the potential target genes at reported loci, which provided insight into the genetic aetiology of persistent HBV infection and related HCC.
Collapse
Affiliation(s)
- Jing Han
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
| | - Congcong Chen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Cheng Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Na Qin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Mingtao Huang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zijian Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Meng Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| |
Collapse
|
34
|
Jiang D, Deng J, Dong C, Ma X, Xiao Q, Zhou B, Yang C, Wei L, Conran C, Zheng SL, Ng IOL, Yu L, Xu J, Sham PC, Qi X, Hou J, Ji Y, Cao G, Li M. Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma. BMC Cancer 2020; 20:403. [PMID: 32393195 PMCID: PMC7216662 DOI: 10.1186/s12885-020-06842-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Recent genome-wide association studies (GWASs) have suggested several susceptibility loci of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) by statistical analysis at individual single-nucleotide polymorphisms (SNPs). However, these loci only explain a small fraction of HBV-related HCC heritability. In the present study, we aimed to identify additional susceptibility loci of HBV-related HCC using advanced knowledge-based analysis. METHODS We performed knowledge-based analysis (including gene- and gene-set-based association tests) on variant-level association p-values from two existing GWASs of HBV-related HCC. Five different types of gene-sets were collected for the association analysis. A number of SNPs within the gene prioritized by the knowledge-based association tests were selected to replicate genetic associations in an independent sample of 965 cases and 923 controls. RESULTS The gene-based association analysis detected four genes significantly or suggestively associated with HBV-related HCC risk: SLC39A8, GOLGA8M, SMIM31, and WHAMMP2. The gene-set-based association analysis prioritized two promising gene sets for HCC, cell cycle G1/S transition and NOTCH1 intracellular domain regulates transcription. Within the gene sets, three promising candidate genes (CDC45, NCOR1 and KAT2A) were further prioritized for HCC. Among genes of liver-specific expression, multiple genes previously implicated in HCC were also highlighted. However, probably due to small sample size, none of the genes prioritized by the knowledge-based association analyses were successfully replicated by variant-level association test in the independent sample. CONCLUSIONS This comprehensive knowledge-based association mining study suggested several promising genes and gene-sets associated with HBV-related HCC risks, which would facilitate follow-up functional studies on the pathogenic mechanism of HCC.
Collapse
Affiliation(s)
- Deke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaen Deng
- Department of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong
| | | | - Xiaopin Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Qianyi Xiao
- Center for Genomic Translational Medicine and Prevention, School of Public Health, Fudan University, Shanghai, China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chou Yang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lin Wei
- Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA.,Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Carly Conran
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Pritzker School of Medicine, University of Chicago, Evanston, IL, USA
| | - S Lilly Zheng
- Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Irene Oi-Lin Ng
- Department of Pathology, the University of Hong Kong, Pokfulam, Hong Kong.,State Key Laboratory of Liver Research, the University of Hong Kong, Pokfulam, Hong Kong
| | - Long Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianfeng Xu
- Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Pak C Sham
- The Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong
| | - Xiaolong Qi
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yuan Ji
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China.
| | - Miaoxin Li
- Department of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong. .,The Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong. .,State Key Laboratory for Cognitive and Brain Sciences, the University of Hong Kong, Pokfulam, Hong Kong. .,Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China. .,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, China.
| |
Collapse
|
35
|
Yang J, Qin T, Liu S, Tang H, Liu M, Wang Q. Interaction analysis of miR-1275/IGF2BP1/IGF2BP3 with the susceptibility to hepatocellular carcinoma. Biomark Med 2020; 14:283-292. [PMID: 32134323 DOI: 10.2217/bmm-2019-0332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: The aim of this study was to investigate the association of miR-1275 rs16759, IGF2BP1 rs11079850 and IGF2BP3 rs34414305 with hepatocellular carcinoma (HCC) risk. Materials & methods: Genotyping of the rs16759 and rs11079850 was performed using a Taqman assay and genotyping of the rs34414305 was performed using PCR. Relative expression of miR-1275, IGF2BP1 and IGF2BP3 was examined using quantitative PCR. Results: Comparison of the rs16759GG, CG/GG and CC genotype showed an increased risk of HCC. When comparing G with C allele, a significantly increased risk of HCC was also found. The rs16759, rs11079850 and rs34414305 had combined the interactive effects on the carcinogenesis of HCC. Moreover, the rs34414305 Del/ATT-Del/Del carriers displayed lower levels of IGF2BP3. Conclusion: The rs16759, rs11079850 and rs34414305 may singly and interactively contribute to carcinogenesis of HCC.
Collapse
Affiliation(s)
- Jun Yang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Tao Qin
- Department of Laboratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, China
| | - Shanshan Liu
- Department of Laboratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, China
| | - Hui Tang
- Department of Laboratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, China
| | - Mengqing Liu
- The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi 541001, China
| | - Qian Wang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, China
| |
Collapse
|
36
|
Li X, Wang H, Li T, Wang L, Wu X, Liu J, Xu Y, Wei W. Circulating tumor DNA/circulating tumor cells and the applicability in different causes induced hepatocellular carcinoma. Curr Probl Cancer 2019; 44:100516. [PMID: 31836136 DOI: 10.1016/j.currproblcancer.2019.100516] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/31/2019] [Accepted: 09/30/2019] [Indexed: 12/25/2022]
Abstract
In 2015, liquid biopsy was rated one of the top 10 breakthrough technologies of the year by MIT Technology Review. Liquid biopsy is a type of in vitro diagnostic method involving a noninvasive blood test. It is also a breakthrough technology used to detect tumors and cancers and assist in therapeutic strategies. The most widely used markers are circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). Primary carcinoma of the liver is a malignancy of hepatocytes or intrahepatic biliary epithelial cells. The most common type of liver cancer is hepatocellular carcinoma (HCC), the causes of which mainly include infection with hepatitis B virus (HBV) and/or hepatitis C virus (HCV), alcohol abuse, aflatoxicosis, and nonalcoholic fatty liver disease/ nonalcoholic steatohepatitis. As there are few typical clinical characteristics during the early stage of the disease, early diagnosis of HCC is very challenging. However, CTCs and ctDNA carry tumor-specific information. Therefore, the detection and analysis of CTCs and ctDNA can provide evidence for the early diagnosis of HCC and guide treatment. Furthermore, several studies have indicated that different inducers of HCC cause different DNA mutations, and accordingly, detection of specific mutations in ctDNA will facilitate the determination of the HCC type and help physicians provide distinctive therapies.
Collapse
Affiliation(s)
- Xuemei Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Huihui Wang
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tao Li
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, China; Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Anti-inflammatory and Immune Medicine innovation team, Hefei, China.
| | - Lianzi Wang
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xian Wu
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jiaqing Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei Wei
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-inflammatory and Immune Medicine, Anhui Anti-inflammatory and Immune Medicine innovation team, Hefei, China.
| |
Collapse
|
37
|
Wang XK, Liao XW, Yang CK, Yu TD, Liu ZQ, Gong YZ, Huang KT, Zeng XM, Han CY, Zhu GZ, Qin W, Peng T. Diagnostic and prognostic biomarkers of Human Leukocyte Antigen complex for hepatitis B virus-related hepatocellular carcinoma. J Cancer 2019; 10:5173-5190. [PMID: 31602270 PMCID: PMC6775598 DOI: 10.7150/jca.29655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 07/25/2019] [Indexed: 01/11/2023] Open
Abstract
Background: Hepatitis B virus infection had been identified its relationship with liver diseases, including liver tumors. We aimed to explore diagnostic and prognostic values between the Human Leukocyte Antigen (HLA) complex and hepatocellular carcinoma (HCC). Methods: We used the GSE14520 dataset to explore diagnostic and prognostic significance between HLA complex and HCC. A nomogram was constructed to predict survival probability of HCC prognosis. Gene set enrichment analysis was explored using gene ontologies and metabolic pathways. Validation of prognostic values of the HLA complex was performed in the Kaplan-Meier Plotter website. Results: We found that HLA-C showed the diagnostic value (P <0.0001, area under curve: 0.784, sensitivity: 93.14%, specificity: 62.26%). In addition, HLA-DQA1 and HLA-F showed prognostic values for overall survival, and HLA-A, HLA-C, HLA-DPA1 and HLA-DQA1 showed prognostic values for recurrence-free survival (all P ≤ 0.05, elevated 0.927, 0.992, 1.023, 0.918, 0.937 multiples compared to non-tumor tissues, respectively). Gene set enrichment analysis found that they were involved in antigen processing and toll like receptor signalling pathway, etc. The nomogram was evaluated for survival probability of HCC prognosis. Validation analysis indicated that HLA-C, HLA-DPA1, HLA-E, HLA-F and HLA-G were associated with HCC prognosis of overall survival (all P ≤ 0.05, elevated 0.988 and 0.997 multiples compared to non-tumor tissues, respectively). Conclusion: HLA-C might be a diagnostic and prognostic biomarker for HCC. HLA-DPA1 and HLA-F might be prognostic biomarkers for HCC.
Collapse
Affiliation(s)
- Xiang-Kun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Xi-Wen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Cheng-Kun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Ting-Dong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Zheng-Qian Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Yi-Zhen Gong
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Ke-Tuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Xian-Min Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Chuang-Ye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Guang-Zhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Wei Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Province, China
| |
Collapse
|
38
|
Zhang Z, Wang C, Liu Z, Zou G, Li J, Lu M. Host Genetic Determinants of Hepatitis B Virus Infection. Front Genet 2019; 10:696. [PMID: 31475028 PMCID: PMC6702792 DOI: 10.3389/fgene.2019.00696] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 07/03/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection is still a major health problem worldwide. Recently, a great number of genetic studies based on single nucleotide polymorphisms (SNPs) and genome-wide association studies have been performed to search for host determinants of the development of chronic HBV infection, clinical outcomes, therapeutic efficacy, and responses to hepatitis B vaccines, with a focus on human leukocyte antigens (HLA), cytokine genes, and toll-like receptors. In addition to SNPs, gene insertions/deletions and copy number variants are associated with infection. However, conflicting results have been obtained. In the present review, we summarize the current state of research on host genetic factors and chronic HBV infection, its clinical type, therapies, and hepatitis B vaccine responses and classify published results according to their reliability. The potential roles of host genetic determinants of chronic HBV infection identified in these studies and their clinical significance are discussed. In particular, HLAs were relevant for HBV infection and pathogenesis. Finally, we highlight the need for additional studies with large sample sizes, well-matched study designs, appropriate statistical methods, and validation in multiple populations to improve the treatment of HBV infection.
Collapse
Affiliation(s)
- Zhenhua Zhang
- Department of Infectious Diseases, the Second Affiliated Hospital of Anhui Medical University, Hefei, China.,College of Pharmacy, Anhui Medical University, Hefei, China
| | - Changtai Wang
- Department of Infectious Diseases, the Affiliated Anqing Hospital of Anhui Medical University, Anqing, China
| | - Zhongping Liu
- Department of Infectious Diseases, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Guizhou Zou
- Department of Infectious Diseases, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jun Li
- College of Pharmacy, Anhui Medical University, Hefei, China
| | - Mengji Lu
- Institute of Virology, University Hospital of Duisburg-Essen, Essen, Germany
| |
Collapse
|
39
|
Xiao B, Kuang Z, Zhang W, Hang J, Chen L, Lei T, He Y, Deng C, Li W, Lu J, Qu J, Zhou Q, Hao W, Sun Z, Li L. Glutamate Ionotropic Receptor Kainate Type Subunit 3 (GRIK3) promotes epithelial-mesenchymal transition in breast cancer cells by regulating SPDEF/CDH1 signaling. Mol Carcinog 2019; 58:1314-1323. [PMID: 30977227 PMCID: PMC6618265 DOI: 10.1002/mc.23014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 01/01/2023]
Abstract
Glutamate Ionotropic Receptor Kainate Type Subunit 3 (GRIK3) is an important excitatory neurotransmitter receptor that plays a significant role in various neurodegenerative diseases. However, the biological functions of GRIK3 in malignancies are largely unknown because of limited related studies. Here, we primarily reported that the expression of GRIK3 was higher in breast cancer tissues than in adjacent noncancerous tissues. GRIK3 expression was also positively correlated with the prognosis of patients with breast cancer. GRIK3 promoted the proliferation and migration abilities of breast cancer cells and enhanced the growth of orthotopically implanted tumors. Mechanically, GRIK3 influenced a range of signaling pathways and key signal transducers, including two epithelial-mesenchymal transition regulators, SPDEF and CDH1. Heterogenous expression of SPDEF and CDH1 counteracted the migration and invasion abilities, respectively, of breast cancer cells induced by GRIK3. Moreover, overexpression of GRIK3 increased the expression of mesenchymal markers and decreased the expression of epithelial markers, resulting in the translocation of β-catenin into the nucleus and the increased β-catenin transcriptional activity. In conclusion, the present study reported a novel oncogenic role of GRIK3. Meanwhile, GRIK3, as a membrane receptor, may also serve as a potential therapeutic target for the treatment of breast cancer.
Collapse
Affiliation(s)
- Bin Xiao
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Zhenzhan Kuang
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Weiyun Zhang
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Jianfeng Hang
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Lidan Chen
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Ting Lei
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Yongyin He
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Chun Deng
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory ScienceGuizhou Medical UniversityGuiyangChina
| | - Weiwei Li
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory ScienceGuizhou Medical UniversityGuiyangChina
| | - Jingrun Lu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory ScienceGuizhou Medical UniversityGuiyangChina
| | - Jing Qu
- Department of Laboratory MedicineNanfang Hospital, Southern Medical UniversityGuangzhouChina
| | - Quan Zhou
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Wenbo Hao
- Institute of Antibody Engineering, School of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhouChina
| | - Zhaohui Sun
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| | - Linhai Li
- Department of Laboratory MedicineGeneral Hospital of Southern Theatre Command of PLAGuangzhouChina
| |
Collapse
|
40
|
Kozuka R, Enomoto M, Sato-Matsubara M, Yoshida K, Motoyama H, Hagihara A, Fujii H, Uchida-Kobayashi S, Morikawa H, Tamori A, Kawada N, Murakami Y. Association between HLA-DQA1/DRB1 polymorphism and development of hepatocellular carcinoma during entecavir treatment. J Gastroenterol Hepatol 2019; 34:937-946. [PMID: 30160782 DOI: 10.1111/jgh.14454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/14/2018] [Accepted: 08/16/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS It remains unclear whether there is an association between single-nucleotide polymorphisms (SNPs) and development of hepatocellular carcinoma (HCC) during entecavir (ETV) treatment in nucleos(t)ide analog-naïve patients with chronic hepatitis B virus infection. We investigated the risk factors for HCC, especially host factors, during ETV treatment. METHODS A total of 127 Japanese patients undergoing ETV treatment were enrolled in this study. Univariate and multivariate analyses for clinical factors, hepatic fibrosis markers, and SNPs associated with HCC development were analyzed. RESULTS A total of 10 patients developed HCC during the follow-up period (median duration, 3.3 years). The 3-, 5-, and 7-year cumulative rates of HCC development were 4.8%, 10.6%, and 13.6%, respectively. Liver fibrosis (cirrhosis; P = 0.0005), age (≥ 49 years; P = 0.0048), platelet count (≤ 115 × 10/mm3 ; P = 0.0007), α-fetoprotein (≥ 8.0 ng/mL; P = 0.030), type IV collagen (≥ 200 ng/mL; P = 0.043), fibrosis-4 index (≥ 4.14; P = 0.0006), and human leukocyte antigen (HLA)-DQA1/DRB1-SNP (AA genotype; P = 0.0092) were significantly associated with HCC development according to the log-rank test. In multivariate analysis, AA genotype in the HLA-DQA1/DRB1 gene (P = 0.013; hazard ratio 4.907; 95% confidence interval 1.407-17.113) and cirrhosis (P = 0.019; hazard ratio 4.789; 95% confidence interval 1.296-17.689) were significantly associated with HCC development. CONCLUSIONS Our findings suggested that patients with AA genotype in the HLA-DQA1/DRB1 gene or cirrhosis should be carefully followed up as a population potentially at higher risk of HCC during ETV treatment.
Collapse
Affiliation(s)
- Ritsuzo Kozuka
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masaru Enomoto
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Misako Sato-Matsubara
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Kanako Yoshida
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hiroyuki Motoyama
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Atsushi Hagihara
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hideki Fujii
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | | | - Hiroyasu Morikawa
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Akihiro Tamori
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Norifumi Kawada
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Yoshiki Murakami
- Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan
| |
Collapse
|
41
|
Wei J, Sheng Y, Li J, Gao X, Ren N, Dong Q, Qin L. Genome-Wide Association Study Identifies a Genetic Prediction Model for Postoperative Survival in Patients with Hepatocellular Carcinoma. Med Sci Monit 2019; 25:2452-2478. [PMID: 30945699 PMCID: PMC6461006 DOI: 10.12659/msm.915511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background As an important aspect of tumor heterogeneity, genetic variation may influence susceptibility and prognosis in different types of cancer. By exploring the prognostic value of genetic variation, this study aimed to establish a model for predicting postoperative survival and assessing the impact of variation on clinical outcomes in patients with hepatocellular carcinoma (HCC). Material/Methods A genome-wide association study of 367 patients with HCC was conducted to identify single nucleotide polymorphisms (SNPs) associated with prognosis. Identified predictors were further evaluated in 758 patients. Two prognostic models were established using Cox proportional hazards regression and Nomogram strategy, and validated in another 316 patients. The effect of the SNP rs2431 was analyzed in detail. Results A prognostic model including 5 SNPs (rs10893585, rs2431, rs34675408, rs6078460, and rs6766361) was established and exhibited high predictive accuracy for HCC prognosis. The panel combined with tumor node metastasis (TNM) stage resulted in a significantly higher c-index (0.723) than the individual c-index values. Stratified by the Nomogram prediction model, the median overall survival for the low-risk and high-risk groups were 100.1 versus 30.8 months (P<0.001) in the training set and 82.2 versus 22.5 months (P<0.001) in the validation set. A closer examination of rs2431 revealed that it may regulate the expression of FNDC3B by disrupting a microRNA-binding site. Conclusions This study established prediction models based on genetic factors alone or in combination with TNM stage for postoperative survival in patients with HCC, and identified FNDC3B as a potential therapeutic target for combating HCC metastasis.
Collapse
Affiliation(s)
- Jinwang Wei
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Yuanyuan Sheng
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Jianhua Li
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Xiaomei Gao
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Ning Ren
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China (mainland)
| | - Qiongzhu Dong
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Lunxiu Qin
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| |
Collapse
|
42
|
Luo YY, Zhang HP, Huang AL, Hu JL. Association between KIF1B rs17401966 genetic polymorphism and hepatocellular carcinoma susceptibility: an updated meta-analysis. BMC MEDICAL GENETICS 2019; 20:59. [PMID: 30947687 PMCID: PMC6449895 DOI: 10.1186/s12881-019-0778-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/03/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Several studies have focused on the association between KIF1B rs17401966 polymorphism and susceptibility to hepatitis B virus-related (HBV-related) hepatocellular carcinoma (HCC), but the conclusions have been inconsistent. We have conducted this updated meta-analysis to explore the association between KIF1B rs17401966 polymorphism and HCC susceptibility. METHODS Eligible studies were identified through systematic searches in PubMed, OVID, ISI Web of Science, Chinese National Knowledge Infrastructure, and Wanfang databases. The quality of evidence was systematically assessed by use of the Newcastle-Ottawa Scale for case control studies in meta-analyses. RESULTS Ten studies containing 18 independent case-control studies were included. The results revealed a significant association between KIF1B rs17401966 polymorphism and susceptibility to HCC under a random-effect allelic model (OR = 0.85, 95% CI 0.76-0.94, P = 0.003); HBV-positive subgroup (OR = 0.82, 95% CI 0.72-0.95, P = 0.007); and Chinese-subgroup (OR = 0.82, 95% CI 0.72-0.93, P = 0.002). CONCLUSIONS G-allele appears to be a protective allele of KIF1B for HCC, especially in HBV-positive and Chinese populations. More well-designed studies with larger sample size and various ethnic groups and risk factors are needed to establish that KIF1B rs17401966 polymorphism is significantly associated with risk of HCC.
Collapse
Affiliation(s)
- Ying-Ying Luo
- Intensive Care Unit, The Third People's Hospital of Chengdu, The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, Sichuan, China.,Institute for Viral Hepatitis, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong-Peng Zhang
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ai-Long Huang
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Jie-Li Hu
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| |
Collapse
|
43
|
O'Brien TR, Yang HI, Groover S, Jeng WJ. Genetic Factors That Affect Spontaneous Clearance of Hepatitis C or B Virus, Response to Treatment, and Disease Progression. Gastroenterology 2019; 156:400-417. [PMID: 30287169 DOI: 10.1053/j.gastro.2018.09.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) and hepatitis B virus (HBV) infections can lead to cirrhosis, end-stage liver disease, and hepatocellular carcinoma. Over the past decade, studies of individuals infected with these viruses have established genetic associations with the probability of developing a chronic infection, risk of disease progression, and likelihood of treatment response. We review genetic and genomic methods that have been used to study risk of HBV and HCV infection and patient outcomes. For example, genome-wide association studies have linked a region containing the interferon lambda genes to spontaneous and treatment-induced clearance of HCV. We review the genetic variants associated with HCV and HBV infection, and how these variants affect specific expression or activities of their products. Further studies of these variants could provide insights into risk factors for and mechanisms of chronic infection and disease progression, as well as new strategies for treatment.
Collapse
Affiliation(s)
- Thomas R O'Brien
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland.
| | - Hwai-I Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Sarah Groover
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma
| | - Wen-Juei Jeng
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan; Liver Research Unit, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| |
Collapse
|
44
|
Shi Z, Yu H, Wu Y, Ford M, Perschon C, Wang C, Zheng SL, Xu J. Genetic risk score modifies the effect of APOE on risk and age onset of Alzheimer's disease. Clin Genet 2018; 95:302-309. [PMID: 30460685 DOI: 10.1111/cge.13479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/25/2018] [Accepted: 11/14/2018] [Indexed: 01/08/2023]
Abstract
Single nucleotide polymorphism (SNP)-based genetic risk score (GRS) and APOE genotype are both important in risk prediction of Alzheimer's disease (AD); however, the interaction between GRS and APOE has not been extensively investigated. Our objective was to determine whether GRS modifies the APOE effect on AD risk and age at onset (AAO). The study included 774 AD cases and 767 controls of European descent. Population standardized GRS was calculated based on 17 previously implicated AD risk-associated SNPs. Association was analyzed using logistic regression, Cox proportional hazards model and Kaplan-Meier curve. We found that GRS was significantly associated with AD risk and the association was stronger among APOE ε4 carriers. Compared to ε4 non-carriers, the Odds Ratio (OR) for AD was 8.09 (95% Confidence Interval [CI]: 4.98-13.63) for ε4 carriers with high-GRS (≥1.5). In contrast, the OR was 2.55 (95% CI: 1.46-4.49) for ε4 carriers with low-GRS (<0.6). In conclusion, these results suggest SNP-based GRS may supplement APOE for better assessment of inherited risk and age of onset of AD.
Collapse
Affiliation(s)
- Zhuqing Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Hongjie Yu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Yishuo Wu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Madison Ford
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Chelsea Perschon
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Chihsiung Wang
- Center for Biomedical Research Informatics, NorthShore University Health System, Evanston, Illinois
| | - Siqun L Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois
| | - Jianfeng Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Center for Genetic Epidemiology, School of Life Sciences, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
45
|
Yang J, Trépo E, Nahon P, Cao Q, Moreno C, Letouzé E, Imbeaud S, Gustot T, Deviere J, Debette S, Amouyel P, Bioulac-Sage P, Calderaro J, Ganne-Carrié N, Laurent A, Blanc JF, Guyot E, Sutton A, Ziol M, Zucman-Rossi J, Nault JC. PNPLA3 and TM6SF2 variants as risk factors of hepatocellular carcinoma across various etiologies and severity of underlying liver diseases. Int J Cancer 2018; 144:533-544. [PMID: 30289982 DOI: 10.1002/ijc.31910] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 01/10/2023]
Abstract
Few single nucleotide polymorphisms (SNPs) have been reproducibly associated with hepatocellular carcinoma (HCC). Our aim was to test the association between nine SNPs and HCC occurrence. SNPs in genes linked to HCC (DEPDC5, GRIK1, KIF1B, STAT4, MICA, DLC1, DDX18) or to liver damage (PNPLA3-rs738409, TM6SF2-rs58542926) in GWAS were genotyped in discovery cohorts including 1,020 HCC, 2,021 controls with chronic liver disease and 2,484 healthy individuals and replication was performed in prospective cohorts of cirrhotic patients with alcoholic liver disease (ALD, n = 249) and hepatitis C (n = 268). In the discovery cohort, PNPLA3 and TM6SF2 SNPs were associated with HCC (OR = 1.67 [CI95%:1.16-2.40], p = 0.005; OR = 1.45 [CI95%:1.08-1.94], p = 0.01) after adjustment for fibrosis, age, gender and etiology. In contrast, STAT4-rs7574865 was associated with HCC only in HBV infected patients (p = 0.03) and the other tested SNP were not linked with HCC risk. PNPLA3 and TM6SF2 variants were independently associated with HCC in patients with ALD (OR = 3.91 [CI95%:2.52-6.06], p = 1.14E-09; OR = 1.79 [CI95%:1.25-2.56], p = 0.001) but not with other etiologies. PNPLA3 SNP was also significantly associated with HCC developed on a nonfibrotic liver (OR = 2.19 [CI95%:1.22-3.92], p = 0.007). The association of PNPLA3 and TM6SF2 with HCC risk was confirmed in the prospective cohort with ALD. A genetic score including PNPLA3 and TM6SF2 minor alleles showed a progressive significant increased risk of HCC in ALD patients. In conclusion, PNPLA3-rs738409 and TM6SF2-rs58542926 are inherited risk variants of HCC development in patients with ALD in a dose dependent manner. The link between PNPLA3 and HCC on nonfibrotic liver suggests a direct role in liver carcinogenesis.
Collapse
Affiliation(s)
- Jie Yang
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France
| | - Eric Trépo
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France.,Department of Gastroenterology, Hepatopancreatology and Digestive Oncology, Cliniques Universitaires de Bruxelles Hôpital Erasme, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Pierre Nahon
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France.,Liver unit, Hôpital Jean Verdier, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bondy, France.,Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris 13, Communauté d'Universités et Etablissements Sorbonne Paris Cité, Paris, France
| | - Qian Cao
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Christophe Moreno
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology, Cliniques Universitaires de Bruxelles Hôpital Erasme, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Eric Letouzé
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France
| | - Sandrine Imbeaud
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France
| | - Thierry Gustot
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology, Cliniques Universitaires de Bruxelles Hôpital Erasme, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Jacques Deviere
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology, Cliniques Universitaires de Bruxelles Hôpital Erasme, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Stéphanie Debette
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, Bordeaux, France.,CHU de Bordeaux, Department of Neurology, Bordeaux, France
| | - Philippe Amouyel
- University of Lille, Institut National de la Santé et de la Recherche Médicale, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Paulette Bioulac-Sage
- Univ. Bordeaux, UMR1053 Bordeaux Research in Translational Oncology, Bordeaux, France.,Service de Pathologie, Hôpital Pellegrin, CHU de Bordeaux, Bordeaux, France
| | - Julien Calderaro
- Service d'anatomopathologie, Hôpital Henri Mondor, Créteil.,Université Paris Est Créteil, Inserm U955, Team 18, Institut Mondor de Recherche Biomédicale, France
| | - Nathalie Ganne-Carrié
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France.,Liver unit, Hôpital Jean Verdier, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bondy, France.,Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris 13, Communauté d'Universités et Etablissements Sorbonne Paris Cité, Paris, France
| | - Alexis Laurent
- Service de chirurgie digestive, Hôpital Henri Mondor, Créteil.,Université Paris Est Créteil, Institut Mondor de Recherche Biomédicale, France
| | - Jean Frédéric Blanc
- Service Hépato-Gastroentérologie et oncologie digestive, Centre Medico-Chirurgical Magellan, Hôpital Haut-Lévêque, CHU de Bordeaux, Bordeaux, France
| | - Erwan Guyot
- Laboratoire de biochimie, Hôpital Jean Verdier, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bondy, France.,INSERM U1148 LVTS, UFR SMBH, Université Paris 13, PRES Paris Sorbonne Cité, Bobigny, France
| | - Angela Sutton
- Laboratoire de biochimie, Hôpital Jean Verdier, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bondy, France.,INSERM U1148 LVTS, UFR SMBH, Université Paris 13, PRES Paris Sorbonne Cité, Bobigny, France
| | - Marianne Ziol
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France.,Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris 13, Communauté d'Universités et Etablissements Sorbonne Paris Cité, Paris, France.,Centre de Ressources Biologiques (BB-0033-00027) Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bondy, France
| | - Jessica Zucman-Rossi
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France.,Hôpital Europeen Georges Pompidou, Paris, France
| | - Jean-Charles Nault
- Inserm UMR-1162, Génomique fonctionnelle des Tumeurs solides, Université Paris Descartes, Université Paris Diderot, Université Paris 13, Labex Immuno-Oncology, Paris, France.,Liver unit, Hôpital Jean Verdier, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bondy, France.,Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris 13, Communauté d'Universités et Etablissements Sorbonne Paris Cité, Paris, France
| |
Collapse
|
46
|
Liu Y, Song C, Ni H, Jiao W, Gan W, Dong X, Liu J, Zhu L, Zhai X, Hu Z, Li J. UBE2L3, a susceptibility gene that plays oncogenic role in hepatitis B-related hepatocellular carcinoma. J Viral Hepat 2018; 25:1363-1371. [PMID: 29969176 DOI: 10.1111/jvh.12963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/11/2018] [Indexed: 12/22/2022]
Abstract
Previously, we identified UBE2L3 as a susceptibility gene for chronic hepatitis B virus (HBV) infection through genome-wide association study. Here, we analysed the association between genetic variants of UBE2L3 and the susceptibility to HBV-related hepatocellular carcinoma (HCC) and further explored its role in HCC. This case-control study included 1344 subjects who cleared HBV, 1560 HBV carriers and 1057 HBV-related HCC patients. Two single nucleotide polymorphisms (SNPs) were genotyped, including rs2266959 and rs4821116. Logistic regression analysis was performed to compute the odds ratio (OR) and 95% confidence interval (CI). We further analysed the expression of UBE2L3 and its association with pathological features based on The Cancer Genome Atlas (TCGA) data and our tissue microarray. Proliferation and migration assays were performed in hepatoma cell lines with or without UBE2L3 knockdown. Further RNA-seq analysis was performed to explore the underlying oncogenic mechanism. The variant genotypes of rs4821116 in UBE2L3 were associated with decreased risk for HCC and chronic HBV infection. Moreover, based on both TCGA and our tissue microarray data, higher levels of UBE2L3 expression were correlated with higher tumour grade, advanced tumour stage and poor survival. In vitro analysis revealed that UBE2L3 may promote hepatocyte proliferation and migration. RNA-seq analysis showed that UBE2L3 was inversely correlated with CDKN2B, a negative regulator of cell cycle, and CLDN1, loss of which may promote cancer metastasis. In conclusion, UBE2L3 may also be a susceptibility gene in HBV-related HCC, and it may promote HCC proliferation and migration by negatively regulating CDKN2B and CLDN1.
Collapse
Affiliation(s)
- Yao Liu
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| | - Ci Song
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hengli Ni
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| | - Weijuan Jiao
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| | - Wenjuan Gan
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaoqiang Dong
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jibin Liu
- Department of Hepatobiliary Surgery, Nantong Tumor Hospital, Nantong, China
| | - Liguo Zhu
- Department of Infection Diseases, Jiangsu Province Center for Disease Prevention and Control, Nanjing, China
| | - Xiangjun Zhai
- Department of Infection Diseases, Jiangsu Province Center for Disease Prevention and Control, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jianming Li
- Department of Pathology, Medical College of Soochow University, Suzhou, China
| |
Collapse
|
47
|
Riazalhosseini B, Mohamed Z, Apalasamy YD, Shafie NS, Mohamed R. Interleukin-6 gene variants are associated with reduced risk of chronicity in hepatitis B virus infection in a Malaysian population. Biomed Rep 2018; 9:213-220. [PMID: 30271596 DOI: 10.3892/br.2018.1126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/29/2018] [Indexed: 02/06/2023] Open
Abstract
Interleukin-6 (IL-6) is a cytokine with a critical role in regulating the immune response to infectious disease. Studies have indicated that polymorphisms in the IL-6 gene may be linked to hepatitis B virus (HBV) infection. The purpose of the present study was to examine the association among IL-6 SNPs and haplotypes with HBV infection risk in a Malaysian population. A total of 1,246 Malaysian subjects with and without chronic hepatitis B were recruited for this study. Three IL-6 polymorphisms (rs2069837, rs1800796 and rs2066992) were genotyped using a Sequenom MassARRAY® platform. The results suggested that GC and CC genotypes of rs1800796 as well as GT and TT genotypes of rs2066992 were associated with protection against HBV infection (P<0.001). Furthermore, haplotypes GG and CT exhibited a significant association with protection against HBV (P=0.003 and =0.005, respectively); and haplotypes GG and CT exhibited a significant association with clearance of HBV infection (P=0.035 and =0.037, respectively). The present study indicates that two IL-6 SNPs (rs1800796 and rs2066992) are associated with clearance of chronic HBV or protection against HBV infection at allelic, genotypic and haplotypic levels.
Collapse
Affiliation(s)
- Behnaz Riazalhosseini
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Zahurin Mohamed
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yamunah Devi Apalasamy
- Social Wellbeing Research Centre, Faculty of Economics and Administration, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Noor Shafila Shafie
- Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Rosmawati Mohamed
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| |
Collapse
|
48
|
Akcay IM, Katrinli S, Ozdil K, Doganay GD, Doganay L. Host genetic factors affecting hepatitis B infection outcomes: Insights from genome-wide association studies. World J Gastroenterol 2018; 24:3347-3360. [PMID: 30122875 PMCID: PMC6092584 DOI: 10.3748/wjg.v24.i30.3347] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/29/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023] Open
Abstract
The clinical outcome of Hepatitis B Virus (HBV) infection depends on the success or failure of the immune responses to HBV, and varies widely among individuals, ranging from asymptomatic self-limited infection, inactive carrier state, chronic hepatitis, cirrhosis, hepatocellular carcinoma, to liver failure. Genome-wide association studies (GWAS) identified key genetic factors influencing the pathogenesis of HBV-related traits. In this review, we discuss GWAS for persistence of HBV infection, antibody response to hepatitis B vaccine, and HBV-related advanced liver diseases. HBV persistence is associated with multiple genes with diverse roles in immune mechanisms. The strongest associations are found within the classical human leukocyte antigen (HLA) genes, highlighting the central role of antigen presentation in the immune response to HBV. Associated variants affect both epitope binding specificities and expression levels of HLA molecules. Several other susceptibility genes regulate the magnitude of adaptive immune responses, determining immunity vs tolerance. HBV persistence and nonresponse to vaccine share the same risk variants, implying overlapping genetic bases. On the other hand, the risk variants for HBV-related advanced liver diseases are largely different, suggesting different host-virus dynamics in acute vs chronic HBV infections. The findings of these GWAS are likely to pave the way for developing more effective preventive and therapeutic interventions by personalizing the management of HBV infection.
Collapse
Affiliation(s)
- Izzet Mehmet Akcay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34469, Turkey
| | - Seyma Katrinli
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34469, Turkey
| | - Kamil Ozdil
- Department of Gastroenterology and Hepatology, Umraniye Teaching and Research Hospital, Istanbul 34764, Turkey
| | - Gizem Dinler Doganay
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul 34469, Turkey
| | - Levent Doganay
- Department of Gastroenterology and Hepatology, Umraniye Teaching and Research Hospital, Istanbul 34764, Turkey
| |
Collapse
|
49
|
Cao P, Yang A, Wang R, Xia X, Zhai Y, Li Y, Yang F, Cui Y, Xie W, Liu Y, Liu T, Jia W, Jiang Z, Li Z, Han Y, Gao C, Song Q, Xie B, Zhang L, Zhang H, Zhang J, Shen X, Yuan Y, Yu F, Wang Y, Xu J, Ma Y, Mo Z, Yu W, He F, Zhou G. Germline Duplication of SNORA18L5 Increases Risk for HBV-related Hepatocellular Carcinoma by Altering Localization of Ribosomal Proteins and Decreasing Levels of p53. Gastroenterology 2018; 155:542-556. [PMID: 29702115 DOI: 10.1053/j.gastro.2018.04.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS Single nucleotide polymorphisms could affect risk for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). We performed a germline copy number variation (CNV)-based genome-wide association study (GWAS) in populations of Chinese ancestry to search for germline CNVs that increase risk of HCC. METHODS We conducted a CNV-based GWAS of 1583 HCC cases (persons with chronic HBV infection and HCC) and 1540 controls (persons with chronic HBV infection without HCC) in Chinese populations. Identified candidates were expressed in L-02, HepG2, or TP53-/- or wild-type HCT116 cells, and knocked down with short hairpin RNAs in HepG2, Bel-7402, and SMMC-7721 cells; proliferation, colony formation, and apoptosis were measured. Formation of xenograft tumors from cell lines was monitored in nude mice. Subcellular localization of ribosome proteins and levels or activity of p53 were investigated by co-immunoprecipitation, immunofluorescence, and immunoblot analyses. Levels of small nucleolar RNA H/ACA box 18-like 5 (SNORA18L5) were quantified by quantitative reverse transcription polymerase chain reaction. RESULTS We identified a low-frequency duplication at chromosome 15q13.3 strongly associated with risk of HBV-related HCC (overall P = 3.17 × 10-8; odds ratio, 12.02). Copy numbers of the 15q13.3 duplication correlated with the expression of SNORA18L5 in liver tissues. Overexpression of SNORA18L5 increased HCC cell proliferation and growth of xenograft tumors in mice; knockdown reduced HCC proliferation and tumor growth. SNORA18L5 overexpression in HepG2 and SMMC-7721 cells inhibited p53-dependent cell cycle arrest and apoptosis. Overexpression of SNORA18L5 led to hyperactive ribosome biogenesis, increasing levels of mature 18S and 28S ribosomal RNAs and causing the ribosomal proteins RPL5 and RPL11 to stay in the nucleolus, which kept them from binding to MDM2. This resulted in increased MDM2-mediated ubiquitination and degradation of p53. Levels of SNORA18L5 were increased in HCC tissues compared with nontumor liver tissues and associated with shorter survival times of patients. CONCLUSIONS In a CNV-based GWAS, we associated duplication at 15q13.3 with increased risk of HBV-related HCC. We found SNORA18L5 at this location to promote HCC cell proliferation and tumor growth in mice. SNORA18L5 increases ribosome biogenesis, facilitates ribosomal RNA maturation, and alters localization of RPL5 and RPL11, allowing for increased MDM2-mediated proteolysis of p53 and cell cycle arrest.
Collapse
Affiliation(s)
- Pengbo Cao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Aiqing Yang
- School of Life Sciences, Tsinghua University, Beijing, P. R. China
| | - Rui Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China; Clinical Medical Institute of General Hospital of Xinjiang Military Area, PLA, Urumqi, Xinjiang, P. R. China
| | - Xia Xia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Yun Zhai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Yuanfeng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Fei Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Ying Cui
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Weimin Xie
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Ying Liu
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Beijing, P. R. China
| | - Taotao Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P. R. China
| | - Weihua Jia
- Department of Experimental Research, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Zhengwen Jiang
- Center for Genetics and Genomics Analysis, Genesky Biotechnologies Inc., Shanghai, P. R. China
| | - Zhuo Li
- Department of Infectious Diseases, Affiliated Youan Hospital, Capital University of Medical Science, Beijing, P. R. China
| | - Yuqing Han
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Chengming Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Qingfeng Song
- Interventional Radiology Department of Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Bobo Xie
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Luo Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Hongxing Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Jinxu Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P. R. China
| | - Yunfei Yuan
- Department of Experimental Research, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Feng Yu
- Center for Genetics and Genomics Analysis, Genesky Biotechnologies Inc., Shanghai, P. R. China
| | - Ying Wang
- Center for Genetics and Genomics Analysis, Genesky Biotechnologies Inc., Shanghai, P. R. China
| | - Jing Xu
- Center for Genetics and Genomics Analysis, Genesky Biotechnologies Inc., Shanghai, P. R. China
| | - Yilong Ma
- Interventional Radiology Department of Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Zengnan Mo
- Department of Urology and Nephrology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, P. R. China
| | - Wuzhong Yu
- Clinical Medical Institute of General Hospital of Xinjiang Military Area, PLA, Urumqi, Xinjiang, P. R. China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China; School of Life Sciences, Tsinghua University, Beijing, P. R. China.
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, P. R. China; National Engineering Research Center for Protein Drugs, Beijing, P. R. China; National Center for Protein Sciences at Beijing, Beijing, P. R. China.
| |
Collapse
|
50
|
Wu XL, Li ZY, Bi XY, Zhao H, Zhao JJ, Zhou JG, Han Y, Huang Z, Zhang YF, Cai JQ. Human leukocyte antigen gene polymorphisms are associated with systemic inflammation in hepatitis B virus-related hepatocellular carcinoma. Cancer Manag Res 2018; 10:2315-2324. [PMID: 30104900 PMCID: PMC6074760 DOI: 10.2147/cmar.s167574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Systemic inflammation (SI) is associated with tumor progression and overall survival (OS) in patients with hepatocellular carcinoma (HCC). The presence of some single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA) region can influence the prognosis of patients with hepatitis B virus (HBV)-related HCC, although the mechanism remains unknown. This study aimed to analyze the correlations between HLA gene polymorphisms and SI. Patients and methods This study included 330 patients with HCC. The clinical parameters were reviewed, and five SNPs, namely rs2647073, rs3997872, rs3077, rs7453920, and rs7768538, were genotyped using the MassARRAY system. Results The rs3997872, rs7453920, and rs7768538 genotypes were found to be significantly associated with OS (P<0.05). The rs7453920 genotype was significantly associated with the neutrophil/lymphocyte ratio (NLR; P=0.001), which was used as an SI index with a threshold determined by receiver operating characteristic analysis. An elevated NLR was also an independent predictor of OS according to univariate and multivariate analyses (P<0.001). Conclusion Our data show that HLA gene polymorphisms are associated with SI in patients with HBV-related HCC, and the absence of minor allele A (rs7453920) promotes SI and shortens OS.
Collapse
Affiliation(s)
| | - Zhi-Yu Li
- Department of Hepatobiliary Surgery,
| | - Xin-Yu Bi
- Department of Hepatobiliary Surgery,
| | - Hong Zhao
- Department of Hepatobiliary Surgery,
| | | | | | - Yue Han
- Department of Interventional Therapies, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | | | | | | |
Collapse
|