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Lu Y, Wang S, Chi T, Zhao Y, Guo H, Wang H, Feng L. DNA damage repair-related gene signature for identifying the immune status and predicting the prognosis of hepatocellular carcinoma. Sci Rep 2023; 13:18978. [PMID: 37923899 PMCID: PMC10624694 DOI: 10.1038/s41598-023-45999-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: 07/31/2023] [Accepted: 10/26/2023] [Indexed: 11/06/2023] Open
Abstract
The heterogeneity of hepatocellular carcinoma (HCC) poses a challenge for accurate prognosis prediction. DNA damage repair genes (DDRGs) have an impact on a wide range of malignancies. However, the relevance of these genes in HCC prognosis has received little attention. In this study, we aimed to develop a prognostic signature to identify novel therapy options for HCC. We acquired mRNA expression profiles and clinical data for HCC patients from The Cancer Genome Atlas (TCGA) database. A polygenic prognostic model for HCC was constructed using selection operator Cox analysis and least absolute shrinkage. The model was validated using International Cancer Genome Consortium (ICGC) data. Overall survival (OS) between the high-risk and low-risk groups was compared using Kaplan‒Meier analysis. Independent predictors of OS were identified through both univariate and multivariate Cox analyses. To determine immune cell infiltration scores and activity in immune-related pathways, a single-sample gene set enrichment analysis was performed. The protein and mRNA expression levels of the prognostic genes between HCC and normal liver tissues were also examined by immunohistochemistry (IHC), immunofluorescence (IF) and quantitative real-time PCR (qRT-PCR). A novel ten-gene signature (CHD1L, HDAC1, KPNA2, MUTYH, PPP2R5B, NEIL3, POLR2L, RAD54B, RUVBL1 and SPP1) was established for HCC prognosis prediction. Patients in the high-risk group had worse OS than those in the low-risk group. Receiver operating characteristic curve analysis confirmed the predictive ability of this prognostic gene signature. Multivariate Cox analysis showed that the risk score was an independent predictor of OS. Functional analysis revealed a strong association with cell cycle and antigen binding pathways, and the risk score was highly correlated with tumor grade, tumor stage, and types of immune infiltrate. High expression levels of the prognostic genes were significantly correlated with increased sensitivity of cancer cells to antitumor drugs. IHC, IF and qRT-PCR all indicated that the prognostic genes were highly expressed in HCC relative to normal liver tissue, consistent with the results of bioinformatics analysis. Ten DDRGs were utilized to create a new signature for identifying the immunological state of HCC and predicting prognosis. In addition, blocking these genes could represent a promising treatment.
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Affiliation(s)
- Yongpan Lu
- Department of Plastic Surgery, Shandong University of Traditional Chinese Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Jingshi Road, Jinan, 250014, Shandong, China
| | - Sen Wang
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Tingting Chi
- Department of Acupuncture and Rehabilitation, The Affiliated Qingdao Hai Ci Hospital of Qingdao University (West Hospital Area), Qingdao, 266000, Shandong, China
| | - Yuli Zhao
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Huimin Guo
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Jining Medical College, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Haizheng Wang
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China
| | - Li Feng
- Department of Medical Ultrasound, Shandong Medicine and Health Key Laboratory of Abdominal Medical Imaging, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qian Foshan Hospital, Shandong First Medical University, No. 16766, Jingshi Road, Jinan, 250014, Shandong, China.
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Adlat S, Vázquez Salgado AM, Lee M, Yin D, Wangensteen KJ. Emerging and potential use of CRISPR in human liver disease. Hepatology 2023:01515467-990000000-00538. [PMID: 37607734 PMCID: PMC10881897 DOI: 10.1097/hep.0000000000000578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 08/24/2023]
Abstract
CRISPR is a gene editing tool adapted from naturally occurring defense systems from bacteria. It is a technology that is revolutionizing the interrogation of gene functions in driving liver disease, especially through genetic screens and by facilitating animal knockout and knockin models. It is being used in models of liver disease to identify which genes are critical for liver pathology, especially in genetic liver disease, hepatitis, and in cancer initiation and progression. It holds tremendous promise in treating human diseases directly by editing DNA. It could disable gene function in the case of expression of a maladaptive protein, such as blocking transthyretin as a therapy for amyloidosis, or to correct gene defects, such as restoring the normal functions of liver enzymes fumarylacetoacetate hydrolase or alpha-1 antitrypsin. It is also being studied for treatment of hepatitis B infection. CRISPR is an exciting, evolving technology that is facilitating gene characterization and discovery in liver disease and holds the potential to treat liver diseases safely and permanently.
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Affiliation(s)
- Salah Adlat
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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3
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Li Y, Xiong C, Wu LL, Zhang BY, Wu S, Chen YF, Xu QH, Liao HF. Tumor subtypes and signature model construction based on chromatin regulators for better prediction of prognosis in uveal melanoma. Pathol Oncol Res 2023; 29:1610980. [PMID: 37362244 PMCID: PMC10287976 DOI: 10.3389/pore.2023.1610980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Background: Uveal Melanoma (UM) is the most prevalent primary intraocular malignancy in adults. This study assessed the importance of chromatin regulators (CRs) in UM and developed a model to predict UM prognosis. Methods: Gene expression data and clinical information for UM were obtained from public databases. Samples were typed according to the gene expression of CRs associated with UM prognosis. The prognostic key genes were further screened by the protein interaction network, and the risk model was to predict UM prognosis using the least absolute shrinkage and selection operator (LASSO) regression analysis and performed a test of the risk mode. In addition, we performed gene set variation analysis, tumor microenvironment, and tumor immune analysis between subtypes and risk groups to explore the mechanisms influencing the development of UM. Results: We constructed a signature model consisting of three CRs (RUVBL1, SIRT3, and SMARCD3), which was shown to be accurate, and valid for predicting prognostic outcomes in UM. Higher immune cell infiltration in poor prognostic subtypes and risk groups. The Tumor immune analysis and Tumor Immune Dysfunction and Exclusion (TIDE) score provided a basis for clinical immunotherapy in UM. Conclusion: The risk model has prognostic value for UM survival and provides new insights into the treatment of UM.
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Affiliation(s)
- Yue Li
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Chao Xiong
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Li Li Wu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Bo Yuan Zhang
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Sha Wu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Yu Fen Chen
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Qi Hua Xu
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
| | - Hong Fei Liao
- School of Ophthalmology and Optometry, Nanchang University, Nanchang, Jiangxi, China
- Affiliated Eye Hospital of Nanchang University, Nanchang, Jiangxi, China
- National Clinical Research Center for Ocular Diseases Jiangxi Province Division, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Ophthalmic Disease, Nanchang, Jiangxi, China
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He Y, Su Y, Duan C, Wang S, He W, Zhang Y, An X, He M. Emerging role of aging in the progression of NAFLD to HCC. Ageing Res Rev 2023; 84:101833. [PMID: 36565959 DOI: 10.1016/j.arr.2022.101833] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 12/10/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
With the aging of global population, the incidence of nonalcoholic fatty liver disease (NAFLD) has surged in recent decades. NAFLD is a multifactorial disease that follows a progressive course, ranging from simple fatty liver, nonalcoholic steatohepatitis (NASH) to liver cirrhosis and hepatocellular carcinoma (HCC). It is well established that aging induces pathological changes in liver and potentiates the occurrence and progression of NAFLD, HCC and other age-related liver diseases. Studies of senescent cells also indicate a pivotal engagement in the development of NAFLD via diverse mechanisms. Moreover, nicotinamide adenine dinucleotide (NAD+), silence information regulator protein family (sirtuins), and mechanistic target of rapamycin (mTOR) are three vital and broadly studied targets involved in aging process and NAFLD. Nevertheless, the crucial role of these aging-associated factors in aging-related NAFLD remains underestimated. Here, we reviewed the current research on the roles of aging, cellular senescence and three aging-related factors in the evolution of NAFLD to HCC, aiming at inspiring promising therapeutic targets for aging-related NAFLD and its progression.
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Affiliation(s)
- Yongyuan He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Frontiers Science Center of Cellular Homeostasis and Human Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinghong Su
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Frontiers Science Center of Cellular Homeostasis and Human Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengcheng Duan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Frontiers Science Center of Cellular Homeostasis and Human Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siyuan Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Frontiers Science Center of Cellular Homeostasis and Human Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Frontiers Science Center of Cellular Homeostasis and Human Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; School of Basic Medicine, Kunming Medical University, China
| | - Yingting Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Frontiers Science Center of Cellular Homeostasis and Human Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaofei An
- Department of Endocrinology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Ming He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Frontiers Science Center of Cellular Homeostasis and Human Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Pathology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.
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Huang L, Guan S, Feng L, Wei J, Wu L. Integrated analysis identified NPNT as a potential key regulator in tumor metastasis of hepatocellular carcinoma. Gene 2022; 825:146436. [PMID: 35304239 DOI: 10.1016/j.gene.2022.146436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/12/2022] [Accepted: 03/11/2022] [Indexed: 01/02/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the lethal malignancies worldwide. Tumor metastasis is the main cause of HCC related death. Although progress has been made in the mechanism study of HCC in the past decades, the underlying mechanism of HCC metastasis has not been fully illustrated. In the present study, bioinformatic analysis including weighted gene co-expression network analysis (WGCNA), differentially expressed gene analysis, and gene enrichment analysis were applied to discover genes correlated with HCC metastasis. Immunohistochemistry (IHC) assays were applied to detect the expression of NPNT in HCC samples. Cell transfection, wound healing, matrigel transwell assays, and western blot assays were utilized to evaluate the effects of NPNT on cell migration and invasion and signaling pathway variation. We found that NPNT was up-regulated in HCC tumor tissues compared with normal tissues. Especially, NPNT was highly expressed in metastatic tumor compared with non-metastatic HCC tumors. Down-regulation of NPNT via siRNA transfection inhibited cell migration, invasion, and FAK/PI3K/AKT signaling pathway in HCC. Our results demonstrate that NPNT is a potential key regulator in HCC metastasis.
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Affiliation(s)
- Lingkun Huang
- Medical College, Guangxi University, Nanning 530004, China
| | - Shuzhen Guan
- Medical College, Guangxi University, Nanning 530004, China
| | - Lin Feng
- Department of Pathology, the first Medical Center of PLA General Hospital, Beijing, China
| | - Jinrui Wei
- Guangxi Scientific Research Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Lichuan Wu
- Medical College, Guangxi University, Nanning 530004, China.
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RUVBL1 promotes enzalutamide resistance of prostate tumors through the PLXNA1-CRAF-MAPK pathway. Oncogene 2022; 41:3239-3250. [PMID: 35508542 DOI: 10.1038/s41388-022-02332-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 12/17/2022]
Abstract
Although enzalutamide improves the overall survival of patients with metastatic prostate cancers, enzalutamide resistance (ENZR) will be inevitably developed. Emerging evidence support that alternative oncogenic pathways may bypass the androgen receptor (AR) signaling to promote ENZR progression, however, the underpinning mechanisms remain poorly defined. Here, we report that the expression of RuvB like AAA ATPase 1 (RUVBL1) is upregulated in ENZR cells and xenograft models and prostate tumors in patients. Enzalutamide increases RUVBL1 accumulation in the cytoplasm, which in turn enhances the recruitment of CRAF proto-oncogene serine/threonine kinase protein to plexin A1 (PLXNA1) and the subsequent activation of the downstream MAPK pathway. Co-overexpression of RUVBL1 and PLXNA1 defines a subgroup of prostate cancer (PCa) patients with a poor prognosis. Furthermore, pharmacological inhibition of RUVBL1 by CB-6644 suppresses ENZR cell proliferation and xenograft growth and allows re-sensitization of ENZR cells and xenografts to enzalutamide, indicating that RUVBL1 may act to substitute the AR signaling to promote cancer cell survival and ENZR development. Together, these findings may lead to the identification of RUVBL1 as a potential therapeutic target for ENZR tumors.
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Dai J, Zhu X, Shen J, Zhang Y, Xie F, Yu Y, Jiang K, Wen T, Li C. The Effect of Metabolic Syndrome on the Outcome of Hepatitis B-Associated Hepatocellular Carcinoma Patients After Hepatectomy: A Multicenter Study. Front Oncol 2022; 12:811084. [PMID: 35356224 PMCID: PMC8959675 DOI: 10.3389/fonc.2022.811084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/10/2022] [Indexed: 02/05/2023] Open
Abstract
Background and Aims With changes in dietary patterns and modern lifestyles, the prevalence of metabolic syndrome (MetS) in hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC) patients is increasing. The purpose of our study is to explore the impact of MetS on the prognosis of HBV-associated HCC patients following radical hepatectomy. Methods Data on consecutive HCC patients who underwent radical hepatectomy were prospectively obtained and retrospectively analyzed from seven medical centers in west areas of China. Propensity score matching (PSM) analysis was conducted to balance the heterogeneity between MetS-HBV-HCC group and HBV-HCC group. Surgical outcomes have been contrasted between the two groups. Results In 984 patients, 179 (18.19%) were diagnosed with MetS. Patients in the MetS-HBV-HCC group had higher CCI score (8.7 [0.0, 12.2] vs. 0.0 [0.0, 8.7], p = 0.048) and a higher rate of severe complications (Clavien–Dindo ≥3, 7.82% vs. 4.10%, p = 0.035), to be more precise: postoperative liver failure, hydrothorax, and hyperglycemia. Patients in the MetS-HBV-HCC group tended to have worse 5-year overall survival (OS) rate (61.45% vs. 69.94%, p = 0.027) and recurrence-free survival (RFS) rate (62.57% vs. 53.66%, p = 0.030), consistent with the results of the competing risk models. Last, MetS was identified to be an independent unfavorable prognostic factor in the multivariate analysis. Conclusion The involvement of MetS increased the risk of postoperative complications and worsens the overall survival and recurrence-free survival time, reminding us to be more prudent to face metabolic disorder among tumor patients.
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Affiliation(s)
- Junlong Dai
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital, Chengdu, China
| | - Xinrui Zhu
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital, Chengdu, China
| | - Junyi Shen
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital, Chengdu, China
| | - Yu Zhang
- Organ Transplantation Center, Sichuan Academy of Medical Sciences (Sichuan Provincial People's Hospital), Chinese Academy of Sciences, Chengdu, China
| | - Fei Xie
- Department of Hepatobiliary and Pancreatic Surgery, the First People's Hospital of Neijiang City, Neijiang, China
| | - Yu Yu
- Department of Hepatopancreatobiliary Surgery, the Second People's Hospital of Yibin City, Yibin, China
| | - Kangyi Jiang
- Department of Hepatobiliary Surgery, People's Hospital of Leshan, Southwest Medical University, Leshan, China
| | - Tianfu Wen
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital, Chengdu, China
| | - Chuan Li
- Liver Transplantation Center, Department of Liver Surgery, West China Hospital, Chengdu, China
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Luo Y, Sun F, Peng X, Dong D, Ou W, Xie Y, Luo Y. Integrated Bioinformatics Analysis to Identify Abnormal Methylated Differentially Expressed Genes for Predicting Prognosis of Human Colon Cancer. Int J Gen Med 2021; 14:4745-4756. [PMID: 34466019 PMCID: PMC8403012 DOI: 10.2147/ijgm.s324483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/06/2021] [Indexed: 12/27/2022] Open
Abstract
Objective To identify the value of key differentially expressed genes (DEGs) regulated by differentially methylated regions (DMRs) in predicting the prognosis of human colon cancer. Materials and Methods RNA sequencing data and DNA methylation data of 455 colon adenocarcinoma (COAD) cases and 41 normal controls were downloaded from The Cancer Genome Atlas (TCGA). Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by the DAVID database. To identify the hub genes regulated by methylation, univariate Cox and multivariate Cox regression analyses were carried out. A nomogram based on the risk score was built to identify the power of the hub genes to predict prognosis in patients with colon cancer. Results A total of 133 DEGs regulated by DMRs were identified through analyzing RNA sequencing data and DNA methylation data from TCGA. GO functional enrichment and KEGG pathway enrichment analysis showed the genes involved in the initiation and progression of colon cancer. Univariate Cox regression analysis and multivariate Cox regression analysis focused on the seven hub genes (CDH4, CR2, KRT85, LGI4, NPAS4, RUVBL1 and SP140) associated with overall survival, the expression of which negatively correlated with their methylation level. The risk score and nomogram model showed that the hub genes served as potential biomarkers for the prognosis prediction of patients with colon cancer. Conclusion Our findings suggest that the DEGs regulated by DMRs are involved in the carcinogenesis and development of colon cancer, and the aberrantly methylated DEGs associated with overall survival of patients may be potential diagnostic and therapeutic targets for colon cancer.
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Affiliation(s)
- Yanbo Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People's Republic of China
| | - Fenglin Sun
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People's Republic of China
| | - Xiaowen Peng
- Department of Laboratory Medicine, Nansha Hospital, Guangzhou First People's Hospital, School of Medicine, Southern China University of Technology, Guangzhou, Guangdong, 511457, People's Republic of China
| | - Dong Dong
- Department of General Surgery, Nansha Hospital, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 511457, Guangdong, People's Republic of China
| | - Wentao Ou
- Department of General Surgery, Nansha Hospital, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 511457, Guangdong, People's Republic of China
| | - Yongke Xie
- Department of General Surgery, Nansha Hospital, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 511457, Guangdong, People's Republic of China
| | - Yuqi Luo
- Department of Gastrointestinal and Hepatobiliary Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People's Republic of China
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Wu ZH, Huang HM, Yang DL. Integrated analysis of the functions and prognostic values of RNA binding proteins in hepatocellular carcinoma. BMC Gastroenterol 2021; 21:265. [PMID: 34130650 PMCID: PMC8204501 DOI: 10.1186/s12876-021-01843-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC), one of the most common malignant tumors worldwide, ranks as the fifth most common cancer and has been the second most frequent cause of cancer-related death. RNA binding proteins (RBPs) are proteins that interact with different classes of RNA and are commonly detected in cells. Methods We used RNA sequencing data from TCGA to display dysfunctional RBPs microenvironments and provide potential useful biomarkers for HCC diagnosis and prognosis. Results 330 differently expressed RBPs (208 upregulated and 122 downregulated) were identified. KEGG were mainly enriched in RNA degradation, Influenza A, Hepatitis C, RIG-I-like receptor signaling pathway, Herpes simplex virus 1 infection and RNA transport. CBioPortal results demonstrated that these genes were altered in 50 samples out of 357 HCC patients (14%) and the amplification of BRCA1 was the largest frequent copy-number alteration. Conclusion Based on the online database, we identified novel RBPs markers for the prognosis of hepatocellular carcinoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-021-01843-0.
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Affiliation(s)
- Zeng-Hong Wu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hong-Ming Huang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Dong-Liang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Javary J, Allain N, Ezzoukhry Z, Di Tommaso S, Dupuy JW, Costet P, Dugot-Senant N, Saltel F, Moreau V, Dubus P, Benhamouche-Trouillet S. Reptin/RUVBL2 is required for hepatocyte proliferation in vivo, liver regeneration and homeostasis. Liver Int 2021; 41:1423-1429. [PMID: 33792165 DOI: 10.1111/liv.14886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/13/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022]
Abstract
Previous studies have shown that Reptin is overexpressed in hepatocellular carcinoma and that it is necessary for in vitro proliferation and cell survival. However, its pathophysiological role in vivo remains unknown. We aimed to study the role of Reptin in hepatocyte proliferation after regeneration using a liver Reptin knock-out model (ReptinLKO ). Interestingly, hepatocyte proliferation is strongly impaired in ReptinLKO mice 36 h after partial hepatectomy, associated with a decrease of cyclin-A expression and mTORC1 and MAPK signalling, leading to an impaired liver regeneration. Moreover, in the ReptinLKO model, we have observed a progressive loss of Reptin invalidation associated with an atypical liver regeneration. Hypertrophic and proliferative hepatocytes gradually replace ReptinKO hypotrophic hepatocytes. To conclude, our results show that Reptin is required for hepatocyte proliferation in vivo and liver regeneration and that it plays a crucial role in hepatocyte survival and liver homeostasis.
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Affiliation(s)
- Joaquim Javary
- INSERM, UMR1053, Bordeaux, France.,BaRITOn (Bordeaux Research in Translational Oncology), Université de Bordeaux, Bordeaux, France
| | - Nathalie Allain
- INSERM, UMR1053, Bordeaux, France.,BaRITOn (Bordeaux Research in Translational Oncology), Université de Bordeaux, Bordeaux, France
| | - Zakaria Ezzoukhry
- INSERM, UMR1053, Bordeaux, France.,BaRITOn (Bordeaux Research in Translational Oncology), Université de Bordeaux, Bordeaux, France
| | - Sylvaine Di Tommaso
- INSERM, UMR1053, Bordeaux, France.,BaRITOn (Bordeaux Research in Translational Oncology), Université de Bordeaux, Bordeaux, France.,Oncoprot TBM Core US005, Bordeaux, France
| | | | - Pierre Costet
- CRYME Centre BROCA Nouvelle Aquitaine (CBNA), Université de Bordeaux service commun des animaleries - Bordeaux, Bordeaux, France
| | | | - Frédéric Saltel
- INSERM, UMR1053, Bordeaux, France.,BaRITOn (Bordeaux Research in Translational Oncology), Université de Bordeaux, Bordeaux, France
| | - Violaine Moreau
- INSERM, UMR1053, Bordeaux, France.,BaRITOn (Bordeaux Research in Translational Oncology), Université de Bordeaux, Bordeaux, France
| | - Pierre Dubus
- INSERM, UMR1053, Bordeaux, France.,BaRITOn (Bordeaux Research in Translational Oncology), Université de Bordeaux, Bordeaux, France.,CHU de Bordeaux, Bordeaux, France
| | - Samira Benhamouche-Trouillet
- INSERM, UMR1053, Bordeaux, France.,BaRITOn (Bordeaux Research in Translational Oncology), Université de Bordeaux, Bordeaux, France
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11
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Adewale Q, Khan AF, Carbonell F, Iturria-Medina Y. Integrated transcriptomic and neuroimaging brain model decodes biological mechanisms in aging and Alzheimer's disease. eLife 2021; 10:e62589. [PMID: 34002691 PMCID: PMC8131100 DOI: 10.7554/elife.62589] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Both healthy aging and Alzheimer's disease (AD) are characterized by concurrent alterations in several biological factors. However, generative brain models of aging and AD are limited in incorporating the measures of these biological factors at different spatial resolutions. Here, we propose a personalized bottom-up spatiotemporal brain model that accounts for the direct interplay between hundreds of RNA transcripts and multiple macroscopic neuroimaging modalities (PET, MRI). In normal elderly and AD participants, the model identifies top genes modulating tau and amyloid-β burdens, vascular flow, glucose metabolism, functional activity, and atrophy to drive cognitive decline. The results also revealed that AD and healthy aging share specific biological mechanisms, even though AD is a separate entity with considerably more altered pathways. Overall, this personalized model offers novel insights into the multiscale alterations in the elderly brain, with important implications for identifying effective genetic targets for extending healthy aging and treating AD progression.
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Affiliation(s)
- Quadri Adewale
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill UniversityMontrealCanada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill UniversityMontrealCanada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill UniversityMontrealCanada
| | - Ahmed F Khan
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill UniversityMontrealCanada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill UniversityMontrealCanada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill UniversityMontrealCanada
| | | | - Yasser Iturria-Medina
- Neurology and Neurosurgery Department, Montreal Neurological Institute, McGill UniversityMontrealCanada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill UniversityMontrealCanada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill UniversityMontrealCanada
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12
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Marin JJ, Macias RI, Monte MJ, Romero MR, Asensio M, Sanchez-Martin A, Cives-Losada C, Temprano AG, Espinosa-Escudero R, Reviejo M, Bohorquez LH, Briz O. Molecular Bases of Drug Resistance in Hepatocellular Carcinoma. Cancers (Basel) 2020; 12:cancers12061663. [PMID: 32585893 PMCID: PMC7352164 DOI: 10.3390/cancers12061663] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022] Open
Abstract
The poor outcome of patients with non-surgically removable advanced hepatocellular carcinoma (HCC), the most frequent type of primary liver cancer, is mainly due to the high refractoriness of this aggressive tumor to classical chemotherapy. Novel pharmacological approaches based on the use of inhibitors of tyrosine kinases (TKIs), mainly sorafenib and regorafenib, have provided only a modest prolongation of the overall survival in these HCC patients. The present review is an update of the available information regarding our understanding of the molecular bases of mechanisms of chemoresistance (MOC) with a significant impact on the response of HCC to existing pharmacological tools, which include classical chemotherapeutic agents, TKIs and novel immune-sensitizing strategies. Many of the more than one hundred genes involved in seven MOC have been identified as potential biomarkers to predict the failure of treatment, as well as druggable targets to develop novel strategies aimed at increasing the sensitivity of HCC to pharmacological treatments.
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Affiliation(s)
- Jose J.G. Marin
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, 28029 Madrid, Spain
- Correspondence: (J.J.G.M.); (O.B.); Tel.: +34-663182872 (J.J.G.M.); +34-923294674 (O.B.)
| | - Rocio I.R. Macias
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, 28029 Madrid, Spain
| | - Maria J. Monte
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, 28029 Madrid, Spain
| | - Marta R. Romero
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, 28029 Madrid, Spain
| | - Maitane Asensio
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
| | - Anabel Sanchez-Martin
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
| | - Candela Cives-Losada
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
| | - Alvaro G. Temprano
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
| | - Ricardo Espinosa-Escudero
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
| | - Maria Reviejo
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
| | - Laura H. Bohorquez
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
| | - Oscar Briz
- Experimental Hepatology and Drug Targeting (HEVEFARM) Group, University of Salamanca, IBSAL, 37007 Salamanca, Spain; (R.I.R.M.); (M.J.M.); (M.R.R.); (M.A.); (A.S.-M.); (C.C.-L.); (A.G.T.); (R.E.-E.); (M.R.); (L.H.B.)
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, 28029 Madrid, Spain
- Correspondence: (J.J.G.M.); (O.B.); Tel.: +34-663182872 (J.J.G.M.); +34-923294674 (O.B.)
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13
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Uchida D, Takaki A, Oyama A, Adachi T, Wada N, Onishi H, Okada H. Oxidative Stress Management in Chronic Liver Diseases and Hepatocellular Carcinoma. Nutrients 2020; 12:nu12061576. [PMID: 32481552 PMCID: PMC7352310 DOI: 10.3390/nu12061576] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic viral hepatitis B and C and non-alcoholic fatty liver disease (NAFLD) have been widely acknowledged to be the leading causes of liver cirrhosis and hepatocellular carcinoma. As anti-viral treatment progresses, the impact of NAFLD is increasing. NAFLD can coexist with chronic viral hepatitis and exacerbate its progression. Oxidative stress has been recognized as a chronic liver disease progression-related and cancer-initiating stress response. However, there are still many unresolved issues concerning oxidative stress, such as the correlation between the natural history of the disease and promising treatment protocols. Recent findings indicate that oxidative stress is also an anti-cancer response that is necessary to kill cancer cells. Oxidative stress might therefore be a cancer-initiating response that should be down regulated in the pre-cancerous stage in patients with risk factors for cancer, while it is an anti-cancer cell response that should not be down regulated in the post-cancerous stage, especially in patients using anti-cancer agents. Antioxidant nutrients should be administered carefully according to the patients’ disease status. In this review, we will highlight these paradoxical effects of oxidative stress in chronic liver diseases, pre- and post-carcinogenesis.
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