1
|
Wang K, Shi JH, Gao J, Sun Y, Wang Z, Shi X, Guo W, Jin Y, Zhang S. Arachidonic acid metabolism CYP450 pathway is deregulated in hepatocellular carcinoma and associated with microvascular invasion. Cell Biol Int 2024; 48:31-45. [PMID: 37655528 DOI: 10.1002/cbin.12086] [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: 04/06/2023] [Revised: 07/08/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023]
Abstract
Arachidonic acid metabolism plays a crucial role in the development and progression of inflammatory and metabolic liver diseases. However, its role in hepatocellular carcinoma (HCC) remains unclear. In this study, we investigated the expression of key genes involved in the arachidonic acid metabolism pathway in HCC using a combination of bioinformatics, proteomics and immunohistochemistry analyses. Through a comprehensive analysis of publicly available datasets, clinical HCC tissues, and tissue microarrays, we compared the expression of hepatic arachidonic acid metabolic genes. We observed significant downregulation of cytochrome P450 (CYP450) pathway genes at both the messenger RNA and protein levels in HCC tissues compared to normal liver tissues. Furthermore, we observed a strong correlation between the deregulation of the arachidonic acid metabolism CYP450 pathway and the pathological features and prognosis of HCC. Specifically, the expression of CYP2C8/9/18/19 was significantly correlated with pathological grade (r = -.484, p < .0001), vascular invasion (r = -.402, p < .0001), aspartate transaminase (r = -.246, p = .025), gamma-glutamyl transpeptidase (r = -.252, p = .022), alkaline phosphatase (r = -.342, p = .002), alpha-fetoprotein (r = -.311, p = .004) and carbohydrate antigen 19-9 (r = -.227, p = .047). Moreover, we discovered a significant association between CYP450 pathway activity and vascular invasion in HCC. Collectively, these data indicate that arachidonic acid CYP450 metabolic pathway deregulation is implicated in HCC progression and may be a potential predictive factor for early recurrence in patients with HCC.
Collapse
Affiliation(s)
- Kai Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Ji-Hua Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Jie Gao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Yaohui Sun
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Zhihui Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Xiaoyi Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| | - Yang Jin
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Diagnosis and Treatment League for Hepatopathy Henan Research Centre for Organ Transplantation, Zhengzhou, China
- Open and Key Laboratory for Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Zhengzhou Key Laboratory for Hepatobiliary and Pancreatic Diseases and Organ Transplantation, Zhengzhou, China
| |
Collapse
|
2
|
Li Q, Wu K, Zhang Y, Liu Y, Wang Y, Chen Y, Sun S, Duan C. Construction of HBV-HCC prognostic model and immune characteristics based on potential genes mining through protein interaction networks. J Cancer Res Clin Oncol 2023; 149:11263-11278. [PMID: 37358667 DOI: 10.1007/s00432-023-04989-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
OBJECTIVE To search for human protein-coding genes related to hepatocellular carcinoma (HCC) in the context of hepatitis B virus (HBV) infection, and perform prognosis risk assessment. METHODS Genes related to HBV-HCC were selected through literature screening and protein-protein interaction (PPI) network database analysis. Prognosis potential genes (PPGs) were identified using Cox regression analysis. Patients were divided into high-risk and low-risk groups based on PPGs, and risk scores were calculated. Kaplan-Meier plots were used to analyze overall survival rates, and the results were predicted based on clinicopathological variables. Association analysis was also conducted with immune infiltration, immune therapy, and drug sensitivity. Experimental verification of the expression of PPGs was done in patient liver cancer tissue and normal liver tissue adjacent to tumors. RESULTS The use of a prognosis potential genes risk assessment model can reliably predict the prognosis risk of patients, demonstrating strong predictive ability. Kaplan-Meier analysis showed that the overall survival rate of the low-risk group was significantly higher than that of the high-risk group. There were significant differences between the two subgroups in terms of immune infiltration and IC50 association analysis. Experimental verification revealed that CYP2C19, FLNC, and HNRNPC were highly expressed in liver cancer tissue, while UBE3A was expressed at a lower level. CONCLUSION PPGs can be used to predict the prognosis risk of HBV-HCC patients and play an important role in the diagnosis and treatment of liver cancer. They also reveal their potential role in the tumor immune microenvironment, clinical-pathological characteristics, and prognosis.
Collapse
Affiliation(s)
- Qingxiu Li
- Department of Cell Biology and Medical Genetics, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Kejia Wu
- Department of Cell Biology and Medical Genetics, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Yiqi Zhang
- Department of Cell Biology and Medical Genetics, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Yuxin Liu
- Department of Cell Biology and Medical Genetics, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Yalan Wang
- Department of Cell Biology and Medical Genetics, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Yong Chen
- Department of Hepatobillary Surgery, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, China
| | - Shuangling Sun
- Chongqing Medical and Pharmaceutical College, No. 82, University Town Middle Road, Shapingba District, Chongqing, 400016, China
| | - Changzhu Duan
- Department of Cell Biology and Medical Genetics, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China.
| |
Collapse
|
3
|
Miki A, Sakuma Y, Watanabe J, Endo K, Sasanuma H, Teratani T, Lefor AK, Shimizu A, Kitayama J, Yasuda Y, Sata N. Remnant liver function is associated with long-term survival in patients with hepatocellular carcinoma undergoing hepatectomy. Sci Rep 2023; 13:15637. [PMID: 37731041 PMCID: PMC10511401 DOI: 10.1038/s41598-023-42929-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023] Open
Abstract
It is important to assess the prognosis and intervene before and after surgery in patients with hepatocellular carcinoma. This study aims to elucidate the association of outcomes and residual liver function after hepatectomy. A total of 176 patients who underwent the initial resection for hepatocellular carcinoma between January 2011 and March 2021 at Jichi Medical University were included. Hepatic clearance of the remnant liver was measured using 99mTc-galactosyl serum albumin scintigraphy. The log-rank test was used to analyze survival using the Kaplan-Meier method. Hazard ratios (HR) and 95% confidence intervals (CI) for overall survival were calculated using Cox's proportional hazard model. In multivariate analysis, microvascular invasion, intraoperative blood loss, and hepatic clearance of the remnant liver were independently associated with overall survival. Hepatic clearance of the remnant liver was independently associated with recurrence free survival. This is the first report to show that lower residual liver function is associated with shorter survival in patients with hepatocellular carcinoma undergoing hepatectomy. Preoperative determination of remnant liver function may allow assessment of prognosis in patients planned to undergo resection of hepatocellular carcinoma. Preservation of liver functional reserve may be crucial for improved long-term outcomes after hepatectomy.
Collapse
Affiliation(s)
- Atsushi Miki
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan.
| | - Yasunaru Sakuma
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Jun Watanabe
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Kazuhiro Endo
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hideki Sasanuma
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Takumi Teratani
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Alan Kawarai Lefor
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Atsushi Shimizu
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Joji Kitayama
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Yoshikazu Yasuda
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Naohiro Sata
- Division of Gastroenterological, General and Transplant Surgery, Department of Surgery, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| |
Collapse
|
4
|
Kim D, Jeong J, Choi J. Exploring the potential of ToxCast™ data for mechanism-based prioritization of chemicals in regulatory context: Case study with priority existing chemicals (PECs) under K-REACH. Regul Toxicol Pharmacol 2023:105439. [PMID: 37392832 DOI: 10.1016/j.yrtph.2023.105439] [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: 01/20/2023] [Revised: 04/26/2023] [Accepted: 06/29/2023] [Indexed: 07/03/2023]
Abstract
Recent studies have highlighted the potential of ToxCast™ database to mechanism-based prioritization of chemicals. To explore the applicability of ToxCast data in the context of regulatory inventory chemicals, we screened 510 priority existing chemicals (PECs) regulated under the Act on the Registration and Evaluation of Chemical Substances (K-REACH) using ToxCast bioassays. In our analysis, a hit-call data matrix containing 298984 chemical-gene interactions was computed for 949 bioassays with the intended target genes, which enabled the identification of the putative toxicity mechanisms. Based on the reactivity to the chemicals, we analyzed 412 bioassays whose intended target gene families were cytochrome P450, oxidoreductase, transporter, nuclear receptor, steroid hormone, and DNA-binding. We also identified 141 chemicals based on their reactivity in the bioassays. These chemicals are mainly in consumer products including colorants, preservatives, air fresheners, and detergents. Our analysis revealed that in vitro bioactivities were involved in the relevant mechanisms inducing in vivo toxicity; however, this was not sufficient to predict more hazardous chemicals. Overall, the current results point to a potential and limitation in using ToxCast data for chemical prioritization in regulatory context in the absence of suitable in vivo data.
Collapse
Affiliation(s)
- Donghyeon Kim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Jaeseong Jeong
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
| |
Collapse
|
5
|
Comparative RNA-Sequencing Analysis Reveals High Complexity and Heterogeneity of Transcriptomic and Immune Profiles in Hepatocellular Carcinoma Tumors of Viral (HBV, HCV) and Non-Viral Etiology. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58121803. [PMID: 36557005 PMCID: PMC9785216 DOI: 10.3390/medicina58121803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Background and Objectives: Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, is the leading cause of cancer-related mortality. It arises and progresses against fibrotic or cirrhotic backgrounds mainly due to infection with hepatitis viruses B (HBV) or C (HCV) or non-viral causes that lead to chronic inflammation and genomic changes. A better understanding of molecular and immune mechanisms in HCC subtypes is needed. Materials and Methods: To identify transcriptional changes in primary HCC tumors with or without hepatitis viral etiology, we analyzed the transcriptomes of 24 patients by next-generation sequencing. Results: We identified common and unique differentially expressed genes for each etiological tumor group and analyzed the expression of SLC, ATP binding cassette, cytochrome 450, cancer testis, and heat shock protein genes. Metascape functional enrichment analysis showed mainly upregulated cell-cycle pathways in HBV and HCV and upregulated cell response to stress in non-viral infection. GeneWalk analysis identified regulator, hub, and moonlighting genes and highlighted CCNB1, ACTN2, BRCA1, IGF1, CDK1, AURKA, AURKB, and TOP2A in the HCV group and HSF1, HSPA1A, HSP90AA1, HSPB1, HSPA5, PTK2, and AURKB in the group without viral infection as hub genes. Immune infiltrate analysis showed that T cell, cytotoxic, and natural killer cell markers were significantly more highly expressed in HCV than in non-viral tumors. Genes associated with monocyte activation had the highest expression levels in HBV, while high expression of genes involved in primary adaptive immune response and complement receptor activity characterized tumors without viral infection. Conclusions: Our comprehensive study underlines the high degree of complexity of immune profiles in the analyzed groups, which adds to the heterogeneous HCC genomic landscape. The biomarkers identified in each HCC group might serve as therapeutic targets.
Collapse
|
6
|
Ji F, Zhang J, Liu N, Gu Y, Zhang Y, Huang P, Zhang N, Lin S, Pan R, Meng Z, Feng XH, Roessler S, Zheng X, Ji J. Blocking hepatocarcinogenesis by a cytochrome P450 family member with female-preferential expression. Gut 2022; 71:2313-2324. [PMID: 34996827 DOI: 10.1136/gutjnl-2021-326050] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022]
Abstract
OBJECTS The incidence of hepatocellular carcinoma (HCC) shows an obvious male dominance in rodents and humans. We aimed to identify the key autosomal liver-specific sex-related genes and investigate their roles in hepatocarcinogenesis. DESIGN Two HCC cohorts (n=551) with available transcriptome and metabolome data were used. Class comparisons of omics data and ingenuity pathway analysis were performed to explore sex-related molecules and their associated functions. Functional assays were employed to investigate roles of the key candidates, including cellular assays, molecular assays and multiple orthotopic HCC mouse models. RESULTS A global comparison of multiple omics data revealed 861 sex-related molecules in non-tumour liver tissues between female and male HCC patients, which denoted a significant suppression of cancer-related diseases and functions in female liver than male. A member of cytochrome P450 family, CYP39A1, was one of the top liver-specific candidates with significantly higher levels in female vs male liver. In HCC tumours, CYP39A1 expression was dramatically reduced in over 90% HCC patients. Exogenous CYP39A1 significantly blocked tumour formation in both female and male mice and partially reduced the sex disparity of hepatocarcinogenesis. The HCC suppressor role of CYP39A1 did not rely on its known P450 enzyme activity but its C-terminal region, by which CYP39A1 impeded the transcriptional activation activity of c-Myc, leading to a significant inhibition of hepatocarcinogenesis. CONCLUSIONS The liver-specific CYP39A1 with female-preferential expression was a strong suppressor of HCC development. Strategies to up-regulate CYP39A1 might be promising methods for HCC treatment in both women and men in future.
Collapse
Affiliation(s)
- Fubo Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jianjuan Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Niya Liu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuanzhuo Gu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Peipei Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Nachuan Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shengda Lin
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ran Pan
- Department of Pathology and Pathophysiology, Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhuoxian Meng
- Department of Pathology and Pathophysiology, Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xin-Hua Feng
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Stephanie Roessler
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Xin Zheng
- Taoharmony Biotech L.L.C, Hangzhou, Zhejiang, China
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China .,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
7
|
Gallon J, Coto-Llerena M, Ercan C, Bianco G, Paradiso V, Nuciforo S, Taha-Melitz S, Meier MA, Boldanova T, Pérez-Del-Pulgar S, Rodríguez-Tajes S, von Flüe M, Soysal SD, Kollmar O, Llovet JM, Villanueva A, Terracciano LM, Heim MH, Ng CKY, Piscuoglio S. Epigenetic priming in chronic liver disease impacts the transcriptional and genetic landscapes of hepatocellular carcinoma. Mol Oncol 2021; 16:665-682. [PMID: 34863035 PMCID: PMC8807355 DOI: 10.1002/1878-0261.13154] [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: 07/20/2021] [Revised: 10/18/2021] [Accepted: 12/02/2021] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinomas (HCCs) usually arise from chronic liver disease (CLD). Precancerous cells in chronically inflamed environments may be 'epigenetically primed', sensitising them to oncogenic transformation. We investigated whether epigenetic priming in CLD may affect HCC outcomes by influencing the genomic and transcriptomic landscapes of HCC. Analysis of DNA methylation arrays from 10 paired CLD-HCC identified 339 shared dysregulated CpG sites and 18 shared differentially methylated regions compared with healthy livers. These regions were associated with dysregulated expression of genes with relevance in HCC, including ubiquitin D (UBD), cytochrome P450 family 2 subfamily C member 19 (CYP2C19) and O-6-methylguanine-DNA methyltransferase (MGMT). Methylation changes were recapitulated in an independent cohort of nine paired CLD-HCC. High CLD methylation score, defined using the 124 dysregulated CpGs in CLD and HCC in both cohorts, was associated with poor survival, increased somatic genetic alterations and TP53 mutations in two independent HCC cohorts. Oncogenic transcriptional and methylation dysregulation is evident in CLD and compounded in HCC. Epigenetic priming in CLD sculpts the transcriptional landscape of HCC and creates an environment favouring the acquisition of genetic alterations, suggesting that the extent of epigenetic priming in CLD could influence disease outcome.
Collapse
Affiliation(s)
- John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland
| | - Mairene Coto-Llerena
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, Switzerland
| | - Caner Ercan
- Institute of Medical Genetics and Pathology, University Hospital Basel, Switzerland
| | - Gaia Bianco
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland
| | - Viola Paradiso
- Institute of Medical Genetics and Pathology, University Hospital Basel, Switzerland
| | - Sandro Nuciforo
- Hepatology Laboratory, Department of Biomedicine, University of Basel, Switzerland
| | - Stephanie Taha-Melitz
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Marie-Anne Meier
- Hepatology Laboratory, Department of Biomedicine, University of Basel, Switzerland
| | - Tujana Boldanova
- Hepatology Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | | | | | - Markus von Flüe
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Savas D Soysal
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Otto Kollmar
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Josep M Llovet
- Translational Research in Hepatic Oncology, Liver Unit, IDIBAPS, Hospital Clínic, University of Barcelona, Spain.,Liver Cancer Program, Divisions of Liver Diseases and Hematology/Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Augusto Villanueva
- Liver Cancer Program, Divisions of Liver Diseases and Hematology/Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luigi M Terracciano
- Department of Pathology, Humanitas Clinical and Research Center, IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Markus H Heim
- Hepatology Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Switzerland.,SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, Switzerland
| |
Collapse
|
8
|
Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma. J Immunol Res 2021; 2021:1801873. [PMID: 34423049 PMCID: PMC8378952 DOI: 10.1155/2021/1801873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/18/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022] Open
Abstract
Despite the advances in the treatment of hepatocellular carcinoma (HCC), the prognosis of HCC patients remains unsatisfactory due to postsurgical recurrence and treatment resistance. Therefore, it is important to reveal the mechanisms underlying HCC and identify potential therapeutic targets against HCC, which could facilitate the development of novel therapies. Based on 12 HCC samples and 12 paired paracancerous normal tissues, we identified differentially expressed mRNAs and lncRNAs using the "limma" package in R software. Moreover, we used the weighted gene coexpression network analysis (WGCNA) to analyze the expression data and screened hub genes. Furthermore, we performed pathway enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In addition, the relative abundance of a given gene set was estimated by single-sample Gene Set Enrichment Analysis. We identified 687 differentially expressed mRNAs and 260 differentially expressed lncRNAs. A total of 6 modules were revealed by WGCNA, and MT1M and MT1E genes from the red module were identified as hub genes. Moreover, pathway analysis revealed the top 10 enriched KEGG pathways of upregulated or downregulated genes. Additionally, we also found that CD58 might act as an immune checkpoint gene in HCC via PD1/CTLA4 pathways and regulate the levels of tumor-infiltrating immune cells in HCC tissues, which might be an immunotherapeutic target in HCC. Our research identified key functional modules and immunomodulatory regulators for HCC, which might offer novel diagnostic biomarkers and/or therapeutic targets for cancer immunotherapy.
Collapse
|
9
|
Wang J, Wang Y, Xu J, Song Q, Shangguan J, Xue M, Wang H, Gan J, Gao W. Global analysis of gene expression signature and diagnostic/prognostic biomarker identification of hepatocellular carcinoma. Sci Prog 2021; 104:368504211029429. [PMID: 34315286 PMCID: PMC10450782 DOI: 10.1177/00368504211029429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. The landscape of HCC's molecular alteration signature has been explored over the last few decades. Even so, more comprehensive research is still needed to improve understanding of tumorigenesis and progression of HCC, as well as to identify potential biomarkers for the malignancy. In this research, a comprehensive bioinformatics analysis was conducted based on the publicly available databases from both the Cancer Genome Atlas (TCGA) program and the gene expression omnibus (GEO) database. R/Bioconductor was used to analyze differentially expressed genes (DEGs) between HCC tumor and normal control (NC) samples, and then a protein-protein interaction (PPI) network of DEGs was established through the STRING platform. Finally, the application of specific candidate genes as diagnostic or prognostic biomarkers of HCC was explored and evaluated by ROC and survival analysis. A total of 310 DEGs were detected in the HCC tumor samples. Thirty-six hub DEGs in the PPI network and 10 candidates of the 36 genes showed significant alterations in tumor expression, including CDKN3, TOP2A, UBE2C, CDC20, PBK, ASPM, KIF20A, NCAPG, CCNB2, CYP3A4. The 10-gene signature had relatively significant effects when distinguishing tumors from normal samples (sensitivity >70%, specificity >70%, AUC >0.8, p < 0.001). Eight candidate genes were negatively correlated with the overall survival rate of the patients (p < 0.05) and were all up-regulated in HCC tumor samples. The age and gender factors had no significant impact on the overall survival rate of HCC patients (p > 0.05), and the TNM stage status factor had a significant negative prognosis correlation (p < 0.05). This research provides evidence for a better understanding of tumorigenesis and progression of HCC and helps to explore candidate targets for disease diagnosis and treatment.
Collapse
Affiliation(s)
- Jihan Wang
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, China
| | - Yangyang Wang
- School of Electronics and Information, Northwestern Polytechnical University, Xi’an, China
| | - Jing Xu
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, China
| | - Qiying Song
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, China
| | - Jingbo Shangguan
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, China
| | - Mengju Xue
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, China
| | - Hanghui Wang
- Department of Nursing, School of Medicine, Xi’an International University, Xi’an, China
| | - Jingyi Gan
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, China
| | - Wenjie Gao
- Department of Spine Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
10
|
Nekvindova J, Mrkvicova A, Zubanova V, Hyrslova Vaculova A, Anzenbacher P, Soucek P, Radova L, Slaby O, Kiss I, Vondracek J, Spicakova A, Bohovicova L, Fabian P, Kala Z, Palicka V. Hepatocellular carcinoma: Gene expression profiling and regulation of xenobiotic-metabolizing cytochromes P450. Biochem Pharmacol 2020; 177:113912. [PMID: 32173367 DOI: 10.1016/j.bcp.2020.113912] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinoma (HCC) remains a highly prevalent and deadly disease, being among the top causes of cancer-related deaths worldwide. Despite the fact that the liver is the major site of biotransformation, studies on drug metabolizing enzymes in HCC are scarce. It is known that malignant transformation of hepatocytes leads to a significant alteration of their metabolic functions and overall deregulation of gene expression. Advanced stages of the disease are thus frequently associated with liver failure, and severe alteration of drug metabolism. However, the impact of dysregulation of metabolic enzymes on therapeutic efficacy and toxicity in HCC patients is largely unknown. Here we demonstrate a significant down-regulation in European Caucasian patients of cytochromes P450 (CYPs), the major xenobiotic-metabolizing enzymes, in HCC tumour samples as compared to their surrounding non-cancerous (reference) tissue. Moreover, we report for the first time the association of the unique CYP profiles with specific transcriptome changes, and interesting correlations with expression levels of nuclear receptors and with the histological grade of the tumours. Integrated analysis has suggested certain co-expression profiles of CYPs with lncRNAs that need to be further characterized. Patients with large tumours with down-regulated CYPs could be more vulnerable to drug toxicity; on the other hand, such tumours would eliminate drugs more slowly and should be more sensitive to pharmacotherapy (except in the case of pro-drugs where activation is necessary).
Collapse
Affiliation(s)
- Jana Nekvindova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
| | - Alena Mrkvicova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic; Department of Medical Biochemistry, Charles University, Faculty of Medicine in Hradec Kralove, Czech Republic.
| | - Veronika Zubanova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
| | - Alena Hyrslova Vaculova
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Pavel Anzenbacher
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
| | - Pavel Soucek
- Center for Toxicology and Health Safety, National Institute of Public Health, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Igor Kiss
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute and Masaryk University, Brno, Czech Republic.
| | - Jan Vondracek
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Alena Spicakova
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
| | - Lucia Bohovicova
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute and Masaryk University, Brno, Czech Republic.
| | - Pavel Fabian
- Department of Oncological and Experimental Pathology, Cancer Institute, Brno, Czech Republic.
| | - Zdenek Kala
- Department of Surgery, University Hospital Brno, Czech Republic.
| | - Vladimir Palicka
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
| |
Collapse
|
11
|
Wang P, Zhang C, Li W, Zhai B, Jiang X, Reddy S, Jiang H, Sun X. Identification of a robust functional subpathway signature for pancreatic ductal adenocarcinoma by comprehensive and integrated analyses. Cell Commun Signal 2020; 18:34. [PMID: 32122386 PMCID: PMC7053133 DOI: 10.1186/s12964-020-0522-4] [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: 11/14/2019] [Accepted: 01/29/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy and its mortality continues to rise globally. Because of its high heterogeneity and complex molecular landscapes, published gene signatures have demonstrated low specificity and robustness. Functional signatures containing a group of genes involved in similar biological functions may display a more robust performance. METHODS The present study was designed to excavate potential functional signatures for PDAC by analyzing maximal number of datasets extracted from available databases with a recently developed method of FAIME (Functional Analysis of Individual Microarray Expression) in a comprehensive and integrated way. RESULTS Eleven PDAC datasets were extracted from GEO, ICGC and TCGA databases. By systemically analyzing these datasets, we identified a robust functional signature of subpathway (path:00982_1), which belongs to the drug metabolism-cytochrome P450 pathway. The signature has displayed a more powerful and robust capacity in predicting prognosis, drug response and chemotherapeutic efficacy for PDAC, particularly for the classical subtype, in comparison with published gene signatures and clinically used TNM staging system. This signature was verified by meta-analyses and validated in available cell line and clinical datasets with chemotherapeutic efficacy. CONCLUSION The present study has identified a novel functional PDAC signature, which has the potential to improve the current systems for predicting the prognosis and monitoring drug response, and to serve a linkage to therapeutic options for combating PDAC. However, the involvement of path:00982_1 subpathway in the metabolism of anti-PDAC chemotherapeutic drugs, particularly its biological interpretation, requires a further investigation. Video Abstract.
Collapse
Affiliation(s)
- Ping Wang
- The Hepatosplenic Surgery Center, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.,Department of Interventional Radiology, the Third Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Weidong Li
- The Hepatosplenic Surgery Center, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.,Department of General Surgery, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Bo Zhai
- The Hepatosplenic Surgery Center, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.,Department of General Surgery, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xian Jiang
- The Hepatosplenic Surgery Center, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Shiva Reddy
- Department of Molecular Medicine & Pathology, Faculty of Medical and Health Sciences, the University of Auckland, Auckland, 1142, New Zealand
| | - Hongchi Jiang
- The Hepatosplenic Surgery Center, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Xueying Sun
- The Hepatosplenic Surgery Center, the First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
| |
Collapse
|
12
|
Takasu S, Yokoo Y, Ishii Y, Kijima A, Ogawa K, Umemura T. Molecular Pathological Differences in Global Gene Expression between Two Sustained Proliferative Lesions, Nodular Regenerative Hepatocellular Hyperplasia and Hepatocellular Adenoma, in Mice. Toxicol Pathol 2018; 47:44-52. [PMID: 30572783 DOI: 10.1177/0192623318810200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Long-term exposure to piperonyl butoxide (PBO) induces multiple nodular masses along with hepatocellular tumors in the liver of mice. The histopathological features of the nodules led to our diagnosis of nodular regenerative hepatocellular hyperplasia (NRH). However, because of the lack of data on the biological characteristics of NRH, whether this lesion is truly nonneoplastic remains unknown. In this study, the molecular characteristics of NRH were compared with those of hepatocellular adenoma (HCA) by global gene expression analysis. Six-week-old male ICR mice were fed a diet containing 6,000 ppm PBO for 43 weeks to induce NRH and HCA development. Complementary DNA microarray analysis was performed using messenger RNA extracted from NRH and HCA frozen sections collected by laser microdissection. Hierarchical cluster analysis showed that all NRH samples clustered together but were separate from the HCA cluster. Pathway analysis revealed activation of the cell cycle and Delta-Notch signaling in both lesions, but the latter was more upregulated in HCA. Downregulation of cytochrome p450 enzymes was observed in NRH, but not in HCA. These results imply that NRH differs from HCA in terms of not only morphological but also molecular characteristics.
Collapse
Affiliation(s)
- Shinji Takasu
- 1 Division of Pathology, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Yuh Yokoo
- 1 Division of Pathology, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Yuji Ishii
- 1 Division of Pathology, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Aki Kijima
- 1 Division of Pathology, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kumiko Ogawa
- 1 Division of Pathology, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Takashi Umemura
- 1 Division of Pathology, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.,2 Laboratory of Animal Pathology, Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Hachioji, Tokyo, Japan
| |
Collapse
|