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Ringlander J, Strömberg LG, Stenbäck JB, Andersson ME, Abrahamsson S, Skoglund C, Castedal M, Larsson SB, Rydell GE, Lindh M. Enrichment Reveals Extensive Integration of Hepatitis B Virus DNA in Hepatitis Delta Virus-Infected Patients. J Infect Dis 2024; 230:e684-e693. [PMID: 38271697 PMCID: PMC11420801 DOI: 10.1093/infdis/jiae045] [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: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) DNA may become integrated into the human genome of infected human hepatocytes. Expression of integrations can produce the surface antigen (HBsAg) that is required for synthesis of hepatitis D virus (HDV) particles and the abundant subviral particles in the blood of HBV- and HDV-infected subjects. Knowledge about the extent and variation of HBV integrations and impact on chronic HDV is still limited. METHODS We investigated 50 pieces of liver explant tissue from 5 patients with hepatitis D-induced cirrhosis, using a deep-sequencing strategy targeting HBV RNA. RESULTS We found that integrations were abundant and highly expressed, with large variation in the number of integration-derived (HBV/human chimeric) reads, both between and within patients. The median number of unique integrations for each patient correlated with serum levels of HBsAg. However, most of the HBV reads represented a few predominant integrations. CONCLUSIONS The results suggest that HBV DNA integrates in a large proportion of hepatocytes, and that the HBsAg output from these integrations vary >100-fold depending on clone size and expression rate. A small proportion of the integrations seems to determine the serum levels of HBsAg and HDV RNA in HBV/HDV coinfected patients with liver cirrhosis.
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Affiliation(s)
- Johan Ringlander
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lucia Gonzales Strömberg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joakim B Stenbäck
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria E Andersson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sanna Abrahamsson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Catarina Skoglund
- The Transplant Institute, Sahlgrenska University Hospital, Gothenburg, Sweden
- Sahlgrenska Academy, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Maria Castedal
- The Transplant Institute, Sahlgrenska University Hospital, Gothenburg, Sweden
- Sahlgrenska Academy, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Simon B Larsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gustaf E Rydell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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2
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Singh V, Mondal A, Adhikary S, Mondal P, Shirgaonkar N, DasGupta R, Roy S, Das C. UBR7 E3 Ligase Suppresses Interferon-β Mediated Immune Signaling by Targeting Sp110 in Hepatitis B Virus-Induced Hepatocellular Carcinoma. ACS Infect Dis 2024. [PMID: 38938101 DOI: 10.1021/acsinfecdis.4c00213] [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: 06/29/2024]
Abstract
A newly discovered E3 ubiquitin ligase, UBR7, plays a crucial role in histone H2BK120 monoubiquitination. Here, we report a novel function of UBR7 in promoting hepatitis B virus (HBV) pathogenesis, which further leads to HBV-induced hepatocellular carcinoma (HCC). Transcriptomics analysis from HCC patients revealed the deregulation of UBR7 in cancer. Remarkably, targeting UBR7, particularly its catalytic function, led to a significant decrease in viral copy numbers. We also identified the speckled family protein Sp110 as an important substrate of UBR7. Notably, Sp110 has been previously shown to be a resident of promyelocytic leukemia nuclear bodies (PML-NBs), where it remains SUMOylated, and during HBV infection, it undergoes deSUMOylation and exits the PML body. We observed that UBR7 ubiquitinates Sp110 at critical residues within its SAND domain. Sp110 ubiquitination downregulates genes in the type I interferon response pathway. Comparative analysis of RNA-Seq from the UBR7/Sp110 knockdown data set confirmed that the IFN-β signaling pathway gets deregulated in HCC cells in the presence of HBV. Single-cell RNA-Seq analysis of patient samples further confirmed the inverse correlation between the expression of Sp110/UBR7 and the inflammation score. Notably, silencing of UBR7 induces IRF7 phosphorylation, thereby augmenting interferon (IFN)-β and the downstream interferon-stimulated genes (ISGs). Further, wild-type but not the ubiquitination-defective mutant of Sp110 could be recruited to the type I interferon response pathway genes. Our study establishes a new function of UBR7 in non-histone protein ubiquitination, promoting viral persistence, and has important implications for the development of therapeutic strategies targeting HBV-induced HCC.
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Affiliation(s)
- Vipin Singh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Atanu Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Niranjan Shirgaonkar
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, A*STAR, 138672 Singapore
| | - Ramanuj DasGupta
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, A*STAR, 138672 Singapore
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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3
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Su PY(A, Chang CH, Yen SCB, Wu HY, Tung WJ, Hu YP, Chen YYI, Lin MH, Shih C, Chen PJ, Tsai K. Epitranscriptomic cytidine methylation of the hepatitis B viral RNA is essential for viral reverse transcription and particle production. Proc Natl Acad Sci U S A 2024; 121:e2400378121. [PMID: 38830096 PMCID: PMC11181118 DOI: 10.1073/pnas.2400378121] [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: 01/08/2024] [Accepted: 04/20/2024] [Indexed: 06/05/2024] Open
Abstract
Epitranscriptomic RNA modifications have emerged as important regulators of the fate and function of viral RNAs. One prominent modification, the cytidine methylation 5-methylcytidine (m5C), is found on the RNA of HIV-1, where m5C enhances the translation of HIV-1 RNA. However, whether m5C functionally enhances the RNA of other pathogenic viruses remains elusive. Here, we surveyed a panel of commonly found RNA modifications on the RNA of hepatitis B virus (HBV) and found that HBV RNA is enriched with m5C as well as ten other modifications, at stoichiometries much higher than host messenger RNA (mRNA). Intriguingly, m5C is mostly found on the epsilon hairpin, an RNA element required for viral RNA encapsidation and reverse transcription, with these m5C mainly deposited by the cellular methyltransferase NSUN2. Loss of m5C from HBV RNA due to NSUN2 depletion resulted in a partial decrease in viral core protein (HBc) production, accompanied by a near-complete loss of the reverse transcribed viral DNA. Similarly, mutations introduced to remove the methylated cytidines resulted in a loss of HBc production and reverse transcription. Furthermore, pharmacological disruption of m5C deposition led to a significant decrease in HBV replication. Thus, our data indicate m5C methylations as a critical mediator of the epsilon elements' function in HBV virion production and reverse transcription, suggesting the therapeutic potential of targeting the m5C methyltransfer process on HBV epsilon as an antiviral strategy.
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Affiliation(s)
- Pei-Yi (Alma) Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei115, Taiwan
| | - Chih-Hsu Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei115, Taiwan
| | - Shin-Chwen Bruce Yen
- Institute of Biomedical Sciences, Academia Sinica, Taipei115, Taiwan
- Taiwan International Graduate Program, National Yang-Ming Chiao-Tung University and Academia Sinica, Taipei115, Taiwan
| | - Hsiu-Yi Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei115, Taiwan
| | - Wan-Ju Tung
- Institute of Biomedical Sciences, Academia Sinica, Taipei115, Taiwan
| | - Yu-Pei Hu
- Institute of Biomedical Sciences Summer Undergraduate Internship Program, Academia Sinica, Taipei115, Taiwan
| | - Yen-Yu Ian Chen
- Institute of Biomedical Sciences Summer Undergraduate Internship Program, Academia Sinica, Taipei115, Taiwan
| | - Miao-Hsia Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei100, Taiwan
| | - Chiaho Shih
- Graduate Institute of Cell Biology, College of Life Sciences, China Medical University, Taichung404, Taiwan
| | - Pei-Jer Chen
- National Taiwan University Center for Genomic Medicine, National Taiwan University, Taipei100, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei100, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei100, Taiwan
| | - Kevin Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei115, Taiwan
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Guo D, Zhang M, Wei T, Zhang X, Shi X, Tang H, Ding M, Li J, Zhang S, Guo W. NFKBIZ regulates NFκB signaling pathway to mediate tumorigenesis and metastasis of hepatocellular carcinoma by direct interaction with TRIM16. Cell Mol Life Sci 2024; 81:167. [PMID: 38581570 PMCID: PMC10998794 DOI: 10.1007/s00018-024-05182-7] [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: 09/19/2023] [Revised: 01/30/2024] [Accepted: 02/20/2024] [Indexed: 04/08/2024]
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with high incidence and mortality rates. NFKBIZ, a member of the nuclear factor kappa B inhibitory family, is closely related to tumor progression. However, the precise role of NFKBIZ in HCC remains unclear. To explore this, we conducted a series of experiments from clinic to cells. Western blot and qPCR revealed a significant downregulation of NFKBIZ in human HCC tissues. Clinical character analysis showed that the patients with lower NFKBIZ expression had poorer prognosis and higher clinical stage. By using CCK-8, wound healing, transwell invasion and migration assay, we discovered that NFKBIZ expression was reversely associated with the proliferation, invasion, and migration ability of HCC cells in vitro. Additionally, the results obtained from xenograft assay and lung metastasis models showed that NFKBIZ overexpression inhibited the growth and metastasis of HCC cells in vivo. Western blot and immunofluorescence assay further revealed that NFKBIZ mediated HCC cell growth and migration by regulating NFκB signaling transduction. Finally, flow cytometry, protein degradation assay and Co-immunoprecipitation indicated that TRIM16 can enhance NFKBIZ ubiquitination by direct interactions at its K48 site, which may thereby alleviate HCC cell apoptosis to induce the insensitivity to sorafenib. In conclusion, our study demonstrated that NFKBIZ regulated HCC tumorigenesis and metastasis by mediating NFκB signal transduction and TRIM16/NFKBIZ/NFκB axis may be the underlying mechanism of sorafenib insensitivity in HCC.
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Affiliation(s)
- Danfeng Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Ming Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Tingju Wei
- Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xiaodan Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xiaoyi Shi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Hongwei Tang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Mingjie Ding
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jie Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Henan Key Laboratory for Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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5
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Zhang X, Li Y, Huan C, Hou Y, Liu R, Shi H, Zhang P, Zheng B, Wang Y, Wang H, Zhang W. LncRNA NKILA inhibits HBV replication by repressing NF-κB signalling activation. Virol Sin 2024; 39:44-55. [PMID: 37832719 PMCID: PMC10877346 DOI: 10.1016/j.virs.2023.10.002] [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: 08/09/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023] Open
Abstract
Hepatitis B virus (HBV) infection results in liver cirrhosis and hepatocellular carcinoma (HCC). HBx/nuclear factor (NF)-κB pathway plays a role in HBV replication. However, whether NF-κB-interacting long noncoding RNA (NKILA), a suppressor of NF-κB activation, regulates HBV replication remains largely unknown. In this study, gain-and-loss experiments showed that NKILA inhibited HBV replication by inhibiting NF-κB activity. In turn, HBV infection down-regulated NKILA expression. In addition, expression levels of NKILA were lower in the peripheral blood-derived monocytes (PBMCs) of HBV-positive patients than in healthy individuals, which were correlated with HBV viral loads. And a negative correlation between NKILA expression level and HBV viral loads was observed in blood serum from HBV-positive patients. Lower levels of endogenous NKILA were also observed in HepG2 cells expressing a 1.3-fold HBV genome, HBV-infected HepG2-NTCP cells, stable HBV-producing HepG2.2.15 and HepAD38 cells, compared to those HBV-negative cells. Furthermore, HBx was required for NKILA-mediated inhibition on HBV replication. NKILA decreased HBx-induced NF-κB activation by interrupting the interaction between HBx and p65, whereas NKILA mutants lack of essential domains for NF-ĸB inhibition, lost the ability to inhibit HBV replication. Together, our data demonstrate that NKILA may serve as a suppressor of HBV replication via NF-ĸB signalling.
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Affiliation(s)
- Xi Zhang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130012, China; Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China; Department of Ophthalmology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Yuanyuan Li
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Chen Huan
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Yubao Hou
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Rujia Liu
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Hongyun Shi
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Peng Zhang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130012, China
| | - Baisong Zheng
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Yingchao Wang
- Hepatobiliary Pancreatic Surgery, The First Hospital of Jilin University, Changchun, 130012, China.
| | - Hong Wang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130012, China; Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China.
| | - Wenyan Zhang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130012, China; Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China.
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6
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Kurokawa S, Kobori T, Yoneda M, Ogawa Y, Honda Y, Kessoku T, Imajo K, Saito S, Nakajima A, Hotta K. Identification of differentially methylated regions associated with both liver fibrosis and hepatocellular carcinoma. BMC Gastroenterol 2024; 24:57. [PMID: 38302914 PMCID: PMC10832174 DOI: 10.1186/s12876-024-03149-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Liver fibrosis is a major risk factor for hepatocellular carcinoma (HCC). We have previously reported that differentially methylated regions (DMRs) are correlated with the fibrosis stages of metabolic dysfunction-associated steatotic liver disease (MASLD). In this study, the methylation levels of those DMRs in liver fibrosis and subsequent HCC were examined. METHODS The methylation levels of DMRs were investigated using alcoholic cirrhosis and HCC (GSE60753). The data of hepatitis C virus-infected cirrhosis and HCC (GSE60753), and two datasets (GSE56588 and GSE89852) were used for replication analyses. The transcriptional analyses were performed using GSE114564, GSE94660, and GSE142530. RESULTS Hypomethylated DMR and increased transcriptional level of zinc finger and BTB domain containing 38 (ZBTB38) were observed in HCC. Hypermethylated DMRs, and increased transcriptional levels of forkhead box K1 (FOXK1) and zinc finger CCCH-type containing 3 (ZC3H3) were observed in HCC. The methylation levels of DMR of kazrin, periplakin interacting protein (KAZN) and its expression levels were gradually decreased as cirrhosis progressed to HCC. CONCLUSIONS Changes in the methylation and transcriptional levels of ZBTB38, ZC3H3, FOXK1, and KAZN are important for the development of fibrosis and HCC; and are therefore potential therapeutic targets and diagnostic tools for cirrhosis and HCC.
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Affiliation(s)
- Suguru Kurokawa
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Takuro Kobori
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Masato Yoneda
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yuji Ogawa
- Department of Gastroenterology, National Hospital Organization Yokohama Medical Center, 3-60-2 Harajyuku, Totsuka, Yokohama, 245-8675, Japan
| | - Yasushi Honda
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Takaomi Kessoku
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
- Department of Palliative Medicine, International University of Health and Welfare Narita Hospital, 852, Hatakeda, Narita, 286-8520, Japan
| | - Kento Imajo
- Department of Gastroenterology, Shin-yurigaoka General Hospital, 255 Furusawatsuko, Asao, Kawasaki, 2150-0026, Japan
| | - Satoru Saito
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Atsushi Nakajima
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kikuko Hotta
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan.
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7
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Chen Z, Shi Q, Zhao Y, Xu M, Liu Y, Li X, Liu L, Sun M, Wu X, Shao Z, Xu Y, Wang L, He X. Long-read transcriptome landscapes of primary and metastatic liver cancers at transcript resolution. Biomark Res 2024; 12:4. [PMID: 38185659 PMCID: PMC10773130 DOI: 10.1186/s40364-023-00554-w] [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: 09/06/2023] [Accepted: 12/29/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND The liver ranks as the sixth most prevalent site of primary cancer in humans, and it frequently experiences metastases from cancers originating in other organs. To facilitate the development of effective treatments and improve survival rates, it is crucial to comprehend the intricate and diverse transcriptome landscape of primary and metastatic liver cancers. METHODS We conducted long-read isoform sequencing and short-read RNA sequencing using a cohort of 95 patients with primary and secondary liver cancer who underwent hepatic resection. We compared the transcriptome landscapes of primary and metastatic liver cancers and systematically investigated hepatocellular carcinoma (HCC), paired primary tumours and liver metastases, and matched nontumour liver tissues. RESULTS We elucidated the full-length isoform-level transcriptome of primary and metastatic liver cancers in humans. Our analysis revealed isoform-level diversity in HCC and identified transcriptome variations associated with liver metastatis. Specific RNA transcripts and isoform switching events with clinical implications were profound in liver cancer. Moreover, we defined metastasis-specific transcripts that may serve as predictors of risk of metastasis. Additionally, we observed abnormalities in adjacent paracancerous liver tissues and characterized the immunological and metabolic alterations occurring in the liver. CONCLUSIONS Our findings underscore the power of full-length transcriptome profiling in providing novel biological insights into the molecular mechanisms underlying tumourigenesis. These insights will further contribute to improving treatment strategies for primary and metastatic liver cancers.
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Affiliation(s)
- Zhiao Chen
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
| | - Qili Shi
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
| | - Yiming Zhao
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
| | - Midie Xu
- Department of Pathology, biobank, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yizhe Liu
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
| | - Xinrong Li
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
| | - Li Liu
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
| | - Menghong Sun
- Department of Pathology, biobank, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
| | - Zhimin Shao
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.
| | - Lu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China.
| | - Xianghuo He
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China.
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China.
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8
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Porukala M, Vinod PK. Gene expression signatures of stepwise progression of Hepatocellular Carcinoma. PLoS One 2023; 18:e0296454. [PMID: 38157373 PMCID: PMC10756545 DOI: 10.1371/journal.pone.0296454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
The molecular pathogenesis of Hepatocellular Carcinoma (HCC) is a complex process progressing from premalignant stages to cancer in a stepwise manner. Mostly, HCC is detected at advanced stages, leading to high mortality rates. Hence, characterising the molecular underpinnings of HCC from normal to cancer state through precancerous state may help in early detection and improve its prognosis and treatment. In this work, we analysed the transcriptomic profile of tumour and premalignant samples from HCC or chronic liver disease patients, who had undergone either total or partial hepatectomy. The normal samples from patients with metastatic cancer/polycystic liver disease/ cholangiocarcinoma were also included. A gene co-expression network approach was applied to identify hierarchical changes: modules, pathways, and genes related to different trajectories of HCC and patient survival. Our analysis shows that the progression from premalignant conditions to tumour is accompanied by differences in the downregulation of genes associated with HNF4A activity and the immune system and upregulation of cell cycle genes, bringing about variability in patient outcomes. However, an increase in immune and cell cycle activity is observed in premalignant samples. Interestingly, co-expression modules and genes from premalignant stages are associated with survival. THBD, a classical marker for dendritic cells, is a predictor of survival at the premalignant stage. Further, genes linked to microtubules, kinetochores, and centromere are altered in both premalignant and tumour conditions and are associated with survival. Our analysis revealed a three-way molecular axis of liver function, immune pathways, and cell cycle driving HCC pathogenesis.
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Affiliation(s)
- Manisri Porukala
- Centre for Computational Natural Sciences and Bioinformatics, IIIT, Hyderabad, India
| | - P. K. Vinod
- Centre for Computational Natural Sciences and Bioinformatics, IIIT, Hyderabad, India
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9
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Fukano K, Wakae K, Nao N, Saito M, Tsubota A, Toyoshima T, Aizaki H, Iijima H, Matsudaira T, Kimura M, Watashi K, Sugiura W, Muramatsu M. A versatile method to profile hepatitis B virus DNA integration. Hepatol Commun 2023; 7:e0328. [PMID: 38051537 PMCID: PMC10697629 DOI: 10.1097/hc9.0000000000000328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/26/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND HBV DNA integration into the host genome is frequently found in HBV-associated HCC tissues and is associated with hepatocarcinogenesis. Multiple detection methods, including hybrid capture-sequencing, have identified integration sites and provided clinical implications; however, each has advantages and disadvantages concerning sensitivity, cost, and throughput. Therefore, methods that can comprehensively and cost-effectively detect integration sites with high sensitivity are required. Here, we investigated the efficiency of RAISING (Rapid Amplification of Integration Site without Interference by Genomic DNA contamination) as a simple and inexpensive method to detect viral integration by amplifying HBV-integrated fragments using virus-specific primers covering the entire HBV genome. METHODS AND RESULTS Illumina sequencing of RAISING products from HCC-derived cell lines (PLC/PRF/5 and Hep3B cells) identified HBV-human junction sequences as well as their frequencies. The HBV-human junction profiles identified using RAISING were consistent with those determined using hybrid capture-sequencing, and the representative junctions could be validated by junction-specific nested PCR. The comparison of these detection methods revealed that RAISING-sequencing outperforms hybrid capture-sequencing in concentrating junction sequences. RAISING-sequencing was also demonstrated to determine the sites of de novo integration in HBV-infected HepG2-NTCP cells, primary human hepatocytes, liver-humanized mice, and clinical specimens. Furthermore, we made use of xenograft mice subcutaneously engrafted with PLC/PRF/5 or Hep3B cells, and HBV-human junctions determined by RAISING-sequencing were detectable in the plasma cell-free DNA using droplet digital PCR. CONCLUSIONS RAISING successfully profiles HBV-human junction sequences with smaller amounts of sequencing data and at a lower cost than hybrid capture-sequencing. This method is expected to aid basic HBV integration and clinical diagnosis research.
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Affiliation(s)
- Kento Fukano
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kousho Wakae
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, HU-IVReD, Hokkaido University, Sapporo, Japan
| | - Masumichi Saito
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akihito Tsubota
- Research Center for Medical Science, The Jikei University School of Medicine, Tokyo, Japan
| | - Takae Toyoshima
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroko Iijima
- Department of Internal Medicine, Division of Hepatobiliary and Pancreatic Disease, Hyogo Medical University, Hyogo, Japan
| | - Takahiro Matsudaira
- Biotechnological Research Support Division, FASMAC Co., Ltd., Kanagawa, Japan
| | - Moto Kimura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Wataru Sugiura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Infectious Disease Research, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
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10
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Yan P, Luo Y, Huang Z, Mou T, Yang H, Peng D, Wu Z. Establishment of a prognostic signature based on fatty acid metabolism genes in HCC associated with hepatitis B. BMC Gastroenterol 2023; 23:390. [PMID: 37957550 PMCID: PMC10644542 DOI: 10.1186/s12876-023-03026-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC) is one of the most common and deadly cancer and often accompanied by varying degrees of liver damage, leading to the dysfunction of fatty acid metabolism (FAM). This study aimed to investigate the relationship between FAM and HBV-associated HCC and identify FAM biomarkers for predicting the prognosis of HBV-associated HCC. METHODS Gene Set Enrichment Analysis (GSEA) was used to analyze the difference of FAM pathway between paired tumor and adjacent normal tissue samples in 58 HBV-associated HCC patients from the Gene Expression Omnibus (GEO) database. Next, 117 HBV-associated HCC patients from The Cancer Genome Atlas (TCGA) database were analyzed to establish a prognostic signature based on 42 FAM genes. Then, the prognostic signature was validated in an external cohort consisting of 30 HBV-associated HCC patients. Finally, immune infiltration analysis was performed to evaluate the FAM-related immune cells in HBV-associated HCC. RESULTS As a result, FAM pathway was clearly downregulated in tumor tissue of HBV-associated HCC, and survival analysis demonstrated that 12 FAM genes were associated with the prognosis of HBV-associated HCC. Lasso-penalized Cox regression analysis identified and established a five-gene signature (ACADVL, ACAT1, ACSL3, ADH4 and ECI1), which showed effective discrimination and prediction for the prognosis of HBV-associated HCC both in the TCGA cohort and the validation cohort. Immune infiltration analysis showed that the high-risk group, identified by FAM signature, of HBV-associated HCC had a higher ratio of Tregs, which was associated with the prognosis. CONCLUSIONS Collectively, these findings suggest that there is a strong connection between FAM and HBV-associated HCC, indicating a potential therapeutic strategy targeting FAM to block the accumulation of Tregs into the tumor microenvironment of HBV-associated HCC.
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Affiliation(s)
- Ping Yan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Yunhai Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Zuotian Huang
- Department of Hepatobiliary Pancreatic Tumor Center, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Tong Mou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Hang Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Dadi Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, China
| | - Zhongjun Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, China.
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11
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Gao N, Guan G, Xu G, Wu H, Xie C, Mo Z, Deng H, Xiao S, Deng Z, Peng L, Lu F, Zhao Q, Gao Z. Integrated HBV DNA and cccDNA maintain transcriptional activity in intrahepatic HBsAg-positive patients with functional cure following PEG-IFN-based therapy. Aliment Pharmacol Ther 2023; 58:1086-1098. [PMID: 37644711 DOI: 10.1111/apt.17670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/04/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Hepatitis B surface antigen (HBsAg) seroclearance marks regression of hepatitis B virus (HBV) infection. However, more than one-fifth of patients with functional cure following pegylated interferon-based therapy may experience HBsAg seroreversion. The mechanisms causing the HBV relapse remain unclear. AIM To investigate the level and origin of HBV transcripts in patients with functional cure and their role in predicting relapse. METHODS Liver tissue obtained from patients with functional cure, as well as uncured and treatment-naïve HBeAg-negative patients with chronic hepatitis B (CHB) were analysed for intrahepatic HBV markers. HBV capture and RNA sequencing were used to detect HBV integration and chimeric transcripts. RESULTS Covalently closed circular DNA (cccDNA) levels and the proportion of HBsAg-positive hepatocytes in functionally cured patients were significantly lower than those in uncured and treatment-naïve HBeAg-negative patients. Integrated HBV DNA and chimeric transcripts declined in functionally cured patients compared to uncured patients. HBsAg-positive hepatocytes present in 25.5% of functionally cured patients, while intrahepatic HBV RNA remained in 72.2%. The levels of intrahepatic HBV RNA, integrated HBV DNA, and chimeric transcripts were higher in functionally cured patients with intrahepatic HBsAg than in those without. The residual intrahepatic HBsAg in functionally cured patients was mainly derived from transcriptionally active integrated HBV DNA; meanwhile, trace transcriptional activity of cccDNA could also remain. Two out of four functionally cured patients with intrahepatic HBsAg and trace active cccDNA experienced HBV relapse. CONCLUSION Integrated HBV DNA and cccDNA maintain transcriptional activity and maybe involved in HBsAg seroreversion in intrahepatic HBsAg-positive patients with functional cure and linked to virological relapse.
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Affiliation(s)
- Na Gao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Guiwen Guan
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Ganlin Xu
- South China Institute of Biomedicine, Guangzhou, Guangdong, China
| | - Haishi Wu
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Chan Xie
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhishuo Mo
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hong Deng
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shuying Xiao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | | | - Liang Peng
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Fengmin Lu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qiyi Zhao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Zhiliang Gao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, Guangdong, China
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12
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Huang X, Lian YE, Qiu L, Yu X, Zhan Z, Zhang Z, Zhang X, Lin H, Xu S, Chen J, Bai Y, Li L. Detection of fibrotic changes in the progression of liver diseases by label-free multiphoton imaging. JOURNAL OF BIOPHOTONICS 2023; 16:e202300153. [PMID: 37403400 DOI: 10.1002/jbio.202300153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/02/2023] [Accepted: 06/28/2023] [Indexed: 07/06/2023]
Abstract
Collagen fibers play an important role in the progression of liver diseases. The formation and progression of liver fibrosis is a dynamic pathological process accompanied by morphological changes in collagen fibers. In this study, we used multiphoton microscopy for label-free imaging of liver tissues, allowing direct detection of various components including collagen fibers, tumors, blood vessels, and lymphocytes. Then, we developed a deep learning classification model to automatically identify tumor regions, and the accuracy reaches 0.998. We introduced an automated image processing method to extract eight collagen morphological features from various stages of liver diseases. Statistical analysis showed significant differences between them, indicating the potential use of these quantitative features for monitoring fibrotic changes during the progression of liver diseases. Therefore, multiphoton imaging combined with automatic image processing method would hold a promising future in rapid and label-free diagnosis of liver diseases.
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Affiliation(s)
- Xingxin Huang
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Yuan-E Lian
- Department of Pathology, The Affiliated Union Hospital of Fujian Medical University, Fuzhou, China
| | - Lida Qiu
- College of Physics and Electronic Information Engineering, Minjiang University, Fuzhou, China
| | - XunBin Yu
- Department of Pathology, Fujian Provincial Hospital, Fuzhou, China
| | - Zhenlin Zhan
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Zheng Zhang
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Xiong Zhang
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Hongxin Lin
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Shuoyu Xu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jianxin Chen
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Yannan Bai
- Shengli Clinical Medical College of Fujian Medical University, Department of Hepatobiliary and Pancreatic Surgery, Fujian Provincial Hospital, Fuzhou, China
| | - Lianhuang Li
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou, China
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13
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Kojima R, Nakamoto S, Kogure T, Ma Y, Ogawa K, Iwanaga T, Qiang N, Ao J, Nakagawa R, Muroyama R, Nakamura M, Chiba T, Kato J, Kato N. Re-analysis of hepatitis B virus integration sites reveals potential new loci associated with oncogenesis in hepatocellular carcinoma. World J Virol 2023; 12:209-220. [PMID: 37396703 PMCID: PMC10311580 DOI: 10.5501/wjv.v12.i3.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/12/2023] [Accepted: 04/12/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC). HBV DNA can get integrated into the hepatocyte genome to promote carcinogenesis. However, the precise mechanism by which the integrated HBV genome promotes HCC has not been elucidated. AIM To analyze the features of HBV integration in HCC using a new reference database and integration detection method. METHODS Published data, consisting of 426 Liver tumor samples and 426 paired adjacent non-tumor samples, were re-analyzed to identify the integration sites. Genome Reference Consortium Human Build 38 (GRCh38) and Telomere-to-Telomere Consortium CHM13 (T2T-CHM13 (v2.0)) were used as the human reference genomes. In contrast, human genome 19 (hg19) was used in the original study. In addition, GRIDSS VIRUSBreakend was used to detect HBV integration sites, whereas high-throughput viral integration detection (HIVID) was applied in the original study (HIVID-hg19). RESULTS A total of 5361 integration sites were detected using T2T-CHM13. In the tumor samples, integration hotspots in the cancer driver genes, such as TERT and KMT2B, were consistent with those in the original study. GRIDSS VIRUSBreakend detected integrations in more samples than by HIVID-hg19. Enrichment of integration was observed at chromosome 11q13.3, including the CCND1 pro-moter, in tumor samples. Recurrent integration sites were observed in mitochondrial genes. CONCLUSION GRIDSS VIRUSBreakend using T2T-CHM13 is accurate and sensitive in detecting HBV integration. Re-analysis provides new insights into the regions of HBV integration and their potential roles in HCC development.
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Affiliation(s)
- Ryuta Kojima
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Shingo Nakamoto
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Tadayoshi Kogure
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Yaojia Ma
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Keita Ogawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Terunao Iwanaga
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Na Qiang
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Junjie Ao
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Ryo Nakagawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Ryosuke Muroyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Masato Nakamura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Jun Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
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14
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Li Z, Zhang H, Li Q, Feng W, Jia X, Zhou R, Huang Y, Li Y, Hu Z, Hu X, Zhu X, Huang S. GepLiver: an integrative liver expression atlas spanning developmental stages and liver disease phases. Sci Data 2023; 10:376. [PMID: 37301898 PMCID: PMC10257690 DOI: 10.1038/s41597-023-02257-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Chronic liver diseases usually developed through stepwise pathological transitions under the persistent risk factors. The molecular changes during liver transitions are pivotal to improve liver diagnostics and therapeutics yet still remain elusive. Cumulative large-scale liver transcriptomic studies have been revealing molecular landscape of various liver conditions at bulk and single-cell resolution, however, neither single experiment nor databases enabled thorough investigations of transcriptomic dynamics along the progression of liver diseases. Here we establish GepLiver, a longitudinal and multidimensional liver expression atlas integrating expression profiles of 2469 human bulk tissues, 492 mouse samples, 409,775 single cells from 347 human samples and 27 liver cell lines spanning 16 liver phenotypes with uniformed processing and annotating methods. Using GepLiver, we have demonstrated dynamic changes of gene expression, cell abundance and crosstalk harboring meaningful biological associations. GepLiver can be applied to explore the evolving expression patterns and transcriptomic features for genes and cell types respectively among liver phenotypes, assisting the investigation of liver transcriptomic dynamics and informing biomarkers and targets for liver diseases.
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Affiliation(s)
- Ziteng Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hena Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Qin Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Wanjing Feng
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiya Jia
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Runye Zhou
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan Li
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xiaodong Zhu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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15
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Carlessi R, Denisenko E, Boslem E, Köhn-Gaone J, Main N, Abu Bakar NDB, Shirolkar GD, Jones M, Beasley AB, Poppe D, Dwyer BJ, Jackaman C, Tjiam MC, Lister R, Karin M, Fallowfield JA, Kendall TJ, Forbes SJ, Gray ES, Olynyk JK, Yeoh G, Forrest AR, Ramm GA, Febbraio MA, Tirnitz-Parker JE. Single-nucleus RNA sequencing of pre-malignant liver reveals disease-associated hepatocyte state with HCC prognostic potential. CELL GENOMICS 2023; 3:100301. [PMID: 37228755 PMCID: PMC10203275 DOI: 10.1016/j.xgen.2023.100301] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/27/2023] [Accepted: 03/17/2023] [Indexed: 05/27/2023]
Abstract
Current approaches to staging chronic liver diseases have limited utility for predicting liver cancer risk. Here, we employed single-nucleus RNA sequencing (snRNA-seq) to characterize the cellular microenvironment of healthy and pre-malignant livers using two distinct mouse models. Downstream analyses unraveled a previously uncharacterized disease-associated hepatocyte (daHep) transcriptional state. These cells were absent in healthy livers but increasingly prevalent as chronic liver disease progressed. Copy number variation (CNV) analysis of microdissected tissue demonstrated that daHep-enriched regions are riddled with structural variants, suggesting these cells represent a pre-malignant intermediary. Integrated analysis of three recent human snRNA-seq datasets confirmed the presence of a similar phenotype in human chronic liver disease and further supported its enhanced mutational burden. Importantly, we show that high daHep levels precede carcinogenesis and predict a higher risk of hepatocellular carcinoma development. These findings may change the way chronic liver disease patients are staged, surveilled, and risk stratified.
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Affiliation(s)
- Rodrigo Carlessi
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Ebru Boslem
- Cellular & Molecular Metabolism Laboratory, Monash Institute of Pharmacological Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Julia Köhn-Gaone
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Nathan Main
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - N. Dianah B. Abu Bakar
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Gayatri D. Shirolkar
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Matthew Jones
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Aaron B. Beasley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Benjamin J. Dwyer
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Connie Jackaman
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - M. Christian Tjiam
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, WA, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Michael Karin
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan A. Fallowfield
- University of Edinburgh Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Timothy J. Kendall
- University of Edinburgh Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
- Edinburgh Pathology, University of Edinburgh, Edinburgh, UK
| | - Stuart J. Forbes
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Elin S. Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia
| | - John K. Olynyk
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia
| | - George Yeoh
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Alistair R.R. Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Grant A. Ramm
- Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Mark A. Febbraio
- Cellular & Molecular Metabolism Laboratory, Monash Institute of Pharmacological Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Janina E.E. Tirnitz-Parker
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
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Teng S, Zheng N, Al-Huqail AA, Lu Y, Ali E, Ali HE, Zhao H. Effect of nanoparticle macroalgae in the treatment of fatty liver disease using logistic regression, and support vector machine. ENVIRONMENTAL RESEARCH 2023; 224:115426. [PMID: 36781010 DOI: 10.1016/j.envres.2023.115426] [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: 12/23/2022] [Revised: 01/26/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
One of the major health issues facing people worldwide is liver fibrosis. Liver fibrosis may be brought on by long-term exposure to harmful substances, medicines, and microorganisms. The development of liver fibrosis in children was particularly worrying due to their longer life-span, which was possibly related to a great risk of developing long-term complications. Marine algae species have provided a biological variety in the research phase of novel approaches to the treatment of numerous ailments. Marine macroalgae have recently been the subject of research due to their rich bioactive chemical composition and potential for the production of various nutraceuticals. Macroalgae are potentially excellent sources of bioactive substances with particular and distinct biological activity when compared to their terrestrial equivalents. Macroalgae in diverse marine cases offer a few biologically active metabolites, comprising sterols, polyunsaturated fatty acids, carotenoids, oligosaccharides, polysaccharides, proteins, polyphenols, vitamins, and minerals. Accordingly, there is great interest in their high potential for supporting immunomodulatory, antimicrobial, antidiabetic, antitumoral, anti-inflammatory, antiangiogenic, and neuroprotective properties. Using an experimental model, the current research intends to collect data on the therapeutic value of macroalgae nanoparticles for fatty liver disease. The researchers' goal of predicting illnesses from the extensive medical datasets is quite difficult. The purpose of this research is to assess the protective effects of a seaweed, Padina pavonia (PP), on liver fibrosis caused by carbon tetrachloride (CCl4). This research presents two models of logistic regression (LR) and support vector machines (SVM) for predicting the likelihood of liver disease incidence. The performance of the model was evaluated using a dataset. PP macro-algae considerably reduce the high blood concentrations of aminotransferases, alkaline phosphatases, and lactate dehydrogenases, as well as causing a considerable (p < 0.05) decrease in serum bilirubin levels. In addition to improving kidney function (urea and creatinine), algal extracts enhance fat metabolism (triglycerides and cholesterol). With an accuracy rate of 70.2%, a sensitivity of 92.3%, a specificity of 74.7%, a type I error of 9.1%, and a type II error of 21.0%, the predictive model has demonstrated excellent performance. The model validated laboratory tests' ability to predict illness (age; direct bilirubin (DB), total proteins (TP), and albumin (ALB). These classifier methods are compared on the basis of their execution time and classification accuracy.
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Affiliation(s)
- Shu Teng
- Department of Pediatric Infection, Hangzhou Children's Hospital, Hangzhou, 310014, China
| | - Nan Zheng
- Zhejiang University of Traditional Chinese Medicine, Hangzhou, 310000, China
| | - Arwa A Al-Huqail
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, Riyadh, 11671, Saudi Arabia.
| | - Yanjie Lu
- Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Elimam Ali
- Department of Civil Engineering, College of Engineering in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - H Elhosiny Ali
- Department of Physics, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, Saudi Arabia; Physics Department, Faculty of Science, Zagazig University, 44519, Zagazig, Egypt; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, 61413, P.O. Box 9004, Saudi Arabia
| | - Huajun Zhao
- University of Traditional Chinese Medicine, Hangzhou, 310000, China.
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Asadpour-Behzadi A, Kariminik A, Kheirkhah B. MicroRNA-155 and 194 alter expression of Th17 and T regulatory-related transcription factors in the patients with severe coronavirus disease 2019 (COVID-19). Immunobiology 2023; 228:152343. [PMID: 36750001 PMCID: PMC9883212 DOI: 10.1016/j.imbio.2023.152343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023]
Abstract
INTRODUCTION It has been demonstrated that the patients with severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) suffer from severe inflammation. Due to the ethnics, the immune responses may be different. Additionally, microRNAs may alter immune responses in the patients. The current study was aimed to evaluate the expression of T helper subsets-related transcription factors, some T helper 17 (Th17) products, and two microRNAs, including miR-155 and miR-194, in the Iranian hospitalized patients. METHODS In this study, T-box expressed in T cells (T-bet), GATA binding protein 3, The retinoid orphan receptor gamma t (RORγt), forkhead box P3 (FOXP3), interleukin (IL)-17A, IL-8, and CC ligand 20 (CCL20) mRNA levels and, miR-155 and miR-194 levels were evaluated in 70 patients suffered from severe coronavirus disease 2019 (COVID-19) and 70 healthy subjects using Real-Time qPCR technique. RESULTS The findings showed that RORγt, and FOXP3 mRNA levels were significantly increased, while IL-17A, IL-8, and CCL20 mRNA levels were significantly decreased in the hospitalized SARS-CoV-2 infected patients. Although the levels of miR-155 and miR-194 were not different between groups, miR-194 has negative and positive correlations with RORγt and IL-17A in the Iranian healthy controls. CONCLUSION This study reports although RORγt was up-regulated, IL-17A, IL-8, and CCL20 mRNA levels were significantly decreased in the hospitalized SARS-CoV-2 infected patients. It may be concluded that up-regulation of FOXP3, via development of T regulatory lymphocytes suppresses Th17 functions and neutralizes Th17 activities. MiR-194 may play crucial roles in regulation of RORγt and IL-17A expression in healthy people, the phenomenon that is disrupted in the severe SARS-CoV-2 infected patients.
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Affiliation(s)
| | - Ashraf Kariminik
- Department of Microbiology, Kerman Branch, Islamic Azad University, Kerman, Iran.
| | - Babak Kheirkhah
- Department of Veterinary Medicine, Baft Branch, Islamic Azad University, Baft, Iran
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Chiang CC, Yeh H, Lim SN, Lin WR. Transcriptome analysis creates a new era of precision medicine for managing recurrent hepatocellular carcinoma. World J Gastroenterol 2023; 29:780-799. [PMID: 36816628 PMCID: PMC9932421 DOI: 10.3748/wjg.v29.i5.780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/23/2022] [Accepted: 01/10/2023] [Indexed: 02/06/2023] Open
Abstract
The high incidence of hepatocellular carcinoma (HCC) recurrence negatively impacts outcomes of patients treated with curative intent despite advances in surgical techniques and other locoregional liver-targeting therapies. Over the past few decades, the emergence of transcriptome analysis tools, including real-time quantitative reverse transcription PCR, microarrays, and RNA sequencing, has not only largely contributed to our knowledge about the pathogenesis of recurrent HCC but also led to the development of outcome prediction models based on differentially expressed gene signatures. In recent years, the single-cell RNA sequencing technique has revolutionized our ability to study the complicated crosstalk between cancer cells and the immune environment, which may benefit further investigations on the role of different immune cells in HCC recurrence and the identification of potential therapeutic targets. In the present article, we summarized the major findings yielded with these transcriptome methods within the framework of a causal model consisting of three domains: primary cancer cells; carcinogenic stimuli; and tumor microenvironment. We provided a comprehensive review of the insights that transcriptome analyses have provided into diagnostics, surveillance, and treatment of HCC recurrence.
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Affiliation(s)
- Chun-Cheng Chiang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
| | - Hsuan Yeh
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Siew-Na Lim
- Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Wey-Ran Lin
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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19
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Nahavandi-Parizi P, Kariminik A, Montazeri M. Retinoic acid-inducible gene 1 (RIG-1) and IFN-β promoter stimulator-1 (IPS-1) significantly down-regulated in the severe coronavirus disease 2019 (COVID-19). Mol Biol Rep 2023; 50:907-911. [PMID: 36309611 PMCID: PMC9617601 DOI: 10.1007/s11033-022-07981-2] [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: 06/24/2022] [Accepted: 09/22/2022] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Retinoic acid-inducible gene 1 (RIG-1) and melanoma differentiation-associated protein 5 (MDA5) are the well-known cytoplasmic sensors that recognize microbial DNA or RNA and active down-stream molecules, including IFN-β promoter stimulator-1 (IPS-1) and receptor interacting protein 1 (RIP1). The roles played by the networked molecules on the infection with SARS-CoV-2 needs more investigations. MATERIAL AND METHOD In this project MDA5, RIG-1, IPS-1 and RIP1 mRNA levels were evaluated in 45 hospitalized patients suffering from coronavirus disease of 2019 (COVID-19) and 45 healthy subjects using Real Time-qPCR technique. RESULT The results showed significant decreased RIG-1 and IPS-1 in the SARS-CoV-2 infected patients when compared to healthy cases. MDA5 and RIP1 did not change when compared two groups. Male patients had similar expression of MDA5, RIG-1, IPS-1 and RIP1 when compared to female patients. CONCLUSION Based on the results, it seems that RIG-1 and its signaling molecule, IPS-1, play key roles in the peripheral blood immune cells against SARS-CoV-2 and, their down-regulation may be induced by the virus to escape from immune responses.
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Affiliation(s)
- Peyman Nahavandi-Parizi
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ashraf Kariminik
- Department of Microbiology, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Maryam Montazeri
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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20
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Li G, Wang Z, Chen D, Yin J, Mo Z, Sun B, Yang T, Zhang X, Zhai Z, Li Y, Chen P, Dai Y, Wang Z, Ma J. Comprehensive analysis of a TPX2-related TRHDE-AS1/PKIA ceRNA network involving prognostic signatures in Hepatitis B virus-infected hepatocellular carcinoma. Front Cell Infect Microbiol 2022; 12:1025900. [PMID: 36204642 PMCID: PMC9530265 DOI: 10.3389/fcimb.2022.1025900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a main carcinogenic factor of hepatocellular carcinoma (HCC). TPX2 microtubule nucleation factor is recently recommended as a novel prognostic biomarker in HBV-infected HCC tissues. This study aimed to explore a TPX2-related ceRNA regulatory network in HBV-infected HCC and the potential impact on HCC prognosis. We comprehensively identified 541 differential expressed lncRNAs (DElncRNAs), 37 DEmiRNAs and 439 DEmRNAs from HBV-related TCGA-HCC cohorts in TPX2low and TPX2high groups. Based on their RNA-RNA interaction and expression analysis, four DElncRNAs (TRHDE-AS1, DLX6-AS1, SNHG14, HOXA11-AS), four DEmiRNAs (miR-23b, miR-320a, miR-589, miR-126) and five DEmRNAs (PKIA, PCDHA2, SHCBP1, PRSS16, KIF18A) in HCC tumor vs normal groups were subjected to the hub regulatory networks analysis and further prognostic value analysis. Importantly, the TRHDE-AS1/miR-23b/PKIA ceRNA network was associated with HCC prognosis. Furthermore, cellular location analysis and base-base interaction analysis indicated that the cytoplasmic lncRNA TRHDE-AS1 was regarded as a ceRNA to sponging miR-23b and then regulating PKIA. Interestingly, correlation analysis suggested the expression correlation between TRHDE-AS1 and PKIA in HCC. Finally, we further performed the methylation and immune infiltration analysis to explore the functional process of PKIA in HCC. We proposed a ceRNA regulatory network may help elucidate the mechanism by which TPX2 contributes to the prognosis of HBV-related HCC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jun Ma
- *Correspondence: Jun Ma, ;
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21
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Zhang J, Pan T, Zhou W, Zhang Y, Xu G, Xu Q, Li S, Gao Y, Wang Z, Xu J, Li Y. Long noncoding RNA LINC01132 enhances immunosuppression and therapy resistance via NRF1/DPP4 axis in hepatocellular carcinoma. J Exp Clin Cancer Res 2022; 41:270. [PMID: 36071454 PMCID: PMC9454129 DOI: 10.1186/s13046-022-02478-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and play fundamental roles in various types of cancer. Current developments in transcriptome analyses unveiled the existence of lncRNAs; however, their functional characterization remains a challenge. Methods A bioinformatics screen was performed by integration of multiple omics data in hepatocellular carcinoma (HCC) prioritizing a novel oncogenic lncRNA, LINC01132. Expression of LINC01132 in HCC and control tissues was validated by qRT-PCR. Cell viability and migration activity was examined by MTT and transwell assays. Finally, our results were confirmed in vivo mouse model and ex vivo patient derived tumor xenograft experiments to determine the mechanism of action and explore LINC01132-targeted immunotherapy. Results Systematic investigation of lncRNAs genome-wide expression patterns revealed LINC01132 as an oncogene in HCC. LINC01132 is significantly overexpressed in tumor and associated with poor overall survival of HCC patients, which is mainly driven by copy number amplification. Functionally, LINC01132 overexpression promoted cell growth, proliferation, invasion and metastasis in vitro and in vivo. Mechanistically, LINC01132 acts as an oncogenic driver by physically interacting with NRF and enhancing the expression of DPP4. Notably, LINC01132 silencing triggers CD8+ T cells infiltration, and LINC01132 knockdown combined with anti-PDL1 treatment improves antitumor immunity, which may prove a new combination therapy in HCC. Conclusions LINC01132 functions as an oncogenic driver that induces HCC development via the NRF1/DPP4 axis. Silencing LINC01132 may enhance the efficacy of anti-PDL1 immunotherapy in HCC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02478-z.
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22
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Cao LL, Peng M, Xie X, Chen GQ, Huang SY, Wang JY, Jiang F, Cui XW, Dietrich CF. Artificial intelligence in liver ultrasound. World J Gastroenterol 2022; 28:3398-3409. [PMID: 36158262 PMCID: PMC9346461 DOI: 10.3748/wjg.v28.i27.3398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/18/2022] [Accepted: 06/20/2022] [Indexed: 02/06/2023] Open
Abstract
Artificial intelligence (AI) is playing an increasingly important role in medicine, especially in the field of medical imaging. It can be used to diagnose diseases and predict certain statuses and possible events that may happen. Recently, more and more studies have confirmed the value of AI based on ultrasound in the evaluation of diffuse liver diseases and focal liver lesions. It can assess the severity of liver fibrosis and nonalcoholic fatty liver, differentially diagnose benign and malignant liver lesions, distinguish primary from secondary liver cancers, predict the curative effect of liver cancer treatment and recurrence after treatment, and predict microvascular invasion in hepatocellular carcinoma. The findings from these studies have great clinical application potential in the near future. The purpose of this review is to comprehensively introduce the current status and future perspectives of AI in liver ultrasound.
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Affiliation(s)
- Liu-Liu Cao
- Department of Medical Ultrasound, The Second Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Mei Peng
- Department of Medical Ultrasound, The Second Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Xiang Xie
- Department of Medical Ultrasound, The Second Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Gong-Quan Chen
- Department of Medical Ultrasound, Minda Hospital of Hubei Minzu University, Enshi 445000, Hubei Province, China
| | - Shu-Yan Huang
- Department of Medical Ultrasound, The First People's Hospital of Huaihua, Huaihua 418000, Hunan Province, China
| | - Jia-Yu Wang
- Department of Medical Ultrasound, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Fan Jiang
- Department of Medical Ultrasound, The Second Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Xin-Wu Cui
- Department of Medical Ultrasound, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Christoph F Dietrich
- Department Allgemeine Innere Medizin, Kliniken Hirslanden Beau Site, Salem und Permanence, Bern 3626, Switzerland
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23
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Wang W, Chen Y, Wu L, Zhang Y, Yoo S, Chen Q, Liu S, Hou Y, Chen XP, Chen Q, Zhu J. HBV genome-enriched single cell sequencing revealed heterogeneity in HBV-driven hepatocellular carcinoma (HCC). BMC Med Genomics 2022; 15:134. [PMID: 35710421 PMCID: PMC9205089 DOI: 10.1186/s12920-022-01264-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/05/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) related hepatocellular carcinoma (HCC) is heterogeneous and frequently contains multifocal tumors, but how the multifocal tumors relate to each other in terms of HBV integration and other genomic patterns is not clear. METHODS To interrogate heterogeneity of HBV-HCC, we developed a HBV genome enriched single cell sequencing (HGE-scSeq) procedure and a computational method to identify HBV integration sites and infer DNA copy number variations (CNVs). RESULTS We performed HGE-scSeq on 269 cells from four tumor sites and two tumor thrombi of a HBV-HCC patient. HBV integrations were identified in 142 out of 269 (53%) cells sequenced, and were enriched in two HBV integration hotspots chr1:34,397,059 (CSMD2) and chr8:118,557,327 (MED30/EXT1). There were also 162 rare integration sites. HBV integration sites were enriched in DNA fragile sites and sequences around HBV integration sites were enriched for microhomologous sequences between human and HBV genomes. CNVs were inferred for each individual cell and cells were grouped into four clonal groups based on their CNVs. Cells in different clonal groups had different degrees of HBV integration heterogeneity. All of 269 cells carried chromosome 1q amplification, a recurrent feature of HCC tumors, suggesting that 1q amplification occurred before HBV integration events in this case study. Further, we performed simulation studies to demonstrate that the sequential events (HBV infecting transformed cells) could result in the observed phenotype with biologically reasonable parameters. CONCLUSION Our HGE-scSeq data reveals high heterogeneity of HCC tumor cells in terms of both HBV integrations and CNVs. There were two HBV integration hotspots across cells, and cells from multiple tumor sites shared some HBV integration and CNV patterns.
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Affiliation(s)
- Wenhui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., New York, NY, 10029, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Yan Chen
- The Hepatic Surgery Centre at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | | | - Yi Zhang
- Department of Mathematics, Hebei University of Science and Technology, Shijiazhuang, Hebei, China
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., New York, NY, 10029, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Quan Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., New York, NY, 10029, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | | | | | - Xiao-Ping Chen
- The Hepatic Surgery Centre at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Qian Chen
- The Division of Gastroenterology, Department of Internal Medicine at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan, China.
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., New York, NY, 10029, USA.
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Sema4, Stamford, CT, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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24
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Wu Q, Zheng X, Leung KS, Wong MH, Tsui SKW, Cheng L. meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data. Bioinformatics 2022; 38:3513-3522. [PMID: 35674358 DOI: 10.1093/bioinformatics/btac379] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/08/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hepatocellular carcinoma (HCC) is a primary malignancy with poor prognosis. Recently, multi-omics molecular-level measurement enables HCC diagnosis and prognosis prediction, which is crucial for early intervention of personalized therapy to diminish mortality. Here, we introduce a novel strategy utilizing DNA methylation and RNA expression data to achieve a multi-omics gene pair signature (GPS) for HCC discrimination. RESULTS The immune genes with negative correlations between expression and promoter methylation are enriched in the highly connected cancer-related pathway network, which are considered as the candidates for HCC detection. After that, we separately construct a methylation GPS (mGPS) and an expression GPS (eGPS), and then assemble them as a meGPS with five gene pairs, in which the significant methylation and expression changes occur between HCC tumor and non-tumor groups. Reliable performance has been validated by independent tissue (age, gender, and etiology) and blood datasets. This study proposes a procedure for multi-omics GPS identification and develops a novel HCC signature using both methylome and transcriptome data, suggesting potential molecular targets for the detection and therapy of HCC. AVAILABILITY AND IMPLEMENTATION Models are available at https://github.com/bioinformaticStudy/meGPS.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qiong Wu
- Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, 518020, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Xubin Zheng
- Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, 518020, China.,Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Man-Hon Wong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Lixin Cheng
- Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, 518020, China
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25
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Péneau C, Imbeaud S, La Bella T, Hirsch TZ, Caruso S, Calderaro J, Paradis V, Blanc JF, Letouzé E, Nault JC, Amaddeo G, Zucman-Rossi J. Hepatitis B virus integrations promote local and distant oncogenic driver alterations in hepatocellular carcinoma. Gut 2022; 71:616-626. [PMID: 33563643 PMCID: PMC8862055 DOI: 10.1136/gutjnl-2020-323153] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Infection by HBV is the main risk factor for hepatocellular carcinoma (HCC) worldwide. HBV directly drives carcinogenesis through integrations in the human genome. This study aimed to precisely characterise HBV integrations, in relation with viral and host genomics and clinical features. DESIGN A novel pipeline was set up to perform viral capture on tumours and non-tumour liver tissues from a French cohort of 177 patients mainly of European and African origins. Clonality of each integration event was determined with the localisation, orientation and content of the integrated sequence. In three selected tumours, complex integrations were reconstructed using long-read sequencing or Bionano whole genome mapping. RESULTS Replicating HBV DNA was more frequently detected in non-tumour tissues and associated with a higher number of non-clonal integrations. In HCC, clonal selection of HBV integrations was related to two different mechanisms involved in carcinogenesis. First, integration of viral enhancer nearby a cancer-driver gene may lead to a strong overexpression of oncogenes. Second, we identified frequent chromosome rearrangements at HBV integration sites leading to cancer-driver genes (TERT, TP53, MYC) alterations at distance. Moreover, HBV integrations have direct clinical implications as HCC with a high number of insertions develop in young patients and have a poor prognosis. CONCLUSION Deep characterisation of HBV integrations in liver tissues highlights new HBV-associated driver mechanisms involved in hepatocarcinogenesis. HBV integrations have multiple direct oncogenic consequences that remain an important challenge for the follow-up of HBV-infected patients.
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Affiliation(s)
- Camille Péneau
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Sandrine Imbeaud
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Tiziana La Bella
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Theo Z Hirsch
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Julien Calderaro
- Service d’Anatomopathologie, Hôpital Henri Mondor, APHP, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Valerie Paradis
- Service de Pathologie, Hôpital Beaujon, APHP, Clichy, France,Université Paris Diderot, CNRS, Centre de Recherche 27 sur l'Inflammation (CRI), Paris, France
| | - Jean-Frederic Blanc
- Service Hépato-Gastroentérologie et Oncologie Digestive, Hôpital Haut-Lévêque, CHU de Bordeaux, Bordeaux, France,Service de Pathologie, CHU Bordeaux GH Pellegrin, Bordeaux, France,Université Bordeaux, Inserm, Research in Translational Oncology, BaRITOn, Bordeaux, France
| | - Eric Letouzé
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France,Service d’Hépatologie, Hôpital Avicenne, Hôpitaux Universitaires Paris-Seine-Saint-Denis, APHP, Bobigny, France
| | - Giuliana Amaddeo
- Service d’Hépato-Gastro-Entérologie, Hôpital Henri Mondor, APHP, Université Paris Est Créteil, Inserm U955, Institut Mondor de recherche biomedicale, Creteil, Île-de-France, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université de Paris, Paris, France .,Functional Genomics of Solid Tumors laboratory, équipe labellisée Ligue Nationale contre le Cancer, Labex OncoImmunology, Paris, France.,Hôpital Européen Georges Pompidou, AP-HP, Paris, France
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26
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Bousali M, Karamitros T. Hepatitis B Virus Integration into Transcriptionally Active Loci and HBV-Associated Hepatocellular Carcinoma. Microorganisms 2022; 10:microorganisms10020253. [PMID: 35208708 PMCID: PMC8879149 DOI: 10.3390/microorganisms10020253] [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: 12/31/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B Virus (HBV) DNA integrations into the human genome are considered major causative factors to HBV-associated hepatocellular carcinoma development. In the present study, we investigated whether HBV preferentially integrates parts of its genome in specific genes and evaluated the contribution of the integrations in HCC development per gene. We applied dedicated in-house developed pipelines on all of the available HBV DNA integration data and performed a statistical analysis to identify genes that could be characterized as hotspots of integrations, along with the evaluation of their association with HBV-HCC. Our results suggest that 15 genes are recurrently affected by HBV integrations and they are significantly associated with HBV-HCC. Further studies that focus on HBV integrations disrupting these genes are mandatory in order to understand the role of HBV integrations in clonal advantage gain and oncogenesis promotion, as well as to determine whether inhibition of the HBV-disrupted genes can provide a therapy strategy for HBV-HCC.
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Affiliation(s)
- Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
- Correspondence: ; Tel.: +30-210-6478871
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27
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Yang Y, Ma Y, Yuan M, Peng Y, Fang Z, Wang J. Identifying the biomarkers and pathways associated with hepatocellular carcinoma based on an integrated analysis approach. Liver Int 2021; 41:2485-2498. [PMID: 34033190 DOI: 10.1111/liv.14972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 02/13/2023]
Abstract
BACKGROUND AND AIMS Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. The molecular mechanism underlying HCC is still unclear. In this study, we conducted a comprehensive analysis to explore the genes, pathways and their interactions involved in HCC. METHODS We analysed the gene expression datasets corresponding to 488 samples from 10 studies on HCC and identified the genes differentially expressed in HCC samples. Then, the genes were compared against Phenolyzer and GeneCards to screen those potentially associated with HCC. The features of the selected genes were explored by mapping them onto the human protein-protein interaction network, and a subnetwork related to HCC was constructed. Hub genes in this HCC specific subnetwork were identified, and their relevance with HCC was investigated by survival analysis. RESULTS We identified 444 differentially expressed genes (177 upregulated and 267 downregulated) related to HCC. Functional enrichment analysis revealed that pathways like p53 signalling and chemical carcinogenesis were eriched in HCC genes. In the subnetwork related to HCC, five disease modules were detected. Further analysis identified six hub genes from the HCC specific subnetwork. Survival analysis showed that the expression levels of these genes were negatively correlated with survival rate of HCC patients. CONCLUSIONS Based on a systems biology framework, we identified the genes, pathways, as well as the disease specific network related to HCC. We also found novel biomarkers whose expression patterns were correlated with progression of HCC, and they could be candidates for further investigation.
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Affiliation(s)
- Yichen Yang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China.,Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Yuequn Ma
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Meng Yuan
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Yonglin Peng
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Zhonghai Fang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
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28
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Chen X, Zhang M, Li N, Pu R, Wu T, Ding Y, Cai P, Zhang H, Zhao J, Yin J, Cao G. Nucleotide variants in hepatitis B virus preS region predict the recurrence of hepatocellular carcinoma. Aging (Albany NY) 2021; 13:22256-22275. [PMID: 34534105 PMCID: PMC8507287 DOI: 10.18632/aging.203531] [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: 03/31/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023]
Abstract
Background: Hepatitis B virus (HBV) variants in the preS region have been associated with hepatocellular carcinoma (HCC). However, the effect of the preS variants on HCC prognosis remains largely unknown. We aimed to identify the preS variants that reliably predict postoperative prognosis in HCC. Methods: RNA-seq data of 203 HCC patients retrieved from public database were screened for the preS variants related to HCC prognosis. The variants in the sera and tumors were then validated in our prospective cohort enrolling 103 HBV-associated HCC patients. Results: By analyzing prognosis-related gene sets in the RNA-seq data, 12 HBV preS variants were associated with HCC recurrence. Of those, G40C and C147T in the sera predicted an unfavorable recurrence-free survival in our cohort (hazard ratio [HR]=2.18, 95% confidence interval [CI]=1.37-3.47, p=0.001 for G40C; HR=1.84, 95% CI=1.15-2.92, p=0.012 for C147T). G40C and C147T were significantly associated with microscopic vascular invasion, larger tumor size, and abnormal liver function. Multivariate Cox regression analysis showed that G40C significantly increased the risk of HCC recurrence in patients with postoperative antiviral treatment. The HCC prognosis-prediction model consisting of α-fetoprotein and G40C in the sera achieved the best performance (sensitivity=0.80, specificity=0.70, and area under the curve=0.79). Functional analysis indicated that these two variants were associated with cell proliferation, chromosome instability, carcinogenesis, metastasis, and anticancer drug resistance. Conclusions: G40C and C147T are serological biomarkers for HCC prognosis and the prognostic model consisting of serological α-fetoprotein and G40C achieved the best performance in predicting postoperative prognosis.
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Affiliation(s)
- Xi Chen
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, Shanghai, China
| | - Minfeng Zhang
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Nan Li
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Rui Pu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, Shanghai, China
| | - Ting Wu
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, Shanghai, China
| | - Yibo Ding
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, Shanghai, China
| | - Peng Cai
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, Shanghai, China
| | - Hongwei Zhang
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, Shanghai, China
| | - Jun Zhao
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Faculty of Navy Medicine, Second Military Medical University, Shanghai, China
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29
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Crouchet E, Bandiera S, Fujiwara N, Li S, El Saghire H, Fernández-Vaquero M, Riedl T, Sun X, Hirschfield H, Jühling F, Zhu S, Roehlen N, Ponsolles C, Heydmann L, Saviano A, Qian T, Venkatesh A, Lupberger J, Verrier ER, Sojoodi M, Oudot MA, Duong FHT, Masia R, Wei L, Thumann C, Durand SC, González-Motos V, Heide D, Hetzer J, Nakagawa S, Ono A, Song WM, Higashi T, Sanchez R, Kim RS, Bian CB, Kiani K, Croonenborghs T, Subramanian A, Chung RT, Straub BK, Schuppan D, Ankavay M, Cocquerel L, Schaeffer E, Goossens N, Koh AP, Mahajan M, Nair VD, Gunasekaran G, Schwartz ME, Bardeesy N, Shalek AK, Rozenblatt-Rosen O, Regev A, Felli E, Pessaux P, Tanabe KK, Heikenwälder M, Schuster C, Pochet N, Zeisel MB, Fuchs BC, Hoshida Y, Baumert TF. A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery. Nat Commun 2021; 12:5525. [PMID: 34535664 PMCID: PMC8448834 DOI: 10.1038/s41467-021-25468-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/03/2021] [Indexed: 12/25/2022] Open
Abstract
Chronic liver disease and hepatocellular carcinoma (HCC) are life-threatening diseases with limited treatment options. The lack of clinically relevant/tractable experimental models hampers therapeutic discovery. Here, we develop a simple and robust human liver cell-based system modeling a clinical prognostic liver signature (PLS) predicting long-term liver disease progression toward HCC. Using the PLS as a readout, followed by validation in nonalcoholic steatohepatitis/fibrosis/HCC animal models and patient-derived liver spheroids, we identify nizatidine, a histamine receptor H2 (HRH2) blocker, for treatment of advanced liver disease and HCC chemoprevention. Moreover, perturbation studies combined with single cell RNA-Seq analyses of patient liver tissues uncover hepatocytes and HRH2+, CLEC5Ahigh, MARCOlow liver macrophages as potential nizatidine targets. The PLS model combined with single cell RNA-Seq of patient tissues enables discovery of urgently needed targets and therapeutics for treatment of advanced liver disease and cancer prevention.
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Grants
- K01 CA140861 NCI NIH HHS
- R21 CA209940 NCI NIH HHS
- R01 DK099558 NIDDK NIH HHS
- R03 AI131066 NIAID NIH HHS
- R01 CA233794 NCI NIH HHS
- ERC CoG grant (HepatoMetaboPath) and EOS grant and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – Project-ID 272983813 – TRR 179, and Project-ID 314905040 SFB TR209.
- NIH CA140861
- NIH DK099558 Irma T. Hirschl/Monique Weill-Caulier Trust
- This work was supported by ARC, Paris and Institut Hospitalo-Universitaire, Strasbourg (TheraHCC1.0 and 2.0 IHUARC IHU201301187 and IHUARC2019 to T.F.B.), the European Union (ERC-AdG-2014-671231-HEPCIR to T.F.B. and Y.H., EU H2020-667273-HEPCAR to T.F.B. and M.H., INTERREG-IV-Rhin Supérieur-FEDER-Hepato-Regio-Net 2012 to T.F.B. and M.B.Z), ANRS, Paris (2013/108 and ECTZ103701 to T.F.B), NIH (DK099558 to Y. H. and CA233794 to Y.H. and T. F. B; CA140861 to B.C.F., CA209940, R21CA209940 and R03AI131066 to N.P. and T.F.B.), Cancer Prevention and Research Institute of Texas (RR180016 to Y.H), US Department of Defense (W81XWH-16-1-0363 to T.F.B. and Y.H.), the Irma T. Hirschl/Monique Weill-Caulier Trust (Y.H.) and the Foundation of the University of Strasbourg (HEPKIN to T. F. B. and Y. H.) and the Institut Universitaire de France (IUF; T. F. B.). M.H. is supported by an ERC CoG grant (HepatoMetaboPath) and EOS grant and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) –Project-ID 272983813 – TRR 179, and Project-ID 314905040 SFB TR209. This work has been published under the framework of the LABEX ANR-10-LABX-0028_HEPSYS and Inserm Plan Cancer and benefits from funding from the state managed by the French National Research Agency as part of the Investments for the future program.
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Affiliation(s)
- Emilie Crouchet
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Simonetta Bandiera
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shen Li
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hussein El Saghire
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Mirian Fernández-Vaquero
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Tobias Riedl
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Xiaochen Sun
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hadassa Hirschfield
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Frank Jühling
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Shijia Zhu
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Natascha Roehlen
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Clara Ponsolles
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Laura Heydmann
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Antonio Saviano
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Tongqi Qian
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anu Venkatesh
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joachim Lupberger
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Eloi R Verrier
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Mozhdeh Sojoodi
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marine A Oudot
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - François H T Duong
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Ricard Masia
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Lan Wei
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christine Thumann
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Sarah C Durand
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Victor González-Motos
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Danijela Heide
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Jenny Hetzer
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Shigeki Nakagawa
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Takaaki Higashi
- Department of Gastroenterological Surgery, Kumamoto University, Kumamoto, Japan
| | - Roberto Sanchez
- Department of Pharmacological Sciences and Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Rosa S Kim
- Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - C Billie Bian
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Karun Kiani
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tom Croonenborghs
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- KU Leuven Technology Campus Geel, AdvISe, Geel, Belgium
| | | | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Beate K Straub
- Institute of Pathology, University Medicine, Johannes Gutenberg University, Mainz, Germany
| | - Detlef Schuppan
- Institute for Translational Immunology and Research Center for Immunotherapy (FZI), Johannes Gutenberg University (JGU) Medical Center, Mainz, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Maliki Ankavay
- University of Lille, CNRS, Inserm, CHU Lille, Pasteur Institute of Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Laurence Cocquerel
- University of Lille, CNRS, Inserm, CHU Lille, Pasteur Institute of Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, Lille, France
| | - Evelyne Schaeffer
- CNRS UPR3572 Immunopathologie et Chimie Thérapeutique, Institut de Biologie Moléculaire et Cellulaire (IBMC), Strasbourg, France
| | - Nicolas Goossens
- Division of Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland
| | - Anna P Koh
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Venugopalan D Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ganesh Gunasekaran
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Myron E Schwartz
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center; Harvard Medical School, Cambridge St. CPZN 4216, Boston, MA, USA
| | - Alex K Shalek
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering Science & Department of Chemistry, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Emanuele Felli
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Patrick Pessaux
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Kenneth K Tanabe
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Catherine Schuster
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Nathalie Pochet
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mirjam B Zeisel
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
- Cancer Research Center of Lyon (CRCL), UMR Inserm 1052 CNRS 5286 Mixte CLB, Université de Lyon 1 (UCBL1), Lyon, France
| | - Bryan C Fuchs
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Ferring Pharmaceuticals Inc 4245 Sorrento Valley Blvd, San Diego, CA, USA.
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Thomas F Baumert
- Institut National de la Santé et de la Recherche Médicale (Inserm), U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France.
- Université de Strasbourg, Strasbourg, France.
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France.
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30
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Bousali M, Papatheodoridis G, Paraskevis D, Karamitros T. Hepatitis B Virus DNA Integration, Chronic Infections and Hepatocellular Carcinoma. Microorganisms 2021; 9:1787. [PMID: 34442866 PMCID: PMC8398950 DOI: 10.3390/microorganisms9081787] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/16/2022] Open
Abstract
Hepatitis B Virus (HBV) is an Old World virus with a high mutation rate, which puts its origins in Africa alongside the origins of Homo sapiens, and is a member of the Hepadnaviridae family that is characterized by a unique viral replication cycle. It targets human hepatocytes and can lead to chronic HBV infection either after acute infection via horizontal transmission usually during infancy or childhood or via maternal-fetal transmission. HBV has been found in ~85% of HBV-related Hepatocellular Carcinomas (HCC), and it can integrate the whole or part of its genome into the host genomic DNA. The molecular mechanisms involved in the HBV DNA integration is not yet clear; thus, multiple models have been described with respect to either the relaxed-circular DNA (rcDNA) or the double-stranded linear DNA (dslDNA) of HBV. Various genes have been found to be affected by HBV DNA integration, including cell-proliferation-related genes, oncogenes and long non-coding RNA genes (lincRNAs). The present review summarizes the advances in the research of HBV DNA integration, focusing on the evolutionary and molecular side of the integration events along with the arising clinical aspects in the light of WHO's commitment to eliminate HBV and viral hepatitis by 2030.
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Affiliation(s)
- Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - George Papatheodoridis
- Department of Gastroenterology, “Laiko” General Hospital of Athens, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
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31
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Shaikh SS, Bawazir A, Yahya BA. Phytochemical, Histochemical and in-vitro Antimicrobial Study of Various Solvent Extracts of Costus speciosus (J.Koenig) Sm. and Costus pictus D. Don. Turk J Pharm Sci 2021; 19:116-124. [DOI: 10.4274/tjps.galenos.2021.08683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Lin SY, Zhang A, Lian J, Wang J, Chang TT, Lin YJ, Song W, Su YH. Recurrent HBV Integration Targets as Potential Drivers in Hepatocellular Carcinoma. Cells 2021; 10:cells10061294. [PMID: 34071075 PMCID: PMC8224658 DOI: 10.3390/cells10061294] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/15/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is the major etiology of hepatocellular carcinoma (HCC), frequently with HBV integrating into the host genome. HBV integration, found in 85% of HBV-associated HCC (HBV–HCC) tissue samples, has been suggested to be oncogenic. Here, we investigated the potential of HBV–HCC driver identification via the characterization of recurrently targeted genes (RTGs). A total of 18,596 HBV integration sites from our in-house study and others were analyzed. RTGs were identified by applying three criteria: at least two HCC subjects, reported by at least two studies, and the number of reporting studies. A total of 396 RTGs were identified. Among the 28 most frequent RTGs, defined as affected in at least 10 HCC patients, 23 (82%) were associated with carcinogenesis and 5 (18%) had no known function. Available breakpoint positions from the three most frequent RTGs, TERT, MLL4/KMT2B, and PLEKHG4B, were analyzed. Mutual exclusivity of TERT promoter mutation and HBV integration into TERT was observed. We present an RTG consensus through comprehensive analysis to enable the potential identification and discovery of HCC drivers for drug development and disease management.
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Affiliation(s)
- Selena Y. Lin
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Adam Zhang
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
| | - Jessica Lian
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
| | - Jeremy Wang
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Ting-Tsung Chang
- Department of Internal Medicine, National Cheng Kung University Medical College, Tainan 704, Taiwan;
| | - Yih-Jyh Lin
- Department of Surgery, National Cheng Kung University Medical College, Tainan 704, Taiwan;
| | - Wei Song
- JBS Science, Inc., Doylestown, PA 18902, USA; (S.Y.L.); (J.W.); (W.S.)
| | - Ying-Hsiu Su
- The Baruch S. Blumberg Research Institute, Doylestown, PA 18902, USA; (A.Z.); (J.L.)
- Correspondence: ; Tel.: +215-489-4907
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33
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Péneau C, Zucman-Rossi J, Nault JC. Genomics of Viral Hepatitis-Associated Liver Tumors. J Clin Med 2021; 10:1827. [PMID: 33922394 PMCID: PMC8122827 DOI: 10.3390/jcm10091827] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/15/2021] [Accepted: 04/18/2021] [Indexed: 12/25/2022] Open
Abstract
Virus-related liver carcinogenesis is one of the main contributors of cancer-related death worldwide mainly due to the impact of chronic hepatitis B and C infections. Three mechanisms have been proposed to explain the oncogenic properties of hepatitis B virus (HBV) infection: induction of chronic inflammation and cirrhosis, expression of HBV oncogenic proteins, and insertional mutagenesis into the genome of infected hepatocytes. Hepatitis B insertional mutagenesis modifies the function of cancer driver genes and could promote chromosomal instability. In contrast, hepatitis C virus promotes hepatocellular carcinoma (HCC) occurrence mainly through cirrhosis development whereas the direct oncogenic role of the virus in human remains debated. Finally, adeno associated virus type 2 (AAV2), a defective DNA virus, has been associated with occurrence of HCC harboring insertional mutagenesis of the virus. Since these tumors developed in a non-cirrhotic context and in the absence of a known etiological factor, AAV2 appears to be the direct cause of tumor development in these patients via a mechanism of insertional mutagenesis altering similar oncogenes and tumor suppressor genes targeted by HBV. A better understanding of virus-related oncogenesis will be helpful to develop new preventive strategies and therapies directed against specific alterations observed in virus-related HCC.
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Affiliation(s)
- Camille Péneau
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
- Hôpital Européen Georges Pompidou, APHP, F-75015 Paris, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006 Paris, France; (C.P.); (J.Z.-R.)
- Functional Genomics of Solid Tumors Laboratory, Équipe Labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, F-75006 Paris, France
- Service d’hépatologie, Hôpital Avicenne, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, F-93000 Bobigny, France
- Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris Nord, F-93000 Bobigny, France
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34
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Bubie A, Zoulim F, Testoni B, Miles B, Posner M, Villanueva A, Losic B. Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling. iScience 2021; 24:102368. [PMID: 33889830 PMCID: PMC8050859 DOI: 10.1016/j.isci.2021.102368] [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: 12/03/2020] [Revised: 03/07/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
The role of oncoviral genotype and co-infection driving oncogenesis remains unclear. We have developed a scalable, high throughput tool for sensitive and precise oncoviral genotype deconvolution. Using tumor RNA sequencing data, we applied it to 537 virally infected liver, cervical, and head and neck tumors, providing the first comprehensive integrative landscape of tumor-viral gene expression, viral antigen immunogenicity, patient survival, and mutational profiling organized by tumor oncoviral genotype. We find that HBV and HPV genotype and co-infection serve as significant predictors of patient survival and immune activation. Finally, we demonstrate that HPV genotype is more associated with viral oncogene expression than cancer type, implying that expression may be similar across episomal and stochastic integration-based infections. While oncoviral infections are known risk factors for oncogenesis, viral genotype and co-infection are shown to strongly associate with disease progression, patient survival, mutational signatures, and putative tumor neoantigen immunogenicity, facilitating novel clinical associations with infections. ViralMine parses oncoviral genotypes and co-infection from in situ tumor data Oncoviral genotyping of TCGA CESC, HNSC, and LIHC cohorts Tumor fitness, immunogenicity, and mutational signatures associate with oncoviral genotype
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Affiliation(s)
- Adrian Bubie
- Departments of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Fabien Zoulim
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France
| | - Barbara Testoni
- INSERM, U1052, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France
| | - Brett Miles
- Department of Otolaryngology Head and Neck Surgery, New York, NY 10029, USA
| | - Marshall Posner
- Division of Hematology Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Augusto Villanueva
- Departments of Genetics and Genomic Sciences, New York, NY 10029, USA.,Division of Liver Diseases, Division of Hematology/Oncology, Department of Medicine, Graduate School of Biomedical Sciences, Tisch Cancer Institute, Diabetes, Obesity, and Metabolism Institute, New York, NY 10029, USA
| | - Bojan Losic
- Departments of Genetics and Genomic Sciences, New York, NY 10029, USA.,Division of Liver Diseases, Division of Hematology/Oncology, Department of Medicine, Graduate School of Biomedical Sciences, Tisch Cancer Institute, Diabetes, Obesity, and Metabolism Institute, New York, NY 10029, USA
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35
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Tu T, Zhang H, Urban S. Hepatitis B Virus DNA Integration: In Vitro Models for Investigating Viral Pathogenesis and Persistence. Viruses 2021; 13:v13020180. [PMID: 33530322 PMCID: PMC7911709 DOI: 10.3390/v13020180] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/12/2021] [Accepted: 01/21/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) is a globally-distributed pathogen and is a major cause of liver disease. HBV (or closely-related animal hepadnaviruses) can integrate into the host genome, but (unlike retroviruses) this integrated form is replication-defective. The specific role(s) of the integrated HBV DNA has been a long-standing topic of debate. Novel in vitro models of HBV infection combined with sensitive molecular assays now enable researchers to investigate this under-characterised phenomenon with greater ease and precision. This review covers the contributions these systems have made to understanding how HBV DNA integration induces liver cancer and facilitates viral persistence. We summarise the current findings into a working model of chronic HBV infection and discuss the clinical implications of this hypothetical framework on the upcoming therapeutic strategies used to curb HBV-associated pathogenesis.
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Affiliation(s)
- Thomas Tu
- Storr Liver Centre, Faculty of Medicine and Health, Westmead Clinical School and Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia;
- Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney at Westmead Hospital, Westmead, NSW 2145, Australia
- Correspondence:
| | - Henrik Zhang
- Storr Liver Centre, Faculty of Medicine and Health, Westmead Clinical School and Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia;
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany;
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
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36
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Guan G, Zheng L, Xi J, Yang X, Chen X, Lu F. Cell Cycle Arrest Protein CDKN2C Is Not an HBV Host Factor. Virol Sin 2021; 36:810-813. [PMID: 33400093 DOI: 10.1007/s12250-020-00337-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Affiliation(s)
- Guiwen Guan
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, 100044, China.,Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Liwei Zheng
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jingyuan Xi
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xingwen Yang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xiangmei Chen
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Fengmin Lu
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, 100044, China. .,Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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37
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Lim CS, Sozzi V, Littlejohn M, Yuen LK, Warner N, Betz-Stablein B, Luciani F, Revill PA, Brown CM. Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes. Microb Genom 2021; 7:mgen000492. [PMID: 33439114 PMCID: PMC8115900 DOI: 10.1099/mgen.0.000492] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV) is a major human pathogen that causes liver diseases. The main HBV RNAs are unspliced transcripts that encode the key viral proteins. Recent studies have shown that some of the HBV spliced transcript isoforms are predictive of liver cancer, yet the roles of these spliced transcripts remain elusive. Furthermore, there are nine major HBV genotypes common in different regions of the world, these genotypes may express different spliced transcript isoforms. To systematically study the HBV splice variants, we transfected human hepatoma cells, Huh7, with four HBV genotypes (A2, B2, C2 and D3), followed by deep RNA-sequencing. We found that 13-28 % of HBV RNAs were splice variants, which were reproducibly detected across independent biological replicates. These comprised 6 novel and 10 previously identified splice variants. In particular, a novel, singly spliced transcript was detected in genotypes A2 and D3 at high levels. The biological relevance of these splice variants was supported by their identification in HBV-positive liver biopsy and serum samples, and in HBV-infected primary human hepatocytes. Interestingly the levels of HBV splice variants varied across the genotypes, but the spliced pregenomic RNA SP1 and SP9 were the two most abundant splice variants. Counterintuitively, these singly spliced SP1 and SP9 variants had a suboptimal 5' splice site, supporting the idea that splicing of HBV RNAs is tightly controlled by the viral post-transcriptional regulatory RNA element.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Vitina Sozzi
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lilly K.W. Yuen
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nadia Warner
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Brigid Betz-Stablein
- Systems Medicine, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Present address: Dermatology Research Centre, Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Fabio Luciani
- Systems Medicine, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter A. Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chris M. Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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38
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Identification of Potential Hub Genes Related to Diagnosis and Prognosis of Hepatitis B Virus-Related Hepatocellular Carcinoma via Integrated Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4251761. [PMID: 33376723 PMCID: PMC7744201 DOI: 10.1155/2020/4251761] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a common malignant cancer with poor survival outcomes, and hepatitis B virus (HBV) infection is most likely to contribute to HCC. But the molecular mechanism remains obscure. Our study intended to identify the candidate potential hub genes associated with the carcinogenesis of HBV-related HCC (HBV-HCC), which may be helpful in developing novel tumor biomarkers for potential targeted therapies. Four transcriptome datasets (GSE84402, GSE25097, GSE94660, and GSE121248) were used to screen the 309 overlapping differentially expressed genes (DEGs), including 100 upregulated genes and 209 downregulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were used to explore the biological function of DEGs. A PPI network based on the STRING database was constructed and visualized by the Cytoscape software, consisting of 209 nodes and 1676 edges. Then, we recognized 17 hub genes by CytoHubba plugin, which were further validated on additional three datasets (GSE14520, TCGA-LIHC, and ICGC-LIRI-JP). The diagnostic effectiveness of hub genes was assessed with receiver operating characteristic (ROC) analysis, and all hub genes displayed good performance in discriminating TNM stage I patient samples and normal tissue ones. For prognostic analysis, two prognostic key genes (TOP2A and KIF11) out of the 17 hub genes were screened and used to develop a prognostic signature, which showed good potential for overall survival (OS) stratification of HBV-HCC patients. Gene Set Enrichment Analysis (GSEA) was performed in order to better understand the function of this prognostic gene signature. Finally, the miRNA-mRNA regulatory relationships of all hub genes in human liver were predicted using miRNet. In conclusion, the current study gives further insight on the pathogenesis and carcinogenesis of HBV-HCC, and the identified DEGs provide a promising direction for improving the diagnostic, prognostic, and therapeutic outcomes of HBV-HCC.
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39
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Zeng XC, Zhang L, Liao WJ, Ao L, Lin ZM, Kang W, Chen WN, Lin X. Screening and Identification of Potential Biomarkers in Hepatitis B Virus-Related Hepatocellular Carcinoma by Bioinformatics Analysis. Front Genet 2020; 11:555537. [PMID: 33193629 PMCID: PMC7556301 DOI: 10.3389/fgene.2020.555537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal cancers globally. Hepatitis B virus (HBV) infection might cause chronic hepatitis and cirrhosis, leading to HCC. To screen prognostic genes and therapeutic targets for HCC by bioinformatics analysis and determine the mechanisms underlying HBV-related HCC, three high-throughput RNA-seq based raw datasets, namely GSE25599, GSE77509, and GSE94660, were obtained from the Gene Expression Omnibus database, and one RNA-seq raw dataset was acquired from The Cancer Genome Atlas (TCGA). Overall, 103 genes were up-regulated and 127 were down-regulated. A protein–protein interaction (PPI) network was established using Cytoscape software, and 12 pivotal genes were selected as hub genes. The 230 differentially expressed genes and 12 hub genes were subjected to functional and pathway enrichment analyses, and the results suggested that cell cycle, nuclear division, mitotic nuclear division, oocyte meiosis, retinol metabolism, and p53 signaling-related pathways play important roles in HBV-related HCC progression. Further, among the 12 hub genes, kinesin family member 11 (KIF11), TPX2 microtubule nucleation factor (TPX2), kinesin family member 20A (KIF20A), and cyclin B2 (CCNB2) were identified as independent prognostic genes by survival analysis and univariate and multivariate Cox regression analysis. These four genes showed higher expression levels in HCC than in normal tissue samples, as identified upon analyses with Oncomine. In addition, in comparison with normal tissues, the expression levels of KIF11, TPX2, KIF20A, and CCNB2 were higher in HBV-related HCC than in HCV-related HCC tissues. In conclusion, our results suggest that KIF11, TPX2, KIF20A, and CCNB2 might be involved in the carcinogenesis and development of HBV-related HCC. They can thus be used as independent prognostic genes and novel biomarkers for the diagnosis of HBV-related HCC and development of pertinent therapeutic strategies.
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Affiliation(s)
- Xian-Chang Zeng
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lu Zhang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wen-Jun Liao
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lu Ao
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Ze-Man Lin
- Fujian Key Laboratory of Medical Bioinformatics, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wen Kang
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wan-Nan Chen
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Xu Lin
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
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40
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Ringlander J, Skoglund C, Prakash K, Andersson ME, Larsson SB, Tang KW, Rydell GE, Abrahamsson S, Castedal M, Norder H, Hellstrand K, Lindh M. Deep sequencing of liver explant transcriptomes reveals extensive expression from integrated hepatitis B virus DNA. J Viral Hepat 2020; 27:1162-1170. [PMID: 32592629 DOI: 10.1111/jvh.13356] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 12/20/2022]
Abstract
Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC). Integration of HBV DNA into the human genome may contribute to oncogenesis and to the production of the hepatitis B surface antigen (HBsAg). Whether integrations contribute to HBsAg levels in the blood is poorly known. Here, we characterize the HBV RNA profile of HBV integrations in liver tissue in patients with chronic HBV infection, with or without concurrent hepatitis D infection, by transcriptome deep sequencing. Transcriptomes were determined in liver tissue by deep sequencing providing 200 million reads per sample. Integration points were identified using a bioinformatic pipeline. Explanted liver tissue from five patients with end-stage liver disease caused by HBV or HBV/HDV was studied along with publicly available transcriptomes from 21 patients. Almost all HBV RNA profiles were devoid of reads in the core and the 3' redundancy (nt 1830-1927) regions, and contained a large number of chimeric viral/human reads. Hence, HBV transcripts from integrated HBV DNA rather than from covalently closed circular HBV DNA (cccDNA) predominated in late-stage HBV infection, in particular in cases with hepatitis D virus co-infection. The findings support the suggestion that integrated HBV DNA can be a significant source of HBsAg in humans.
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Affiliation(s)
- Johan Ringlander
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Catarina Skoglund
- The Transplant Institute, Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kasthuri Prakash
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria E Andersson
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Simon B Larsson
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ka-Wei Tang
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gustaf E Rydell
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sanna Abrahamsson
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria Castedal
- The Transplant Institute, Department of Surgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Heléne Norder
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kristoffer Hellstrand
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Liu X, Qin J, Gao T, Li C, He B, Pan B, Xu X, Chen X, Zeng K, Xu M, Zhu C, Pan Y, Sun H, Sun L, Xu T, Wang S. YTHDF1 Facilitates the Progression of Hepatocellular Carcinoma by Promoting FZD5 mRNA Translation in an m6A-Dependent Manner. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:750-765. [PMID: 33230473 PMCID: PMC7595883 DOI: 10.1016/j.omtn.2020.09.036] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/30/2020] [Indexed: 01/27/2023]
Abstract
Hepatocellular carcinoma (HCC), one of the most aggressive malignancies, ranks as the fourth leading cause of cancer-related deaths worldwide. Emerging evidence indicates that RNA N6-methyladenosine (m6A) plays a critical role in tumor progression. However, the biological function of YTHDF1 in HCC remains unclear. Here, we found that YTHDF1 expression was strikingly elevated in HCC tissues and cell lines and significantly associated with prognosis of HCC patients. Moreover, YTHDF1 expression was transcriptionally regulated by USF1 and c-MYC in HCC. Functional studies showed that YTHDF1 can promote HCC cell proliferation and metastasis both in vitro and in vivo. Multi-omics analysis revealed that YTHDF1 can accelerate the translational output of FZD5 mRNA in an m6A-dependent manner and function as an oncogene through the WNT/β-catenin pathway. Taken together, our study revealed an essential role of YTHDF1 in the progression of HCC cells, which indicated that targeting YTHDF1 may be a potential therapeutic strategy in HCC.
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Affiliation(s)
- Xiangxiang Liu
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Jian Qin
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Tianyi Gao
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Chenmeng Li
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Bangshun He
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Bei Pan
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Xueni Xu
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Xiaoxiang Chen
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Kaixuan Zeng
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Mu Xu
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Chengbin Zhu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Yuqin Pan
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Huiling Sun
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Li Sun
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Tao Xu
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
| | - Shukui Wang
- School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
- Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211100, Jiangsu, China
- Corresponding author: Shukui Wang, School of Medicine, Southeast University, Nanjing 210096, Jiangsu, China.
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Yang Y, Deng X, Chen X, Chen S, Song L, Meng M, Han Q, Imani S, Li S, Zhong Z, Li X, Deng Y. Landscape of active enhancers developed de novo in cirrhosis and conserved in hepatocellular carcinoma. Am J Cancer Res 2020; 10:3157-3178. [PMID: 33163263 PMCID: PMC7642653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023] Open
Abstract
Hepatocellular carcinoma (HCC) patients always have a background of cirrhosis. Aberrant epigenetic changes in cirrhosis provide a conductive environment for HCC tumorigenesis. Active enhancers (AEs) are essential for epigenetic regulation and play an important role in cell development and the progression of many diseases. However, the role of AEs in the progression from cirrhosis to HCC remains unclear. We systemically constructed a landscape of AEs that developed de novo in cirrhosis and were conserved in HCC, referred to as CL-HCC AEs. We observed significant upregulation of these CL-HCC AE-associated genes in cirrhosis and HCC, with no other epigenetic changes. Enrichment analysis of these CL-HCC AE-associated genes revealed enrichment in both hepatocyte-intrinsic tumorigenesis and tumor immune response, which might contribute to HCC tumorigenesis. Analysis of the diagnostic ability of these CL-HCC AE-associated genes provided a five-gene (THBS4, OLFML2B, CDKN3, GABRE, and HDAC11) diagnostic biomarker for HCC. Molecular subtype (MS) identification based on the CL-HCC AE-associated genes identified 3 MSs. Samples representing the 3 MSs showed differences in CL-HCC AE-associated gene expression levels, prognosis, copy number variation (CNV)/mutation frequencies, functional pathways, tumor microenvironment (TME) cell subtypes, immunotherapy responses and putative drug responses. We also found that the BET bromodomain inhibitor JQ1 downregulated the expression of CL-HCC AE-associated genes. Collectively, our results suggest that CL-HCC AEs and their associated genes contribute to HCC tumorigenesis and evolution, and could be used to distinguish the different landscapes of HCC and help explore the mechanism, classification, prediction, and precision therapy of HCC.
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Affiliation(s)
- Yao Yang
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University)Chongqing 400038, China
| | - Xiaoyu Deng
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University)Chongqing 400038, China
| | - Xinjian Chen
- Department of Cardiovascularology, Airforce Hospital of Southern Theater CommandGuangzhou, Guangdong 510062, China
| | - Shihan Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Army Medical University (Third Military Medical University)Chongqing 400038, China
| | - Liang Song
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University)Chongqing 400038, China
| | - Meng Meng
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University)Chongqing 400038, China
| | - Qi Han
- The General Hospital of Tibet Military RegionLhasa, Tibet 850000, China
| | - Saber Imani
- Department of Oncology, The Affiliated Hospital of Southwest Medical UniversityLuzhou, Sichuan 646000, China
| | - Shuhui Li
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University (Third Military Medical University)Chongqing 400038, China
| | - Zhaoyang Zhong
- Cancer Center, Daping Hospital and Research Institute of Surgery, Army Medical University (Third Military Medical University)Chongqing 400042, China
| | - Xiaohui Li
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University)Chongqing 400038, China
| | - Youcai Deng
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University)Chongqing 400038, China
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Qi J, Zhou J, Tang XQ, Wang Y. Gene Biomarkers Derived from Clinical Data of Hepatocellular Carcinoma. Interdiscip Sci 2020; 12:226-236. [PMID: 32297074 DOI: 10.1007/s12539-020-00366-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/05/2020] [Accepted: 04/02/2020] [Indexed: 12/25/2022]
Abstract
Hepatocellular carcinoma (HCC) is a common cancer of high mortality, mainly due to the difficulty in diagnosis during its clinical stage. Here we aim to find the gene biomarkers, which are of important significance for diagnosis and treatment. In this work, 3682 differentially expressed genes on HCC were firstly differentiated based on the Cancer Genome Atlas database (TCGA). Co-expression modules of these differentially expressed genes were then constructed based on the weighted correlation network algorithm. The correlation coefficient between the co-expression module and clinical data from the Broad GDAC Firehose was thereafter derived. Finally, the interactive network of genes was then constructed. Then, the hub genes were used to implement enrichment analysis and pathway analysis in the Database for Annotation, Visualization and Integrated Discovery (DAVID) database. Results revealed that the abnormally expressed genes in the module played an important role in the biological process including cell division, sister chromatid cohesion, DNA repair, and G1/S transition of mitotic cell cycle. Meanwhile, these genes also enriched in a few crucial pathways related to Cell cycle, Oocyte meiosis, and p53 signaling. Via investigating the closeness centrality of the interactive network, eight gene biomarkers including the CKAP2, TPX2, CDCA8, KIFC1, MELK, SGO1, RACGAP1, and KIAA1524 gene were discovered, whose functions had been indeed revealed to be correlated with HCC. This study, therefore, suggests that the abnormal expression of those eight genes may be taken as gene biomarkers of HCC.
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Affiliation(s)
- Jiaming Qi
- School of Science, Jiangnan University, Wuxi, 214122, China
| | - Jiaxing Zhou
- School of Science, Jiangnan University, Wuxi, 214122, China
| | - Xu-Qing Tang
- School of Science, Jiangnan University, Wuxi, 214122, China. .,Wuxi Engineering Research Center for Biocomputing, Jiangnan University, Wuxi, 214122, China.
| | - Yaolai Wang
- Wuxi Engineering Research Center for Biocomputing, Jiangnan University, Wuxi, 214122, China
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Mining TCGA Database for Tumor Microenvironment-Related Genes of Prognostic Value in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2408348. [PMID: 31828095 PMCID: PMC6885833 DOI: 10.1155/2019/2408348] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/29/2019] [Accepted: 10/09/2019] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common and lethal malignancies. Recent studies reveal that tumor microenvironment (TME) components significantly affect HCC growth and progression, particularly the infiltrating stromal and immune cells. Thus, mining of TME-related biomarkers is crucial to improve the survival of patients with HCC. Public access of The Cancer Genome Atlas (TCGA) database allows convenient performance of gene expression-based analysis of big data, which contributes to the exploration of potential association between genes and prognosis of a variety of malignancies, including HCC. The "Estimation of STromal and Immune cells in MAlignant Tumors using Expression data" algorithm renders the quantification of the stromal and immune components in TME possible by calculating the stromal and immune scores. Differentially expressed genes (DEGs) were screened by dividing the HCC cohort of TCGA database into high- and low-score groups according to stromal and immune scores. Further analyses of functional enrichment and protein-protein interaction networks show that the DEGs are mainly involved in immune response, cell adhesion, and extracellular matrix. Finally, seven DEGs have significant association with HCC poor outcomes. These genes contain FABP3, GALNT5, GPR84, ITGB6, MYEOV, PLEKHS1, and STRA6 and may be candidate biomarkers for HCC prognosis.
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Safari-Arababadi M, Modarressi MH, Arababadi MK. Up-regulation of RIP1 and IPS-1 in chronic HBV infected patients. Genet Mol Biol 2019; 42:337-343. [PMID: 31429854 PMCID: PMC6726166 DOI: 10.1590/1678-4685-gmb-2018-0071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/02/2018] [Indexed: 12/28/2022] Open
Abstract
IPS-1 and RIP1 are the main downstream molecules of RIG1 and MDA5, as
intracytoplasmic receptors, which are the main receptors involved in recognition
of internal and external viral double-stranded RNA. In this project, mRNA levels
of IPS-1 and RIP1 were investigated in the peripheral blood immune cells of
chronic hepatitis B (CHB) patients. IPS-1 and RIP1 mRNA levels were measured in
60 CHB patients and 120 healthy subjects, using RT-qPCR technique. A significant
increase in expression levels of IPS-1 and
RIP1 was found in patients when compared to healthy
individuals. There was no correlation between IPS-1 and RIP1expression levels
with the serum levels of hepatitis B e-Antigen (HBeAg) and liver enzymes in
patients. Based on the results, it seems that IPS-1 and RIP1 can participate in
the induction of low chronic inflammation, which is a main cause of liver
cirrhosis and hepatocellular carcinoma.
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Affiliation(s)
- Minoo Safari-Arababadi
- Department of Genetics, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad Hossein Modarressi
- Department of Genetics, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Kazemi Arababadi
- Immunology of Infectious Diseases Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.,Department of Laboratory Sciences, Faculty of Paramedicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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46
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Xie S, Jiang X, Zhang J, Xie S, Hua Y, Wang R, Yang Y. Identification of significant gene and pathways involved in HBV-related hepatocellular carcinoma by bioinformatics analysis. PeerJ 2019; 7:e7408. [PMID: 31392101 PMCID: PMC6677124 DOI: 10.7717/peerj.7408] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/04/2019] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a common malignant tumor affecting the digestive system and causes serious financial burden worldwide. Hepatitis B virus (HBV) is the main causative agent of HCC in China. The present study aimed to investigate the potential mechanisms underlying HBV-related HCC and to identify core biomarkers by integrated bioinformatics analyses. Methods In the present study, HBV-related HCC GSE19665, GSE55092, GSE94660 and GSE121248 expression profiles were downloaded from the Gene Expression Omnibus database. These databases contain data for 299 samples, including 145 HBV-related HCC tissues and 154 non-cancerous tissues (from patients with chronic hepatitis B). The differentially expressed genes (DEGs) from each dataset were integrated and analyzed using the RobustRankAggreg (RRA) method and R software, and the integrated DEGs were identified. Subsequently, the gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID online tool, and the protein-protein interaction (PPI) network was constructed using STRING and visualized using Cytoscape software. Finally, hub genes were identified, and the cBioPortal online platform was used to analyze the association between the expression of hub genes and prognosis in HCC. Results First, 341 DEGs (117 upregulated and 224 downregulated) were identified from the four datasets. Next, GO analysis showed that the upregulated genes were mainly involved in cell cycle, mitotic spindle, and adenosine triphosphate binding. The majority of the downregulated genes were involved in oxidation reduction, extracellular region, and electron carrier activity. Signaling pathway analysis showed that the integrated DEGs shared common pathways in retinol metabolism, drug metabolism, tryptophan metabolism, caffeine metabolism, and metabolism of xenobiotics by cytochrome P450. The integrated DEG PPI network complex comprised 288 nodes, and two important modules with high degree were detected using the MCODE plug-in. The top ten hub genes identified from the PPI network were SHCBP1, FOXM1, KIF4A, ANLN, KIF15, KIF18A, FANCI, NEK2, ECT2, and RAD51AP1. Finally, survival analysis revealed that patients with HCC showing altered ANLN and KIF18A expression profiles showed worse disease-free survival. Nonetheless, patients with FOXM1, NEK2, RAD51AP1, ANLN, and KIF18A alterations showed worse overall survival. Conclusions The present study identified key genes and pathways involved in HBV-related HCC, which improved our understanding of the mechanisms underlying the development and recurrence of HCC and identified candidate targets for the diagnosis and treatment of HBV-related HCC.
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Affiliation(s)
- Shucai Xie
- Department of Hepatobiliary Surgery, Haikou People's Hospital/Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, China
| | - Xili Jiang
- Department of Radiology, The Second People's Hospital of Hunan Province/Brain Hospital of Hunan Province, Changsha, China
| | - Jianquan Zhang
- Department of Hepatobiliary Surgery, Haikou People's Hospital/Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, China
| | - Shaowei Xie
- Department of Hepatobiliary Surgery, Haikou People's Hospital/Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, China
| | - Yongyong Hua
- Department of Hepatobiliary Surgery, Haikou People's Hospital/Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, China
| | - Rui Wang
- Department of Hepatobiliary Surgery, Haikou People's Hospital/Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, China
| | - Yijun Yang
- Department of Hepatobiliary Surgery, Haikou People's Hospital/Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, China
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47
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Zhang F, Ding L, Cui L, Barber R, Deng B. Identification of long non-coding RNA-related and -coexpressed mRNA biomarkers for hepatocellular carcinoma. BMC Med Genomics 2019; 12:25. [PMID: 30704465 PMCID: PMC6357343 DOI: 10.1186/s12920-019-0472-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND While changes in mRNA expression during tumorigenesis have been used widely as molecular biomarkers for the diagnosis of a number of cancers, the approach has limitations. For example, traditional methods do not consider the regulatory and positional relationship between mRNA and lncRNA. The latter has been largely shown to possess tumor suppressive or oncogenic properties. The combined analysis of mRNA and lncRNA is likely to facilitate the identification of biomarkers with higher confidence. RESULTS Therefore, we have developed an lncRNA-related method to identify traditional mRNA biomarkers. First we identified mRNAs that are differentially expressed in Hepatocellular Carcinoma (HCC) by comparing cancer and matched adjacent non-tumorous liver tissues. Then, we performed mRNA-lncRNA relationship and coexpression analysis and obtained 41 lncRNA-related and -coexpressed mRNA biomarkers. Next, we performed network analysis, gene ontology analysis and pathway analysis to unravel the functional roles and molecular mechanisms of these lncRNA-related and -coexpressed mRNA biomarkers. Finally, we validated the prediction and performance of the 41 lncRNA-related and -coexpressed mRNA biomarkers using Support Vector Machine model with five-fold cross-validation in an independent HCC dataset from RNA-seq. CONCLUSIONS Our results suggested that mRNAs expression profiles coexpressed with positionally related lncRNAs can provide important insights into early diagnosis and specific targeted gene therapy of HCC.
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Affiliation(s)
- Fan Zhang
- Vermont Genetics Network, University of Vermont, Burlington, VT 05405 USA
- Department of Biology, University of Vermont, Burlington, VT 05405 USA
| | - Linda Ding
- School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0606 USA
| | - Li Cui
- Department of Neurosciences, School of Medicine, University of California, San Diego, 9500 Gilman Drive #0949, La Jolla, CA 92093 USA
| | - Robert Barber
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX USA
| | - Bin Deng
- Vermont Genetics Network, University of Vermont, Burlington, VT 05405 USA
- Department of Biology, University of Vermont, Burlington, VT 05405 USA
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48
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Li H, Zhao X, Li C, Sheng C, Bai Z. Integrated analysis of lncRNA-associated ceRNA network reveals potential biomarkers for the prognosis of hepatitis B virus-related hepatocellular carcinoma. Cancer Manag Res 2019; 11:877-897. [PMID: 30697079 PMCID: PMC6340501 DOI: 10.2147/cmar.s186561] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background There is evidence that abnormal expression of lncRNAs is associated with hepatitis B virus (HBV) infection-induced hepatocellular carcinoma (HCC). However, the mechanisms remain not fully elucidated. The study aimed to identify novel lncRNAs and explore their underlying mechanisms based on the ceRNA hypothesis. Methods The RNA and miRNA expression profiling in 20 tumor and matched adjacent tissues from HBV–HCC patients were retrieved from the Gene Expression Omnibus database under accession numbers GSE77509 and GSE76903, respectively. Differentially expressed lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs) were identified using the EdgeR package. Protein–protein interaction (PPI) network was constructed for DEGs followed by module analysis. The ceRNA network was constructed based on interaction relationships between miRNAs and mRNAs/lncRNAs. The functions of DEGs were predicted using DAVID and BinGO databases. The prognosis values (overall survival [OS] and recurrence-free survival [RFS]) of ceRNA network genes were determined using The Cancer Genome Atlas (TCGA) data with Cox regression analysis and Kaplan–Meier method. Results The present study screened 643 DELs, 83 DEMs, and 1,187 DEGs. PPI network analysis demonstrated that CDK1 and CCNE1 were hub genes and extracted in functionally related modules. E2F2, CDK1, and CCNE1 were significantly enriched into cell cycle pathway. FAM182B-miR-125b-5p-E2F2 and LINC00346-miR-10a-5p-CDK1/CCNE1 ceRNA axes were obtained by constructing the ceRNA network. Patients with high expressions of DELs and DEGs in the above ceRNA axes had poor OS, while patients with the high expression of DEMs possessed excellent OS. CDK1 was also an RFS-related biomarker, with its high expression predicting poor RFS. The upregulation of LINC00346 and CDK1 but the downregulation of miR-10a-5p in HCC was validated in other microarray datasets and TCGA database. Conclusion The LINC00346-miR-10a-5p-CDK1 axis may be an important mechanism for HBV-related HCC, and genes in this ceRNA axis may be potential prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Hongyan Li
- Infectious Department, China-Japan Union Hospital, Jilin University, Changchun 130033, China,
| | - Xiaonan Zhao
- Infectious Department, China-Japan Union Hospital, Jilin University, Changchun 130033, China,
| | - Chenghua Li
- Infectious Department, China-Japan Union Hospital, Jilin University, Changchun 130033, China,
| | - Chuanlun Sheng
- Infectious Department, China-Japan Union Hospital, Jilin University, Changchun 130033, China,
| | - Zhenzi Bai
- Infectious Department, China-Japan Union Hospital, Jilin University, Changchun 130033, China,
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49
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Ni JS, Zheng H, Huang ZP, Hong YG, Ou YL, Tao YP, Wang MC, Wang ZG, Yang Y, Zhou WP. MicroRNA-197-3p acts as a prognostic marker and inhibits cell invasion in hepatocellular carcinoma. Oncol Lett 2018; 17:2317-2327. [PMID: 30675297 PMCID: PMC6341871 DOI: 10.3892/ol.2018.9848] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 11/16/2018] [Indexed: 01/27/2023] Open
Abstract
MicroRNAs (miRNAs) serve an important regulatory role in carcinogenesis and cancer progression. Aberrant expression of miR-197-3p has been reported in various human malignancies. However, the role of miR-197-3p in the progression and prognosis of hepatocellular carcinoma (HCC) remains unknown. The present study demonstrated that miR-197-3p was downregulated in HCC tissues and that the low level of miR-197-3p expression in HCC tumours correlated with aggressive clinicopathological characteristics; thus, miR-197-3p may serve as a predictor for poor prognosis in patients with HCC. Additionally, miR-197-3p markedly inhibited the metastasis of HCC cells in vitro and in vivo. Bioinformatics analysis further identified zinc finger protein interacted with K protein 1 (ZIK1) as a novel target of miR-197-3p in HCC cells. These findings suggest that miR-197-3p may regulate the survival of HCC cells, partially through the downregulation of ZIK1. Therefore, the miR-197-3p/ZIK1 axis may serve as a novel therapeutic target in patients with HCC.
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Affiliation(s)
- Jun-Sheng Ni
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Hao Zheng
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Zhi-Ping Huang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China.,Department of Hepatobiliary Surgery, General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, P.R. China
| | - Yong-Gang Hong
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yang-Liu Ou
- Department of Colorectal Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yuan-Ping Tao
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Meng-Chao Wang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Zhen-Guang Wang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Yuan Yang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
| | - Wei-Ping Zhou
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China.,Key Laboratory of Signalling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai 200438, P.R. China.,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai 200438, P.R. China
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Ruan P, Dai X, Sun J, He C, Huang C, Zhou R, Cao Z, Ye L. Different types of viral‑host junction found in HBV integration breakpoints in HBV‑infected patients. Mol Med Rep 2018; 19:1410-1416. [PMID: 30535432 PMCID: PMC6323230 DOI: 10.3892/mmr.2018.9709] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/29/2018] [Indexed: 12/13/2022] Open
Abstract
The present study surveyed the characteristics of hepatitis B virus (HBV) integration in the liver genomes of patients with acute hepatitis B (AHB), carriers of inactive hepatitis B surface antigen (HBsAg), and patients with chronic hepatitis B (CHB) receiving antiviral treatment. 'Short‑read' whole genome sequencing (WGS) with an average of 4,879x coverage for HBV integration was performed in three patients with AHB, two carriers of inactive HBsAg, and 13 patients with CHB receiving antiviral treatment. Conventional polymerase chain reaction and Sanger sequencing were used to verify integration breakpoints supported by at least two paired‑end reads, and viral‑host chimeric transcripts were surveyed simultaneously. HBV integration breakpoints were 100% identified with an average of 138.2±379.9 breakpoints per sample. The numbers of HBV integration breakpoints were positively associated with the sequencing depth coverage numbers and levels of intrahepatic covalently closed circular DNA, respectively (P<0.0001 and P<0.0001). Four types of viral‑host junction in 14 HBV integration breakpoints were detected (two viral junctions mapped in the HBs gene, one in the Precore gene, and others within the HBx gene): Forward simple junction, reverse simple junction, forward and reverse complicated junction, and microhomology were found in many of the junctions. Expression of viral‑human chimeric transcripts was observed in several breakpoints, including the HBs gene. As a result, HBV can integrate into the host gene in the same manner as non‑homologous end joining and microhomology‑mediated end joining with numerous sites, and a close association may exist between HBV integration and patient prognosis. HBx integration may be indispensable for viral‑host chimeric transcription and HBsAg may be produced from integrated DNA.
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Affiliation(s)
- Peng Ruan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xiufang Dai
- Department of Breast Surgery, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Jun Sun
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Chunping He
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Chao Huang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Rui Zhou
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Zhuo Cao
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Lan Ye
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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