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Zhang Y, Mou Y, Chen M, Lin X, Zhao Y, Luo X. Binary split fluorescent biosensor based on lettuce DNA aptamer for label-free and enzyme-free analysis of hepatitis B viral DNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4561-4569. [PMID: 38912590 DOI: 10.1039/d4ay00713a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Hepatitis B virus (HBV) acts as a severe public health threat, causing chronic liver diseases. Although the quantified evaluation of HBV infection can be obtained by estimating the capacity of the HBV DNA genome, it still lacks an effective and robust detection method without using enzymes or chemical labeling. Herein, we have designed a binary split fluorescent DNA aptasensor (bsFDA) by rationally splitting the lettuce aptamer into two functional DNA short chains and utilizing the HBV DNA segment complementary sequences (HDs). In this strategy, the bsFDA has been investigated to specifically recognize the HDs, forming a triplex DNA with the lettuce aptamer structure. Meanwhile, the turn-on fluorescence of bsFDA is obtained upon formation of a fluorescent complex between DFHO and the triplex DNA structure, allowing the enzyme-free, label-free, fast-responsive, and reliable fluorescence readout for detecting HDs and the potential HDs mutants. Moreover, bsFDA has been applied for spiked HDs analysis in different real matrixes, including human serum and cell lysate. The satisfactory recovery rates and reproducibility of the bsFDA reveal its potential detection efficacy for HDs analysis in biological samples. Overall, bsFDA holds great potential in developing functionalized aptasensors and realizing viral genome analysis in biological research.
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Affiliation(s)
- Yanfei Zhang
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Yue Mou
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Meiyun Chen
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Xinru Lin
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
| | - Yujie Zhao
- Medical College, Guangxi University, Nanning 530004, P. R. China.
| | - Xingyu Luo
- Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China.
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Allweiss L, Testoni B, Yu M, Lucifora J, Ko C, Qu B, Lütgehetmann M, Guo H, Urban S, Fletcher SP, Protzer U, Levrero M, Zoulim F, Dandri M. Quantification of the hepatitis B virus cccDNA: evidence-based guidelines for monitoring the key obstacle of HBV cure. Gut 2023; 72:972-983. [PMID: 36707234 PMCID: PMC10086470 DOI: 10.1136/gutjnl-2022-328380] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/15/2023] [Indexed: 01/29/2023]
Abstract
OBJECTIVES A major goal of curative hepatitis B virus (HBV) treatments is the reduction or inactivation of intrahepatic viral covalently closed circular DNA (cccDNA). Hence, precise cccDNA quantification is essential in preclinical and clinical studies. Southern blot (SB) permits cccDNA visualisation but lacks sensitivity and is very laborious. Quantitative PCR (qPCR) has no such limitations but inaccurate quantification due to codetection of viral replicative intermediates (RI) can occur. The use of different samples, preservation conditions, DNA extraction, nuclease digestion methods and qPCR strategies has hindered standardisation. Within the ICE-HBV consortium, available and novel protocols for cccDNA isolation and qPCR quantification in liver tissues and cell cultures were compared in six laboratories to develop evidence-based guidance for best practices. DESIGN Reference material (HBV-infected humanised mouse livers and HepG2-NTCP cells) was exchanged for cross-validation. Each group compared different DNA extraction methods (Hirt extraction, total DNA extraction with or without proteinase K treatment (+PK/-PK)) and nuclease digestion protocols (plasmid-safe ATP-dependent DNase (PSD), T5 exonuclease, exonucleases I/III). Samples were analysed by qPCR and SB. RESULTS Hirt and -PK extraction reduced coexisting RI forms. However, both cccDNA and the protein-free relaxed circular HBV DNA (pf-rcDNA) form were detected by qPCR. T5 and Exo I/III nucleases efficiently removed all RI forms. In contrast, PSD did not digest pf-rcDNA, but was less prone to induce cccDNA overdigestion. In stabilised tissues (eg, Allprotect), nucleases had detrimental effects on cccDNA. CONCLUSIONS We present here a comprehensive evidence-based guidance for optimising, controlling and validating cccDNA measurements using available qPCR assays.
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Affiliation(s)
- Lena Allweiss
- I. Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Munich and Heidelberg sites, Germany
| | - Barbara Testoni
- Cancer Research Center of Lyon, INSERM U1052, Lyon University, Hospices de Lyon, Lyon, France
- ANRS HBV Cure Task Force, Lyon, France
| | - Mei Yu
- Gilead Sciences, Foster City, California, USA
| | - Julie Lucifora
- Cancer Research Center of Lyon, INSERM U1052, Lyon University, Hospices de Lyon, Lyon, France
- ANRS HBV Cure Task Force, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, Lyon, France
| | - Chunkyu Ko
- Institute of Virology, Technical University of Munich, Munchen, Germany
- Infectious Diseases Therapeutic Research Center, Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Korea (the Republic of)
| | - Bingqian Qu
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- Division of Veterinary Medicine, Paul-Ehrlich-Institut, Langen, Germany
| | - Marc Lütgehetmann
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Munich and Heidelberg sites, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf Hamburg, Hamburg, Germany
| | - Haitao Guo
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Microbiology and Molecular Genetics, Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Stephan Urban
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Munich and Heidelberg sites, Germany
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Ulrike Protzer
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Munich and Heidelberg sites, Germany
- Institute of Virology, Technical University of Munich, Munchen, Germany
| | - Massimo Levrero
- Cancer Research Center of Lyon, INSERM U1052, Lyon University, Hospices de Lyon, Lyon, France
- ANRS HBV Cure Task Force, Lyon, France
| | - Fabien Zoulim
- Cancer Research Center of Lyon, INSERM U1052, Lyon University, Hospices de Lyon, Lyon, France
- ANRS HBV Cure Task Force, Lyon, France
| | - Maura Dandri
- I. Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Munich and Heidelberg sites, Germany
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Hsu CW, Chu YD, Lai MW, Lin CL, Liang KH, Lin YH, Yeh CT. Hepatitis B Virus Covalently Closed Circular DNA Predicts Postoperative Liver Cancer Metastasis Independent of Virological Suppression. Cancers (Basel) 2021; 13:cancers13030538. [PMID: 33572617 PMCID: PMC7867012 DOI: 10.3390/cancers13030538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023] Open
Abstract
New antiviral therapies against hepatitis B virus (HBV) focus on the elimination of covalently closed circular DNA (cccDNA). However, traditional cccDNA-specific quantitative PCR (qPCR) has a narrow effective range, hindering a reliable comparison between the levels of biopsy-derived cccDNAs. Collaterally, the prognostic role of cccDNA in HBV-related hepatocellular carcinoma (HCC) cannot be clearly defined. Here, we developed a peptide nucleic acid (PNA)-clamping qPCR method to provide a wider range of specific cccDNA quantification (up to 5 logs of effective range). Extrachromosomal DNA was extracted from para-neoplastic tissues for cccDNA quantification. In total, 350 HBV-related HCC patients were included for an outcome analysis. Without differential pre-dilution, cccDNA levels in para-neoplastic liver tissues were determined, ranging from < 2 × 103 to 123.0 × 106 copies/gram. The multivariate linear regression analysis showed that cccDNA was independently correlated with the HBV e antigen (p < 0.001) and serum HBV-DNA levels (p = 0.012). The Cox proportional hazard model analysis showed that cccDNA independently predicted overall survival (p = 0.003) and extrahepatic metastasis-free survival (p = 0.001). In virologically suppressed HCC patients, cccDNA still effectively predicted intrahepatic recurrence-free (p = 0.003) and extrahepatic metastasis-free (p = 0.009) survivals. In conclusion, cccDNA independently predicted postoperative extrahepatic metastasis-free survival.
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Affiliation(s)
- Chao-Wei Hsu
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (C.-W.H.); (Y.-D.C.); (M.-W.L.); (Y.-H.L.)
- Department of Hepatogastroenterology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Yu-De Chu
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (C.-W.H.); (Y.-D.C.); (M.-W.L.); (Y.-H.L.)
| | - Ming-Wei Lai
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (C.-W.H.); (Y.-D.C.); (M.-W.L.); (Y.-H.L.)
- Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Chih-Lang Lin
- Liver Research Unit, Chang Gung Memorial Hospital, Keelung 204, Taiwan;
| | - Kung-Hao Liang
- Medical Research Department, Taipei Veterans General Hospital, Taipei 112, Taiwan;
| | - Yang-Hsiang Lin
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (C.-W.H.); (Y.-D.C.); (M.-W.L.); (Y.-H.L.)
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (C.-W.H.); (Y.-D.C.); (M.-W.L.); (Y.-H.L.)
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: ; Tel.: +886-3-3281200 (ext. 8129)
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Li FC, Li YK, Fan YC. Biomarkers for hepatitis B virus replication: an overview and a look to the future. Expert Rev Gastroenterol Hepatol 2020; 14:1131-1139. [PMID: 32887529 DOI: 10.1080/17474124.2020.1815530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Hepatitis B virus (HBV) infection is a major public health issue but there are no powerful drugs to eradicate the virus. HBV markers including HBsAg, HBcrAg, HBV RNA, HBcAb, and HBV DNA are becoming promising biomarkers to reflect the natural phases of chronic HBV infection and predict the outcome of anti-HBV treatment. AREAS COVERED The authors summarized the biomarkers of HBV replication and presented the current advances of these biomarkers on predicting the outcome of anti-HBV treatment and identifying the progression of chronic HBV infection. EXPERT OPINION HBsAg, HBcrAg, HBV RNA, HBcAb, and HBV DNA are noninvasive and feasible biomarkers for monitoring the process of anti-HBV therapy and predicting the progress of HBV infection. However, there are still no strong biomarkers with high sensitivity and specificity for clinical application. Combination of two or more HBV biomarkers, new technique for measuring HBV cccDNA, and searching novel HBV biomarkers are essential for anti-HBV treatment in the future.
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Affiliation(s)
- Feng-Cai Li
- Department of Hepatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University , Jinan, China
| | - Yue-Kai Li
- Department of Nuclear Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University , Jinan, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital, Cheeloo College of Medicine, Shandong University , Jinan, China.,Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University , Jinan, China
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Wong DKH, Cheng SCY, Mak LLY, To EWP, Lo RCL, Cheung TT, Seto WK, Fung J, Man K, Lai CL, Yuen MF. Among Patients with Undetectable Hepatitis B Surface Antigen and Hepatocellular Carcinoma, a High Proportion Has Integration of HBV DNA into Hepatocyte DNA and No Cirrhosis. Clin Gastroenterol Hepatol 2020; 18:449-456. [PMID: 31252193 DOI: 10.1016/j.cgh.2019.06.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/03/2019] [Accepted: 06/16/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS In some individuals with undetectable serum levels of hepatitis B surface antigen (HBsAg), hepatitis B virus (HBV) DNA can still be detected in serum or hepatocytes and HBV replicates at low levels-this is called occult HBV infection (OBI). OBI has been associated with increased risk of hepatocellular carcinoma (HCC). We investigated the incidence of OBI in patients with HCC and other liver diseases. We also investigated whether, in patients with OBI and HCC, HBV DNA has integrated into the DNA of hepatocytes. METHODS We collected clinical information and liver tissues from 110 HBsAg-negative patients (90 with HCC and 20 without HCC; median ages at surgical resection and biopsy collection, 64.1 and 48.6 years, respectively) who underwent liver resection or liver biopsy from November 2002 through July 2017 in Hong Kong. HBV DNA and covalently closed circular DNA (cccDNA) were analyzed and quantified by PCR in liver tissues. Integration of HBV DNA into the DNA of liver cells was detected by Alu-PCR. RESULTS Of the 90 HBsAg-negative patients with HCC, 18 had alcoholic liver disease (20%), 14 had non-alcoholic fatty liver disease or steatohepatitis (16%), 2 had primary biliary cholangitis, 2 had recurrent pyogenic cholangitis, 1 had autoimmune hepatitis, and 53 had none of these (59%). Among the 20 patients without HCC, 7 had non-alcoholic fatty liver disease or steatohepatitis, 7 had primary biliary cholangitis, and 6 had autoimmune hepatitis. OBI was detected in 62/90 patients with HCC (69%) and 3/20 patients without HCC (15%) (P < .0001). cccDNA was detectable in liver cells of 29 patients with HCC and OBI (47%) and HBV DNA had integrated into DNA of liver cells of 43 patients with HCC and OBI (69%); cccDNA and integrated HBV DNA were not detected in the 3 patients who had OBI without HCC. There were 29 patients with integration of HBV DNA among 33 patients with undetectable cccDNA in liver tissues (88%) and 14 patients with integration of HBV DNA among the 29 patients with cccDNA in liver tissues (48%) (P = .001). HBV DNA was found to integrate near genes associated with hepatocarcinogenesis, such as those encoding telomerase reverse transcriptase, lysine methyltransferase 2B, and cyclin A2. Among the 43 patients with integration of HBV DNA, 39 (91%) did not have cirrhosis. CONCLUSIONS In an analysis of clinical data and liver tissues from 90 HBsAg-negative patients with HCC, we found that almost 70% had OBI, of whom 70% had integration of HBV DNA into liver cell DNA; 90% of these patients did not have cirrhosis. HBV DNA integrated near hepatic oncogenes; these integrations might promote development of liver cancer.
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Affiliation(s)
- Danny Ka-Ho Wong
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China; State Key Laboratory of Liver Research, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Serene Ching Yan Cheng
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Loey Lung-Yi Mak
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Elvis Wai-Pan To
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Regina Cheuk-Lam Lo
- State Key Laboratory of Liver Research, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China; Department of Pathology, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Tan-To Cheung
- State Key Laboratory of Liver Research, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China; Department of Surgery, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Wai-Kay Seto
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China; State Key Laboratory of Liver Research, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - James Fung
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China; State Key Laboratory of Liver Research, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Kwan Man
- State Key Laboratory of Liver Research, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China; Department of Surgery, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Ching-Lung Lai
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China; State Key Laboratory of Liver Research, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China
| | - Man-Fung Yuen
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China; State Key Laboratory of Liver Research, University of Hong Kong, Queen Mary Hospital, Hong Kong SAR, China.
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Mohd-Ismail NK, Lim Z, Gunaratne J, Tan YJ. Mapping the Interactions of HBV cccDNA with Host Factors. Int J Mol Sci 2019; 20:ijms20174276. [PMID: 31480501 PMCID: PMC6747236 DOI: 10.3390/ijms20174276] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infection is a major health problem affecting about 300 million people globally. Although successful administration of a prophylactic vaccine has reduced new infections, a cure for chronic hepatitis B (CHB) is still unavailable. Current anti-HBV therapies slow down disease progression but are not curative as they cannot eliminate or permanently silence HBV covalently closed circular DNA (cccDNA). The cccDNA minichromosome persists in the nuclei of infected hepatocytes where it forms the template for all viral transcription. Interactions between host factors and cccDNA are crucial for its formation, stability, and transcriptional activity. Here, we summarize the reported interactions between HBV cccDNA and various host factors and their implications on HBV replication. While the virus hijacks certain cellular processes to complete its life cycle, there are also host factors that restrict HBV infection. Therefore, we review both positive and negative regulation of HBV cccDNA by host factors and the use of small molecule drugs or sequence-specific nucleases to target these interactions or cccDNA directly. We also discuss several reporter-based surrogate systems that mimic cccDNA biology which can be used for drug library screening of cccDNA-targeting compounds as well as identification of cccDNA-related targets.
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Affiliation(s)
- Nur K Mohd-Ismail
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore 117545, Singapore
| | - Zijie Lim
- Department of Medicine, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore 119228, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Yee-Joo Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore 117545, Singapore.
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.
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