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Husain B, Ramani SR, Chiang E, Lehoux I, Paduchuri S, Arena TA, Patel A, Wilson B, Chan P, Franke Y, Wong AW, Lill JR, Turley SJ, Gonzalez LC, Grogan JL, Martinez-Martin N. A Platform for Extracellular Interactome Discovery Identifies Novel Functional Binding Partners for the Immune Receptors B7-H3/CD276 and PVR/CD155. Mol Cell Proteomics 2019; 18:2310-2323. [PMID: 31308249 PMCID: PMC6823854 DOI: 10.1074/mcp.tir119.001433] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/10/2019] [Indexed: 12/21/2022] Open
Abstract
Receptors expressed on the plasma membrane and their interacting partners critically regulate cellular communication during homeostasis and disease, and as such represent main therapeutic targets. Despite its importance for drug development, receptor-ligand proteomics has remained a daunting field, in part because of the challenges associated to the study of membrane-expressed proteins. Here, to enable sensitive detection of receptor-ligand interactions in high throughput, we implement a new platform, the Conditioned Media AlphaScreen, for interrogation of a library consisting of most single transmembrane human proteins. Using this method to study key immune receptors, we identify and further validate the interleukin receptor IL20RA as the first binding partner for the checkpoint inhibitor B7-H3. Further, KIR2DL5, a natural killer cell protein that had remained orphan, is uncovered as a functional binding partner for the poliovirus receptor (PVR). This interaction is characterized using orthogonal assays, which demonstrate that PVR specifically engages KIR2DL5 on natural killer cells leading to inhibition of cytotoxicity. Altogether, these results reveal unappreciated links between protein families that may importantly influence receptor-driven functions during disease. Applicable to any target of interest, this technology represents a versatile and powerful approach for elucidation of receptor-ligand interactomes, which is essential to understand basic aspects of the biology of the plasma membrane proteins and ultimately inform the development of novel therapeutic strategies.
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Affiliation(s)
- Bushra Husain
- Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, CA
| | - Sree R Ramani
- Portfolio Management and Operations, Genentech, South San Francisco, CA
| | - Eugene Chiang
- Cancer Immunology Department, Genentech, South San Francisco, CA
| | | | - Sairupa Paduchuri
- Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, CA
| | - Tia A Arena
- Cell Culture, Genentech, South San Francisco, CA
| | - Ashka Patel
- 23 & me Therapeutics, South San Francisco, CA
| | - Blair Wilson
- Biochemical Cellular Pharmacology, Genentech, South San Francisco, CA
| | - Pamela Chan
- Biochemical Cellular Pharmacology, Genentech, South San Francisco, CA
| | - Yvonne Franke
- BioMolecular Resources, Genentech, South San Francisco, CA
| | | | - Jennie R Lill
- Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, CA
| | - Shannon J Turley
- Cancer Immunology Department, Genentech, South San Francisco, CA
| | - Lino C Gonzalez
- Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, CA; 23 & me Therapeutics, South San Francisco, CA
| | - Jane L Grogan
- Cancer Immunology Department, Genentech, South San Francisco, CA
| | - Nadia Martinez-Martin
- Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, CA.
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Shao W, Earley LF, Chai Z, Chen X, Sun J, He T, Deng M, Hirsch ML, Ting J, Samulski RJ, Li C. Double-stranded RNA innate immune response activation from long-term adeno-associated virus vector transduction. JCI Insight 2018; 3:120474. [PMID: 29925692 DOI: 10.1172/jci.insight.120474] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/17/2018] [Indexed: 12/16/2022] Open
Abstract
Data from clinical trials for hemophilia B using adeno-associated virus (AAV) vectors have demonstrated decreased transgenic coagulation factor IX (hFIX) expression 6-10 weeks after administration of a high vector dose. While it is likely that capsid-specific cytotoxic T lymphocytes eliminate vector-transduced hepatocytes, thereby resulting in decreased hFIX, this observation is not intuitively consistent with restored hFIX levels following prednisone application. Although the innate immune response is immediately activated following AAV vector infection via TLR pathways, no studies exist regarding the role of the innate immune response at later time points after AAV vector transduction. Herein, activation of the innate immune response in cell lines, primary human hepatocytes, and hepatocytes in a human chimeric mouse model was observed at later time points following AAV vector transduction. Mechanistic analysis demonstrated that the double-stranded RNA (dsRNA) sensor MDA5 was necessary for innate immune response activation and that transient knockdown of MDA5, or MAVS, decreased IFN-β expression while increasing transgene production in AAV-transduced cells. These results both highlight the role of the dsRNA-triggered innate immune response in therapeutic transgene expression at later time points following AAV transduction and facilitate the execution of effective strategies to block the dsRNA innate immune response in future clinical trials.
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Affiliation(s)
| | | | | | | | - Junjiang Sun
- Gene Therapy Center.,Division of Pharmacoengineering and Molecular Pharmaceutics, School of Pharmacy
| | | | - Meng Deng
- Lineberger Comprehensive Cancer Center
| | | | | | | | - Chengwen Li
- Gene Therapy Center.,Department of Pediatrics, School of Medicine, and.,Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Huang WL, Tsai MJ, Hsu KT, Wang JR, Chen YH, Ho SY. Prediction of linear B-cell epitopes of hepatitis C virus for vaccine development. BMC Med Genomics 2015; 8 Suppl 4:S3. [PMID: 26680271 PMCID: PMC4682406 DOI: 10.1186/1755-8794-8-s4-s3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background High genetic heterogeneity in the hepatitis C virus (HCV) is the major challenge of the development of an effective vaccine. Existing studies for developing HCV vaccines have mainly focused on T-cell immune response. However, identification of linear B-cell epitopes that can stimulate B-cell response is one of the major tasks of peptide-based vaccine development. Owing to the variability in B-cell epitope length, the prediction of B-cell epitopes is much more complex than that of T-cell epitopes. Furthermore, the motifs of linear B-cell epitopes in different pathogens are quite different (e. g. HCV and hepatitis B virus). To cope with this challenge, this work aims to propose an HCV-customized sequence-based prediction method to identify B-cell epitopes of HCV. Results This work establishes an experimentally verified dataset comprising the B-cell response of HCV dataset consisting of 774 linear B-cell epitopes and 774 non B-cell epitopes from the Immune Epitope Database. An interpretable rule mining system of B-cell epitopes (IRMS-BE) is proposed to select informative physicochemical properties (PCPs) and then extracts several if-then rule-based knowledge for identifying B-cell epitopes. A web server Bcell-HCV was implemented using an SVM with the 34 informative PCPs, which achieved a training accuracy of 79.7% and test accuracy of 70.7% better than the SVM-based methods for identifying B-cell epitopes of HCV and the two general-purpose methods. This work performs advanced analysis of the 34 informative properties, and the results indicate that the most effective property is the alpha-helix structure of epitopes, which influences the connection between host cells and the E2 proteins of HCV. Furthermore, 12 interpretable rules are acquired from top-five PCPs and achieve a sensitivity of 75.6% and specificity of 71.3%. Finally, a conserved promising vaccine candidate, PDREMVLYQE, is identified for inclusion in a vaccine against HCV. Conclusions This work proposes an interpretable rule mining system IRMS-BE for extracting interpretable rules using informative physicochemical properties and a web server Bcell-HCV for predicting linear B-cell epitopes of HCV. IRMS-BE may also apply to predict B-cell epitopes for other viruses, which benefits the improvement of vaccines development of these viruses without significant modification. Bcell-HCV is useful for identifying B-cell epitopes of HCV antigen to help vaccine development, which is available at http://e045.life.nctu.edu.tw/BcellHCV.
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HCV genome-wide genetic analyses in context of disease progression and hepatocellular carcinoma. PLoS One 2014; 9:e103748. [PMID: 25079603 PMCID: PMC4117537 DOI: 10.1371/journal.pone.0103748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/01/2014] [Indexed: 12/20/2022] Open
Abstract
Hepatitis C virus (HCV) is a major cause of hepatitis and hepatocellular carcinoma (HCC) world-wide. Most HCV patients have relatively stable disease, but approximately 25% have progressive disease that often terminates in liver failure or HCC. HCV is highly variable genetically, with seven genotypes and multiple subtypes per genotype. This variation affects HCV's sensitivity to antiviral therapy and has been implicated to contribute to differences in disease. We sequenced the complete viral coding capacity for 107 HCV genotype 1 isolates to determine whether genetic variation between independent HCV isolates is associated with the rate of disease progression or development of HCC. Consensus sequences were determined by sequencing RT-PCR products from serum or plasma. Positions of amino acid conservation, amino acid diversity patterns, selection pressures, and genome-wide patterns of amino acid covariance were assessed in context of the clinical phenotypes. A few positions were found where the amino acid distributions or degree of positive selection differed between in the HCC and cirrhotic sequences. All other assessments of viral genetic variation and HCC failed to yield significant associations. Sequences from patients with slow disease progression were under a greater degree of positive selection than sequences from rapid progressors, but all other analyses comparing HCV from rapid and slow disease progressors were statistically insignificant. The failure to observe distinct sequence differences associated with disease progression or HCC employing methods that previously revealed strong associations with the outcome of interferon α-based therapy implies that variable ability of HCV to modulate interferon responses is not a dominant cause for differential pathology among HCV patients. This lack of significant associations also implies that host and/or environmental factors are the major causes of differential disease presentation in HCV patients.
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El-Fatah Fahmy Hanno A, Mohiedeen KM, Deghedy A, Sayed R. Serum complements C3 and C4 in chronic HCV infection and their correlation with response to pegylated interferon and ribavirin treatment. Arab J Gastroenterol 2014; 15:58-62. [PMID: 25097047 DOI: 10.1016/j.ajg.2014.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 01/13/2014] [Accepted: 04/22/2014] [Indexed: 01/16/2023]
Abstract
BACKGROUND AND STUDY AIMS To search for an immunological parameter that may correlate with the response to interferon (IFN) treatment is very crucial. The objective of this study was to correlate the levels of C3 and C4 complement components with the response to IFN treatment in patients with chronic hepatitis C virus (HCV) infection. PATIENTS AND METHODS This study was conducted on 100 patients and control subjects classified into three groups. Group (I) consisted of 50 patients with chronic hepatitis C who were receiving IFN treatment and showed various responses; group (II) included 25 patients with chronic hepatitis C naive to IFN treatment; and group (III) included 25 healthy subjects matched for age and sex who served as controls. Measurement of the level of complement C3 and C4 was done by a quantitative turbidimetric test. Measurement of complement levels in group (I) was done at the end of treatment at the 48th week. RESULTS Serum levels of C3 and C4 were found to be significantly reduced in all patients with chronic HCV infection in both groups (I and II) compared to the healthy control group (III) (p<0.05). Moreover, chronic HCV patients treated with IFN and ribavirin had significantly lower levels of C3 and C4 compared with patients naive to IFN and ribavirin treatment. At the end of treatment, both C3 and C4 had significantly increased in responders to IFN when compared to non-responders (p=0.025 and 0.05, respectively). There was a significant negative correlation between C3 and C4 levels and the concentration of serum alanine aminotransferase (ALT) measured simultaneously. CONCLUSION Higher C3 and C4 serum concentrations were found to be positively correlated to the end-of-treatment response in patients with chronic HCV infection treated with IFN and ribavirin.
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Affiliation(s)
- Abd El-Fatah Fahmy Hanno
- Tropical Medicine and clinical pathology Departments, Alexandria Faculty of Medicine, Alexandria, Egypt
| | - Khaled Mahmoud Mohiedeen
- Tropical Medicine and clinical pathology Departments, Alexandria Faculty of Medicine, Alexandria, Egypt.
| | - Akram Deghedy
- Tropical Medicine and clinical pathology Departments, Alexandria Faculty of Medicine, Alexandria, Egypt
| | - Reeham Sayed
- Tropical Medicine and clinical pathology Departments, Alexandria Faculty of Medicine, Alexandria, Egypt
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Kawaguchi-Suzuki M, Frye RF. The role of pharmacogenetics in the treatment of chronic hepatitis C infection. Pharmacotherapy 2014; 34:185-201. [PMID: 24114761 DOI: 10.1002/phar.1349] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hepatitis C virus (HCV) chronically infects 170 million people worldwide. Until recently, combination therapy with peginterferon-α (pegIFN) and ribavirin (RBV) has been the standard of care. However, for many patients, especially those infected with the most common HCV genotype 1 (HCV-1), this treatment has resulted in unsatisfactory treatment response rates. Many clinical factors, including pharmacogenetics, influence the treatment response rate. Genetic variation in the interleukin 28B (IL28B) gene is the major determinant of treatment response, a finding that has been replicated in multiple independent cohorts. This review focuses on the association between pharmacogenetics and conventional pegIFN/RBV therapy in patients infected with HCV non-genotype 1; patients reinfected with HCV after liver transplantation; and patients coinfected with HCV and human immunodeficiency virus. We also review the pharmacogenetic data for boceprevir and telaprevir triple therapy in patients with HCV-1 infection, as well as viral genomic polymorphisms and genetic variants that may protect against anemia. Pharmacogenetic information offers a personalized medicine approach to help clinicians and patients make better informed decisions to maximize response and minimize toxicity for the treatment of chronic HCV infection.
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Affiliation(s)
- Marina Kawaguchi-Suzuki
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida
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Thueng-in K, Thanongsaksrikul J, Srimanote P, Bangphoomi K, Poungpair O, Maneewatch S, Choowongkomon K, Chaicumpa W. Cell penetrable humanized-VH/V(H)H that inhibit RNA dependent RNA polymerase (NS5B) of HCV. PLoS One 2012; 7:e49254. [PMID: 23145135 PMCID: PMC3493538 DOI: 10.1371/journal.pone.0049254] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/04/2012] [Indexed: 12/13/2022] Open
Abstract
NS5B is pivotal RNA dependent RNA polymerase (RdRp) of HCV and NS5B function interfering halts the virus infective cycle. This work aimed to produce cell penetrable humanized single domain antibodies (SdAb; VH/VHH) that interfere with the RdRp activity. Recombinant NS5BΔ55 of genotype 3a HCV with de novo RNA synthetic activity was produced and used in phage biopanning for selecting phage clones that displayed NS5BΔ55 bound VH/VHH from a humanized-camel VH/VHH display library. VH/VHH from E. coli transfected with four selected phage clones inhibited RdRp activity when tested by ELISA inhibition using 3′di-cytidylate 25 nucleotide directed in vitro RNA synthesis. Deduced amino acid sequences of two clones showed VHH hallmark and were designated VHH6 and VHH24; other clones were conventional VH, designated VH9 and VH13. All VH/VHH were linked molecularly to a cell penetrating peptide, penetratin. The cell penetrable VH9, VH13, VHH6 and VHH24 added to culture of Huh7 cells transfected with JHF-1 RNA of genotype 2a HCV reduced the amounts of RNA intracellularly and in culture medium implying that they inhibited the virus replication. VH/VHH mimotopes matched with residues scattered on the polymerase fingers, palm and thumb which were likely juxtaposed to form conformational epitopes. Molecular docking revealed that the antibodies covered the RdRp catalytic groove. The transbodies await further studies for in vivo role in inhibiting HCV replication.
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Affiliation(s)
- Kanyarat Thueng-in
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Potjanee Srimanote
- Graduate Program, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
| | - Kunan Bangphoomi
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ornnuthchar Poungpair
- Department of Research and Development, Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
| | - Santi Maneewatch
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
- * E-mail:
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Tseng CW, Hsieh YH, Chang CK, Lai NS, Hung TH, Wu SF, Tseng KC. HLA-B*15:02 is associated with anemia in patients with chronic hepatitis C treated with pegylated interferon-α and ribavirin. ACTA ACUST UNITED AC 2012; 80:424-30. [PMID: 22931407 DOI: 10.1111/j.1399-0039.2012.01956.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 06/30/2012] [Accepted: 08/06/2012] [Indexed: 01/23/2023]
Abstract
To investigate the relationship between human leukocyte antigen (HLA) class I and II alleles and treatment-induced anemia in chronic hepatitis C (CHC) patients receiving combination therapy with pegylated interferon-α (PEG-IFN-α) and ribavirin (RBV). One hundred six naïve CHC patients (59 females and 47 males; mean age, 53.08 years) who underwent combination treatment were enrolled. The patients were considered positive for hemoglobin (Hb)-related side effects if the Hb concentrations dropped below 10 g/dl during PEG-IFN-α plus RBV treatment. The HLA-A, -B, -C, -DR, and -DQ loci were investigated by sequence-based genotyping. The effects of the clinical characteristics, virologic variables, and the HLA alleles on treatment-induced anemia were evaluated by a logistic regression analysis. Forty patients (37.7%) had Hb levels below 10 g/dl during the treatment course. Low baseline Hb levels and an advanced liver fibrosis stage were associated with decreases in Hb levels to below 10 g/dl. The occurrence of treatment-related anemia (Hb < 10 g/dl) was significantly associated with HLA-B*15:02 as shown by multivariate analysis (adjusted odds ratio, 8.13; 95% confidence interval: 1.19-55.70; P-value after Holm's procedure, 0.03). HLA-B*15:02 is associated with treatment-induced anemia in Taiwanese CHC patients receiving combination therapy with PEG-IFN-α plus RBV.
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Affiliation(s)
- C-W Tseng
- Department of Internal Medicine, Buddhist Dalin Tzu Chi General Hospital, Chia-Yi, Taiwan
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Hepatitis C virus infection modulates expression of interferon stimulatory gene IFITM1 by upregulating miR-130A. J Virol 2012; 86:10221-5. [PMID: 22787204 DOI: 10.1128/jvi.00882-12] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We have examined the underlying mechanism of hepatitis C virus (HCV)-mediated IFITM1 regulation. IFITM1 is a potential target of miR-130a. Our results demonstrated that miR-130a expression was significantly higher in HCV-infected hepatocytes and liver biopsy specimens than in controls. Introduction of anti-miR-130a in hepatocytes increased IFITM1 expression. Hepatocytes stably expressing IFITM1 reduced HCV replication. Together, these results suggested that HCV infection of hepatocytes upregulates miR-130a and that use of anti-miR-130a may have potential for restriction of HCV replication.
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Holmes JA, Sievert W, Thompson AJ. IL28B polymorphism and genetic biomarkers of viral clearance in hepatitis C virus infection. Biomark Med 2011; 5:461-78. [PMID: 21861668 DOI: 10.2217/bmm.11.47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Infection with hepatitis C virus (HCV) is a major global health issue. Only a small proportion of patients clear the virus spontaneously and the majority develop chronic hepatitis C infection. Chronic hepatitis C is one of the most common causes of advanced liver disease in the western world and is now the leading indication for liver transplantation. Unfortunately, the standard treatment, consisting of pegylated-interferon and ribavirin, is suboptimal. Less than 50% of patients infected with HCV genotype 1 are cured, treatment is costly and is associated with significant toxicity. Therefore, there has been a need to identify accurate predictors of treatment outcome to facilitate treatment decision-making. Four independent genome-wide association studies have recently confirmed an association between genetic variation in the region of the IL28B gene and treatment outcome in HCV-1 patients. Patients who carry the good response variant are two- to three-fold more likely to be cured. The difference in the frequency of the good response variant between patients of different ethnic background explains much of the recognized ethnic disparity in treatment response rates. The IL28B variants are also associated with likelihood of spontaneous clearance of HCV infection. This discovery represents a significant advance in our ability to personalize HCV therapy, as well as suggesting novel avenues for research into viral pathogenesis and therapeutic development.
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Affiliation(s)
- Jacinta A Holmes
- Department of Gastroenterology & Hepatology, St Vincent's Hospital, 41 Victoria Parade, Fitzroy, Melbourne, Victoria 3065, Australia
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