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Bartosh UI, Dome AS, Zhukova NV, Karitskaya PE, Stepanov GA. CRISPR/Cas9 as a New Antiviral Strategy for Treating Hepatitis Viral Infections. Int J Mol Sci 2023; 25:334. [PMID: 38203503 PMCID: PMC10779197 DOI: 10.3390/ijms25010334] [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: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatitis is an inflammatory liver disease primarily caused by hepatitis A (HAV), B (HBV), C (HCV), D (HDV), and E (HEV) viruses. The chronic forms of hepatitis resulting from HBV and HCV infections can progress to cirrhosis or hepatocellular carcinoma (HCC), while acute hepatitis can lead to acute liver failure, sometimes resulting in fatality. Viral hepatitis was responsible for over 1 million reported deaths annually. The treatment of hepatitis caused by viral infections currently involves the use of interferon-α (IFN-α), nucleoside inhibitors, and reverse transcriptase inhibitors (for HBV). However, these methods do not always lead to a complete cure for viral infections, and chronic forms of the disease pose significant treatment challenges. These facts underscore the urgent need to explore novel drug developments for the treatment of viral hepatitis. The discovery of the CRISPR/Cas9 system and the subsequent development of various modifications of this system have represented a groundbreaking advance in the quest for innovative strategies in the treatment of viral infections. This technology enables the targeted disruption of specific regions of the genome of infectious agents or the direct manipulation of cellular factors involved in viral replication by introducing a double-strand DNA break, which is targeted by guide RNA (spacer). This review provides a comprehensive summary of our current knowledge regarding the application of the CRISPR/Cas system in the regulation of viral infections caused by HAV, HBV, and HCV. It also highlights new strategies for drug development aimed at addressing both acute and chronic forms of viral hepatitis.
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Affiliation(s)
| | | | | | | | - Grigory A. Stepanov
- The Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; (U.I.B.); (A.S.D.); (N.V.Z.); (P.E.K.)
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Zhang H, Quadeer AA, McKay MR. Direct-acting antiviral resistance of Hepatitis C virus is promoted by epistasis. Nat Commun 2023; 14:7457. [PMID: 37978179 PMCID: PMC10656532 DOI: 10.1038/s41467-023-42550-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023] Open
Abstract
Direct-acting antiviral agents (DAAs) provide efficacious therapeutic treatments for chronic Hepatitis C virus (HCV) infection. However, emergence of drug resistance mutations (DRMs) can greatly affect treatment outcomes and impede virological cure. While multiple DRMs have been observed for all currently used DAAs, the evolutionary determinants of such mutations are not currently well understood. Here, by considering DAAs targeting the nonstructural 3 (NS3) protein of HCV, we present results suggesting that epistasis plays an important role in the evolution of DRMs. Employing a sequence-based fitness landscape model whose predictions correlate highly with experimental data, we identify specific DRMs that are associated with strong epistatic interactions, and these are found to be enriched in multiple NS3-specific DAAs. Evolutionary modelling further supports that the identified DRMs involve compensatory mutational interactions that facilitate relatively easy escape from drug-induced selection pressures. Our results indicate that accounting for epistasis is important for designing future HCV NS3-targeting DAAs.
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Affiliation(s)
- Hang Zhang
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Ahmed Abdul Quadeer
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China.
| | - Matthew R McKay
- Department of Electrical and Electronic Engineering, University of Melbourne, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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Xie Z, Deng K, Xia Y, Zhang C, Xu M, Li F, Liu J, Zhou Y, Chen X, Chen X, Yan Q, Huang J, Chen W, Wu S, Bai H, Li J, Guan Y. Efficacy and safety of direct-acting antiviral therapies and baseline predictors for treatment outcomes in hepatitis C patients: a multi-center, real-world study in Guangdong, China. J Med Virol 2022; 94:4459-4469. [PMID: 35545872 DOI: 10.1002/jmv.27851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 11/09/2022]
Abstract
: The data on direct acting antivirals (DAA) in chronic hepatitis C (CHC) patients in southern China with multiple genotypes circulating are limited. This study aims to evaluate the efficacy and safety of DAA regimens among CHC patients in Guangdong, China. A total of 220 patients receiving a variety of DAA were enrolled. The primary outcome was sustained virologic response (SVR) at 12 weeks. Resistance associated substations (RAS) were evaluated by deep sequencing. The overall SVR rate was 96.4%, and was 97.7% for genotype 1, 100% for genotype 2, 91.9% for genotype 3, 95.7% for genotype 6, and 100% for untyped. The overall incidence of adverse events (AEs) was 8.2% (18/220) and all the AEs were mild. Nonstructural protein 5A RAS, 30K/31M and Y93H, were most prevalent at baseline and the end of treatment in non-SVR patients, respectively. Logistics regression showed that elevated ALT and AST at baseline were specifically associated with non-SVR in patients with genotype 3 and 6 infections (P = 0.029 and P = 0.017) but not genotype 1 infection (P = 0.746 and P = 0.971), and baseline AST was the best predictor for SVR in genotype 3 and 6 patients (area under curve = 0.890). CONCLUSION: All DAA regimens achieved ideal SVR and were well tolerated. NS5A RAS were prevalent in non-SVR patients. ALT and AST as baseline predictors for non-SVR in genotype 3 and 6 infections warrant further research in a larger cohort. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zhiwei Xie
- Department of Hepatology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Kai Deng
- Infectious Disease Institute, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yang Xia
- Department of Hepatology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chunlan Zhang
- Department of Hepatology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Min Xu
- Department of Hepatology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Feng Li
- Infectious Disease Institute, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jinfeng Liu
- Institution of Clinical Research, the First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Yuanping Zhou
- Department of Infectious Disease, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoping Chen
- Department of Infectious Disease, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Xuefu Chen
- Department of Infectious Disease, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Qin Yan
- Department of Hepatology, Shenzhen Union Hospital of Huazhong University of Science and Technology, Shenzhen, Guangdong, China
| | - Jing Huang
- Department of Infectious Disease, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Wenli Chen
- Department of Infectious Disease, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Shuduo Wu
- Department of Hepatology, Guangdong Province Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Honglian Bai
- Institution of Clinical Research, the First People's Hospital of Foshan, Foshan, Guangdong, China
| | - Jianping Li
- Department of Hepatology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yujuan Guan
- Department of Hepatology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
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Pabjan P, Brzdęk M, Chrapek M, Dziedzic K, Dobrowolska K, Paluch K, Garbat A, Błoniarczyk P, Reczko K, Stępień P, Zarębska-Michaluk D. Are There Still Difficult-to-Treat Patients with Chronic Hepatitis C in the Era of Direct-Acting Antivirals? Viruses 2022; 14:96. [PMID: 35062302 PMCID: PMC8779728 DOI: 10.3390/v14010096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022] Open
Abstract
Difficult-to-treat populations with chronic hepatitis C (CHC), in the era of interferon treatment, included patients with liver cirrhosis, kidney impairment, treatment-experienced individuals, and those coinfected with the human immunodeficiency virus. The current study aimed to determine whether, in the era of direct-acting antivirals (DAA), there are still patients that are difficult-to-treat. The study included all consecutive patients chronically infected with hepatitis C virus (HCV) who started interferon-free therapy between July 2015 and December 2020 in the Department of Infectious Diseases in Kielce. The analyzed real-world population consisted of 963 patients, and most of them were infected with genotype 1 (87.6%) with the predominance of subtype 1b and were treatment-naïve (78.8%). Liver cirrhosis was determined in 207 individuals (21.5%), of whom 82.6% were compensated. The overall sustained virologic response, after exclusion of non-virologic failures, was achieved in 98.4%. The univariable analysis demonstrated the significantly lower response rates in males, patients with liver cirrhosis, decompensation of hepatic function at baseline, documented esophageal varices, concomitant diabetes, body mass index ≥25, and previous ineffective antiviral treatment. Despite an overall very high effectiveness, some unfavorable factors, including male gender, genotype 3 infection, liver cirrhosis, and treatment experience, significantly reduce the chances for a virologic response were identified.
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Affiliation(s)
- Paweł Pabjan
- Department of Infectious Diseases, Voivodship Hospital, Jan Kochanowski University, 25-317 Kielce, Poland; (P.P.); (K.P.); (A.G.); (P.B.); (K.R.); (P.S.)
| | - Michał Brzdęk
- Collegium Medicum, Jan Kochanowski University, 25-369 Kielce, Poland; (M.B.); (K.D.); (K.D.)
| | - Magdalena Chrapek
- Faculty of Natural Sciences, Jan Kochanowski University, 25-369 Kielce, Poland;
| | - Kacper Dziedzic
- Collegium Medicum, Jan Kochanowski University, 25-369 Kielce, Poland; (M.B.); (K.D.); (K.D.)
| | - Krystyna Dobrowolska
- Collegium Medicum, Jan Kochanowski University, 25-369 Kielce, Poland; (M.B.); (K.D.); (K.D.)
| | - Katarzyna Paluch
- Department of Infectious Diseases, Voivodship Hospital, Jan Kochanowski University, 25-317 Kielce, Poland; (P.P.); (K.P.); (A.G.); (P.B.); (K.R.); (P.S.)
| | - Anna Garbat
- Department of Infectious Diseases, Voivodship Hospital, Jan Kochanowski University, 25-317 Kielce, Poland; (P.P.); (K.P.); (A.G.); (P.B.); (K.R.); (P.S.)
| | - Piotr Błoniarczyk
- Department of Infectious Diseases, Voivodship Hospital, Jan Kochanowski University, 25-317 Kielce, Poland; (P.P.); (K.P.); (A.G.); (P.B.); (K.R.); (P.S.)
| | - Katarzyna Reczko
- Department of Infectious Diseases, Voivodship Hospital, Jan Kochanowski University, 25-317 Kielce, Poland; (P.P.); (K.P.); (A.G.); (P.B.); (K.R.); (P.S.)
| | - Piotr Stępień
- Department of Infectious Diseases, Voivodship Hospital, Jan Kochanowski University, 25-317 Kielce, Poland; (P.P.); (K.P.); (A.G.); (P.B.); (K.R.); (P.S.)
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases, Voivodship Hospital, Jan Kochanowski University, 25-317 Kielce, Poland; (P.P.); (K.P.); (A.G.); (P.B.); (K.R.); (P.S.)
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Santos APDT, Silva VCM, Mendes-Corrêa MC, Lemos MF, Malta FDM, Santana RAF, Dastoli GTF, Castro VFDD, Pinho JRR, Moreira RC. Characterization of primary direct-acting antiviral (DAA) drugs resistance mutations in NS5A/NS5B regions of hepatitis C virus with genotype 1a and 1b from patients with chronic hepatitis. Rev Inst Med Trop Sao Paulo 2022; 64:e61. [PMID: 36197422 PMCID: PMC9528309 DOI: 10.1590/s1678-9946202264061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | - João Renato Rebello Pinho
- Universidade de São Paulo, Brazil; Universidade de São Paulo, Brazil; Hospital Israelita Albert Einstein, Brazil
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Ren S, Wei F, Jin Y, Lu J, He Z, Ma L, Zheng Y, Wang J, Chen X. Baseline resistance-associated substitutions may impact DAA response among treatment failure chronic hepatitis C patients with pegylated interferon and ribavirin in real life. Antivir Ther 2020; 25:245-255. [PMID: 32936785 DOI: 10.3851/imp3369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND To evaluate the impact of baseline resistance-associated substitutions (RASs) on direct-acting antiviral (DAA) treatment response among pegylated interferon in combination with ribavirin (PR) failing patients in a real-life setting. METHODS Blood samples and clinical data from 171 patients who failed PR treatment were collected. All of them received rescue DAA regimens. RAS identified in the NS3, NS5A and NS5B regions by Sanger sequencing method were compared by DAA regimen and HCV subtypes. We assessed sustained virological response at 12 weeks (SVR12) and evaluated the impact of baseline RASs on the effectiveness of DAA regimens in clinical practice. RESULTS The overall SVR12 rates were: 89.47% (153/171), 92.1% (117/127) in patients without cirrhosis versus 81.8% (36/44) in those with cirrhosis, without significant difference (χ2=3.69, P=0.08); 87.9% in genotype (GT)1b patients (n=116) versus 93.8% in GT2a (n=32) versus 90.5% in GT3 (n=21) versus 100% in GT6 (n=2), without significant difference (χ2=1.02, P=0.84); 66.7% in asunaprevir (ASV) + daclatasvir (DCV) regimen (n=24) versus 94.0% in sofosbuvir (SOF)-based regimen (n=133), with significant difference (χ2=19.7, P=0.001). Our results showed that the prevalence of NS3, NS5A, NS5B RASs was 45.02%, 39.76% and 71.34%, respectively, and higher incidence of RASs in cirrhosis than without cirrhosis (81.8% versus 63.8%), with a statistically significant difference (χ2=4.92, P=0.03). In the ASV/DCV cohort (n=24), 4 of 11 patients (36.4%) with baseline NS3/NS5A RASs achieved SVR12, whereas 12 of 13 patients (92.3%) without RASs achieved SVR12, with significant difference (χ2=8.39, P=0.008). However, this relationship was not seen in the SOF-based subgroup (94.6% versus 92.7%; χ2=0.18, P=0.7). Treatment failure with DAAs occurred in 10.53% (n=18) of our study population, baseline NS5A substitution including L31M or Y93H (n=13) was the most frequently detected RAS, rescue regimen with velpatasvir (VEL)/SOF + ribavirin (RBV) for 12 weeks or 24 weeks was highly effective in patients who failed previous use of NS5A inhibitors, regardless of GT or cirrhosis. CONCLUSIONS Natural RASs are common in Chinese patients failing with PR treatment. High prevalence of clinically relevant RASs (such as L31M, Y93H) supports the appropriateness of HCV resistance tests to properly guide DAA-based therapy. These findings might be used to select salvage therapies.
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Affiliation(s)
- Shan Ren
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Feili Wei
- Beijing Institute of Hepatology, Beijing, China
| | - Yi Jin
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junfeng Lu
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Zhimin He
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Lina Ma
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yanhong Zheng
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junli Wang
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xinyue Chen
- Beijing Youan Hospital, Capital Medical University, Beijing, China
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Structurally distinct cyclosporin and sanglifehrin analogs CRV431 and NV556 suppress established HCV infection in humanized-liver mice. PLoS One 2020; 15:e0237236. [PMID: 32764799 PMCID: PMC7413547 DOI: 10.1371/journal.pone.0237236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
We previously reported that the non-immunosuppressive cyclophilin inhibitors (CypIs)—cyclosporin A analog CRV431 and sanglifehrin analog NV556—efficiently inhibit HCV replication in vitro. In this study, we asked whether they can also reduce HCV replication in vivo. We found that a single oral administration of CRV431 and NV556 to HCV-infected humanized-liver mice drastically reduced HCV blood levels. The antiviral effect was observed when CRV431 or NV556 were each individually administered with HCV, 3, 6 weeks or even 3 months post-infection when viral replication is robust. These results were confirmed in chimeric mice implanted with human hepatocytes isolated from three distinct donors. Remarkably, no viral rebound was observed 5 months after a single dose administration of 50 mg/kg of CRV431 or NV556 four weeks post-HCV infection, indicating the possibility of suppression of an established viral infection. Since we recently demonstrated that both CRV431 and NV556 also inhibit the development of liver fibrosis and hepatocellular carcinoma in nonviral-induced non-alcoholic steatohepatitis mouse models, our present data suggest that the two entirely structurally different CypIs—CRV431 and NV556—derived from unrelated natural products, represent attractive partners to current direct-acting agent (DAA) regimens for the treatment of hepatitis C and liver diseases.
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