key: cord-0876703-lgxjov2r authors: Li, Hui-Chun; Yang, Chee-Hing; Lo, Shih-Yen title: Cellular factors involved in the hepatitis C virus life cycle date: 2021-07-28 journal: World J Gastroenterol DOI: 10.3748/wjg.v27.i28.4555 sha: eb2c93652e4de8ce880e855cf046f449d5100469 doc_id: 876703 cord_uid: lgxjov2r The hepatitis C virus (HCV), an obligatory intracellular pathogen, highly depends on its host cells to propagate successfully. The HCV life cycle can be simply divided into several stages including viral entry, protein translation, RNA replication, viral assembly and release. Hundreds of cellular factors involved in the HCV life cycle have been identified over more than thirty years of research. Characterization of these cellular factors has provided extensive insight into HCV replication strategies. Some of these cellular factors are targets for anti-HCV therapies. In this review, we summarize the well-characterized and recently identified cellular factors functioning at each stage of the HCV life cycle. Around 50%-80% of patients infected with the hepatitis C virus (HCV) will develop chronic infection. Approximately 71 million individuals are chronically infected by the HCV worldwide according to an estimation by the World Health Organization ( https://www.who.int/hepatitis/publications/global-hepatitis-report2017/en/). Chronic hepatitis C (CHC) patients are at high risk of developing liver cirrhosis and even hepatocellular carcinoma. Although CHC can now be cured using various directacting antivirals, the majority of CHC patients remain undiagnosed and, thus, untreated. Furthermore, a successful antiviral treatment does not prevent HCV reinfection. Therefore, HCV eradication remains a challenge and will probably require an effective vaccine[1] (for a review see References [2, 3] ). HCV belongs to the family Flaviviridae and genus Hepacivirus. Its genome is a singlestranded RNA with positive polarity that is packaged by viral core protein and enveloped by a lipid membrane containing two viral glycoproteins (i.e., E1 and E2) to form the virion. HCV genomic RNA sequences are highly heterogeneous among different isolates. At present, HCV is classified into at least six major genotypes (1 to 6). HCV heterogeneity hinders the development of an effective vaccine to protect against infection from all HCV genotypes. Despite the sequence variations, all currently recognized HCV genotypes are pathogenic, hepatotropic and preserve the similarity of the life cycle in cells (for a review see References [4, 5] ). The HCV life cycle begins with the binding of a virion to its specific entry factors (or receptors) on hepatocytes. After binding, the virion is internalized into the cytoplasm and its genomic RNA is released. Then, the HCV genomic RNA is used for both polyprotein translation and viral replication. HCV replication takes place within the membranous web (MW) in the endoplasmic reticulum (ER). At last, HCV uses the biosynthetic pathway of very-low-density lipoprotein (VLDL) to assemble and release the viral particles from cells (for a review see Reference [6] ). HCV relies significantly on its host cells to establish a successful infection due to the fact of its limited genetic content. Hundreds of cellular factors have been identified as being involved in the HCV life cycle over more than thirty years of research. In this review article, due to the limited space, we can only summarize the well-characterized and recently identified cellular factors involved in the HCV life cycle but not including immune responses against viral infections (for a review see Reference [7] ). It has been demonstrated that purified HCV particles are spherical and heterogeneous in size (40-100 nm in diameter) with no obvious symmetry under cryo-EM [8] . The density of HCV particles in the plasma of CHC patients also varied (from 1.03 to 1.25 g/mL). Low-density HCV particles with 81-85 nm diameters are highly infectious [8, 9] . The HCV particles with low density are associated with apolipoproteins (Apo such as Apo-E, Apo-AI, Apo-CI and Apo-B), phospholipids (such as phosphatidylcholine and sphingomyelin) and cholesterol (free and esterified), while they have almost no phosphatidylserine (PS) and very little amounts of phosphatidylethanolamine[8, [10] [11] [12] . HCV particles derived from cultured cells show characteristics similar to those from CHC patients[9,10,13]. Thus, these circulating HCV particles are referred to as "lipo-viro particles" (LVPs) [14] and have very low buoyant densities due to the fact of their interactions with lipoproteins in the blood[15] (Figure 1) More than 40 cellular proteins were found in the HCV particles recently using proteomics analyses, including heat shock cognate protein 70 (HSC70) and nucleoporin 98 (Nup98); both proteins play a role in virus assembly/release[22,23]. Model of cell-free virus entry into hepatocytes. Hepatitis C virus (HCV) lipo-viral particles (LPVs) may be captured by DC-SIGN on the dendritic cells or L-SIGN on the endothelium in the sinusoidal space. After transfer to Space of Disse, HCV LPVs could attach to the hepatocytes through interacting with highly sulfated heparan sulfate proteoglycans, low-density lipoprotein receptor and scavenger receptor class B type 1 (1). This attachment allows the engagement of LPVs to cluster of differentiation 81 (CD81) and then induces the epidermal growth factor receptor receptor signaling (2). Lateral diffusion of the CD81-HCV complexes results in the association of CD81-HCV with Claudin-1 (3) and then OCLIN (4). Formation of the HCV-CD81-CLDN1-OCLIN complex allows viral particles internalized through clathrin-dependent endocytosis (5). Endosomal acidification induces the fusion of viral particles possibly through E1 and leads to the release of the viral genomic RNA into cytosol (6). HSPGs: Heparan sulfate proteoglycans; HCV: Hepatitis C virus; EGFR: Epidermal growth factor receptor; LDLR: Low-density lipoprotein receptor. interactions with viral glycoproteins. Entry cofactors, although not interacting directly with the virus, play an important role in supporting viral entry. To infect a new hepatocyte, the HCV needs to interact with the attachment factors on the basolateral side of hepatocytes first ( Figure 2 . SR-B1, as both an entry factor and an attachment factor, has been shown to bind viral envelope proteins [29, 40] . Interaction of HCV with CD81 activates epidermal growth factor receptor (EGFR) signaling and also facilitates CD81 diffusion and formation of the HCV-CD81-CLDN1 complex [39, [41] [42] [43] . The HCV-CD81-CLDN1 complex then interacts with OCLN, which is believed to mediate the clathrin-dependent internalization through interacting with GTPase dynamin [44] [45] [46] . SR-B1, CD81, CLDN1 and OCLN are four well-characterized entry factors for HCV entry [28] . In addition, LRL-R could interact with both HCV and E2 proteins and, thus, function as an entry factor [47] . HCV particles are then internalized, mature in the acidic endosomes that promote low pH-dependent HCV fusion and, ultimately, release HCV genomic RNAs (uncoating) into cytosol[48-50] (Figure 2 ). Low endosomal pH and interactions of viral glycoproteins with CD81 are thought to induce conformational rearrangements of viral glycoproteins for HCV fusion[51], which is controlled by E1 protein [52] . Recently, cell death-inducing DFFA-like effector B (CIDEB) protein was identified as an entry cofactor to act at a late membrane fusion event [53] . Both HCV and coronavirus [e.g., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)][54] are positive-strand RNA viruses. These two viruses enter their target cells through receptor-mediated endocytosis and release their genomic RNAs for translation in the cytosol. However, unlike HCV, coronavirus fusion for viral entry is unusual in that it is often biphasic and can occur at or near the cell's surface or in late endosomes [55] . In addition to HSPGs, LDLR, and SR-B1, interferon receptor IFNAR2 was found as a novel attachment factor to facilitate HCV entry through interacting with Apo-E[56]. VLDL receptor (VLDLR), similar to LDLR, could also serve as an attachment factor for HCV entry [57] . Niemann-Pick C1-like 1 (NPC1L1) contributes to HCV entry possibly through its role as a cholesterol receptor, thus functioning as an HCV entry cofactor [58] . Similarly, PS receptor (TIM-1/human hepatitis A virus cellular receptor 1/CD365) has also been identified as an attachment factor through binding with PS on HCV In addition to cell-free virus entry into hepatocytes, HCV particles can also transmit directly from an infected hepatocyte to an adjacent hepatocyte [94] [95] [96] . A recent study demonstrated that the HCV core, E1, E2 and P7 genes were essential for not only cellfree viral transmission but also cell-to-cell transmission [ After the fusion between the viral envelope and the endosomal membrane, HCV positive-strand RNA will be released into the cytosol ( Figure 2 [320] ; D: Then, NS3, NS4A, NS4B, NS5A and NS5B proteins will form the replication complex. Core and NS5A proteins will be transferred to lipid droplets, while E1 and E2 proteins will stay in the assembly sites. IRES: Internal ribosome entry site; 5'UTR: 5'-untranslated region. In addition to the synthesis of HCV polyprotein, another viral protein is produced through the core+1 reading frame (for a review see References [151, 152] To shape an ER membrane into an RO requires not only viral and cellular proteins but also lipid synthesis (for a review see Refenence [236] ). Many studies have shown that HCV could modulate lipid metabolism (e.g., cholesterol and fatty acid biosynthesis) to promote viral replication [237] [238] [239] . Furthermore, to achieve robust HCV replication, it is necessary to limit the oxidative degradation of lipids [240] . Sphingolipid is also required for HCV replication and might contribute to detergent resistance of HCV replication sites [241] . Modulation of the lipid environment of RO by HCV includes the recruitment and activation of the lipid kinase PI4KIIIα by NS5A and NS5B proteins to generate enhanced levels of phosphatidylinositol 4-phosphate (PI4P) at the RO[200] . PI4P could attract lipid transport proteins [oxysterolbinding protein (OSBP), four-phosphate adaptor protein 2 and CERT)] to deliver glycosphingolipids, cholesterol and ceramide respectively to the RO[242,243]. OSBP and CERT could interact with the human VAP residing in the ER [244] . Both VAP-A and VAP-B, enriched in purified DMVs [245] , interact with NS5A and NS5B and assist in the formation of the replicase complex [204, 245] . Two types of lncRNAs, lin-IGF2-AS and lnc-7SK, are involved in HCV replication through regulating PI4P [246] . Recently, HCV NS3/4A protease was reported to control the activity of 24-dehydrocholesterol reductase, catalyzing the conversion of desmosterol to cholesterol, to regulate the lipid environment for HCV RNA replication [247] . FUSE binding protein 1 is reported to be an essential cellular factor required for HCV replication through inhibiting the function of tumor suppressor p53 [248] . Several other cellular factors were involved in the HCV RNA replication, mTORC1 [249] and chloride channel [250] , but their exact roles are not yet defined. Assembly of HCV particles requires a viral genomic RNA, core proteins (for the capsid formation) and the viral envelope glycoproteins (E1 and E2). In addition to these viral factors, other viral nonstructural proteins and cellular factors, especially VLDL synthesis and secretion, are essential for the HCV assembly (for a review see Reference [251] ). Cleavage at the HCV core protein C-terminus by the intramembrane signal peptide peptidase is required for its maturation and targeting to LDs [252] . The mature core protein, forming the viral capsid, comprises two domains: The amino-terminal domain (D1; a.a. 1-118) and a central domain (D2; a.a. 119-177) [253] . D1 harbors basic aa residues that interact with viral RNA [254] , while D2 is hydrophobic and associated with LDs [252] . LDs are important for the production of infectious HCV particles [255] . As expected, a reduction in the volume of LDs by the suppression of HSC70 expression[23] or disruption of LDs by the inhibitor of aryl hydrocarbon (AhR) [256] would inhibit HCV production. Thus, ADP-ribosylation factor-related protein 1 essential for LD growth is required for HCV propagation [257] , while N-Myc Downstream-Regulated Gene 1 restricts HCV assembly by limiting LD formation [258] . Several cellular factors are involved in the association of the core with LDs. Diacylglycerol acyltransferase-1 (DGAT1) interacts with both the core and NS5A proteins and is required for the trafficking of these two proteins to LDs [259] . PLA2G4A also plays a role in recruiting core to LDs, and its specific cleavage of lipids containing arachidonic acid is essential for the production of infectious viral particles [260] . Interaction of core and Nup98 in LDs is important for HCV propagation [22] , while heterogeneous nuclear ribonucleoprotein K is recruited to sites in close proximity to LDs and suppress HCV production [261] . HCV genomic RNAs synthesized by the HCV replication complex (NS3-NS5B proteins) in the DMVs will be transferred by NS5A and NS3-4A proteins and encapsidated by the viral capsid to form the nucleocapsid. The HCV RNA structure [262] responsible for its encapsidation by core proteins has been suggested to be (1) a highly conserved secondary structure within the core D2 region [263] ; (2) the conserved apical motifs of the 3'X region [264] ; or (3) multiple RNA motifs with a secondary structure [265] . Lipid mobilization from cytoplasmic LDs favors the morphogenesis and secretion of HCV particles [266, 267] . HCV infection suppresses the cellular lysophosphatidylcholine acyltransferase 1 expression resulting in altered lipid metabolism and, in turn, increases the production of infectious viral particles with low density [267] . α/β hydrolase domain-containing protein 5/CGI-58[266] and ATGL lipase [268] also mobilize lipids in LDs for the production of HCV particles. PLA2G4C [215] and AAM-B [269] recruit the NS4B protein to LDs. Thus, these two proteins may bridge the steps of HCV RNA replication and assembly by translocation of RCs to LDs. In addition to DGAT1, CD2AP also participates in the transfer of NS5A to LDs[270] . Interactions between NS5A and core proteins are crucial for productive HCV infection [271] . Protein kinase C and CK substrate in neurons protein 2 [272] and cortactin [273] promote interactions between HCV core and NS5A in the LDs. HCV NS5A protein domain I interacts with the D1 region of core protein [274] . Indeed, core and NS5A proteins are found associated with LDs at 12 h post-infection [275] . The LDs associated with core and NS5A proteins are close to the DMVs and the assembly sites on the ER membrane (Figure 4) . Several studies suggested that the NS5A protein might link DMVs with assembly sites. Two LD-associated proteins, Rab18[226] and TIP47 [276, 277] , were found to interact with NS5A and might help the juxtaposition of replication and assembly sites. Formation of HCV nucleocapsid may occur in the LDs and/or assembly sites ( Figure 4) . Then, HCV nucleocapsid will move to the assembly sites and interact with viral E1/E2 proteins (envelopment) and bud into the ER lumen (egress) (Figure 4) . All viral proteins are involved in HCV assembly [278, 279] . The core and E1/E2 proteins are the integral protein components of an HCV particle. The other viral proteins do help viral assembly and egress, especially NS5A, p7, and NS2 [278] [279] [280] [281] . NS2, ubiquitinated by MARCH8 [282] , is a key regulator of viral assembly by bringing together the structural and nonstructural proteins required for particle formation. The cellular signal peptidase complex subunit 1 interacts with both NS2 and E2 proteins and mediates membrane association of the NS2-E2 complex to control HCV assembly [283] . Then, PLA1A plays a role in bridging NS2-E2 complex and NS5A-associated replication complex through its interaction with E2, NS2 and NS5A [284, 285] . It is likely that NS2 protein brings E1, E2, NS3, NS5A and core proteins together to form a complex within the detergent-resistant membranes in the ER as an assembly platform to initiate HCV assembly [286] . Meanwhile, the clathrin Adaptor Related Protein Complex 2 Subunit Mu 1 [287] and a small GTPase, Rab32 [288] , may transfer nucleocapsids to the sites of envelopment. HRS (hepatocyte growth factor-regulated tyrosine kinase substrate), an endosomal-sorting complex required for transport (ESCRT)-0 complex component, is involved in the viral envelopment [289] . HCV assembly and envelopment are linked to the VLDL synthesis and secretion [290] . Indeed, CIDEB, an important regulator of the VLDL pathway, contributes to the HCV assembly through interacting with NS5A [291] . However, inhibitors of microsomal triglyceride transfer protein (MTTP) affect secretion of HCV more severely than that of VLDL [292] . HCV is also reported to modify VLDL secretion [293, 294] . These results suggest that HCV assembly occurs possibly through modification of the VLDL secretion. Indeed, colocalization of the core with Apo-E but not with Apo-B was demonstrated [295] . Therefore, it is more likely that HCV suppresses VLDL secretion and then uses the excess lipid to produce lipid-rich viral particles. Components of VLDL synthesis, such as MTTP [290] , Apo-B [296] and especially Apo-E[10], have been implicated in HCV assembly. HCV production in HuH7 cells with double knockout of Apo-B/Apo-E was reduced significantly compared to that of single knockout cells, and ectopic expression of Apo-E in cells with double knockout of Apo-B/Apo-E restored production of infectious viruses. Furthermore, ectopic expression of Apo-E or MTTP in cells with double knockout of Apo-B/MTTP could restore infectious virus production [297] . These studies suggested that there are Apo-B-dependent and -July 28, 2021 Volume 27 Issue 28 and assembly sites. HCV genomic RNA synthesized by the replication complex (NS3-NS5B proteins) in the DMVs will be transferred by NS5A and NS3-4A proteins and encapsidated by the core proteins to form the nucleocapsid. Then, the HCV nucleocapsid will interact with glycoproteins E1/E2 in the assembly sites and bud into the ER lumen. Both Apo-B-dependent andindependent mechanisms are possibly involved in HCV particle assembly. One model shows the production of a fused form of HCV with very-low-density lipoproteins. Another model shows the budding of HCV particles with several apolipoproteins but not Apo-B. Nascent viral particles may be further lipidated by luminal lipoproteins and incorporated with exchangeable apolipoproteins. ER: Endoplasmic reticulum. independent virus assembly pathways (Figure 4) . Similar to the effect of ectopic expression of Apo-E in Apo-B/Apo-E double knockout cells, expression of exchangeable apolipoproteins (e.g., Apo-A1, A2, C1, C2 and C3), the peptides of amphipathic α-helices containing the amino-terminal domain of Apo-E [297] or even human cathelicidin antimicrobial peptide [298] also restored infectious virus production. These results suggest that infectious virus production is regulated redundantly by exchangeable apolipoproteins expressed in the liver. Annexin A3 (ANXA3) through facilitating the incorporation of Apo-E [299] and Golgi protein 73, a resident Golgi membrane protein, through facilitating the interaction of HCV NS5A with Apo-E [300] , promote HCV virion maturation. Recently, Apo-M, interacting with E2, was reported to be a novel virus particle-associated protein [301] . After envelopment, HCV particles then traffic to Golgi likely within COPII secretory vesicles [295, 302] . Secretion of infectious HCV particles relies in part on components of the ESCRT pathway [303] . HCV egress but not VLDL secretion is blocked by silencing Rabs and the transGolgi network (TGN)-associating adaptors [304] . Moreover, inhibition of Apo-E secretion using monensin does not impair HCV release. These results suggested that HCV and VLDL use distinct secretion pathways [305] . Altogether, these results suggest that the release of HCV particles occur via a TGNendosomal secretion pathway that is different from that of VLDL. The lipid-associated TM6SF2 (transmembrane 6 superfamily 2) has been demonstrated to promote lipidation and secretion of HCV particles [306] . The secreted HCV particle is likely a single particle fusion of viral structural proteins with various apolipoproteins and lipids (Figure 1) . Autophagy triggered by HCV-induced oxidative stress favors the release of HCV particles [307] . Thus, autophagy may play a role not only in the induction of DMVs but also in the secretion of HCV particles (for a review see Reference [235] ). HCV particles from the sera of HCV-infected patients harbor higher amounts of Apo-E than those derived from cell culture [308] . The interaction of Apo-E and HCV enhances specific infectivity and may aid HCV in evading neutralizing antibodies July 28, 2021 Volume 27 Issue 28 [309] . HCV particles from the blood of HCV-infected patients contain Apo-B100 or Apo-B48, indicating that a significant fraction of HCV particles in blood is also associated with Apo-B48-containing lipoproteins [310] . These results suggested that the interactions between HCV particles and lipoproteins (e.g., Apo-E and Apo-B48) in the blood of HCV patients ( Figure 1B ). Besides lipoproteins, specific serum factors, including albumin, also promote extracellular maturation of HCV particles [311] . Several cellular factors were involved in the assembly and secretion of HCV particles, such as ANXA2 [312] , sorcin (soluble resistance-related calcium-binding protein) [313] , AP-1A, AP-1B, AP-4[101] and O-linked N-acetylglucosamine transferase [314] , but their exact roles are not yet defined. Study on the life cycle of the HCV has progressed tremendously after the development of in vitro HCV culture systems [315] . Understanding the HCV replication cycle led to the huge success of direct-acting anti-virals (DAAs) targeting NS3, NS5A, and NS5B. Hundreds of cellular factors involved in various stages of the HCV's life cycle have also been identified after more than 30 years of research on HCV-host cell interactions. Some of these cellular factors have been selected as targets for anti-HCV therapy (e.g., SR-B1, EGFR, NPC1L1, miR122, CypA) [7] . Inhibitors against these cellular factors may complement existing DAAs. A successful vaccine for HCV is still a challenge in the near future. Understanding the mechanisms of viral entry, especially E2-CD81 interactions, should help in the development of a vaccine. HCV particle, a hybrid lipo-viro-particle, does not look like a canonical enveloped virus. Thus, HCV has become a unique model for studying virus-host interactions, e.g., between HCV and cellular lipid metabolisms. Furthermore, all positive-strand RNA viruses, including coronaviruses and picornaviruses, induce the reorganization of cellular membranes to replicate their genomes, similar to HCV [316] . Using HCV as a paradigm to study how HCV induces cellular membrane re-organization may lead to identification of broad-spectrum antivirals targeting cellular factors commonly used by these viruses. Despite the impressive advances, many issues are still far from being clarified regarding HCV-host cell interactions. More studies are needed to understand the detailed mechanisms. 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functional studies of nonstructural protein 2 of the hepatitis C virus reveal its key role as organizer of virion assembly MARCH8 Ubiquitinates the Hepatitis C Virus Nonstructural 2 Protein and Mediates Viral Envelopment Signal peptidase complex subunit 1 participates in the assembly of hepatitis C virus through an interaction with E2 and NS2 Phosphatidylserine-Specific Phospholipase A1 is the Critical Bridge for Hepatitis C Virus Assembly Phosphatidylserine-specific phospholipase A1 involved in hepatitis C virus assembly through NS2 complex formation Endoplasmic Reticulum Detergent-Resistant Membranes Accommodate Hepatitis C Virus Proteins for Viral Assembly Identification and targeting of an interaction between a tyrosine motif within hepatitis C virus core protein and AP2M1 essential for viral assembly Hepatitis C Virus-Induced Rab32 Aggregation and Its Implications for Virion Assembly Hepatitis C Virus Proteins Interact with the Endosomal Sorting Complex Required for Transport (ESCRT) Machinery via Ubiquitination To Facilitate Viral Envelopment Hepatitis C virus production by human hepatocytes dependent on assembly and secretion of very low-density lipoproteins Cell-death-inducing DFFA-like Effector B Contributes to the Assembly of Hepatitis C Virus (HCV) Particles and Interacts with HCV NS5A Apolipoprotein E but not B is required for the formation of infectious hepatitis C virus particles Hepatitis C virus core protein inhibits microsomal triglyceride transfer protein activity and very low density lipoprotein secretion: a model of viral-related steatosis Ferritin heavy chain is the host factor responsible for HCV-induced inhibition of apoB-100 production and is required for efficient viral infection Molecular determinants and dynamics of hepatitis C virus secretion Secretion of hepatitis C virus envelope glycoproteins depends on assembly of apolipoprotein B positive lipoproteins Amphipathic α-helices in apolipoproteins are crucial to the formation of infectious hepatitis C virus particles Human Cathelicidin Compensates for the Role of Apolipoproteins in Hepatitis C Virus Infectious Particle Formation Quantitative Lipid Droplet Proteome Analysis Identifies Annexin A3 as a Cofactor for HCV Particle Production Golgi protein 73 facilitates the interaction of hepatitis C virus NS5A with apolipoprotein E to promote viral particle secretion identified as a novel hepatitis C virus (HCV) particle associated protein, contributes to HCV assembly and interacts with E2 protein Hepatitis C Virus Lipoviroparticles Assemble in the Endoplasmic Reticulum (ER) and Bud off from the ER to the Golgi Compartment in COPII Vesicles Vps4 and the ESCRT-III complex are required for the release of infectious hepatitis C virus particles Release of Infectious Hepatitis C Virus from Huh7 Cells Occurs via a trans-Golgi Network-to-Endosome Pathway Independent of Very-Low-Density Lipoprotein Secretion TM6SF2 Promotes Lipidation and Secretion of Hepatitis C Virus in 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