Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus–mediated liver disease posttransplantation

Abstract

Liver transplant tissues offer the unique opportunity to model the longitudinal protein abundance changes occurring during hepatitis C virus (HCV)-associated liver disease progression in vivo. In this study, our goal was to identify molecular signatures, and potential key regulatory proteins, representative of the processes influencing early progression to fibrosis. We performed global protein profiling analyses on 24 liver biopsy specimens obtained from 15 HCV+ liver transplant recipients at 6 and/or 12 months post-transplantation. Differentially regulated proteins associated with early progression to fibrosis were identified by analysis of the area under the receiver operating characteristic curve (AUC). Analysis of serum metabolites was performed on samples obtained from an independent cohort of 60 HCV+ liver transplant patients. Computational modeling approaches were applied to identify potential key regulatory proteins of liver fibrogenesis. Among 4,324 proteins identified, 250 exhibited significant differential regulation in patients with rapidly progressive fibrosis. Patients with rapid fibrosis progression exhibited enrichment in differentially regulated proteins associated with various immune, hepatoprotective, and fibrogenic processes. The observed increase in pro-inflammatory activity and impairment in anti-oxidant defenses suggests that patients who develop significant liver injury experience elevated oxidative stresses. This was supported by an independent study demonstrating the altered abundance of oxidative stress associated serum metabolites in patients who develop severe liver injury. Computational modeling approaches further highlight a potentially important link between HCV-associated oxidative stress and epigenetic regulatory mechanisms impacting on liver fibrogenesis. In conclusion, our proteome and metabolome analyses provide new insights into the role for increased oxidative stress in the rapid fibrosis progression observed in HCV+ liver transplant recipients. These findings may prove useful in prognostic applications for predicting early progression to fibrosis.

Endogenous intrahepatic IFNs and association with IFN-free HCV treatment outcome

“…24), whereas expression of other matrix-associated genes (COL1A1, COL1A2, and SPP1) and immunoregulatory genes (IL10 and TGFB1) was not affected (data not shown). In situ hybridization (ISH) in liver biopsies confirmed reduced expression of an ISG mRNA transcript, IFI44, during treatment, regardless of SVR or relapse status, followed by reactivation of its expression at the time of viral relapse ( Figure 2C and Supplemental Figure 1).…”

Metabolic Phenotyping for Enhanced Mechanistic Stratification of Chronic Hepatitis C-Induced Liver Fibrosis

“…Th e robustness of the ELF model is therefore perhaps a refl ection of an increased specifi city achieved through modeling a continuous gradient of metabolic distributions against the continuous ELF parameter, thus producing a metabolic phenotype of fi brosis less prone to infl uences of confounding factors or patient characteristics coincidentally mapping with categorically scored METAVIR classes. It is not perhaps surprising that better correlation is observed between metabolic plasma biomarkers and key serum fi brosis markers accumulation of methionine ( 34,35 ), which has also been linked to oxidative stress in CHC liver transplant patients ( 36 ). Impaired conversion of methionine to S -adenosyl-methionine, resulting in a lack of labile methyl groups for the conversion of creatine from guanidinoacetate ( 37,38 ), may also account for the lower creatine levels observed in patients with higher fi brosis.…”

Can Proteomic Profiling Identify Biomarkers and/or Therapeutic Targets for Liver Fibrosis?

“…Diamond et al demonstrated the effect of oxidative stress proteins to fibrosis progression in biopsy samples of HCV-infected patients [76]. The same group recently analyzed proteomic mechanisms of HCV-mediated liver fibrosis in posttransplant recipients by LC-MS (liquid chromatography coupled mass spectrometry) and demonstrated once again the important role of enhanced oxidative stress in the rapid fibrosis progression observed in HCV-infected liver transplant patients [77]. Ferrin et al studied liver biopsies of HCV-infected alcoholic patients with cirrhosis for altered proteins in the progression of HCC and observed deregulation of ceruloplasmin (CP), paraoxanase (PON1), complement component 4a (CD4a), and fibrinogen-α (FGA) expression [78].…”