Proteomic profiling of human liver biopsies: Hepatitis C virus–induced fibrosis and mitochondrial dysfunction

Abstract

Liver biopsies from hepatitis C virus (HCV)-infected patients offer the unique opportunity to study human liver biology and disease in vivo. However, the low protein yields associated with these small samples present a significant challenge for proteomic analysis. In this study we describe the application of an ultrasensitive proteomics platform for performing robust quantitative proteomic studies on microgram amounts of HCV-infected human liver tissue from 15 patients at different stages of fibrosis. A high-quality liver protein database containing 5,920 unique protein identifications supported high throughput quantitative studies using 16 C hronic infection with hepatitis C virus (HCV), a bloodborne pathogen persistently infecting more than 170 million individuals worldwide, often leads to progressive liver disease, including fibrosis, cirrhosis, and hepatocellular carcinoma. 1 Unfortunately, efforts to manage this growing public health problem have been hindered by the lack of an efficient vaccine and limited efficacy of current treatment modalities (for example, interferon and ribavirin therapy). These observations point to the importance of continued efforts to better understand the molecular mechanisms of viral replication and pathogenesis of HCV-associated disease syndromes. To this end, functional genomics technologies have enormous potential to enhance our understanding of virushost interactions, as well as providing practical insights that will impact medical practice. The identification and characterization of altered regulatory pathways is expected to provide new insights into HCV infection biology and new avenues for drug and vaccine development.

Proteomics analysis of mitochondrial proteins reveals overexpression of a mitochondrial protein chaperon, prohibitin, in cells expressing hepatitis C virus core protein†

“…Mitochondria were purified using Nycodenz (Nycomed Pharma, Zürich, Switzerland) according to the protocols reported by Okado-Matsumoto et al 17 For transient transfection experiments, HepG2 cells were transfected with a core-expression plasmid using TransIT-LT1 (Mirus Bio, Madison, WI). Huh7 cells harboring HCV genotype 1b full-genomic (RCYM1) 18 or subgenomic replicon (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15), and livers of 3-month-old core-gene transgenic mice 2 were also used for the analysis.…”

“…[7][8][9] A recent study found, by the proteomic profiling of biopsy specimens, that an impairment in key mitochondrial processes, including fatty acid oxidation and oxidative phosphorylation, and in the response to oxidative stress occurs in HCV-infected human liver with advanced fibrosis. 10 Therefore, it is probable that the HCV core protein affects mitochondrial functions because such pathogenesis is observed in both HCV core-transgenic mice and HCV-infected patients. [11][12][13] The recent progress in proteomics has opened new avenues for disease-related biomarker discovery.…”

Host–virus interactions during hepatitis C virus infection: a complex and dynamic molecular biosystem

“…[137][138][139][140] One of the first detailed proteomics study related to HCV biology was performed by Yan et al 141 In this study, they used isotope-coded affinity tags (ICAT) to examine differentially expressed proteins during interferon treatment of Huh-7 cells. Their study identified novel IFN regulated proteins and pathways including metabolism and dynamics of microtubule function, thereby providing further insights to the possible mechanisms of antiviral effects of interferon at the protein level and a global view of the antiviral state that the host cell undertakes during interferon treatment.…”

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

“…There are few studies that investigated proteomic changes in HCV-associated fibrogenesis. 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].…”