Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
+44 1223 790975
ISSN: 0974-276X
+44 1223 790975
Bevin Gangadharan, Manisha Bapat, Jan Rossa, Robin Antrobus, David Chittenden, Bettina Kampa, Eleanor Barnes, Paul Klenerman, Raymond A. Dwek and Nicole Zitzmann
Accepted Abstracts: J Proteomics Bioinform
Two-dimensional gel electrophoresis (2-DE) is often used to separate plasma or serum proteins in an attempt to identify novel biomarkers. A major difficulty with this approach is due to high abundant plasma/serum proteins which limits the detection of low abundance features. To overcome this problem a novel proteomics approach was developed and used to identify new fibrosis biomarkers in patients with different stages of liver fibrosis. Plasma samples from healthy individuals and patients with hepatitis C virus (HCV) induced cirrhosis were analysed using 2-DE over a narrow pH 3-5.6 range, a range outside the pH of highly abundant albumin, transferrin and immunoglobulins. Novel markers identified by this approach were validated across all fibrosis stages by Western blotting. 44 candidate biomarkers were revealed of which 20 were novel. Western blot analysis with newly identified biomarkers showed a consistent change with increasing fibrosis stage and were promising when compared to the markers used in established fibrosis tests. This is the first time the pH 3−5.6 range has been used to separate plasma by 2-DE. This pH range is useful for discovering novel biomarkers in all diseases. The novel fibrosis markers identified by this new proteomics approach may help to assess hepatic fibrosis and eliminate the need for invasive liver biopsies.
Bevin Gangadharan is a research associate in the Oxford Glycobiology Institute, Department of Biochemistry at the University of Oxford (http:// www.bioch.ox.ac.uk/glycob/) in the Oxford Antiviral Drug Discovery Unit headed by Dr. Nicole Zitzmann (http://www.bioch.ox.ac.uk/aspsite/index. asp?pageid=608). The Oxford Antiviral Drug Discovery Unit is involved in developing antiviral iminosugars, studying HCV p7 as a drug target and identifying novel fibrosis biomarkers in Hepatitis C patients. Liver biopsy is currently the gold standard for assessing liver fibrosis and since no reliable non-invasive diagnostic approach is currently available, a suitable serologic biomarker of liver fibrosis is urgently needed. The main focus of Dr. Bevin Gangadharan?s research is to use proteomics to identify novel serum biomarker candidates for liver fibrosis in hepatitis C patients and to validate these biomarkers. He has used proteomics to identify potential fibrosis biomarkers by comparing serum from healthy controls with serum from patients with varying degrees of hepatic fibrosis induced by infection with HCV (1,2). He has identified numerous candidate biomarkers for liver fibrosis which could help to establish a less invasive way of diagnosing hepatic scarring. He is currently following up the work in the liver fibrosis biomarker study by using other proteomics techniques to identify more biomarkers in plasma (3,4,5,6,7), validate these markers by Western blotting and use immunoassays to determine the concentrations of the biomarkers in plasma samples from patients with varying degrees of hepatic scarring. He works with others in the Oxford Antiviral Drug Discovery Unit and collaborators to help use proteomics to investigate several viral systems. This includes the identification of protein expression changes in cells infected with HCV (8), hepatitis B virus (HBV) (9), herpes simplex virus (HSV) (10) and also using proteomics to investigate cell signalling in HIV (11) and the effect of HCV p7 on cellular proteins. He also trains students to use proteomics techniques for their projects such as analysing the effect of interferon and liposomes on cellular protein expression in HCV infected and mock infected cells.