Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics

Proteomics. 2004 Oct;4(10):3235-45. doi: 10.1002/pmic.200400839.


Liver cirrhosis is a worldwide health problem. Reliable, noninvasive methods for early detection of liver cirrhosis are not available. Using a three-step approach, we classified sera from rats with liver cirrhosis following different treatment insults. The approach consisted of: (i) protein profiling using surface-enhanced laser desorption/ionization (SELDI) technology; (ii) selection of a statistically significant serum biomarker set using machine learning algorithms; and (iii) identification of selected serum biomarkers by peptide sequencing. We generated serum protein profiles from three groups of rats: (i) normal (n=8), (ii) thioacetamide-induced liver cirrhosis (n=22), and (iii) bile duct ligation-induced liver fibrosis (n=5) using a weak cation exchanger surface. Profiling data were further analyzed by a recursive support vector machine algorithm to select a panel of statistically significant biomarkers for class prediction. Sensitivity and specificity of classification using the selected protein marker set were higher than 92%. A consistently down-regulated 3495 Da protein in cirrhosis samples was one of the selected significant biomarkers. This 3495 Da protein was purified on-chip and trypsin digested. Further structural characterization of this biomarkers candidate was done by using cross-platform matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) peptide mass fingerprinting (PMF) and matrix-assisted laser desorption/ionization time of flight/time of flight (MALDI-TOF/TOF) tandem mass spectrometry (MS/MS). Combined data from PMF and MS/MS spectra of two tryptic peptides suggested that this 3495 Da protein shared homology to a histidine-rich glycoprotein. These results demonstrated a novel approach to discovery of new biomarkers for early detection of liver cirrhosis and classification of liver diseases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Biomarkers, Tumor
  • Computational Biology / methods*
  • Down-Regulation
  • Liver / metabolism
  • Liver Cirrhosis / metabolism*
  • Male
  • Peptides / chemistry
  • Proteins / chemistry
  • Proteomics / methods*
  • Rats
  • Sensitivity and Specificity
  • Software
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Trypsin / chemistry
  • Trypsin / pharmacology


  • Biomarkers, Tumor
  • Peptides
  • Proteins
  • histidine-rich proteins
  • Trypsin