High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors

PLoS Genet. 2017 Jan 27;13(1):e1006565. doi: 10.1371/journal.pgen.1006565. eCollection 2017 Jan.


To date, no large scale, systematic description of the blood serum proteome has been performed in inflammatory bowel disease (IBD) patients. By using microarray technology, a more complete description of the blood proteome of IBD patients is feasible. It may help to achieve a better understanding of the disease. We analyzed blood serum profiles of 1128 proteins in IBD patients of European descent (84 Crohn's Disease (CD) subjects and 88 Ulcerative Colitis (UC) subjects) as well as 15 healthy control subjects, and linked protein variability to patient age (all cohorts) and genetic components (genotype data generated from CD patients). We discovered new, previously unreported aging-associated proteomic traits (such as serum Albumin level), confirmed previously reported results from different tissues (i.e., upregulation of APOE with aging), and found loss of regulation of MMP7 in CD patients. In carrying out a genome wide genotype-protein association study (proteomic Quantitative Trait Loci, pQTL) within the CD patients, we identified 41 distinct proteomic traits influenced by cis pQTLs (underlying SNPs are referred to as pSNPs). Significant overlaps between pQTLs and cis eQTLs corresponding to the same gene were observed and in some cases the QTL were related to inflammatory disease susceptibility. Importantly, we discovered that serum protein levels of MST1 (Macrophage Stimulating 1) were regulated by SNP rs3197999 (p = 5.96E-10, FDR<5%), an accepted GWAS locus for IBD. Filling the knowledge gap of molecular mechanisms between GWAS hits and disease susceptibility requires systematically dissecting the impact of the locus at the cell, mRNA expression, and protein levels. The technology and analysis tools that are now available for large-scale molecular studies can elucidate how alterations in the proteome driven by genetic polymorphisms cause or provide protection against disease. Herein, we demonstrated this directly by integrating proteomic and pQTLs with existing GWAS, mRNA expression, and eQTL datasets to provide insights into the biological processes underlying IBD and pinpoint causal genetic variants along with their downstream molecular consequences.

Trial registration: ClinicalTrials.gov NCT00771667.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aging / blood*
  • Biomarkers / blood
  • Case-Control Studies
  • Female
  • Genetic Predisposition to Disease*
  • Hepatocyte Growth Factor / blood
  • High-Throughput Screening Assays
  • Humans
  • Inflammatory Bowel Diseases / blood*
  • Inflammatory Bowel Diseases / epidemiology
  • Inflammatory Bowel Diseases / genetics
  • Male
  • Middle Aged
  • Polymorphism, Single Nucleotide
  • Proteome / genetics
  • Proteome / metabolism*
  • Proto-Oncogene Proteins / blood
  • Quantitative Trait Loci


  • Biomarkers
  • Proteome
  • Proto-Oncogene Proteins
  • macrophage stimulating protein
  • Hepatocyte Growth Factor

Associated data

  • ClinicalTrials.gov/NCT00771667

Grants and funding

This work is partially supported by Janssen R&D, LLC. The contributions of Janssen R&D, LLC included study design, data generation, analysis, interpretation of the results and preparation of the manuscript. Dr. Ke Hao is partially supported by the National Natural Science Foundation of China (Grant No. 21477087, 91643201) and by the Ministry of Science and Technology of China (Grant No. 2016YFC0206507).