Serum Proteomic Profiles Associated with IL28B Genotype among CHC Patients
1
McCarthy ,
1
Cyr ,
1
Lucas,
1
Thompson,
2
Patel , Alexander
Jeanette J.
Derek
Joseph
J. Will
Keyur
Hans L. Tillmann,2, Paul J. Clark2, M. Arthur Moseley1 and John G. McHutchison2.
1
2
Thompson ,
Institute for Genome Sciences and Policy, Duke University, Durham, NC ; 2 Duke Clinical Research Institute and Duke University Medical Center, Durham, NC
Background
Results
• SNP near the gene IL28B (encoding IFN-λ3) are
associated with both spontaneous and treatment (Peg-IFN
& Riba) induced clearance of hepatitis C virus (HCV).
• Subject characteristics: Caucasian (78%); males (61%);
mean age 47.4 years; sustained virologic responders to
treatment (63%).
• The underlying genetic variant(s) responsible for this
observed association remains to be identified, yet several
SNPs, including rs12979860, appear to be robust markers
of its effect.
• LC-MS/MS generated 4,186 peptides with positive
identifications, which latent factor modeling grouped
into 110 metaproteins.
• In an effort to gain further insight into the function of this
locus, we carried out association analysis of rs12979860
with expression of serum protein quantitative traits in a
cohort of patients with chronic hepatitis C (CHC).
Methods
• Subjects: 41 HCV genotype 1 CHC patients from the
Duke Liver Clinic with serum samples available prior to
treatment and DNA available for genetic analysis.
• IL28B rs12979860 genotyping method: TaqMan.
• Two metaproteins significantly associated with IL28B
genotype: the liver protein Corticosteroid Binding
Globulin (CBG; p = 9.2×10-6) and complement
component C5 (p = 0.005). Only CBG remained
significant after correction for multiple testing.
• rs12979860 ‘C’ (responder) allele was associated with
lower levels of CBG metaprotein and explained 38% of
the variance in CBG metaprotein. (Figure 1).
Figure 1.
• CBG metaprotein composition shown in Figure 2.
Figure 2. CBG metaprotein peptide composition.
Each gray bar is a representation of the labeled protein. Red sections
represent polypeptides from isotope groups that are in the factor and
black sections represent polypeptides from the isotope groups that are
identified in the data set but are not in the factor. Gray represents
sections of the protein that are not identified in the data set. % Coverage
is the percent of identified peptides from that protein that are in the factor
and % signature is the percent of the factor that comes from the
associated protein. Note that the sum of % signature is <1 because there
are unidentified peptides in the factor that are not shown in the figure.
• Proteomic data: generated using LC-MS/MS analysis of
pre-treatment serum samples immunodepleted using
MARS14 columns and digested with trypsin.
• Associations also found between the IL28B rs12979860
genotype and SVR (p = 5.06×10-5) and between CBG
metaprotein expression and SVR (p = 0.0011).
• Analysis: Peptides with protein identifications were
grouped using a latent factor model with informative
priors to classify the peptides into 110 metaproteins.
Metaproteins were each analyzed for association with
IL28B genotype using one-way analysis of variance.
• Ingenuity Pathway analysis linked IL28B and CBG via
steroid hormones (corticosteroids and progestins) and
proinflammatory cytokines (tumor necrosis factor and
interferon gamma) (Figure 3) .
Figure 3. Ingenuity Pathway Analysis.
Conclusions
• IL28B rs12979860 is strongly associated with serum
levels of corticosteroid binding globulin peptides.
• CBG, also known as Transcortin, is a major high-affinity
plasma transport protein for glucocorticoids and
progestins and is expressed primarily in the liver.
• IL28B’s effect on viral clearance may be partly mediated
through the action of steroid hormones.
• Studies that incorporate direct measures of cortisol and
CBG may provide further validation of the role of
corticosteroids in IL28B-associated viral clearance.
This study was funded in large part by a generous grant from the David H
Murdock Institute for Business and Culture via the M.U.R.D.O.C.K. Study and
NIH CTSA award 1 UL1 RR024128-01 to Duke University.