| Literature DB >> 23143602 |
David C Whitcomb1, Jessica LaRusch, Alyssa M Krasinskas, Lambertus Klei, Jill P Smith, Randall E Brand, John P Neoptolemos, Markus M Lerch, Matt Tector, Bimaljit S Sandhu, Nalini M Guda, Lidiya Orlichenko, Samer Alkaade, Stephen T Amann, Michelle A Anderson, John Baillie, Peter A Banks, Darwin Conwell, Gregory A Coté, Peter B Cotton, James DiSario, Lindsay A Farrer, Chris E Forsmark, Marianne Johnstone, Timothy B Gardner, Andres Gelrud, William Greenhalf, Jonathan L Haines, Douglas J Hartman, Robert A Hawes, Christopher Lawrence, Michele Lewis, Julia Mayerle, Richard Mayeux, Nadine M Melhem, Mary E Money, Thiruvengadam Muniraj, Georgios I Papachristou, Margaret A Pericak-Vance, Joseph Romagnuolo, Gerard D Schellenberg, Stuart Sherman, Peter Simon, Vijay P Singh, Adam Slivka, Donna Stolz, Robert Sutton, Frank Ulrich Weiss, C Mel Wilcox, Narcis Octavian Zarnescu, Stephen R Wisniewski, Michael R O'Connell, Michelle L Kienholz, Kathryn Roeder, M Michael Barmada, Dhiraj Yadav, Bernie Devlin.
Abstract
Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR and SPINK1 variants were associated with pancreatitis risk. We now report two associations at genome-wide significance identified and replicated at PRSS1-PRSS2 (P < 1 × 10(-12)) and X-linked CLDN2 (P < 1 × 10(-21)) through a two-stage genome-wide study (stage 1: 676 cases and 4,507 controls; stage 2: 910 cases and 4,170 controls). The PRSS1 variant likely affects disease susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous (or hemizygous in males) CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men (male hemizygote frequency is 0.26, whereas female homozygote frequency is 0.07).Entities:
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Year: 2012 PMID: 23143602 PMCID: PMC3510344 DOI: 10.1038/ng.2466
Source DB: PubMed Journal: Nat Genet ISSN: 1061-4036 Impact factor: 38.330
Characterization of case subjects used for GWAS[*].
| chronic pancreatitis | recurrent acute pancreatitis | chronic pancreatitis + recurrent acute pancreatitis | |||
|---|---|---|---|---|---|
| Stage 1 | 676 | -- | 676 | ||
| Alcohol-related pancreatitis [ | Yes | 264 | -- | 264 | |
| No | 411 | -- | 411 | ||
| Unknown | 1 | -- | 1 | ||
| Stage 2 | 331 | 579 | 910 | ||
| Alcohol-related pancreatitis [ | Yes | 70 | 113 | 183 | |
| No | 256 | 462 | 718 | ||
| Unknown | 5 | 4 | 9 | ||
| Combined | 930 | 579 | 1506 | ||
| Alcohol-related pancreatitis [ | Yes | 334 | 113 | 447 | |
| No | 667 | 462 | 1129 | ||
| Unknown | 6 | 4 | 10 | ||
Does not include information from controls in Stage 1 (n=4514) or from Stage 2 (n=4053). For more complete characterization of samples, please see Supplementary Table 1 in the Appendix.
Alcohol-related pancreatitis was assigned by the study physician at enrollment.
Figure 1Manhattan plot showing the negative log (base 10) of the p-value for the association of SNP genotype with affection status for all SNPs passing quality control filters and falling within a selected region of the PRSS1-PRSS2 and CLDN2 loci. Regions selected to highlight the most associated SNPs. Squares indicate Stage 1 results, circles for Stage 2, diamonds for combined Stage 1 and 2 data. After accounting for the most highly associated SNP at each locus, no other SNP approached genomewide-significant association.
Results for leading SNPs at the PRSS1-PRSS2 and CLDN2 loci from Stage 1, Stage 2, and joint analysis.
| CP + RAP | CP | CP + RAP | CP + RAP | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Allele Frequency (A1) | Stage 1 | Stage 2 | Combined | ||||||||||||
| CHR | SNP | BP | A1[ | A2 | cases | controls | OR | se(OR) | P | OR | se(OR) | P | OR | se(OR) | P |
| 7 | rs10273639 | 142456928 | T | C | 0.350 | 0.424 | 0.712 | 0.044 | 3.0×10-8 | 0.748 | 0.039 | 7.5×10-8 | 0.734 | 0.029 | 2.0×10-14 |
| X | rs7057398 | 106144529 | C | T | 0.374 | 0.281 | 1.493 | 0.075 | 1.4×10-15 | 1.210 | 0.066 | 1.8×10-5 | 1.321 | 0.049 | 4.6×10-17 |
| X | rs12688220 | 106244767 | T | C | 0.367 | 0.261 | 1.612 | 0.081 | 2.4×10-21 | 1.238 | 0.073 | 2.3×10-6 | 1.385 | 0.054 | 2.3×10-22 |
A1 is the allele counted for purposes of computing odds ratio and associated statistics. The model used here includes covariates to control for the two leading eigenvectors for ancestry, as was done in the Plink analyses, but differs in its treatment of the minor allele count for the CLDN2 locus, which resides on the × chromosome (as described in Online Methods). Alleles given are refSNP alleles according to dbSNP. See Supplementary Table 2 for all SNPs passing quality control and showing p-value < 5×10-7 for Stage 1 or Stage 2 or the joint analysis.
Figure 2Expression and localization of claudin-2 in the human pancreas using mouse anti-claudin-2 antibodies based on rs12688220 genotype. A. Western blot of anti-claudin-2 antibody from 3 control samples genotyped at rs12688220 (TT is high risk). The antibody reacts with a protein at ~22-23 kDa, consistent with claudin-2. Samples had inflammation and/or fibrosis on histology of adjacent tissue. α-tubulin, loading control. Blots from all controls are presented in Supplementary Figure 8. B. Anti-claudin-2 staining (brown color) of normal-appearing control tissue localizing to ducts but not to acinar cells (scale bar=50μm). C. Severe chronic pancreatitis from a case with the high-risk (T male or TT female) genotype. Claudin-2 staining localizes to the intralobular duct (Duct), atrophic acini (*), and cells with morphologic appearance of macrophages (arrow)(scale bar=50μm). D. Chronic pancreatitis tissue from a patient with the low-risk genotype (CC or CT) with staining localizing to the duct and granular staining in acinar cells (scale bar = 100 μm). E. Chronic pancreatitis, high-risk genotype with intense staining of acinar cell basolateral membrane (scale bar=100 μm, enlarged in inset, scale bar=10μm). F. Immunofluorescence staining of control human pancreatic tissue claudin-2 staining (red) localizing to the ducts (*) and co-localizing with the macrophage marker CD68 (green, colocalized with red is yellow, arrows. Nuclei stained with Hoechst's dye, blue, scale bar = 100μm).
Allele frequencies for rs10273639 (risk allele C) and rs12688220 (risk allele T) when data are stratified by controls or pancreatitis ± alcohol-related diagnosis.
| Status | Alcohol-related | Number of individuals | rs10273639[ | rs12688220[ |
|---|---|---|---|---|
| Control | -- | 8029 | 0.576 | 0.261 |
| Pancreatitis | No | 1129 | 0.634 | 0.322 |
| Yes | 447 | 0.696 | 0.427 |
Using data from cases only and in a joint analysis of both SNPs, rs12688220 predicts alcohol-related pancreatitis as genotypes (χ2=29.57; DF=2; p-value = 4×10-7) or count of risk alleles (χ2=13.17; DF=1; p-value = 3×10-4). rs10273639 (PRSS1-PRSS2 locus) is a significant predictor (count of risk alleles: χ2=5.68; DF=1; p-value = 0.017; genotypes: χ2=6.05; DF=2; p-value = 0.049), even after accounting for the effects of rs12688220.