Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis

Melis A Aksit, Hua Ling, Rhonda G Pace, Karen S Raraigh, Frankline Onchiri, Anna V Faino, Kymberleigh Pagel, Elizabeth Pugh, Adrienne M Stilp, Quan Sun, Elizabeth E Blue, Fred A Wright, Yi-Hui Zhou, Michael J Bamshad, Ronald L Gibson, Michael R Knowles, Garry R Cutting, Scott M Blackman, CF Genome Project, Melis A Aksit, Michael J Bamshad, Scott M Blackman, Elizabeth Blue, Kati Buckingham, Jessica X Chong, J Michael Collaco, Garry R Cutting, Hong Dang, Alice Eastman, Anna Faino, Paul J Gallins, Ronald Gibson, Beth Godwin, William W Gordon, Kurt Hetrick, Le Huang, Michael R Knowles, Anh-Thu N Lam, Hua Ling, Weifang Liu, Yun Li, Frankline Onchiri, Wanda K O'Neal, Rhonda G Pace, Kymberleigh Pagel, Mark Porter, Elizabeth Pugh, Karen S Raraigh, Rebekah Mikeasky, Margaret Rosenfeld, Jonathan Rosen, Adrienne Stilp, Jaclyn R Stonebraker, Quan Sun, Jia Wen, Fred A Wright, Yingxi Yang, Peng Zhang, Yan Zhang, Yi-Hui Zhou, Melis A Aksit, Hua Ling, Rhonda G Pace, Karen S Raraigh, Frankline Onchiri, Anna V Faino, Kymberleigh Pagel, Elizabeth Pugh, Adrienne M Stilp, Quan Sun, Elizabeth E Blue, Fred A Wright, Yi-Hui Zhou, Michael J Bamshad, Ronald L Gibson, Michael R Knowles, Garry R Cutting, Scott M Blackman, CF Genome Project, Melis A Aksit, Michael J Bamshad, Scott M Blackman, Elizabeth Blue, Kati Buckingham, Jessica X Chong, J Michael Collaco, Garry R Cutting, Hong Dang, Alice Eastman, Anna Faino, Paul J Gallins, Ronald Gibson, Beth Godwin, William W Gordon, Kurt Hetrick, Le Huang, Michael R Knowles, Anh-Thu N Lam, Hua Ling, Weifang Liu, Yun Li, Frankline Onchiri, Wanda K O'Neal, Rhonda G Pace, Kymberleigh Pagel, Mark Porter, Elizabeth Pugh, Karen S Raraigh, Rebekah Mikeasky, Margaret Rosenfeld, Jonathan Rosen, Adrienne Stilp, Jaclyn R Stonebraker, Quan Sun, Jia Wen, Fred A Wright, Yingxi Yang, Peng Zhang, Yan Zhang, Yi-Hui Zhou

Abstract

Individuals with cystic fibrosis (CF) develop complications of the gastrointestinal tract influenced by genetic variants outside of CFTR. Cystic fibrosis-related diabetes (CFRD) is a distinct form of diabetes with a variable age of onset that occurs frequently in individuals with CF, while meconium ileus (MI) is a severe neonatal intestinal obstruction affecting ∼20% of newborns with CF. CFRD and MI are slightly correlated traits with previous evidence of overlap in their genetic architectures. To better understand the genetic commonality between CFRD and MI, we used whole-genome-sequencing data from the CF Genome Project to perform genome-wide association. These analyses revealed variants at 11 loci (6 not previously identified) that associated with MI and at 12 loci (5 not previously identified) that associated with CFRD. Of these, variants at SLC26A9, CEBPB, and PRSS1 associated with both traits; variants at SLC26A9 and CEBPB increased risk for both traits, while variants at PRSS1, the higher-risk alleles for CFRD, conferred lower risk for MI. Furthermore, common and rare variants within the SLC26A9 locus associated with MI only or CFRD only. As expected, different loci modify risk of CFRD and MI; however, a subset exhibit pleiotropic effects indicating etiologic and mechanistic overlap between these two otherwise distinct complications of CF.

Keywords: CFRD; cystic fibrosis; cystic fibrosis-related diabetes; diabetes; genetic modifier; intestinal obstruction; meconium ileus; pleiotropy.

Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Copyright © 2022 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Figures

Figure 1
Figure 1
Kaplan-Meier plots for age of onset of CFRD Plots divided by history of meconium ileus and site of enrollment in (A) everyone, (B) individuals born after 1970, (C) F508del homozygotes, and (D) F508del homozygotes born after 1970.
Figure 2
Figure 2
Manhattan plots of phase 1 + 2 combined association analyses Association analysis was performed on all variants with minor allele frequency (MAF) > 0.5% that passed quality control criteria. The x axis indicates chromosomal position, and the y axis indicates the strength of evidence for association with meconium ileus (−log10[p value]) (top) or cystic fibrosis-related diabetes (bottom). Adjusted models include additional covariates of MI or CFRD. The black line corresponds to the genome-wide significance threshold (p value 5e−8). Labels in bold exceed genome-wide significance and in regular font exceeded suggestive significance. Labels in blue are not previously identified for MI, purple are not previously identified for CFRD, and black are previously known. CEBPB falls below the suggestive threshold in the adjusted analyses, so it is labeled in parentheses.
Figure 3
Figure 3
Comparison of the genetic risk architectures of CFRD and MI Comparison of p values of each variant for association with MI and CFRD. All variants have been plotted. The MI log10(p value) was defined as positive when the risk alleles were concordant between CFRD and MI.
Figure 4
Figure 4
Forest plot of significant loci (genome-wide significant, suggestive significant, or candidate-based significant) Summary statistics in the adjusted analyses are shown. Genomic positions are in GRCh38. §Aksit et al. ‡Gong et al. EA, effect allele; OA, other allele; EAF: effect allele frequency.
Figure 5
Figure 5
LocusZoom plots for the SLC26A9 locus (A) LocusZoom plot for association with MI in the CFGP cohort, adjusted with a covariate of CFRD Martingale residuals. (B) LocusZoom plot for association with CFRD Martingale residuals in the CFGP cohort, adjusted with a covariate of MI. (C) D′ linkage disequilibrium plot created on Haploview demonstrating the linkage disequilibrium between key SNPs in the region in the CFGP cohort.
Figure 6
Figure 6
LocusZoom plots for the CEBPB locus (A) LocusZoom plot for association with MI in the CFGP cohort, adjusted with a covariate of CFRD Martingale residuals. (B) LocusZoom plot for association with CFRD Martingale residuals in the CFGP cohort, adjusted with a covariate of MI. (C) R-squared linkage disequilbrium plot created on Haploview demonstrating the linkage disequilibrium between key SNPs in the region in the CFGP cohort.
Figure 7
Figure 7
LocusZoom and linkage disequilibrium plots for the PRSS1 locus (A) LocusZoom plot for association with MI, adjusted with a covariate of CFRD Martingale residuals. (B) LocusZoom plot for association with CFRD Martingale residuals, adjusted with a covariate of MI. (C) R-squared linkage disequilibrium plot created on Haploview demonstrating the linkage disequilibrium between key SNPs in the region in the CFGP cohort.
Figure 8
Figure 8
LocusZoom plots for the CLPS locus (A) LocusZoom plot for association with MI, adjusted with a covariate of CFRD Martingale residuals. (B) LocusZoom plot for association with CFRD Martingale residuals, adjusted with a covariate of MI.

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