Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci

Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes....

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Published inPLoS genetics Vol. 15; no. 2; p. e1008007
Main Authors Gong, Jiafen, Wang, Fan, Xiao, Bowei, Panjwani, Naim, Lin, Fan, Keenan, Katherine, Avolio, Julie, Esmaeili, Mohsen, Zhang, Lin, He, Gengming, Soave, David, Mastromatteo, Scott, Baskurt, Zeynep, Kim, Sangook, O'Neal, Wanda K, Polineni, Deepika, Blackman, Scott M, Corvol, Harriet, Cutting, Garry R, Drumm, Mitchell, Knowles, Michael R, Rommens, Johanna M, Sun, Lei, Strug, Lisa J
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 26.02.2019
Public Library of Science (PLoS)
Subjects
Amino Acid Transport Systems, Neutral - genetics
Amino Acid Transport Systems, Neutral - metabolism
Antiporters - genetics
Antiporters - metabolism
Biochemistry, Molecular Biology
Bioinformatics
Biology
Biology and Life Sciences
CF gene
Chromosome 1
Chromosome 13
Chromosome 7
Cystic fibrosis
Cystic Fibrosis - genetics
Cystic Fibrosis - metabolism
Disease susceptibility
Female
Fibrosis
Funding
Gastrointestinal diseases
Gene expression
Gene Expression Profiling - methods
Gene Expression Regulation
Genes
Genetic aspects
Genetics
Genome-Wide Association Study - methods
Genomes
Genomics
Genotype & phenotype
H(+)-K(+)-Exchanging ATPase - genetics
H(+)-K(+)-Exchanging ATPase - metabolism
Haplotypes
Health aspects
Hospitals
Human genetics
Humans
Intestinal obstruction
Intestine
Life Sciences
Lung - metabolism
Lung diseases
Male
Meconium
Medical research
Medicine
Medicine and Health Sciences
Morbidity
Organ Specificity
Pancreas
Pancreas, Exocrine - metabolism
Pancreatitis
Pediatrics
Precision medicine
Public health
Quantitative genetics
Quantitative trait loci
Research and Analysis Methods
Respiratory tract
Respiratory tract diseases
Social Sciences
Sulfate Transporters - genetics
Sulfate Transporters - metabolism
Susceptibility
Trypsin - genetics
Trypsin - metabolism
North Carolina
Canada
United States > US
Ohio
France
Maryland
Baltimore Maryland
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Abstract Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10(-10)); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p<2.2x10(-16), 2.81x10(-11), respectively); and replicated a suggestive locus on chromosome 7 near PRSS1 (min p = 2.55x10(-7)). PRSS1 is exclusively expressed in the exocrine pancreas and was previously associated with non-CF pancreatitis with functional characterization demonstrating impact on PRSS1 gene expression. We thus asked whether the other meconium ileus modifier loci impact gene expression and in which organ. We developed and applied a colocalization framework called the Simple Sum (SS) that integrates regulatory and genetic association information, and also contrasts colocalization evidence across tissues or genes. The associated modifier loci colocalized with expression quantitative trait loci (eQTLs) for ATP12A (p = 3.35x10(-8)), SLC6A14 (p = 1.12x10(-10)) and SLC26A9 (p = 4.48x10(-5)) in the pancreas, even though meconium ileus manifests in the intestine. The meconium ileus susceptibility locus on chromosome X appeared shifted in location from a previously identified locus for CF lung disease severity. Using the SS we integrated the lung disease association locus with eQTLs from nasal epithelia of 63 CF participants and demonstrated evidence of colocalization with airway-specific regulation of SLC6A14 (p = 2.3x10(-4)). Cystic Fibrosis is realizing the promise of personalized medicine, and identification of the contributing organ and understanding of tissue specificity for a gene modifier is essential for the next phase of personalizing therapeutic strategies.
AbstractList Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10(-10)); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p<2.2x10(-16), 2.81x10(-11), respectively); and replicated a suggestive locus on chromosome 7 near PRSS1 (min p = 2.55x10(-7)). PRSS1 is exclusively expressed in the exocrine pancreas and was previously associated with non-CF pancreatitis with functional characterization demonstrating impact on PRSS1 gene expression. We thus asked whether the other meconium ileus modifier loci impact gene expression and in which organ. We developed and applied a colocalization framework called the Simple Sum (SS) that integrates regulatory and genetic association information, and also contrasts colocalization evidence across tissues or genes. The associated modifier loci colocalized with expression quantitative trait loci (eQTLs) for ATP12A (p = 3.35x10(-8)), SLC6A14 (p = 1.12x10(-10)) and SLC26A9 (p = 4.48x10(-5)) in the pancreas, even though meconium ileus manifests in the intestine. The meconium ileus susceptibility locus on chromosome X appeared shifted in location from a previously identified locus for CF lung disease severity. Using the SS we integrated the lung disease association locus with eQTLs from nasal epithelia of 63 CF participants and demonstrated evidence of colocalization with airway-specific regulation of SLC6A14 (p = 2.3x10(-4)). Cystic Fibrosis is realizing the promise of personalized medicine, and identification of the contributing organ and understanding of tissue specificity for a gene modifier is essential for the next phase of personalizing therapeutic strategies.
Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10 -10 ); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p<2.2x10 -16 , 2.81x10 −11 , respectively); and replicated a suggestive locus on chromosome 7 near PRSS1 (min p = 2.55x10 -7 ). PRSS1 is exclusively expressed in the exocrine pancreas and was previously associated with non-CF pancreatitis with functional characterization demonstrating impact on PRSS1 gene expression. We thus asked whether the other meconium ileus modifier loci impact gene expression and in which organ. We developed and applied a colocalization framework called the Simple Sum (SS) that integrates regulatory and genetic association information, and also contrasts colocalization evidence across tissues or genes. The associated modifier loci colocalized with expression quantitative trait loci (eQTLs) for ATP12A (p = 3.35x10 -8 ), SLC6A14 (p = 1.12x10 -10 ) and SLC26A9 (p = 4.48x10 -5 ) in the pancreas, even though meconium ileus manifests in the intestine. The meconium ileus susceptibility locus on chromosome X appeared shifted in location from a previously identified locus for CF lung disease severity. Using the SS we integrated the lung disease association locus with eQTLs from nasal epithelia of 63 CF participants and demonstrated evidence of colocalization with airway-specific regulation of SLC6A14 (p = 2.3x10 -4 ). Cystic Fibrosis is realizing the promise of personalized medicine, and identification of the contributing organ and understanding of tissue specificity for a gene modifier is essential for the next phase of personalizing therapeutic strategies. Cystic Fibrosis (CF) impacts the normal functioning of several organs including the pancreas, intestines and lungs. CF is caused by mutations in the CF transmembrane conductance regulator, but individuals with the same mutations have different disease severity. For example, only ~15% of individuals with CF are born with intestinal obstruction at birth (meconium ileus) while all have progressive lung disease with varying severity. Modifier genes contribute to variation across individuals with CF. In this study we identified modifiers of meconium ileus susceptibility, encompassing the previously identified SLC26A9 and SLC6A14 , and two new loci ATP12A and PRSS1 . To understand the mechanism by which these modifier genes impact CF severity we developed a new statistical method that assesses colocalization with regulatory information. Using this methodology we show, surprisingly, that all the meconium ileus association signals colocalize with gene expression in the pancreas rather than in intestinal tissues. A distinct and neighbouring locus near SLC6A14 also contributes to CF lung disease. Aided by transcriptomics of nasal epithelia from CF patients we found that each locus impacts variation in gene expression of SLC6A14 with tissue specificity. Understanding the contributing tissue and responsible gene are necessary to prioritize modifiers as alternative therapeutic targets.
Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10-10); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p<2.2x10-16, 2.81x10−11, respectively); and replicated a suggestive locus on chromosome 7 near PRSS1 (min p = 2.55x10-7). PRSS1 is exclusively expressed in the exocrine pancreas and was previously associated with non-CF pancreatitis with functional characterization demonstrating impact on PRSS1 gene expression. We thus asked whether the other meconium ileus modifier loci impact gene expression and in which organ. We developed and applied a colocalization framework called the Simple Sum (SS) that integrates regulatory and genetic association information, and also contrasts colocalization evidence across tissues or genes. The associated modifier loci colocalized with expression quantitative trait loci (eQTLs) for ATP12A (p = 3.35x10-8), SLC6A14 (p = 1.12x10-10) and SLC26A9 (p = 4.48x10-5) in the pancreas, even though meconium ileus manifests in the intestine. The meconium ileus susceptibility locus on chromosome X appeared shifted in location from a previously identified locus for CF lung disease severity. Using the SS we integrated the lung disease association locus with eQTLs from nasal epithelia of 63 CF participants and demonstrated evidence of colocalization with airway-specific regulation of SLC6A14 (p = 2.3x10-4). Cystic Fibrosis is realizing the promise of personalized medicine, and identification of the contributing organ and understanding of tissue specificity for a gene modifier is essential for the next phase of personalizing therapeutic strategies.
Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10.sup.-10 ); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p<2.2x10.sup.-16, 2.81x10.sup.-11, respectively); and replicated a suggestive locus on chromosome 7 near PRSS1 (min p = 2.55x10.sup.-7). PRSS1 is exclusively expressed in the exocrine pancreas and was previously associated with non-CF pancreatitis with functional characterization demonstrating impact on PRSS1 gene expression. We thus asked whether the other meconium ileus modifier loci impact gene expression and in which organ. We developed and applied a colocalization framework called the Simple Sum (SS) that integrates regulatory and genetic association information, and also contrasts colocalization evidence across tissues or genes. The associated modifier loci colocalized with expression quantitative trait loci (eQTLs) for ATP12A (p = 3.35x10.sup.-8 ), SLC6A14 (p = 1.12x10.sup.-10) and SLC26A9 (p = 4.48x10.sup.-5) in the pancreas, even though meconium ileus manifests in the intestine. The meconium ileus susceptibility locus on chromosome X appeared shifted in location from a previously identified locus for CF lung disease severity. Using the SS we integrated the lung disease association locus with eQTLs from nasal epithelia of 63 CF participants and demonstrated evidence of colocalization with airway-specific regulation of SLC6A14 (p = 2.3x10.sup.-4). Cystic Fibrosis is realizing the promise of personalized medicine, and identification of the contributing organ and understanding of tissue specificity for a gene modifier is essential for the next phase of personalizing therapeutic strategies.
Audience Academic
Author Polineni, Deepika
Panjwani, Naim
Mastromatteo, Scott
Avolio, Julie
He, Gengming
Xiao, Bowei
Cutting, Garry R
Knowles, Michael R
Zhang, Lin
Kim, Sangook
O'Neal, Wanda K
Rommens, Johanna M
Baskurt, Zeynep
Lin, Fan
Keenan, Katherine
Blackman, Scott M
Esmaeili, Mohsen
Sun, Lei
Wang, Fan
Corvol, Harriet
Soave, David
Gong, Jiafen
Drumm, Mitchell
Strug, Lisa J
AuthorAffiliation 3 Program in Physiology and Experimental Medicine, The Hospital for Sick Children, Toronto, ON, Canada
14 Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
17 The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
12 Sorbonne Universités, Université Pierre et Marie (UPMC) Paris, Paris, France
1 Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
11 Assistance Publique-Hôpitaux de Paris (AP-HP), Hôspital Trousseau, Pediatric Pulmonary Department; Institut National de la Santé et la Recherche Médicale (INSERM) U938, Paris, France
Newcastle University, UNITED KINGDOM
2 Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
8 Marsico Lung Institute and Cystic Fibrosis Pulmonary Research and Treatment Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
4 Program in Translational Medicine, The Hospital for Sick Childre
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/30807572$$D View this record in MEDLINE/PubMed
https://hal.sorbonne-universite.fr/hal-02090361$$DView record in HAL
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Snippet Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium...
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SubjectTerms Amino Acid Transport Systems, Neutral - genetics
Amino Acid Transport Systems, Neutral - metabolism
Antiporters - genetics
Antiporters - metabolism
Biochemistry, Molecular Biology
Bioinformatics
Biology
Biology and Life Sciences
CF gene
Chromosome 1
Chromosome 13
Chromosome 7
Cystic fibrosis
Cystic Fibrosis - genetics
Cystic Fibrosis - metabolism
Disease susceptibility
Female
Fibrosis
Funding
Gastrointestinal diseases
Gene expression
Gene Expression Profiling - methods
Gene Expression Regulation
Genes
Genetic aspects
Genetics
Genome-Wide Association Study - methods
Genomes
Genomics
Genotype & phenotype
H(+)-K(+)-Exchanging ATPase - genetics
H(+)-K(+)-Exchanging ATPase - metabolism
Haplotypes
Health aspects
Hospitals
Human genetics
Humans
Intestinal obstruction
Intestine
Life Sciences
Lung - metabolism
Lung diseases
Male
Meconium
Medical research
Medicine
Medicine and Health Sciences
Morbidity
Organ Specificity
Pancreas
Pancreas, Exocrine - metabolism
Pancreatitis
Pediatrics
Precision medicine
Public health
Quantitative genetics
Quantitative trait loci
Research and Analysis Methods
Respiratory tract
Respiratory tract diseases
Social Sciences
Sulfate Transporters - genetics
Sulfate Transporters - metabolism
Susceptibility
Trypsin - genetics
Trypsin - metabolism
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Title Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci
URI https://www.ncbi.nlm.nih.gov/pubmed/30807572
https://www.proquest.com/docview/2251042722
https://search.proquest.com/docview/2186617045
https://hal.sorbonne-universite.fr/hal-02090361
https://pubmed.ncbi.nlm.nih.gov/PMC6407791
https://doaj.org/article/3c571d7e43ec4d68b05079348aa2ac8e
http://dx.doi.org/10.1371/journal.pgen.1008007
Volume 15
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