Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients

Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD's heritability. In order to discover the missing heritability due to rare variants, we have...

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Published inPloS one Vol. 12; no. 5; p. e0176664
Main Authors Al-Aama, Jumana Yousuf, Shaik, Noor Ahmad, Banaganapalli, Babajan, Salama, Mohammed A, Rashidi, Omran, Sahly, Ahmed N, Mohsen, Mohammed O, Shawoosh, Harbi A, Shalabi, Hebah Ahmad, Edreesi, Mohammad Al, Alharthi, Sameer E, Wang, Jun, Elango, Ramu, Saadah, Omar I
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 15.05.2017
Public Library of Science (PLoS)
Subjects
Adenylate kinase
Adenylate Kinase - chemistry
Adenylate Kinase - genetics
Alleles
Amino acids
Antigens
Autoimmune diseases
Biology and Life Sciences
CD4 antigen
Celiac disease
Celiac Disease - genetics
Chromosome Mapping
Chromosomes
Computational Biology
Computer applications
Consanguinity
Development and progression
Evolution, Molecular
Exome
Exome sequencing
Female
Gastroenterology
Gene loci
Genes
Genetic aspects
Genetic Variation
Genomes
Genotype
Gluten
Heritability
High-Throughput Nucleotide Sequencing
Histocompatibility antigen HLA
Humans
Hydrogen Bonding
Inheritance Patterns
Insertion
Lymphocytes T
Male
Medicine
Medicine and Health Sciences
Models, Molecular
Mutation
Pediatrics
Pedigree
Penetrance
Phosphates
Protein Conformation
Protein structure
Proteins
Research and Analysis Methods
Saudi Arabia
Secondary structure
Small intestine
Social Sciences
Saudi Arabia
Middle East
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Abstract Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD's heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400th and 556th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4+ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.
AbstractList Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD’s heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400 th and 556 th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5 , which may eventually down-regulates the reactivity potential of CD4 + T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.
Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD's heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400th and 556th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4+ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.
Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD's heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p&lt;0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400th and 556th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4+ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.
Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD's heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400.sup.th and 556.sup.th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4.sup.+ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.
Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD’s heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400 th and 556 th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5 , which may eventually down-regulates the reactivity potential of CD4 + T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.
Audience Academic
Author Mohsen, Mohammed O
Elango, Ramu
Shaik, Noor Ahmad
Sahly, Ahmed N
Saadah, Omar I
Alharthi, Sameer E
Wang, Jun
Shawoosh, Harbi A
Al-Aama, Jumana Yousuf
Banaganapalli, Babajan
Salama, Mohammed A
Edreesi, Mohammad Al
Rashidi, Omran
Shalabi, Hebah Ahmad
AuthorAffiliation 2 Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
6 Division of Gastroenterology, Department of Pediatrics, Dhahran Health Center, Saudi Aramco Medical Services Organization, Dhahran, Saudi Arabia
1 Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
7 Division of Pediatric Gastroenterology, Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
Huashan Hospital Fudan University, CHINA
4 Department of Pediatrics, King Fahd Armed Forces Hospital, Jeddah, Saudi Arabia
3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
5 Primary Healthcare Center, Ministry of Health, Jeddah, Saudi Arabia
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/28505210$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
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2017 Al-Aama et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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DocumentTitleAlternate Celiac disease exome analysis discovery of AK5 gene as potential candidate
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Conceptualization: JYA OIS NAS BB RE.Data curation: NAS BB RE.Formal analysis: NAS BB RE JW.Funding acquisition: OIS.Investigation: MAS OR BB.Methodology: NAS BB RE.Project administration: SEA.Resources: OIS ANS MOM H. Shawoosh H. Shalabi MAE.Software: BB.Supervision: NAS BB RE OIS.Validation: JYA NAS BB RE.Visualization: BB.Writing – original draft: NAS BB RE.Writing – review & editing: NAS BB RE OIS ANS MOM H. Shawoosh H. Shalabi MAE MAS OR.
Competing Interests: The authors have declared that no competing interests exist.
OpenAccessLink https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5432167/
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Snippet Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA...
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StartPage e0176664
SubjectTerms Adenylate kinase
Adenylate Kinase - chemistry
Adenylate Kinase - genetics
Alleles
Amino acids
Antigens
Autoimmune diseases
Biology and Life Sciences
CD4 antigen
Celiac disease
Celiac Disease - genetics
Chromosome Mapping
Chromosomes
Computational Biology
Computer applications
Consanguinity
Development and progression
Evolution, Molecular
Exome
Exome sequencing
Female
Gastroenterology
Gene loci
Genes
Genetic aspects
Genetic Variation
Genomes
Genotype
Gluten
Heritability
High-Throughput Nucleotide Sequencing
Histocompatibility antigen HLA
Humans
Hydrogen Bonding
Inheritance Patterns
Insertion
Lymphocytes T
Male
Medicine
Medicine and Health Sciences
Models, Molecular
Mutation
Pediatrics
Pedigree
Penetrance
Phosphates
Protein Conformation
Protein structure
Proteins
Research and Analysis Methods
Saudi Arabia
Secondary structure
Small intestine
Social Sciences
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Title Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients
URI https://www.ncbi.nlm.nih.gov/pubmed/28505210
https://www.proquest.com/docview/1899020509
https://search.proquest.com/docview/1899414884
https://pubmed.ncbi.nlm.nih.gov/PMC5432167
https://doaj.org/article/131ed546c31e47ea901ac980cfc0d987
http://dx.doi.org/10.1371/journal.pone.0176664
Volume 12
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