Investigation of Pathogenic Genes in Peri-Implantitis from Implant Clustering Failure Patients: A Whole-Exome Sequencing Pilot Study
Identifieur interne : 000756 ( Pmc/Curation ); précédent : 000755; suivant : 000757Investigation of Pathogenic Genes in Peri-Implantitis from Implant Clustering Failure Patients: A Whole-Exome Sequencing Pilot Study
Auteurs : Soohyung Lee [Corée du Sud] ; Ji-Young Kim [Corée du Sud] ; Jihye Hwang [Corée du Sud] ; Sanguk Kim [Corée du Sud] ; Jae-Hoon Lee [Corée du Sud] ; Dong-Hoo Han [Corée du Sud]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Peri-implantitis is a frequently occurring gum disease linked to multi-factorial traits with various environmental and genetic causalities and no known concrete pathogenesis. The varying severity of peri-implantitis among patients with relatively similar environments suggests a genetic aspect which needs to be investigated to understand and regulate the pathogenesis of the disease. Six unrelated individuals with multiple clusterization implant failure due to severe peri-implantitis were chosen for this study. These six individuals had relatively healthy lifestyles, with minimal environmental causalities affecting peri-implantitis. Research was undertaken to investigate pathogenic genes in peri-implantitis albeit with a small number of subjects and incomplete elimination of environmental causalities. Whole-exome sequencing was performed on collected saliva samples via self DNA collection kit. Common variants with minor allele frequencies (MAF) > = 0.05 from all control datasets were eliminated and variants having high and moderate impact and loss of function were used for comparison. Gene set enrichment analysis was performed to reveal functional groups associated with the genetic variants. 2,022 genes were left after filtering against dbSNP, the 1000 Genomes East Asian population, and healthy Korean randomized subsample data (GSK project). 175 (p-value <0.05) out of 927 gene sets were obtained via GSEA (DAVID). The top 10 was chosen (p-value <0.05) from cluster enrichment showing significance of cytoskeleton, cell adhesion, and metal ion binding. Network analysis was applied to find relationships between functional clusters. Among the functional groups, ion metal binding was located in the center of all clusters, indicating dysfunction of regulation in metal ion concentration might affect cell morphology or cell adhesion, resulting in implant failure. This result may demonstrate the feasibility of and provide pilot data for a larger research project aimed at discovering biomarkers for early diagnosis of peri-implantitis.
Url:
DOI: 10.1371/journal.pone.0099360
PubMed: 24921256
PubMed Central: 4055653
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xml:lang="en" level="a" type="main">Investigation of Pathogenic Genes in Peri-Implantitis from Implant Clustering Failure Patients: A Whole-Exome Sequencing Pilot Study</title><author><name sortKey="Lee, Soohyung" sort="Lee, Soohyung" uniqKey="Lee S" first="Soohyung" last="Lee">Soohyung Lee</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Prosthodontics, Oral Science Research Center, College of Dentistry, Yonsei University, Seoul, Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Prosthodontics, Oral Science Research Center, College of Dentistry, Yonsei University, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Ji Young" sort="Kim, Ji Young" uniqKey="Kim J" first="Ji-Young" last="Kim">Ji-Young Kim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Prosthodontics, Oral Science Research Center, College of Dentistry, Yonsei University, Seoul, Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Prosthodontics, Oral Science Research Center, College of Dentistry, Yonsei University, Seoul</wicri:regionArea></affiliation></author><author><name sortKey="Hwang, Jihye" sort="Hwang, Jihye" uniqKey="Hwang J" first="Jihye" last="Hwang">Jihye Hwang</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of IT Convergence and Engineering, Pohang University of Science and Technology, Pohang, Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of IT Convergence and Engineering, Pohang University of Science and Technology, Pohang</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Sanguk" sort="Kim, Sanguk" uniqKey="Kim S" first="Sanguk" last="Kim">Sanguk Kim</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of IT Convergence and Engineering, Pohang University of Science and 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Research Center, College of Dentistry, Yonsei University, Seoul, Korea</addr-line></nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Prosthodontics, Oral Science Research Center, College of Dentistry, Yonsei University, Seoul</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Peri-implantitis is a frequently occurring gum disease linked to multi-factorial traits with various environmental and genetic causalities and no known concrete pathogenesis. The varying severity of peri-implantitis among patients with relatively similar environments suggests a genetic aspect which needs to be investigated to understand and regulate the pathogenesis of the disease. Six unrelated individuals with multiple clusterization implant failure due to severe peri-implantitis were chosen for this study. These six individuals had relatively healthy lifestyles, with minimal environmental causalities affecting peri-implantitis. Research was undertaken to investigate pathogenic genes in peri-implantitis albeit with a small number of subjects and incomplete elimination of environmental causalities. Whole-exome sequencing was performed on collected saliva samples via self DNA collection kit. Common variants with minor allele frequencies (MAF) > = 0.05 from all control datasets were eliminated and variants having high and moderate impact and loss of function were used for comparison. Gene set enrichment analysis was performed to reveal functional groups associated with the genetic variants. 2,022 genes were left after filtering against dbSNP, the 1000 Genomes East Asian population, and healthy Korean randomized subsample data (GSK project). 175 (p-value <0.05) out of 927 gene sets were obtained via GSEA (DAVID). The top 10 was chosen (p-value <0.05) from cluster enrichment showing significance of cytoskeleton, cell adhesion, and metal ion binding. Network analysis was applied to find relationships between functional clusters. Among the functional groups, ion metal binding was located in the center of all clusters, indicating dysfunction of regulation in metal ion concentration might affect cell morphology or cell adhesion, resulting in implant failure. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24921256</article-id><article-id pub-id-type="pmc">4055653</article-id><article-id pub-id-type="publisher-id">PONE-D-14-08914</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0099360</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Medicine and Health Sciences</subject><subj-group><subject>Clinical Genetics</subject></subj-group><subj-group><subject>Diagnostic Medicine</subject></subj-group><subj-group><subject>Health Care</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Research and Analysis Methods</subject><subj-group><subject>Database and Informatics Methods</subject></subj-group></subj-group></article-categories><title-group><article-title>Investigation of Pathogenic Genes in Peri-Implantitis from Implant Clustering Failure Patients: A Whole-Exome Sequencing Pilot Study</article-title><alt-title alt-title-type="running-head">Investigation of Peri-Implantitis Pathogenic Genes</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Lee</surname><given-names>Soohyung</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kim</surname><given-names>Ji-Young</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hwang</surname><given-names>Jihye</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kim</surname><given-names>Sanguk</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lee</surname><given-names>Jae-Hoon</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Han</surname><given-names>Dong-Hoo</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Department of Prosthodontics, Oral Science Research Center, College of Dentistry, Yonsei University, Seoul, Korea</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Department of IT Convergence and Engineering, Pohang University of Science and Technology, Pohang, Korea</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Department of Prosthodontics, Oral Science Research Center, College of Dentistry, Yonsei University, Seoul, Korea</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Schönbach</surname><given-names>Christian</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Nazarbayev University, Kazakhstan</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>jaehoon115@yuhs.ac</email> (JHL); <email>donghoohan@yuhs.ac</email> (DHH)</corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: JHL DHH. Analyzed the data: JH SK. Wrote the paper: SL JYK.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>12</day><month>6</month><year>2014</year></pub-date><volume>9</volume><issue>6</issue><elocation-id>e99360</elocation-id><history><date date-type="received"><day>25</day><month>2</month><year>2014</year></date><date date-type="accepted"><day>13</day><month>5</month><year>2014</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Lee et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>Peri-implantitis is a frequently occurring gum disease linked to multi-factorial traits with various environmental and genetic causalities and no known concrete pathogenesis. The varying severity of peri-implantitis among patients with relatively similar environments suggests a genetic aspect which needs to be investigated to understand and regulate the pathogenesis of the disease. Six unrelated individuals with multiple clusterization implant failure due to severe peri-implantitis were chosen for this study. These six individuals had relatively healthy lifestyles, with minimal environmental causalities affecting peri-implantitis. Research was undertaken to investigate pathogenic genes in peri-implantitis albeit with a small number of subjects and incomplete elimination of environmental causalities. Whole-exome sequencing was performed on collected saliva samples via self DNA collection kit. Common variants with minor allele frequencies (MAF) > = 0.05 from all control datasets were eliminated and variants having high and moderate impact and loss of function were used for comparison. Gene set enrichment analysis was performed to reveal functional groups associated with the genetic variants. 2,022 genes were left after filtering against dbSNP, the 1000 Genomes East Asian population, and healthy Korean randomized subsample data (GSK project). 175 (p-value <0.05) out of 927 gene sets were obtained via GSEA (DAVID). The top 10 was chosen (p-value <0.05) from cluster enrichment showing significance of cytoskeleton, cell adhesion, and metal ion binding. Network analysis was applied to find relationships between functional clusters. Among the functional groups, ion metal binding was located in the center of all clusters, indicating dysfunction of regulation in metal ion concentration might affect cell morphology or cell adhesion, resulting in implant failure. This result may demonstrate the feasibility of and provide pilot data for a larger research project aimed at discovering biomarkers for early diagnosis of peri-implantitis.</p></abstract><funding-group><funding-statement>This work is supported by research funding provided by Oral Science Research Center and School of Dentistry Intramural Research (6-2012-0207). This research was supported by Basic Science Research Program through the National research Foundation of Korea (NRF) funded by the Ministy of Science, ICT and Future Planning (2011-0014268). This research was also supported by funding provided by National Research Foundation of Korea (NRF) (2013018606). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="9"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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