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Transcriptome Analysis Reveals Modulation of Human Stem Cells from the Apical Papilla by Species Associated with Dental Root Canal Infection
Interaction of oral bacteria with stem cells from the apical papilla (SCAP) can negatively affect the success of regenerative endodontic treatment (RET). Through RNA-seq transcriptomic analysis, we studied the effect of the oral bacteria and , as well as their supernatants enriched by bacterial meta...
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| Published in: | International journal of molecular sciences 2022-11, Vol.23 (22), p.14420 |
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| container_issue | 22 |
| container_start_page | 14420 |
| container_title | International journal of molecular sciences |
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| creator | Razghonova, Yelyzaveta Zymovets, Valeriia Wadelius, Philip Rakhimova, Olena Manoharan, Lokeshwaran Brundin, Malin Kelk, Peyman Romani Vestman, Nelly |
| description | Interaction of oral bacteria with stem cells from the apical papilla (SCAP) can negatively affect the success of regenerative endodontic treatment (RET). Through RNA-seq transcriptomic analysis, we studied the effect of the oral bacteria
and
, as well as their supernatants enriched by bacterial metabolites, on the osteo- and dentinogenic potential of SCAPs in vitro. We performed bulk RNA-seq, on the basis of which differential expression analysis (DEG) and gene ontology enrichment analysis (GO) were performed. DEG analysis showed that
supernatant had the greatest effect on SCAPs, whereas
supernatant had the least effect (Tanimoto coefficient = 0.05). GO term enrichment analysis indicated that
upregulates the immune and inflammatory response of SCAPs, and
suppresses cell proliferation and cell division processes. SCAP transcriptome profiles showed that under the influence of
the upregulation of
,
, and
genes occurred, which may negatively affect the SCAP's osteo- and odontogenic differentiation.
downregulates the expression of
and
and upregulates the expression of
and
in SCAPs, the upregulation of which may be detrimental for SCAPs' differentiation potential. In conclusion, the present study shows that in vitro,
,
, and their metabolites are capable of up- or downregulating the expression of genes that are necessary for dentinogenic and osteogenic processes to varying degrees, which eventually may result in unsuccessful RET outcomes. Transposition to the clinical context merits some reservations, which should be approached with caution. |
| doi_str_mv | 10.3390/ijms232214420 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_ba14ccd35f5f4d61afbd798d26de511d</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><doaj_id>oai_doaj_org_article_ba14ccd35f5f4d61afbd798d26de511d</doaj_id><sourcerecordid>2740507341</sourcerecordid><originalsourceid>FETCH-LOGICAL-c588t-cfd423ba4bc6eef57db6dd1ff338e8cc04173a2ed3976ec7ac65d27193f669163</originalsourceid><addsrcrecordid>eNp1kk1v0zAYxyMEYmNw5IosceFS8LuTC1LVAatUBNoGV8uxH6-ukjiLk039Dnxo3HWMFYmDZcvP7_k_r0XxmuD3jFX4Q9i0iTJKCecUPymOCad0hrFUTx-9j4oXKW0wzqConhdHTHKGy6o8Ln5dDqZLdgj9GFtA88402xQSOocbME1CX6ObGjOG2KHo0dnUmg5djNCiBTTZ7IfYonGdHftgTYO-mz40jUH1Fl30YAMkNE8p2mBGcOg2jGt0Ct2YyfMYR7QwOR5adh7sLsTL4pnPQeHV_X1S_Pj86XJxNlt9-7JczFczK8pynFnvOGW14bWVAF4oV0vniPeMlVBaizlRzFBwrFISrDJWCkcVqZiXsiKSnRTLva6LZqP7IbRm2Opogr77iMOVNsMYbAO6NoRb65jwwnMnifG1U1XpqHQgCHFZa7XXSrfQT_WBWjP1-dT56AS6Eopbg0EbSaTmTCpdAxfaE4ZpaQj1SmW52X_lTsPP-V1yUztpiokoaeY_7vkMt-Bsbu5gmgO3Q0sX1voq3uhKVqKsdr14dy8wxOsJ0qjbkGwerukgTklTxbHAinGS0bf_oJs4DXmCO4pVnDNB6N8K7BBTGsA_JEOw3q2sPljZzL95XMED_WdH2W_S0eni</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2739443512</pqid></control><display><type>article</type><title>Transcriptome Analysis Reveals Modulation of Human Stem Cells from the Apical Papilla by Species Associated with Dental Root Canal Infection</title><source>Access via ProQuest (Open Access)</source><source>PubMed Central</source><creator>Razghonova, Yelyzaveta ; Zymovets, Valeriia ; Wadelius, Philip ; Rakhimova, Olena ; Manoharan, Lokeshwaran ; Brundin, Malin ; Kelk, Peyman ; Romani Vestman, Nelly</creator><creatorcontrib>Razghonova, Yelyzaveta ; Zymovets, Valeriia ; Wadelius, Philip ; Rakhimova, Olena ; Manoharan, Lokeshwaran ; Brundin, Malin ; Kelk, Peyman ; Romani Vestman, Nelly</creatorcontrib><description>Interaction of oral bacteria with stem cells from the apical papilla (SCAP) can negatively affect the success of regenerative endodontic treatment (RET). Through RNA-seq transcriptomic analysis, we studied the effect of the oral bacteria
and
, as well as their supernatants enriched by bacterial metabolites, on the osteo- and dentinogenic potential of SCAPs in vitro. We performed bulk RNA-seq, on the basis of which differential expression analysis (DEG) and gene ontology enrichment analysis (GO) were performed. DEG analysis showed that
supernatant had the greatest effect on SCAPs, whereas
supernatant had the least effect (Tanimoto coefficient = 0.05). GO term enrichment analysis indicated that
upregulates the immune and inflammatory response of SCAPs, and
suppresses cell proliferation and cell division processes. SCAP transcriptome profiles showed that under the influence of
the upregulation of
,
, and
genes occurred, which may negatively affect the SCAP's osteo- and odontogenic differentiation.
downregulates the expression of
and
and upregulates the expression of
and
in SCAPs, the upregulation of which may be detrimental for SCAPs' differentiation potential. In conclusion, the present study shows that in vitro,
,
, and their metabolites are capable of up- or downregulating the expression of genes that are necessary for dentinogenic and osteogenic processes to varying degrees, which eventually may result in unsuccessful RET outcomes. Transposition to the clinical context merits some reservations, which should be approached with caution.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms232214420</identifier><identifier>PMID: 36430898</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Bacteria ; Basic Medicine ; Biofilms ; Bone marrow ; Cbfa-1 protein ; Cell and Molecular Biology ; Cell Differentiation ; Cell division ; Cell proliferation ; Cell- och molekylärbiologi ; Dental pulp ; Dental Pulp Cavity ; dentinogenesis ; Dentistry ; differential gene expression analysis (DEG) ; Differentiation ; Endodontics ; Enrichment ; Enterococcus faecalis ; Environmental conditions ; Fusobacterium nucleatum ; Gene expression ; Gene Expression Profiling ; Genes ; Genomes ; Humans ; Infections ; Inflammation ; Inflammatory response ; Intracellular Signaling Peptides and Proteins - metabolism ; Medical and Health Sciences ; Medicin och hälsovetenskap ; Medicinska och farmaceutiska grundvetenskaper ; Metabolites ; Microorganisms ; Mineralization ; odontologi ; Odontology ; Osteogenesis ; regenerative endodontic treatment (RET) ; Root canals ; Stem cells ; Stem Cells - metabolism ; stem cells from the apical papilla (SCAP) ; Teeth ; transcriptome analysis ; Transcriptomes ; Transcriptomics ; Transposition</subject><ispartof>International journal of molecular sciences, 2022-11, Vol.23 (22), p.14420</ispartof><rights>2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 by the authors. 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c588t-cfd423ba4bc6eef57db6dd1ff338e8cc04173a2ed3976ec7ac65d27193f669163</citedby><cites>FETCH-LOGICAL-c588t-cfd423ba4bc6eef57db6dd1ff338e8cc04173a2ed3976ec7ac65d27193f669163</cites><orcidid>0000-0002-8747-3307 ; 0000-0001-9751-5745 ; 0000-0002-5674-8179 ; 0000-0003-1594-1738 ; 0000-0002-3536-4467</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2739443512/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2739443512?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36430898$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-201582$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://lup.lub.lu.se/record/9574ca0e-a616-4367-be45-f13028a12f77$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Razghonova, Yelyzaveta</creatorcontrib><creatorcontrib>Zymovets, Valeriia</creatorcontrib><creatorcontrib>Wadelius, Philip</creatorcontrib><creatorcontrib>Rakhimova, Olena</creatorcontrib><creatorcontrib>Manoharan, Lokeshwaran</creatorcontrib><creatorcontrib>Brundin, Malin</creatorcontrib><creatorcontrib>Kelk, Peyman</creatorcontrib><creatorcontrib>Romani Vestman, Nelly</creatorcontrib><title>Transcriptome Analysis Reveals Modulation of Human Stem Cells from the Apical Papilla by Species Associated with Dental Root Canal Infection</title><title>International journal of molecular sciences</title><addtitle>Int J Mol Sci</addtitle><description>Interaction of oral bacteria with stem cells from the apical papilla (SCAP) can negatively affect the success of regenerative endodontic treatment (RET). Through RNA-seq transcriptomic analysis, we studied the effect of the oral bacteria
and
, as well as their supernatants enriched by bacterial metabolites, on the osteo- and dentinogenic potential of SCAPs in vitro. We performed bulk RNA-seq, on the basis of which differential expression analysis (DEG) and gene ontology enrichment analysis (GO) were performed. DEG analysis showed that
supernatant had the greatest effect on SCAPs, whereas
supernatant had the least effect (Tanimoto coefficient = 0.05). GO term enrichment analysis indicated that
upregulates the immune and inflammatory response of SCAPs, and
suppresses cell proliferation and cell division processes. SCAP transcriptome profiles showed that under the influence of
the upregulation of
,
, and
genes occurred, which may negatively affect the SCAP's osteo- and odontogenic differentiation.
downregulates the expression of
and
and upregulates the expression of
and
in SCAPs, the upregulation of which may be detrimental for SCAPs' differentiation potential. In conclusion, the present study shows that in vitro,
,
, and their metabolites are capable of up- or downregulating the expression of genes that are necessary for dentinogenic and osteogenic processes to varying degrees, which eventually may result in unsuccessful RET outcomes. Transposition to the clinical context merits some reservations, which should be approached with caution.</description><subject>Bacteria</subject><subject>Basic Medicine</subject><subject>Biofilms</subject><subject>Bone marrow</subject><subject>Cbfa-1 protein</subject><subject>Cell and Molecular Biology</subject><subject>Cell Differentiation</subject><subject>Cell division</subject><subject>Cell proliferation</subject><subject>Cell- och molekylärbiologi</subject><subject>Dental pulp</subject><subject>Dental Pulp Cavity</subject><subject>dentinogenesis</subject><subject>Dentistry</subject><subject>differential gene expression analysis (DEG)</subject><subject>Differentiation</subject><subject>Endodontics</subject><subject>Enrichment</subject><subject>Enterococcus faecalis</subject><subject>Environmental conditions</subject><subject>Fusobacterium nucleatum</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Genes</subject><subject>Genomes</subject><subject>Humans</subject><subject>Infections</subject><subject>Inflammation</subject><subject>Inflammatory response</subject><subject>Intracellular Signaling Peptides and Proteins - 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metabolism</topic><topic>Medical and Health Sciences</topic><topic>Medicin och hälsovetenskap</topic><topic>Medicinska och farmaceutiska grundvetenskaper</topic><topic>Metabolites</topic><topic>Microorganisms</topic><topic>Mineralization</topic><topic>odontologi</topic><topic>Odontology</topic><topic>Osteogenesis</topic><topic>regenerative endodontic treatment (RET)</topic><topic>Root canals</topic><topic>Stem cells</topic><topic>Stem Cells - metabolism</topic><topic>stem cells from the apical papilla (SCAP)</topic><topic>Teeth</topic><topic>transcriptome analysis</topic><topic>Transcriptomes</topic><topic>Transcriptomics</topic><topic>Transposition</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Razghonova, Yelyzaveta</creatorcontrib><creatorcontrib>Zymovets, Valeriia</creatorcontrib><creatorcontrib>Wadelius, Philip</creatorcontrib><creatorcontrib>Rakhimova, Olena</creatorcontrib><creatorcontrib>Manoharan, Lokeshwaran</creatorcontrib><creatorcontrib>Brundin, Malin</creatorcontrib><creatorcontrib>Kelk, Peyman</creatorcontrib><creatorcontrib>Romani Vestman, Nelly</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>ProQuest Health and Medical</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest Research Library</collection><collection>Research Library (Corporate)</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - 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Through RNA-seq transcriptomic analysis, we studied the effect of the oral bacteria
and
, as well as their supernatants enriched by bacterial metabolites, on the osteo- and dentinogenic potential of SCAPs in vitro. We performed bulk RNA-seq, on the basis of which differential expression analysis (DEG) and gene ontology enrichment analysis (GO) were performed. DEG analysis showed that
supernatant had the greatest effect on SCAPs, whereas
supernatant had the least effect (Tanimoto coefficient = 0.05). GO term enrichment analysis indicated that
upregulates the immune and inflammatory response of SCAPs, and
suppresses cell proliferation and cell division processes. SCAP transcriptome profiles showed that under the influence of
the upregulation of
,
, and
genes occurred, which may negatively affect the SCAP's osteo- and odontogenic differentiation.
downregulates the expression of
and
and upregulates the expression of
and
in SCAPs, the upregulation of which may be detrimental for SCAPs' differentiation potential. In conclusion, the present study shows that in vitro,
,
, and their metabolites are capable of up- or downregulating the expression of genes that are necessary for dentinogenic and osteogenic processes to varying degrees, which eventually may result in unsuccessful RET outcomes. Transposition to the clinical context merits some reservations, which should be approached with caution.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>36430898</pmid><doi>10.3390/ijms232214420</doi><orcidid>https://orcid.org/0000-0002-8747-3307</orcidid><orcidid>https://orcid.org/0000-0001-9751-5745</orcidid><orcidid>https://orcid.org/0000-0002-5674-8179</orcidid><orcidid>https://orcid.org/0000-0003-1594-1738</orcidid><orcidid>https://orcid.org/0000-0002-3536-4467</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1422-0067 |
| ispartof | International journal of molecular sciences, 2022-11, Vol.23 (22), p.14420 |
| issn | 1422-0067 1661-6596 1422-0067 |
| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_ba14ccd35f5f4d61afbd798d26de511d |
| source | Access via ProQuest (Open Access); PubMed Central |
| subjects | Bacteria Basic Medicine Biofilms Bone marrow Cbfa-1 protein Cell and Molecular Biology Cell Differentiation Cell division Cell proliferation Cell- och molekylärbiologi Dental pulp Dental Pulp Cavity dentinogenesis Dentistry differential gene expression analysis (DEG) Differentiation Endodontics Enrichment Enterococcus faecalis Environmental conditions Fusobacterium nucleatum Gene expression Gene Expression Profiling Genes Genomes Humans Infections Inflammation Inflammatory response Intracellular Signaling Peptides and Proteins - metabolism Medical and Health Sciences Medicin och hälsovetenskap Medicinska och farmaceutiska grundvetenskaper Metabolites Microorganisms Mineralization odontologi Odontology Osteogenesis regenerative endodontic treatment (RET) Root canals Stem cells Stem Cells - metabolism stem cells from the apical papilla (SCAP) Teeth transcriptome analysis Transcriptomes Transcriptomics Transposition |
| title | Transcriptome Analysis Reveals Modulation of Human Stem Cells from the Apical Papilla by Species Associated with Dental Root Canal Infection |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-28T11%3A26%3A50IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Transcriptome%20Analysis%20Reveals%20Modulation%20of%20Human%20Stem%20Cells%20from%20the%20Apical%20Papilla%20by%20Species%20Associated%20with%20Dental%20Root%20Canal%20Infection&rft.jtitle=International%20journal%20of%20molecular%20sciences&rft.au=Razghonova,%20Yelyzaveta&rft.date=2022-11-20&rft.volume=23&rft.issue=22&rft.spage=14420&rft.pages=14420-&rft.issn=1422-0067&rft.eissn=1422-0067&rft_id=info:doi/10.3390/ijms232214420&rft_dat=%3Cproquest_doaj_%3E2740507341%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c588t-cfd423ba4bc6eef57db6dd1ff338e8cc04173a2ed3976ec7ac65d27193f669163%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2739443512&rft_id=info:pmid/36430898&rfr_iscdi=true |