{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T18:14:07Z","timestamp":1770315247523,"version":"3.49.0"},"reference-count":50,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T00:00:00Z","timestamp":1747008000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T00:00:00Z","timestamp":1747008000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["aap.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Periodontology"],"published-print":{"date-parts":[[2025,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Granulation tissue is routinely discarded in periodontal surgical procedures, but few studies have characterized it. The present study aimed to compare global gene expression in granulation tissue derived from different types of periodontal osseous defects.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Total RNA was isolated from granulation tissue harvested during routine periodontal surgical procedures. Nineteen sites were analyzed\u2014seven infrabony, six suprabony, and six furcation defects. Following quality control checks, samples underwent bulk mRNA sequencing (20\u201330 million read pairs per sample) before bioinformatic analyses utilizing gene ontology and associated pathway\/enrichment analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>No statistically significant differentially expressed genes (DEG) were detected between different osseous defect types. An increase in the expression of 11 genes with a false discovery rate of &lt;0.05 was detected when a comparison was made in terms of healing duration post nonsurgical periodontal therapy (NSPT). Notably, the genes involved included those regulating collagen synthesis and osteogenic activity. Analysis based on sex differences revealed 38 DEG. Gene enrichment analysis revealed that 24 DEG without Y\u2010linked attachment are mostly involved in immune regulation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Routinely discarded periodontal granulation tissue exhibits epithelial characteristics due to a substantial period of maturation post NSPT. Confirmation of ongoing maturation beyond traditional periodontal re\u2010evaluation timepoints warrants further investigation on tissue differentiation potential. More research is needed to elucidate the role of sex as a biological variable affecting periodontal immune response.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Plain language summary<\/jats:title>\n                    <jats:p>Granulation (wound) tissue is routinely removed during gum (periodontal) surgical procedures, but knowledge on its characteristics is scarce. This study aimed to compare gene expression in granulation tissue derived from different types of periodontal bone defects via high\u2010throughput RNA sequencing. Total RNA was extracted from 95 samples harvested from gum disease patients during surgery. After quality control checks, 19 samples (seven infrabony, six suprabony, and six furcation defects) were eligible for sequencing. Subsequent analyses were done utilizing software with known cell biological pathways and processes. Analysis revealed no differentially expressed genes (DEG) in terms of periodontal defect category. There was statistically significantly increased expression of 11 genes when a comparison was made in terms of healing duration following deep scaling treatment. These genes are involved in collagen synthesis and osteogenic activity. Interestingly, analysis based on sex differences detected 38 DEG. Gene enrichment analysis revealed that 24 DEG without association with Y chromosomes are mostly involved in the regulation of immune system response. Routinely discarded periodontal granulation tissue exhibits lining cell characteristics that change over time following deep scaling treatment. More research is needed to unravel the role of sex as a biological variable affecting periodontal immune response in this type of tissue.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/jper.24-0821","type":"journal-article","created":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T05:50:03Z","timestamp":1747029003000},"page":"1379-1390","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Transcriptome analysis of granulation tissue from periodontal osseous defects"],"prefix":"10.1002","volume":"96","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2283-6816","authenticated-orcid":false,"given":"Ye Han","family":"Sam","sequence":"first","affiliation":[{"name":"Periodontology Unit, Centre for Host\u2010Microbiome Interactions Faculty of Dentistry, Oral and Craniofacial Sciences King's College London  London UK"},{"name":"Centre of Periodontology Studies, Faculty of Dentistry MARA University of Technology, Universiti Teknologi MARA Sungai Buloh  Sungai Buloh Selangor Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4588-3241","authenticated-orcid":false,"given":"Ana J.","family":"Caetano","sequence":"additional","affiliation":[{"name":"Institute of Dentistry Faculty of Medicine and Dentistry Queen Mary University of London  London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2738-1603","authenticated-orcid":false,"given":"Dewi R.","family":"Owen","sequence":"additional","affiliation":[{"name":"Periodontology Unit, Centre for Host\u2010Microbiome Interactions Faculty of Dentistry, Oral and Craniofacial Sciences King's College London  London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2778-9756","authenticated-orcid":false,"given":"Giuseppe","family":"Mainas","sequence":"additional","affiliation":[{"name":"Periodontology Unit, Centre for Host\u2010Microbiome Interactions Faculty of Dentistry, Oral and Craniofacial Sciences King's College London  London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7750-5010","authenticated-orcid":false,"given":"Luigi","family":"Nibali","sequence":"additional","affiliation":[{"name":"Periodontology Unit, Centre for Host\u2010Microbiome Interactions Faculty of Dentistry, Oral and Craniofacial Sciences King's College London  London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8927-0741","authenticated-orcid":false,"given":"Mandeep","family":"Ghuman","sequence":"additional","affiliation":[{"name":"Periodontology Unit, Centre for Host\u2010Microbiome Interactions Faculty of Dentistry, Oral and Craniofacial Sciences King's College London  London UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2025,5,12]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/9781118704509"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/jre.13074"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1902\/jop.1991.62.1.5"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aap8798"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/prd.12057"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.5051\/jpis.2105780289"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.13474"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/jre.12551"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/JPER.22\u20100242"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/JPER.18\u20100006"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.13290"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jclinepi.2007.11.008"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2024.02.018"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.13849"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.14034"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469\u20107580.2009.01066.x"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1902\/jop.1971.42.11.678"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600\u2010051X.2008.01245.x"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1111\/jre.12465"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1111\/jre.12118"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1155\/2016\/8239258"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.13245"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1002\/JPER.23\u20100285"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1902\/jop.2006.050358"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1034\/j.1600-051X.29.s2.4.x"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600\u2010051X.2005.00776.x"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.13703"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1902\/jop.1999.70.10.1209"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.1159\/000339613"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365\u20102133.2001.04006.x"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1743\u20106109.2006.00107.x"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1902\/jop.2013.130002"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddm060"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.270.11.5872"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41591\u2010018\u20100020\u2010z"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.200906014"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2016.01.106"},{"key":"e_1_2_10_39_1","doi-asserted-by":"publisher","DOI":"10.1002\/jbmr.133"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00784\u2010024\u201005754\u20108"},{"key":"e_1_2_10_41_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00784\u2010023\u201005122\u2010y"},{"key":"e_1_2_10_42_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600\u2010051X.2005.00649.x"},{"key":"e_1_2_10_43_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.13246"},{"key":"e_1_2_10_44_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcpe.13259"},{"key":"e_1_2_10_45_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12020\u2010024\u201003766\u20108"},{"key":"e_1_2_10_46_1","doi-asserted-by":"publisher","DOI":"10.1902\/jop.2015.140530"},{"key":"e_1_2_10_47_1","doi-asserted-by":"publisher","DOI":"10.1111\/jre.13272"},{"key":"e_1_2_10_48_1","doi-asserted-by":"publisher","DOI":"10.1902\/jop.2010.100045"},{"key":"e_1_2_10_49_1","doi-asserted-by":"publisher","DOI":"10.1111\/jre.12401"},{"key":"e_1_2_10_50_1","doi-asserted-by":"publisher","DOI":"10.1111\/jre.12102"},{"key":"e_1_2_10_51_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41368\u2010021\u201000146\u20100"}],"container-title":["Journal of Periodontology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/aap.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/JPER.24-0821","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/aap.onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/JPER.24-0821","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/aap.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/JPER.24-0821","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T03:54:10Z","timestamp":1770263650000},"score":1,"resource":{"primary":{"URL":"https:\/\/aap.onlinelibrary.wiley.com\/doi\/10.1002\/JPER.24-0821"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,12]]},"references-count":50,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["10.1002\/JPER.24-0821"],"URL":"https:\/\/doi.org\/10.1002\/jper.24-0821","archive":["Portico"],"relation":{},"ISSN":["0022-3492","1943-3670"],"issn-type":[{"value":"0022-3492","type":"print"},{"value":"1943-3670","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,12]]},"assertion":[{"value":"2024-12-19","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-03-26","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-05-12","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}