{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T16:23:39Z","timestamp":1791908619733,"version":"4.3.4"},"reference-count":40,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T00:00:00Z","timestamp":1716336000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The periodontium comprising periodontal ligament (PDL), gingiva, and epithelium play crucial roles in maintaining tooth integrity and function. Understanding tissue cellular composition and gene expression is crucial for illuminating periodontal pathophysiology. This study aimed to identify tissue-specific markers via scRNA-Seq. Primary human PDL, gingiva, and epithelium tissues (n = 7) were subjected to cell hashing and sorting. scRNA-Seq library preparation using 10\u00d7 Genomics protocol and Illumina sequencing was conducted. The analysis was performed using Cellranger (v3.1.0), with downstream analysis via R packages Seurat (v5.0.1) and SCORPIUS (v1.0.9). Investigations identified eight distinct cellular clusters, revealing the ubiquitous presence of epithelial and gingival cells. PDL cells evolved in two clusters with numerical superiority. The other clusters showed varied predominance regarding gingival and epithelial cells or an equitable distribution of both. The cluster harboring most cells mainly consisted of PDL cells and was present in all donors. Some of the other clusters were also tissue-inherent, while the presence of others was environmentally influenced, revealing variability across donors. Two clusters exhibited genetic profiles associated with tissue development and cellular integrity, respectively, while all other clusters were distinguished by genes characteristic of immune responses. Developmental trajectory analysis uncovered that PDL cells may develop after epithelial and gingival cells, suggesting the inherent PDL cell-dominated cluster as a final developmental stage. This single-cell RNA sequencing study delineates the hierarchical organization of periodontal tissue development, identifies tissue-specific markers, and reveals the influence of environmental factors on cellular composition, advancing our understanding of periodontal biology and offering potential insights for therapeutic interventions.<\/jats:p>","DOI":"10.3390\/ijms25115617","type":"journal-article","created":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T07:56:11Z","timestamp":1716364571000},"page":"5617","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Unraveling Divergent Transcriptomic Profiles: A Comparative Single-Cell RNA Sequencing Study of Epithelium, Gingiva, and Periodontal Ligament Tissues"],"prefix":"10.3390","volume":"25","author":[{"given":"Ali T.","family":"Abdallah","sequence":"first","affiliation":[{"name":"Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), Medical Faculty and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"},{"name":"Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, 50924 Cologne, Germany"},{"name":"Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Mathematics and Natural Sciences, University of Cologne, 50931 Cologne, Germany"},{"name":"Interdisciplinary Center for Clinical Research, University Hospital RWTH, 52074 Aachen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0266-6095","authenticated-orcid":false,"given":"Anna","family":"Konermann","sequence":"additional","affiliation":[{"name":"Department of Orthodontics, University Hospital Bonn, 53111 Bonn, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,5,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/j.1600-0757.2005.00135.x","article-title":"Proteomics for the periodontium: Current strategies and future promise","volume":"40","author":"McCulloch","year":"2006","journal-title":"Periodontology 2000"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Pereira, D., and Sequeira, I. 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