{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["van den Akker GGH"],"funding":["BMM IDiDAS","ReumaFonds","Dutch Arthritis Foundation"],"pagination":["203-220"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7097986"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["11(2)"],"pubmed_abstract":["<h4>Objective</h4>Lack of specific marker-sets prohibits definition and functional distinction of cellular subtypes in the intervertebral disc (IVD), such as those from the annulus fibrosus (AF) and the nucleus pulposus (NP).<h4>Design</h4>We recently generated immortalized cell lines from human NP and AF tissues; these comprise a set of functionally distinct clonal subtypes. Whole transcriptome analyses were performed of 12 phenotypically distinct clonal cell lines (4× NP-Responder, 4× NP-nonResponder, 2× AF-Sheet forming, and 2× AF-nonSheet forming). Data sets were filtered for membrane-associated marker genes and compared to literature.<h4>Results</h4>Comparison of our immortal cell lines to published primary NP, AF, and articular chondrocytes (AC) transcriptome datasets revealed preservation of AF and NP phenotypes. NP-specific membrane-associated genes were defined by comparison to AF cells in both the primary dataset (46 genes) and immortal cell-lines (161 genes). Definition of AF-specific membrane-associated genes yielded 125 primary AF cell and 92 immortal cell-line markers. Overlap between primary and immortal NP cells yielded high-confidence NP-specific marker genes for NP-R (<i>CLDN11, TMEFF2, CA12, ANXA2, CD44</i>) and NP-nR (EFNA1, NETO2, SLC2A1). Overlap between AF and immortal AF subtypes yielded specific markers for AF-S (<i>COLEC12, LPAR1</i>) and AF-nS (<i>CHIC1</i>).<h4>Conclusions</h4>The current study provides a reference platform for preclinical evaluation of novel membrane-associated cell type-specific markers in the IVD. Future research will focus on their biological relevance for IVD function in development, homeostasis, and degenerate conditions."],"journal":["Cartilage"],"pubmed_title":["A Membranome-Centered Approach Defines Novel Biomarkers for Cellular Subtypes in the Intervertebral Disc."],"pmcid":["PMC7097986"],"funding_grant_id":["LLP14","LLP-14","Project P2.01"],"pubmed_authors":["Rhijn LWV","van den Akker GGH","Richardson SM","Eijssen LMT","Welting TJM","Voncken JW","Hoyland JA"],"additional_accession":[]},"is_claimable":false,"name":"A Membranome-Centered Approach Defines Novel Biomarkers for Cellular Subtypes in the Intervertebral Disc.","description":"<h4>Objective</h4>Lack of specific marker-sets prohibits definition and functional distinction of cellular subtypes in the intervertebral disc (IVD), such as those from the annulus fibrosus (AF) and the nucleus pulposus (NP).<h4>Design</h4>We recently generated immortalized cell lines from human NP and AF tissues; these comprise a set of functionally distinct clonal subtypes. Whole transcriptome analyses were performed of 12 phenotypically distinct clonal cell lines (4× NP-Responder, 4× NP-nonResponder, 2× AF-Sheet forming, and 2× AF-nonSheet forming). Data sets were filtered for membrane-associated marker genes and compared to literature.<h4>Results</h4>Comparison of our immortal cell lines to published primary NP, AF, and articular chondrocytes (AC) transcriptome datasets revealed preservation of AF and NP phenotypes. NP-specific membrane-associated genes were defined by comparison to AF cells in both the primary dataset (46 genes) and immortal cell-lines (161 genes). Definition of AF-specific membrane-associated genes yielded 125 primary AF cell and 92 immortal cell-line markers. Overlap between primary and immortal NP cells yielded high-confidence NP-specific marker genes for NP-R (<i>CLDN11, TMEFF2, CA12, ANXA2, CD44</i>) and NP-nR (EFNA1, NETO2, SLC2A1). Overlap between AF and immortal AF subtypes yielded specific markers for AF-S (<i>COLEC12, LPAR1</i>) and AF-nS (<i>CHIC1</i>).<h4>Conclusions</h4>The current study provides a reference platform for preclinical evaluation of novel membrane-associated cell type-specific markers in the IVD. Future research will focus on their biological relevance for IVD function in development, homeostasis, and degenerate conditions.","dates":{"release":"2020-01-01T00:00:00Z","publication":"2020 Apr","modification":"2024-11-20T08:29:24.078Z","creation":"2020-10-08T07:17:52Z"},"accession":"S-EPMC7097986","cross_references":{"pubmed":["29629573"],"doi":["10.1177/1947603518764260"]}}