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We conducted a comparison of the expression profiles of mRNAs, lncRNAs, and circRNAs via whole-transcriptome sequencing in eight KBD and ten OA individuals. To facilitate functional annotation-enriched analysis for differentially expressed (DE) genes, DE lncRNAs, and DE circRNAs, we employed bioinformatic analysis utilizing Gene Ontology (GO) and KEGG. Additionally, using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), we validated the expression levels of four cartilage-related genes in chondrocytes. We identified a total of 43 DE mRNAs, 1451 DE lncRNAs, and 305 DE circRNAs in KBD cartilage tissue compared to OA (q value &lt; 0.05; |log2FC| &gt; 1). We also performed competing endogenous RNA network analysis, which identified a total of 65 lncRNA-mRNA interactions and 4714 miRNA-circRNA interactions. In particular, we observed that circRNA12218 had binding sites for three miRNAs targeting ACAN, while circRNA12487 had binding sites for seven miRNAs targeting COL2A1. Our results add a novel set of genes and non-coding RNAs that could potentially serve as candidate diagnostic biomarkers or therapeutic targets for KBD patients.<\/jats:p>","DOI":"10.3390\/ijms25084348","type":"journal-article","created":{"date-parts":[[2024,4,15]],"date-time":"2024-04-15T10:24:26Z","timestamp":1713176666000},"page":"4348","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Whole-Transcriptome Sequencing of Knee Joint Cartilage from Kashin\u2013Beck Disease and Osteoarthritis Patients"],"prefix":"10.3390","volume":"25","author":[{"given":"Lixin","family":"Han","sequence":"first","affiliation":[{"name":"Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi\u2019an Jiaotong University, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Trace Elements and Endemic Diseases (Xi\u2019an Jiaotong University), National Health and Family Planning Commission, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Environment and Genes Related to Diseases (Xi\u2019an Jiaotong University), Ministry of Education, Xi\u2019an 710061, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2915-5535","authenticated-orcid":false,"given":"Bolun","family":"Cheng","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi\u2019an Jiaotong University, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Trace Elements and Endemic Diseases (Xi\u2019an Jiaotong University), National Health and Family Planning Commission, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Environment and Genes Related to Diseases (Xi\u2019an Jiaotong University), Ministry of Education, Xi\u2019an 710061, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenming","family":"Wei","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi\u2019an Jiaotong University, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Trace Elements and Endemic Diseases (Xi\u2019an Jiaotong University), National Health and Family Planning Commission, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Environment and Genes Related to Diseases (Xi\u2019an Jiaotong University), Ministry of Education, Xi\u2019an 710061, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0527-9250","authenticated-orcid":false,"given":"Li","family":"Liu","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi\u2019an Jiaotong University, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Trace Elements and Endemic Diseases (Xi\u2019an Jiaotong University), National Health and Family Planning Commission, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Environment and Genes Related to Diseases (Xi\u2019an Jiaotong University), Ministry of Education, Xi\u2019an 710061, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiqiang","family":"Cheng","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi\u2019an Jiaotong University, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Trace Elements and Endemic Diseases (Xi\u2019an Jiaotong University), National Health and Family Planning Commission, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Environment and Genes Related to Diseases (Xi\u2019an Jiaotong University), Ministry of Education, Xi\u2019an 710061, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huan","family":"Liu","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi\u2019an Jiaotong University, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Trace Elements and Endemic Diseases (Xi\u2019an Jiaotong University), National Health and Family Planning Commission, Xi\u2019an 710061, China"},{"name":"Key Laboratory of Environment and Genes Related to Diseases (Xi\u2019an Jiaotong University), Ministry of Education, Xi\u2019an 710061, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumeng","family":"Jia","sequence":"additional","affiliation":[{"name":"Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science 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