We retrieved 159 OA-related per-view publications from the Web of Science (a list of publicaitons used by this release see below) and read and collected genes associated OA reported by the publications. At least one evidence was found to support the corresponding gene as a biomarker for OA: genome-wide association study (GWAS), differential expressed gene (DEG) or differential methylation region (DMR) analysis (Boer et al., 2021; Ramos et al. 2014; Dunn et al., 2019; Ali et al., 2020; Ji et al., 2018).
As a results, a total of 2,405 OA marker genes which have been identified from different joints were collected (Table 1). The 2,405 OA marker genes have diverse evidences, such as 167 by GWAS, 899 by DEG analysis based on transcriptomic (bull RNA, 65 were further experimentally validated) and 1,212 by DMR analysis (56 further validated). In the 167 marker genes or OA-associated effector genes by GWAS, most 126 (17.5%) were also included in the gene set independently identified by DEG or DMR analysis.
DEG analysis base on small RNAs and single-cell RNAs (scRNA), also found several hundreds of mark genes, including 154 genes coding genes that were regulated by 176 non-coding genes (11 lncRNAs, five circRNAs and 160 miRNAs), and 251 genes identified by scRNA-seq data.
With more clinical significance, 112 OA marker genes (22 experimentally validated) were identified from blood of OA patients, which had significantly different expression or methylation level relative to normal (Table 1).
Additionally, a total of 30 OA marker genes can be targeted by available drugs based on DrugBank database, which provide another useful clinical approach to cure OA.
The above marker genes are predictive of OA progression and valuable diagnosis biomarkers with superior ability to measure early and subtle changes in OA progression compared to traditional radiographic measures.
(Qinjie Chu, Lingjuan Xie, Xiaoxu Xu, Xiaotian Yang, Longjiang Fan)
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