Elucidating Epigenetic Regulation by Identifying Functional cis‐Acting Long Noncoding RNAs and Their Targets in Osteoarthritic Articular Cartilage

Abstract

Objective To identify robustly differentially expressed long noncoding RNAs (lncRNAs) with osteoarthritis (OA) pathophysiology in cartilage and to explore potential target messenger RNA (mRNA) by establishing coexpression networks, followed by functional validation. Methods RNA sequencing was performed on macroscopically lesioned and preserved OA cartilage from patients who underwent joint replacement surgery due to OA (n = 98). Differential expression analysis was performed on lncRNAs that were annotated in GENCODE and Ensembl databases. To identify potential interactions, correlations were calculated between the identified differentially expressed lncRNAs and the previously reported differentially expressed protein‐coding genes in the same samples. Modulation of chondrocyte lncRNA expression was achieved using locked nucleic acid GapmeRs. Results By applying our in‐house pipeline, we identified 5,053 lncRNAs that were robustly expressed, of which 191 were significantly differentially expressed (according to false discovery rate) between lesioned and preserved OA cartilage. Upon integrating mRNA sequencing data, we showed that intergenic and antisense differentially expressed lncRNAs demonstrate high, positive correlations with their respective flanking sense genes. To functionally validate this observation, we selected P3H2‐AS1, which was down‐regulated in primary chondrocytes, resulting in the down‐regulation of P3H2 gene expression levels. As such, we can confirm that P3H2‐AS1 regulates its sense gene P3H2. Conclusion By applying an improved detection strategy, robustly differentially expressed lncRNAs in OA cartilage were detected. Integration of these lncRNAs with differential mRNA expression levels in the same samples provided insight into their regulatory networks. Our data indicates that intergenic and antisense lncRNAs play an important role in regulating the pathophysiology of OA.

Whole Transcriptome Mapping Identifies an Immune- and Metabolism-Related Non-coding RNA Landscape Remodeled by Mechanical Stress in IL-1β-Induced Rat OA-like Chondrocytes

“…Moreover, mechanical stress gives promise to the novel lncRNA expression, and the number of the novel DELs was more than 10-fold of the known DELs, which suggests that this part is more responsive to mechanical stress in the lncRNA transcriptome. Indeed, the roles of lncRNAs are highlighted in chondrocyte biology and OA pathogenesis ( Tu et al, 2020 ; van Hoolwerff et al, 2020 ), such as lncRNA Pvt1 ( Li et al, 2017 ). In spite of the fact that increased Pvt1 is proven to be a promoter of chondrocyte apoptosis contributing OA, we found that Pvt1 was decreased instead in our system, suggesting that apoptosis might not be robustly induced by this mechanical stress.…”

Osteoarthritis year in review: genetics, genomics, epigenetics

“…To rationalize the lncRNAs most important in OA, van Hoolwerff et al. established lncRNA-mRNA co-expression networks using paired (lesion vs intact cartilage) RNA-seq data from almost 100 OA patients 58 . This identified 5,053 robustly expressed lncRNAs, of which 191 were significantly differentially expressed.…”

Insights into the molecular landscape of osteoarthritis in human tissues

“…This study pointed out 191 differentially expressed lncRNAs in degraded cartilage and demonstrated the importance of intergenic and antisense lncRNA in osteoarthritis pathophysiology. The authors also indicated P3H2-AS1 lncRNA as a potential preclinical target through regulation of its sense gene P3H2 [ 15 ]. Another study focused on microRNAs and their interactions with mRNAs by comparing the synovium between five osteoarthritis patients and three healthy controls.…”