Probes for INS

To understand the subcellular localization of RUNX2 and two lncRNAs, LINC02035 and LOC100130207, immunocytochemistry (for RUNX2 protein) and RNA _in situ_ hybridization assays (for both lncRNAs) were performed using human primary chondrocytes isolated from knee cartilage of OA patients. We confirmed that the RUNX2 protein was strongly detected in the nucleus of chondrocytes isolated from damaged cartilage (Figure 4A). The fractionated western blot results also showed that the RUNX2 protein was detected only in the nucleus of chondrocytes isolated from damaged cartilage (Figure 4B). To further understand the molecular mechanisms of the lncRNAs LINC02035 and LOC100130207, we performed an _in situ_ assay using primary chondrocytes derived from patients, because primary chondrocytes are a valuable model for studying OA pathogenesis. The results showed that both LINC02035 and LOC100130207 were highly expressed in chondrocytes isolated from the knee cartilage of patients with OA (Figure 4C). We then evaluated the mRNA levels and subcellular localization of both lncRNAs to elucidate their site of action using a commercially available kits in primary chondrocytes isolated from intact or damaged cartilage tissues. The results showed that both lncRNAs were more upregulated in primary chondrocytes isolated from damaged cartilage tissue than in intact cartilage tissue (Figure 4D). In primary chondrocytes, LINC02035 and LOC100130207 were merely detected in the cytoplasm of human primary chondrocytes and both lncRNAs were localized to nucleus (Figure 4E). Likewise, we also studied the subcellular localization of both lncRNAs in TC28a2 cells. The results showed that LINC02035 and LOC100130207 were evenly distributed in the nucleus and cytoplasm of normal chondrocytes (Figure 4F, left). However, both lncRNAs were preferentially localized to the nucleus and to a lesser extent to the cytoplasm after TC28a2 cells were treated with hypertrophic medium or TNF-α (Figure 4F, middle and right). To investigate whether RUNX2 is regulated at the post-translational level during hypertrophic changes in chondrocytes, human primary chondrocytes or TC28a2 cells were treated with the proteasome inhibitor MG132. The results showed that the protein level of RUNX2 was dose-dependently increased by MG132 treatment (Figure 4G-H), indicating that the upregulation of RUNX2 in osteoarthritic or hypertrophic chondrocytes occurs at the post-translational level. To examine whether both lncRNAs are involved in the stabilization of RUNX2 protein during hypertrophic differentiation and the inflammatory response in chondrocytes, IP was conducted to confirm the ubiquitination of RUNX2 protein. First, we investigated how the ubiquitination of RUNX2 protein is regulated during hypertrophic differentiation or the inflammatory response of chondrocytes, and as a result, it was confirmed that ubiquitination of RUNX2 was reduced by hypertrophic medium or TNF-α treatment (Figure 4I). However, ubiquitination of RUNX2 protein was clearly increased in TC28a2 cells transfected with siRNAs targeting LINC02035 or LOC100130207, even though the cells were treated with hypertrophic medium or TNF-α (Figure 4J-K). These results suggest that both lncRNAs upregulated during hypertrophic differentiation and the inflammatory response in chondrocytes contribute to the stabilization of the RUNX2 protein.

Diseases of the renal filtration unit—the glomerulus—are the most common cause of chronic kidney disease. Podocytes are the pivotal cell type for the function of this filter and focal-segmental glomerulosclerosis (FSGS) is a classic example of a podocytopathy leading to proteinuria and glomerular scarring. Currently, no targeted treatment of FSGS is available. This lack of therapeutic strategies is explained by a limited understanding of the defects in podocyte cell biology leading to FSGS. To date, most studies in the field have focused on protein-coding genes and their gene products. However, more than 80% of all transcripts produced by mammalian cells are actually non-coding. Here, long non-coding RNAs (lncRNAs) are a relatively novel class of transcripts and have not been systematically studied in FSGS to date. The appropriate tools to facilitate lncRNA research for the renal scientific community are urgently required due to a row of challenges compared to classical analysis pipelines optimized for coding RNA expression analysis. Here, we present the bioinformatic pipeline CALINCA as a solution for this problem. CALINCA automatically analyzes datasets from murine FSGS models and quantifies both annotated and de novo assembled lncRNAs. In addition, the tool provides in-depth information on podocyte specificity of these lncRNAs, as well as evolutionary conservation and expression in human datasets making this pipeline a crucial basis to lncRNA studies in FSGS.