Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis

Abstract

31Background: Osteoarthritis (OA) is a common joint disorder with increasing impact 32 in an aging society; however, there is no cure or effective treatments so far due to lack 33 of sufficient understanding of its pathogenesis. While genome-wide association studies 34 (GWAS) and DNA methylation profiling identified many non-coding loci associated 35 to OA, the interpretation of them remains challenging. 36Methods: Here, we employed Assay for Transposase-Accessible Chromatin with high 37 throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in 38 articular knee cartilage of OA patients and to identify the chromatin signatures relevant 39 to OA. 40 Results:We identified 109,215 accessible chromatin regions in cartilage and 71% of 41 these regions were annotated as enhancers. We found these accessible chromatin 42 regions are enriched for OA GWAS single nucleotide polymorphisms (SNPs) and OA 43 differentially methylated loci, implying their relevance to OA. By linking these 44 enhancers to their potential target genes, we have identified a list of candidate enhancers 45 that may be relevant to OA. Through integration of ATAC-seq data with RNA-seq data, 46we identified genes that are altered both at epigenomic and transcriptomic levels. These 47 enriched for mesenchymal stem cell-specific enhancers and motifs of transcription 50 factor families involved in osteoblast differentiation (e.g. bZIP and ETS). 51 Conclusions: This study marks the first investigation of accessible chromatin 52 landscape on clinically relevant hard tissues and demonstrates how accessible 53 chromatin profiling can provide comprehensive epigenetic information of a disease. 54 Our analyses provide supportive evidence towards the model of endochondral 55 ossification-like cartilage-to-bone conversion in OA knee cartilage, which is consistent 56 with the OA characteristic of thicker subchondral bone. The identified OA-relevant 57 genes and their enhancers may have a translational potential for diagnosis or drug 58 targets. 59 60 Keywords 61 osteoarthritis, epigenomics, enhancer, ATAC-seq, endochondral ossification. 62 63 Background 64Osteoarthritis (OA) is a degenerative joint disease [1,2] that is one of the most common 65 causes of chronic disability in the world [3,4], of which the knee OA is the most 66 common. Main features of OA include cartilage degradation, subchondral bone 67 thickening, joint space narrowing and osteophytes formation [5], resulting in stiffness, 68 swelling, and pain in the joint. Currently available treatments are either pain relief or 69 joint function improvement by strengthening the supporting muscles. However, OA 70 progression ultimately leads to costly total joint replacement surgery, making it a 71 growing global health burden. 72Although the causes of OA are not well understood, risk factors such as age, 73 weight, gender, and genetic factors have been identified [4]. Several models for OA 74 initiation, such as mechanical injury, inflammatory mediators from synovium, defects 75 4 in meta...

Knee Osteoarthritis: A Review of Pathogenesis and State-Of-The-Art Non-Operative Therapeutic Considerations

“…Likewise, by mapping the chromatin regulatory regions (promoters and enhancers) applying ATAC-seq on the knee joint cartilages from OA patients, Liu and colleagues investigated enhancers’ alterations associated with OA. During the study, the authors have verified 7 OA associated SNPs (rs10851630, rs10851631, rs10851632, rs12905608, rs12910752, rs4238326 and rs35246600) reside in three chondrocyte-accessible enhancers of the predicted target gene ALDH1A2 [ 161 ].…”

The Landscape of Chromatin Accessibility in Skeletal Muscle During Embryonic Development in Pigs

“…ACRs vary dramatically among different tissues and cell types during the developmental stage [68][69][70]. For example, widespread decreases in chromatin accessibility have been demonstrated to occur in age-related macular degeneration, and a few common ACRs have been found to be shared among different tissues [71].…”

“…In this study, to investigate the dynamics of chromatin accessibility during muscle development in pig embryos, we used ATAC-seq and RNA-seq to analyze the chromatin accessibility and transcriptome of longissimus dorsi tissue at different embryonic stages (45,70, and 100 days post coitus (dpc)) in Large White (LW) pigs (LW45, LW70, and LW100, respectively). The results of this work will provide a theoretical basis for comparison of the molecular mechanisms of embryonic muscle development among different stages, which will broaden our knowledge of epigenetics during muscle development.…”

Comparison of differential accessibility analysis strategies for ATAC-seq data

“…We further used another published ATAC-seq data of human healthy cartilage and Osteoarthritis cartilage 33 . After removal of three unwanted variations by using RUVSeq, we could observe significant improvement in the PCA plot [ Fig.…”

“…Down-sampling of ATAC-seq data. ATAC-seq data of mouse liver and kidney 39 , DLFC 24 , and human cartilage 33 were downloaded from GEO, and the QC check, data processing, and peak calling were performed by using AIAP (https://github.com/Zhang-lab/ATAC-seq_QC_analysis) 30 . Peaks identified in all samples were merged together if they had ≥1 bp overlap to generate common open chromatin regions (OCRs).…”