Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands.
Department of Orthopaedics, Leiden University Medical Center, Leiden, The Netherlands.
Rheumatology (Oxford). 2023 Apr 3;62(4):1669-1676. doi: 10.1093/rheumatology/keac498.
To present an unbiased approach to identify positional transcript single nucleotide polymorphisms (SNPs) of osteoarthritis (OA) risk loci by allelic expression imbalance (AEI) analyses using RNA sequencing of articular cartilage and subchondral bone from OA patients.
RNA sequencing from 65 articular cartilage and 24 subchondral bone from OA patients was used for AEI analysis. AEI was determined for all genes present in the 100 regions reported by the genome-wide association studies (GWAS) catalog that were also expressed in cartilage or bone. The count fraction of the alternative allele (φ) was calculated for each heterozygous individual with the risk SNP or with the SNP in linkage disequilibrium (LD) with it (r2 > 0.6). Furthermore, a meta-analysis was performed to generate a meta-φ (null hypothesis median φ = 0.49) and P-value for each SNP.
We identified 30 transcript SNPs (28 in cartilage and two in subchondral bone) subject to AEI in 29 genes. Notably, 10 transcript SNPs were located in genes not previously reported in the GWAS catalog, including two long intergenic non-coding RNAs (lincRNAs), MALAT1 (meta-φ = 0.54, FDR = 1.7×10-4) and ILF3-DT (meta-φ = 0.6, FDR = 1.75×10-5). Moreover, 12 drugs were interacting with seven genes displaying AEI, of which seven drugs have been already approved.
By prioritizing proxy transcript SNPs that mark AEI in cartilage and/or subchondral bone at loci harbouring GWAS signals, we present an unbiased approach to identify the most likely functional OA risk-SNP and gene. We identified 10 new potential OA risk genes ready for further translation towards underlying biological mechanisms.
通过对骨关节炎（OA）患者关节软骨和软骨下骨的 RNA 测序进行等位基因表达失衡（AEI）分析，提出一种公正的方法来识别 OA 风险基因座的位置转录单核苷酸多态性（SNP）。
使用 65 例 OA 患者的关节软骨和 24 例软骨下骨的 RNA 测序进行 AEI 分析。对全基因组关联研究（GWAS）目录中报告的 100 个区域中所有在软骨或骨中表达的基因进行 AEI 分析。对于具有风险 SNP 或与风险 SNP 连锁不平衡（LD）的 SNP（r2>0.6）的每个杂合个体，计算替代等位基因的计数分数（φ）。此外，还进行了荟萃分析，以生成每个 SNP 的荟萃 φ（零假设中位数 φ=0.49）和 P 值。
我们在 29 个基因中确定了 30 个受 AEI 影响的转录 SNP（28 个在软骨中，2 个在软骨下骨中）。值得注意的是，10 个转录 SNP 位于 GWAS 目录中未报道的基因中，包括两个长非编码 RNA（lncRNA），MALAT1（荟萃 φ=0.54， FDR=1.7×10-4）和 ILF3-DT（荟萃 φ=0.6， FDR=1.75×10-5）。此外，有 12 种药物与 7 种显示 AEI 的基因相互作用，其中 7 种药物已获得批准。
通过优先考虑在含有 GWAS 信号的基因座中标记软骨和/或软骨下骨 AEI 的替代转录 SNP，我们提出了一种公正的方法来识别最有可能的 OA 风险 SNP 和基因。我们确定了 10 个新的潜在 OA 风险基因，为进一步转化为潜在的生物学机制做好了准备。
