全基因组关联研究(GWAS)指导的数据整合与非编码CRISPR干扰筛选揭示骨密度的遗传病因

GWAS-Informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density.

作者信息

Conery Mitchell, Pippin James A, Wagley Yadav, Trang Khanh, Pahl Matthew C, Villani David A, Favazzo Lacey J, Ackert-Bicknell Cheryl L, Zuscik Michael J, Katsevich Eugene, Wells Andrew D, Zemel Babette S, Voight Benjamin F, Hankenson Kurt D, Chesi Alessandra, Grant Struan F A

机构信息

Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.

Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.

出版信息

bioRxiv. 2024 Dec 29:2024.03.19.585778. doi: 10.1101/2024.03.19.585778.

Abstract

Over 1,100 independent signals have been identified with genome-wide association studies (GWAS) for bone mineral density (BMD), a key risk factor for mortality-increasing fragility fractures; however, the effector gene(s) for most remain unknown. Informed by a variant-to-gene mapping strategy implicating 89 non-coding elements predicted to regulate osteoblast gene expression at BMD GWAS loci, we executed a single-cell CRISPRi screen in human fetal osteoblasts (hFOBs). The BMD relevance of hFOBs was supported by heritability enrichment from stratified LD-score regression involving 98 cell types grouped into 15 tissues. 23 genes showed perturbation in the screen, with four (ARID5B, CC2D1B, EIF4G2, and NCOA3) exhibiting consistent effects upon siRNA knockdown on three measures of osteoblast maturation and mineralization. Lastly, additional heritability enrichments, genetic correlations, and multi-trait fine-mapping revealed unexpectedly that many BMD GWAS signals are pleiotropic and likely mediate their effects via non-bone tissues. Extending our CRISPRi screening approach to these tissues could play a key role in fully elucidating the etiology of BMD.

摘要

全基因组关联研究(GWAS)已识别出1100多个与骨密度(BMD)相关的独立信号,骨密度是导致死亡率增加的脆性骨折的关键风险因素;然而,大多数信号的效应基因仍不为人知。基于一种变异到基因的映射策略,该策略涉及89个预测在BMD GWAS位点调控成骨细胞基因表达的非编码元件,我们在人胎儿成骨细胞(hFOB)中进行了单细胞CRISPR干扰筛选。通过对15个组织中98种细胞类型进行分层LD评分回归的遗传力富集,支持了hFOB与BMD的相关性。筛选中有23个基因显示出扰动,其中四个基因(ARID5B、CC2D1B、EIF4G2和NCOA3)在对成骨细胞成熟和矿化的三项指标进行siRNA敲低时表现出一致的效应。最后,额外的遗传力富集、遗传相关性和多性状精细定位意外地发现,许多BMD GWAS信号具有多效性,可能通过非骨组织介导其效应。将我们的CRISPR干扰筛选方法扩展到这些组织可能在全面阐明BMD的病因方面发挥关键作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/76f0/11687569/cd3b2ad557a4/nihpp-2024.03.19.585778v2-f0001.jpg

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