Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual

Abstract

Background Bone accrual impacts lifelong skeletal health, but genetic discovery has been primarily limited to cross-sectional study designs and hampered by uncertainty about target effector genes. Here, we capture this dynamic phenotype by modeling longitudinal bone accrual across 11,000 bone scans in a cohort of healthy children and adolescents, followed by genome-wide association studies (GWAS) and variant-to-gene mapping with functional follow-up. Results We identify 40 loci, 35 not previously reported, with various degrees of supportive evidence, half residing in topological associated domains harboring known bone genes. Of several loci potentially associated with later-life fracture risk, a candidate SNP lookup provides the most compelling evidence for rs11195210 (SMC3). Variant-to-gene mapping combining ATAC-seq to assay open chromatin with high-resolution promoter-focused Capture C identifies contacts between GWAS loci and nearby gene promoters. siRNA knockdown of gene expression supports the putative effector gene at three specific loci in two osteoblast cell models. Finally, using CRISPR-Cas9 genome editing, we confirm that the immediate genomic region harboring the putative causal SNP influences PRPF38A expression, a location which is predicted to coincide with a set of binding sites for relevant transcription factors. Conclusions Using a new longitudinal approach, we expand the number of genetic loci putatively associated with pediatric bone gain. Functional follow-up in appropriate cell models finds novel candidate genes impacting bone accrual. Our data also raise the possibility that the cell fate decision between osteogenic and adipogenic lineages is important in normal bone accrual.

Targeting circular RNAs as a therapeutic approach: current strategies and challenges

“…Furthermore, CRISPR/Cas13d- and shRNA-based circRNA functional screenings were performed, and shRNA screenings were found to result in significantly higher false positive rates. 36 Altogether, these studies suggest that the CRISPR/Cas13 system could serve as a highly effective tool to directly target circRNAs in a specific and robust manner, and they provide a basis for future in vivo studies.…”

“…This study evaluated the knockdown of several circRNAs and found that 24–30 nt spacers have comparable knockdown efficiency, with 24 nt spacers showing greater sensitivity to single and double mismatches compared to 30 nt spacers. 36 It was demonstrated that Cas13d and shRNA could achieve a similar circRNA knockdown efficiency, but Cas13d produced substantially less off-target effects. Furthermore, CRISPR/Cas13d- and shRNA-based circRNA functional screenings were performed, and shRNA screenings were found to result in significantly higher false positive rates.…”

“… 33 , 34 Furthermore, CRISPR technology and Cas13 systems in particular have demonstrated great potential in knocking down circRNAs in a specific and robust manner. 35 , 36 …”

scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured

“…In addition to selecting experimental protocols before conducting scRNA-seq experiments, a common challenge after collecting scRNA-seq data is to choose among the many available data analysis methods in an unbiased manner. For example, many algorithms have been developed for missing gene expression imputation [ 36 , 37 ], dimensionality reduction [ 38 – 40 ], cell clustering [ 41 – 44 ], rare cell type detection [ 45 – 47 ], differentially expressed gene identification [ 48 – 52 ], and trajectory inference [ 53 – 57 ]. Even though several benchmark and comparative studies have been carried out for common analysis tasks [ 58 – 63 ], most of them have only evaluated a subset of available computational methods using data from limited experimental protocols.…”

ABE8e with Polycistronic tRNA-gRNA Expression Cassette Sig-Nificantly Improves Adenine Base Editing Efficiency in Nicotiana benthamiana

“…The efficiency of ABE8e is significantly improved in human cells, especially at poorly edited targets with ABE7.10, which could provide a useful tool for broadening adenine base editing capability [ 12 ]. While we prepared this manuscript, the ABE8e has been reported in rice [ 14 , 15 , 16 ]. However, the comparison between ABE7.10 and ABE8e and the effects of the sgRNA expression system on ABE8e have not been investigated.…”