5.9
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5.9
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2021 Vol. 48, No. 4

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Original research
Comprehensive validation of a diagnostic strategy for sequencing genes with one or multiple pseudogenes using pseudoxanthoma elasticum as a model
Wouter Steyaert, Shana Verschuere, Paul J. Coucke, Olivier M. Vanakker
2021, 48(4): 289-299. doi: 10.1016/j.jgg.2021.02.009
Abstract (168) HTML PDF (9)
Abstract:
Pseudogenes are frequently encountered noncoding sequences with a high sequence similarity to their protein-coding paralogue. For this reason, their presence is often considered troublesome in molecular diagnostics. In pseudoxanthoma elasticum (PXE), a disease predominantly caused by mutations in ATPbinding cassette family C member 6 (ABCC6), the presence of two pseudogenes complicates the analysis of sequence data. With whole-exome sequencing (WES) becoming the standard of care in molecular diagnostics, we wanted to evaluate whether this technique is as reliable as gene-specific targeted enrichment analysis for the analysis of ABCC6. We established a PCR-based targeted enrichment and next-generation sequencing testing approach and demonstrated that the ABCC6-specific enrichment combined with the applied mapping algorithm overcomes the complication of ABCC6 pseudogene aspecificities, contrary to WES. We propose a time- and cost-efficient diagnostic strategy for comprehensive and accurate molecular genetic testing of PXE, which is highly automatable.
Geranylgeranyl pyrophosphate-mediated protein geranylgeranylation regulates endothelial cell proliferation and apoptosis during vasculogenesis in mouse embryo
Danyang Chong, Zhong Chen, Shan Gua, Tongyu Zhang, Na Xu, Yue Zhao, Chaojun Li
2021, 48(4): 300-311. doi: 10.1016/j.jgg.2021.03.009
Abstract (99) HTML PDF (7)
Abstract:
Vascular development is essential for the establishment of the circulatory system during embryonic development and requires the proliferation of endothelial cells. However, the underpinning regulatory mechanisms are not well understood. Here, we report that geranylgeranyl pyrophosphate (GGPP), a metabolite involved in protein geranylgeranylation, plays an indispensable role in embryonic vascular development. GGPP is synthesized by geranylgeranyl pyrophosphate synthase (GGPPS) in the mevalonate pathway. The selective knockout of Ggpps in endothelial cells led to aberrant vascular development and embryonic lethality, resulting from the decreased proliferation and enhanced apoptosis of endothelial cells during vasculogenesis. The defect in protein geranylgeranylation induced by GGPP depletion inhibited the membrane localization of RhoA and enhanced yes-associated protein (YAP) phosphorylation, thereby prohibiting the entry of YAP into the nucleus and the expression of YAP target genes related to cell proliferation and the antiapoptosis process. Moreover, inhibition of the mevalonate pathway by simvastatin induced endothelial cell proliferation defects and apoptosis, which were ameliorated by GGPP. Geranylgeraniol (GGOH), a precursor of GGPP, ameliorated the harmful effects of simvastatin on vascular development of developing fetuses in pregnant mice. These results indicate that GGPP-mediated protein geranylgeranylation is essential for endothelial cell proliferation and the antiapoptosis process during embryonic vascular development.
Targeted sequencing and integrative analysis of 3,195 Chinese patients with neurodevelopmental disorders prioritized 26 novel candidate genes
Tao Wang, Yi Zhang, Liqui Liu, Yan Wang, Huiqian Chen, Tianda Fan, Jinchen Li, Kun Xia, Zhongsheng Sun
2021, 48(4): 312-323. doi: 10.1016/j.jgg.2021.03.002
Abstract (142) HTML PDF (10)
Abstract:
Neurodevelopmental disorders (NDDs) are a set of complex disorders characterized by diverse and cooccurring clinical symptoms. The genetic contribution in patients with NDDs remains largely unknown. Here, we sequence 519 NDD-related genes in 3,195 Chinese probands with neurodevelopmental phenotypes and identify 2,522 putative functional mutations consisting of 137 de novo mutations (DNMs) in 86 genes and 2,385 rare inherited mutations (RIMs) with 22 X-linked hemizygotes in 13 genes, 2 homozygous mutations in 2 genes and 23 compound heterozygous mutations in 10 genes. Furthermore, the DNMs of 16,807 probands with NDDs are retrieved from public datasets and combine in an integrated analysis with the mutation data of our Chinese NDD probands by taking 3,582 in-house controls of Chinese origin as background. We prioritize 26 novel candidate genes. Notably, six of these genes — ITSN1, UBR3, CADM1, RYR3, FLNA, and PLXNA3 — preferably contribute to autism spectrum disorders (ASDs), as demonstrated by high co-expression and/or interaction with ASD genes confirmed via rescue experiments in a mouse model. Importantly, these genes are differentially expressed in the ASD cortex in a significant manner and involved in ASD-associated networks. Together, our study expands the genetic spectrum of Chinese NDDs, further facilitating both basic and translational research.
Phosphorylation of Ago2 is required for its role in DNA doublestrand break repair
Xiaolu Hu, Yan Li, Tianfang Zhang, Lin Li, She Chen, Xiaohong Wu, Haijun Li, Binjie Qi, Zuobing Chen
2021, 48(4): 333-340. doi: 10.1016/j.jgg.2021.03.011
Abstract (114) HTML PDF (8)
Abstract:
Repair of DNA double-strand break (DSB) is critical for the maintenance of genome integrity. A class of DSB-induced small RNAs (diRNAs) has been shown to play an important role in DSB repair. In humans, diRNAs are associated with Ago2 and guide the recruitment of Rad51 to DSB sites to facilitate repair by homologous recombination (HR). Ago2 activity has been reported to be regulated by phosphorylation under normal and hypoxic conditions. However, the role of Ago2 phosphorylation in DNA damage repair is unexplored. Here, we show that S672, S828, T830, and S831 of human Ago2 are phosphorylated in response to ionizing radiation (IR). S672A mutation of Ago2 leads to significant reduction in Rad51 foci formation and HR efficiency. We further show that defective association of Ago2 S672A variant with DSB sites, instead of defects in diRNA and Rad51 binding, may account for decreased Rad51 foci formation and HR efficiency. Our study reveals a novel regulatory mechanism for the function of Ago2 in DNA repair.
Letter to the editor
PARK16 locus: Differential effects of the non-coding rs823114 on Parkinson's disease risk, RNA expression, and DNA methylation
Orly Goldstein, Mali Gana-Weisz, Fergal Casey, Hila Meltzer-Fridrich, Or Yaacov, Yedael Y. Waldman, Dongdong Lin, Yael Mordechai, Jing Zhu, Patrick F. Cullen, Nurit Omer, Tamara Shiner, Avner Thaler, Anat Mirelman, Sally John, Nir Giladi, Avi Orr-Urtreger
2021, 48(4): 341-345. doi: 10.1016/j.jgg.2020.10.010
Abstract (135) HTML PDF (14)
Abstract: