Browsing by Author "Yang, Qingxin"

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Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response
(2021-03-10) Lin, Jing-wen; Tang, Chao; Wei, Han-cheng; Du, Baowen; Chen, Chuan; Wang, Minjin; Zhou, Yongzhao; Yu, Ming-xia; Cheng, Lu; Kuivanen, Suvi; Ogando, Natacha S.; Levanov, Lev; Zhao, Yuancun; Li, Chang-ling; Zhou, Ran; Li, Zhidan; Zhang, Yiming; Sun, Ke; Wang, Chengdi; Chen, Li; Xiao, Xia; Zheng, Xiuran; Chen, Sha-sha; Yang, Ruirui; Zhang, Dan; Xu, Mengying; Song, Junwei; Wang, Danrui; Li, Yupeng; Lei, ShiKun; Zeng, Wanqin; Yang, Qingxin; He, Ping; Zhang, Yaoyao; Zhou, Lifang; Cao, Ling; Luo, Feng; Liu, Huayi; Wang, Liping; Ye, Fei; Zhang, Ming; Li, Mengjiao; Li, Xinqiong; Li, Kaiju; Ke, Bowen; Xu, Jiannan; Yang, Huiping; He, Shusen; Pan, Ming; Yan, Yichen; Zha, Yi; Jiang, Lingyu; Yu, Changxiu; Liu, Yingfen; Xu, Zhiyong; Li, Qingfeng; Jiang, Yongmei; Sun, Jiufeng; Hong, Wei; Wei, Hongping; Lu, Guangwen; Vapalahti, Olli; Luo, Yunzi; Wei, Yuquan; Connor, Thomas; Tan, Wenjie; Snijder, Eric J.; Smura, Teemu; Li, Weimin; Geng, Jia; Ying, Binwu; Chen, Lu
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
SCAPE: a mixture model revealing single-cell polyadenylation diversity and cellular dynamics during cell differentiation and reprogramming
(2022-06-24) Zhou, Ran; Xiao, Xia; He, Ping; Zhao, Yuancun; Xu, Mengying; Zheng, Xiuran; Yang, Ruirui; Chen, Shasha; Zhou, Lifang; Zhang, Dan; Yang, Qingxin; Song, Junwei; Tang, Chao; Zhang, Yiming; Lin, Jing-wen; Cheng, Lu; Chen, Lu
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Alternative polyadenylation increases transcript diversities at the 3’ end, regulating biological processes including cell differentiation, embryonic development and cancer progression. Here, we present a Bayesian method SCAPE, which enables de novo identification and quantification of polyadenylation (pA) sites at single-cell level by utilizing insert size information. We demonstrated its accuracy and robustness and identified 31 558 sites from 36 mouse organs, 43.8% (13 807) of which were novel. We illustrated that APA isoforms were associated with miRNAs binding and regulated in tissue-, cell type-and tumor-specific manners where no difference was found at gene expression level, providing an extra layer of information for cell clustering. Furthermore, we found genome-wide dynamic changes of APA usage during erythropoiesis and induced pluripotent stem cell (iPSC) differentiation, suggesting APA contributes to the functional flexibility and diversity of single cells. We expect SCAPE to aid the analyses of cellular dynamics and diversities in health and disease.