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SeqCor:correct the effect of guide RNA sequences in clustered regularly interspaced short palindromic repeats/Cas9 screening by machine learning algorithm

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Journal of Genetics and Genomics 2020年第11期47卷 672-680页

作者： Xiaojian Liu Yuanyuan Yang Yan Qiu Md Reyad-ul-ferdous qiurong ding Yi Wang CAS Key Laboratory of Nutrition Metabolism and Food SafetyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China Ministry of Education Key Laboratory of Contemporary Anthropology Department of Anthropology and Human GeneticsSchool of Life SciencesFudan UniversityShanghai 200438China Human Phenome Institute Fudan UniversityShanghai 200438China

Clustered regularly interspaced short palindromic repeats(CRISPR)/Cas9-based screening using various guide RNA(g RNA)libraries has been executed to identify functional components for a wide range of phenotypes with regard to numerous cell types and *** data from public CRISPR/Cas9-based screening experiments,we found that the sequences of g RNAs in the library influence CRISPR/Cas9-based *** building a standard strategy for correcting results of all g RNA libraries is impractical,we developed Seq Cor,an open-source programming bundle that enables researchers to address the result bias potentially triggered by the composition of g RNA sequences via the organization of g RNA in the library used in CRISPR/Cas9-based ***,Seq Cor completely computerizes the extraction of sequence features that may influence single-guide RNA knockout efficiency using a machine learning *** together,we have developed a software program bundle that ought to be beneficial to the CRISPR/Cas9-based screening platform.

关键词： SeqCor CRISPR/Cas9-based screening Machine learning

Modeling drug-induced liver injury and screening for anti-hepatofibrotic compounds using human PSC-derived organoids

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Cell Regeneration 2023年第1期12卷 338-350页

作者： Xiaoshan Wu Dacheng Jiang Yi Yang Shuang Li qiurong ding School of Biotechnology East China University of Science and TechnologyShanghai 200237P.R.China CAS Key Laboratory of Nutrition Metabolism and Food SafetyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031P.R.China School of Pharmacy Fujian Health CollegeFujian 350101P.R.China Shanghai Jiao Tong University Affiliated Sixth People’s Hospital Shanghai 200233China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101P.R.China

Preclinical models that can accurately predict the toxicity and efficacy of candidate drugs to human liver tissue are in urgent *** liver organoid(HLO)derived from human pluripotent stem cells offers a possible ***,we generated HLOs,and demonstrated the utility of these HLOs in modeling a diversity of phenotypes associated with drug-induced liver injury(DILI),including steatosis,fibrosis,and immune *** changes in HLOs after treatment with tool compounds such as acetaminophen,fialuridine,methotrexate,or TAK-875 showed high concordance with human clinical data in drug safety ***,HLOs were able to model liver fibrogenesis induced by TGFβ or LPS *** further devised a high-content analysis system,and established a high-throughput anti-fibrosis drug screening system using ***208 and Imatinib were identified that can significantly suppress fibrogenesis induced by TGFβ,LPS,or *** together,our studies demonstrated the potential applications of HLOs in drug safety testing and anti-fibrotic drug screening.

关键词： Human liver organoid Pluripotent stem cell Drug-induced liver injury Anti-fibrotic compounds High-content analysis

In Situ Saturating Mutagenesis Screening Identifies a Functional Genomic Locus that Regulates Ucp1 Expression

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Phenomics 2021年第1期1卷 15-21页

作者： Yan Qiu Xiaojian Liu Yingmin Sun Shuang Li Yuda Wei Cheng Tian qiurong ding CAS Key Laboratory of Nutrition Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031People’s Republic of China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101People’s Republic of China

A better understanding of the molecular mechanisms that control the UCP1 expression in brown and beige adipocytes is essential for us to modulate adipose cell fate and promote thermogenesis,which may provide a therapeutic view for the treatment of obesity and obesity-related *** systematically identify cis-element(s)that transcriptionally regulates Ucp1,we here took advantage of the high-throughput CRIPSR-Cas9 screening system,and performed an in situ saturating mutagenesis screen,by using a customized sgRNA library targeting the~20 kb genomic region near *** the screening,we have identified several genomic loci that may contain key regulatory element for Ucp1 expression in cultured brown and white adipocytes in vitro,and in inguinal white adipose tissue in *** study highlights a broadly useful approach for studying cis-regulatory elements in a high-throughput manner.

关键词： In situ saturating mutagenesis screen Brown and beige adipocytes UCP1 sgRNA-9768

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心血管疾病的基因治疗

上海大学学报（自然科学版） 2016年第3期22卷 270-279页

作者：丁秋蓉陈彦好中国科学院上海生命科学研究院营养科学研究所上海200031

基因治疗在先天遗传性以及后天获得性心血管疾病治疗中均具有广阔的发展前景.对心血管疾病致病机理的深入认识和疾病基因组学研究的发展,进一步促进了临床前基因治疗的研究进展.但基因治疗过程中存在的机体细胞免疫反应、外源基因表达... 详细信息

基因治疗在先天遗传性以及后天获得性心血管疾病治疗中均具有广阔的发展前景.对心血管疾病致病机理的深入认识和疾病基因组学研究的发展,进一步促进了临床前基因治疗的研究进展.但基因治疗过程中存在的机体细胞免疫反应、外源基因表达水平不足、在体基因转导效率低下等因素都成为基因治疗临床应用转化的瓶颈.近年来,基因导入载体和基因组编辑技术的发展为上述问题的改善和解决提供了新的思路.目前成族规律间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)/Cas9基因组编辑技术已经成功应用于动物模型的在体基因编辑,达到了显著改善血脂指标的疗效.进一步研究体内组织特异和高效的基因导入方式,提高基因编辑的靶向效率和特异性,并建立全面有效的安全评估实验体系,将推动基因治疗向临床应用的转化.针对心血管疾病基因治疗中基因导入载体的研究以及CRISPR/Cas9基因组编辑技术的应用展开讨论.

关键词：心血管疾病基因治疗基因导入载体 CRISPR/Cas9基因组编辑技术

LENG8 regulation of mRNA processing controls mitochondria activity

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LENG8 regulation of mRNA processing controls mitochondria ac...

基因组编辑技术在干细胞疾病模型建立和精准医疗中的应用

中国生物化学与分子生物学会2020全国学术在线会议

作者： Yongxu Zhao Xiaoting Wang Yuenan Liu Niannian Li Shengming Wang Hongliang Yi Nan Zhang qiurong ding Feng Liu Department of Otolaryngology-Head and Neck Surgery Otolaryngology Institute of Shanghai JiaoTong UniversityShanghai JiaoTong University Affiliated Sixth People's Hospital CAS Key Laboratory of Nutrition Metabolism and Food SafetyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of Sciences Shanghai Key Laboratory of Sleep Disordered Breathing Department of Oncology Jinan Central HospitalCheeloo College of MedicineShandong University

mRNA processing is essential for the maintenance of cellular and tissue ***,how this process is precisely regulated in mammalian cells remains largely *** we demonstrate that LENG8 is the mammalian orthologous counterpart of yeast mRNA processing factor *** show that LENG8 binds mRNA,associates with components of mRNA processing machinery TREX complex and contributes to mRNA *** of LENG8 leads to aberrant accumulation of poly(A) RNA in nucleus in both Hela cells and murine ***8 precipitates shows high enrichment of mRNAs and lncRNAs,about half of which are also bound by THO/TREX component *** when compared to THOC1,LENG8 preferentially bound mRNA encoding mitochondria proteins and depletion of LENG8 dramatically destroys mitochondria structures and reduces mitochondrial respiratory *** work therefore reveals an evolutionarily conserved mRNA processing factor that controls mitochondria activity.

关键词： RNA metabolism mRNA export mRNP biogenesis mitochondria

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遗传 2015年第10期37卷 983-991页

作者：韦余达李爽刘改改张永贤丁秋蓉中国科学院上海生命科学研究院营养科学研究所上海200031

精准医疗强调针对不同个体定制个性化治疗方案,其推行需要精准疾病模型的建立。人类干细胞因其具有多能性而成为体外不同类型的成体细胞和器官小体的潜在来源,其强增殖能力保证了充足原材料用于科研分析和大规模药物筛选。基因组编辑技... 详细信息

精准医疗强调针对不同个体定制个性化治疗方案,其推行需要精准疾病模型的建立。人类干细胞因其具有多能性而成为体外不同类型的成体细胞和器官小体的潜在来源,其强增殖能力保证了充足原材料用于科研分析和大规模药物筛选。基因组编辑技术(尤其是CRISPR/Cas9技术)的快速发展使得在人多能干细胞和成体干细胞中进行高效基因组编辑成为可能。两者的有效结合能建立起针对不同遗传致病背景的"个性化"疾病模型,有利于深入解析不同遗传突变的致病机制和开发高针对性的精准医疗方案。本文对基因组编辑技术在人类干细胞中的应用以及利用干细胞疾病模型模拟罕见病和肿瘤发生的研究进行了综述。

关键词： CRISPR/Cas9技术人多能干细胞人成体干细胞罕见病模型肿瘤模型

Identification of small-molecule ion channel modulators in *** channelopathy models

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Identification of small-molecule ion channel modulators in *...

利用CRISPR/Cas9技术对人多能干细胞进行高效基因组编辑

第五届中国秀丽线虫大会

作者： Qiang Jiang Kai Li Wen-Jing Lu Shuang Li Xin Chen Xi-Juan Liu Jie Yuan qiurong ding Feng Lan Shi-Qing Cai Institute of Neuroscience and State Key Laboratory of Neuroscience CAS Center for Excellence in Brain Science and Intelligence TechnologyChinese Academy of Sciences Beijing Laboratory for Cardiovascular Precision Medicine Beijing Anzhen HospitalCapital Medical University CAS Key Laboratory of Nutrition and Metabolism Institute for Nutritional SciencesShanghai Institutes for Biological SciencesChinese Academy of Sciences

Ion channels are important drug targets,but in vitro high-throughput systems for channel-targeting drug discovery are often unreliable due to non-physiological context for ion *** we report a *** phenotype-based in vi...

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遗传 2015年第11期37卷 1167-1173页

作者：刘改改李爽韦余达张永贤丁秋蓉中国科学院上海生命科学研究院营养科学研究所上海200031

CRISPR/Cas9技术提供了一个全新的基因组编辑体系。本文利用CRISPR/Cas9平台,在人胚胎干细胞株中对选取的一段特定基因组区域进行了多种基因组编辑:通过在基因编码框中引入移码突变进行基因敲除;通过单链DNA提供外源模板经由同源重组定... 详细信息

CRISPR/Cas9技术提供了一个全新的基因组编辑体系。本文利用CRISPR/Cas9平台,在人胚胎干细胞株中对选取的一段特定基因组区域进行了多种基因组编辑:通过在基因编码框中引入移码突变进行基因敲除;通过单链DNA提供外源模板经由同源重组定点敲入FLAG序列;通过同时靶向多个位点诱导基因组大片段删除。研究结果表明CRISPR/Cas9可以对多能干细胞进行高效基因编辑,获得的突变干细胞株有助于对基因和基因组区域的功能进行分析和干细胞疾病模型的建立。

关键词： CRISPR/Cas9基因编辑人多能干细胞基因敲除 DNA序列定点插入基因组大片段删除

RACK1 as a signaling adaptor in regulating glucosestimulated IREla Activation in pancreatic b-cells

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RACK1 as a signaling adaptor in regulating glucosestimulated...