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Computer-aided engineering of CRISPR-Cas proteins for enhanced human genome editing

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Science China(Life Sciences) 2023年第4期66卷 883-886页

作者： Yangcan Chen Yanping Hu Shengqiu Luo Xinge Wang Bangwei Mao Yi Chen Jing Xu Zhikun Li Qi Zhou Wei Li State Key Laboratory of stem cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China institute for stem cell and regenerative medicine Chinese Academy of SciencesBeijing 100101China Bejing institute for stem cell and regenerative medicine Beijing 100101China

Dear editor.The remarkably diversified CRISPR-Cas systems in nature have provided unlimited valuable resources to develop genome editing tools that are revolutionizing the fields of biotechnology and medicine.However,due to their microbial origin,the activity of most naturally occurring CRISPR-Cas nucleases is relatively poor in mammalian cells(Ran et al.,2015).Thus,improving the mammalian genome editing efficiency becomes the priority for harnessing more CRISPRCas systems for widespread applications.Rational protein engineering serves as a powerful approach to enhance the catalytic activity of enzymes.Whereas,this approach largely relies on proteinic three-dimension(3D)structure information as guide for design.The fact is that of the large numbers of the CRISPR-Cas systems discovered in recent years,only a small number of them with the 3D structures were reported.To bypass this limitation,here,we report an efficient and simple strategy for rational engineering of Cas nucleases without the need of 3D structure information and successfully optimized nucleases from Cas9 and Cas12 families.

关键词： rational editor editing

A framework for the responsible reform of the 14-day rule in human embryo research

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Protein & cell 2022年第8期13卷 552-558页

作者： Yaojin Peng Jianwei Lv Zhenyu Xiao Lulu Ding Qi Zhou State Key Laboratory of stem cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China institute for stem cell and Regeneration Chinese Academy of SciencesBeijing 100101China University of the Chinese Academy of Sciences Beijing 100049China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China

Ever since the world's first"test-tube"baby was bom in 1978,the use of human embryos in research has become highly controversial ethically and thus created a significant challenge for jurisdictions,especially in Europ... 详细信息

关键词： framework rule created

Deciphering the placental abnormalities associated with somatic cell nuclear transfer at single-nucleus resolution

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Protein & cell 2023年第12期14卷 924-928页

作者： Liyuan Jiang Xin Wang Leyun Wang Sinan Ma Yali Ding Chao Liu Siqi Wang Xuan Shao Ying Zhang Zhikun Li Wei Li Guihai Feng Qi Zhou College of Life Sciences Northeast Agricultural UniversityHarbin 150030China State Key Laboratory of stem cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China institute for stem cell and regenerative medicine Chinese Academy of SciencesBeijing 100101China Savaid Medical School University of Chinese Academy of SciencesBeijing 100049China University of Chinese Academy of Sciences Beijing 100049China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China

Dear Editor,The placenta connecting the fetus to the matermal uterus provides material exchange and an immune-tolerant environment for the embryo in all eutherian mammals(Shao et al.,2022).The representative mouse placenta displays a multilayered structure with distinct characteristics and functions,including the matermal decidua,junctional zone,and labyrinth layer(Marsh and Blelloch,2020).The decidua,which is thought to be derived from the matermal endometrium(and further undergoes decidualization),provides an anchor for fetal trophoblast invasion.The junctional zone predominantly contains spongiotrophoblasts(SpT),glycogen trophoblasts(GlyT),and trophoblast giant cells(TGCs).The labyrinth is the innermost two-layer structure,which mainly consists of syncytiotrophoblast cells(SynTI and SynTII),sinusoidal TGCs(S-TGCs),and fetal endothelial cells(Simmons and Cross,2005).

关键词： fetal invasion fetus

Connecting past and present:single-cell lineage tracing

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Protein & cell 2022年第11期13卷 790-807页

作者： Cheng Chen Yuanxin Liao Guangdun Peng Center for cell Lineage and Development CAS Key Laboratory of Regenerative BiologyGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineGIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research CentreGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China Center for cell Lineage and Atlas Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory)Guangzhou 510005China institute for stem cell and Regeneration Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Central to the core principle of cell theory,depicting cells'history,state and fate is a fundamental goal in modern biology.By leveraging clonal analysis and sin-gle-cell RNA-seq technologies,single-cell lineage trac-ing provides new opportunities to interrogate both cell states and lineage histories.During the past few years,many strategies to achieve lineage tracing at single-cell resolution have been developed,and three of them(in-tegration barcodes,polylox barcodes,and CRISPR barcodes)are noteworthy as they are amenable in experimentally tractable systems.Although the above strategies have been demonstrated in animal develop-ment and stem cell research,much care and effort are still required to implement these methods.Here we review the development of single-cell lineage tracing,major characteristics of the cell barcoding strategies,applications,as well as technical considerations and limitations,providing a guide to choose or improve the single-cell barcoding lineage tracing.

关键词： single-cell lineage tracing integration barcodes polylox barcodes CRISPR barcodes

Placental Development and Pregnancy-Associated Diseases

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Maternal-Fetal medicine 2022年第1期4卷 36-51页

作者： Xin Yu Hongyu Wu Yun Yang Feiyang Wang Yan-Ling Wang Xuan Shao State Key Laboratory of stem cell and Reproductive Biology Institute of ZoologyInstitute for Stem Cell and RegenerationChinese Academy of SciencesBeijing 100101China University of the Chinese Academy of Sciences Beijing 101408China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China

Serving as the interface between the fetal and maternal environments during gestation,the placenta plays critical roles in the protection of the developing fetus and the maintenance of maternal health.The placenta is primarily derived from the embryonic trophectoderm which differentiates into various subtypes of trophoblast cells through villous and extravillous pathways.The interactions among trophoblasts and multiple decidual cells and immune cells at the maternal-fetal interface fundamentally form the functional units of the placenta,which are responsible for blood perfusion and maternal-fetal material exchange,immune tolerance,and the regulation of pregnancy adaptation.Defects in placental development and functional maintenance are in tight association with adverse pregnancy outcomes such as preeclampsia.In this article,we review recent advances on human trophoblast cell differentiation and the construction of placental functional units and discuss the placental and maternal factors that may contribute to the occurrence of preeclampsia.

关键词： Placenta Human placenta Trophoblast cell differentiation Functional units Preeclampsia

Mesenchymal stem cells in tissue repairing and regeneration: Progress and future

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Burns & Trauma 2013年第1期1卷 13-20页

作者： Jiafei Xi Xinlong Yan Junnian Zhou Wen Yue Xuetao Pei stem cell and regenerative medicine Lab Beijing Institute of Transfusion Medicine Beijing China

The presence of mesenchymal progenitor cells within bone marrow has been known since the late nineteenth century. To date, mesenchymal stem cells (MSCs) have been isolated from several different connective tissues, such as adipose tissue, muscle, placenta, umbilical cord matrix, blood, liver, and dental pulp. Bone marrow, however, is still one of the major sources of MSCs for preclinical and clinical research. MSCs were first evaluated for regenerative applications and have since been shown to directly influence the immune system and to promote neovascularization of ischemic tissues. These observations have prompted a new era of MSC transplantation as a treatment for various diseases. In this review, we summarize the important studies that have investigated the use of MSCs as a therapeutic agent for regenerative medicine, immune disorders, cancer, and gene therapy. Furthermore, we discuss the mechanisms involved in MSC-based therapies and clinical-grade MSC manufacturing.

关键词： Mesenchymal stem cells regenerative medicine gene therapy anticancer immune disorder

Chemical journey of somatic cells to pluripotency

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cell Regeneration 2022年第1期11卷 290-292页

作者： Deepti Abbey institute for stem cell Science and regenerative medicine GKVK-PostBellary RoadBangalore 560065India

Reprogramming somatic cells to pluripotent stem cells has revolutionized the biomedical field by providing enor-mous hopes and opportunities for the regeneration of tissues and organs for transplantation.Using a small molecule cocktail of epigenetic modifiers and cell signalling inhibitors,a chemical-based easy and controllable technique for converting human somatic cells into chemically induced pluripotent stem cells was recently reported(Guan,Nature 605:325–31,2022).This novel approach offers well-defined,safe,simple,easy,and clinical-grade manufacturing strate-gies for modifying the fate of human cells required for regenerative therapeutics.

关键词： organs programming somatic

Synergistic engineering of CRISPR-Cas nucleases enables robust mammalian genome editing

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The Innovation 2022年第4期3卷 74-82页

作者： Yangcan Chen Yanping Hu Xinge Wang Shengqiu Luo Ning Yang Yi Chen Zhikun Li Qi Zhou Wei Li State Key Laboratory of stem cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China institute for stem cell and regenerative medicine Chinese Academy of SciencesBeijing 100101China Bejing institute for stem cell and regenerative medicine Beijing 100101China

The naturally occurring prokaryotic CRISPR-Cas systems provide valuable resources for the development of new genome-editing tools.However,the majority of prokaryotic Cas nucleases exhibit poor editing efficiency in mammalian cells,which significantly limits their utility.Here,we have developed a method termed Improving Editing Activity by Synergistic Engineering(MIDAS).This method exerts a synergistic effect to improve mammalian genome-editing efficiency of a wide range of CRISPR-Cas systems by enhancing the interactions of Cas nuclease with the protospacer adjacent motif(PAM)and the single-stranded DNA(ssDNA)substrate in the catalytic pocket simultaneously.MIDAS robustly and significantly increased the gene-editing efficiency of Cas12i,Cas12b,and CasX in human cells.Notably,a Cas12i variant,Cas12iMax,exhibited robust activity with a very broad PAM range(NTNN,NNTN,NAAN,and NCAN)and higher efficiency than the current widely used Cas nucleases.A high-fidelity version of Cas12iMax(Cas12iHiFi)has been further engineered to minimize off-target effects.Our work provides an expandable and efficacious method for engineering Cas nucleases for robust mammalian genome editing.

关键词： editing engineering mammalian

Two kinds of macrophage memory:innate and adaptive immune-like macrophage memory

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cellular & Molecular Immunology 2022年第7期19卷 852-854页

作者： Changhong Wu Yanan Xu Yong Zhao State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijingChina Cunji Medical School University of Chinese Academy of SciencesBeijingChina Beijing Institute for Stem Cell and Regenerative Medicine BeijingChina

It is believed that the adaptive immune system responds to nonself entities with its specificity and memory properties.In contrast,the innate immune system lacks adaptive characteristics.Whether innate immune cells ca... 详细信息

关键词： properties characteristics system