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CRISPR,CAR-T,and NK:Current applications and future perspectives

genes & Diseases 2024年第4期11卷 246-257页

作者： Mohadeseh Khoshandam Hossein Soltaninejad Amir Ali Hamidieh Saman Hosseinkhani department of Reproductive Biology Academic Center for EducationCultureand Research(ACECR)Qom branch***Iran National Institute of genetic Engineering and Biotechnology(NIGEB) Tehran 14965/161Iran department of stem cells technology and Tissue Regeneration Faculty of Interdisciplinary Science and TechnologiesTarbiat Modares UniversityTehran 15614Iran Pediatric Cell Therapy and gene Therapy Research Center GeneCell&Tissue Research InstituteTehran University of Medical SciencesTehran ***Iran department of Biochemistry Faculty of Biological SciencesTarbiat Modares UniversityTehran 15614Iran

Chimeric antigen receptor T(CAR-T)cell therapy represents a breakthrough in personalized cancer treatments.In this regard,synthetic receptors comprised of antigen recognition domains,signaling,and stimulatory domains are used to reprogram T-cells to target tum or cells and destroy them.Despite the success of this approach in refractory B-cell malignancies,the optimal potency of CAR T-cell therapy for many other cancers,particularly solid tumors,has not been validated.Natural killer cells are powerful cytotoxic lymphocytes specialized in recognizing and dispensing the tumor cells in coordination with other anti-tumor immunity cells.Based on these studies,many investigations are focused on the accurate designing of CAR T-cells with clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)system or other novel gene editing tools that can induce hereditary changes with or without the presence of a double-stranded break into the genome.These methodologies can be specifically focused on negative controllers of T-cells,induce modifications to a particular gene,and produce reproducible,safe,and powerful allogeneic CAR T-cells for on-demand cancer immunotherapy.The improvement of the CRISPR/Cas9 innovation offers an adaptable and proficient gene-editing capability in activating different pathways to help natural killer cells interact with novel CARs to particularly target tumor cells.Novel achievements and future challenges of combining next-generation CRISPR-Cas9 gene editing tools to optimize CAR T-cell and natural killer cell treatment for future clinical trials toward the foundation of modern cancer treatments have been assessed inthis review.

关键词： Cancer CAR T-cell CRISPR gene editing Immunotherapy NK cell

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Clinical applications of the CRISPR/Cas9 genome-editing system: Delivery options and challenges in precision medicine

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genes & Diseases 2024年第1期11卷 268-282页

作者： Mohadeseh Khoshandam Hossein Soltaninejad Marziyeh Mousazadeh Amir Ali Hamidieh Saman Hosseinkhani department of Reproductive Biology Academic Center for EducationCultureand Research(ACECR)Qom BranchQom ***Iran National Institute of genetic Engineering and Biotechnology(NIGEB) Tehran 14155-6463Iran Faculty of Interdisciplinary Science and Technology Tarbiat Modares UniversityTehran 14117-13116Iran Pediatric Cell and gene Therapy Research Center GeneCell&Tissue Research InstituteTehran UniversityofMedical SciencesTehran14155-6559Iran department of Nanobiotechnology Faculty of Biological SciencesTarbiat Modares UniversityTehran 14117-13116Iran department of Biochemistry Faculty of Biological SciencesTarbiat Modares UniversityTehran 14117-13116Iran

CRISPR/Cas9 is an effective gene editing tool with broad applications for the pre-vention or treatment of numerous diseases.It depends on CRiSPR(clustered regularly inter-spaced short palindromic repeats)as a bacterial immune system and plays as a gene editing tool.Due to the higher specificity and efficiency of CRISPR/Cas9 compared to other editing ap-proaches,it has been broadly investigated to treat numerous hereditary and acquired ill-nesses,including cancers,hemolytic diseases,immunodeficiency disorders,cardiovascular diseases,visual maladies,neurodegenerative conditions,and a few X-linked disorders.CRISPR/Cas9 system has been used to treat cancers through a variety of approaches,with sta-ble gene editing techniques.Here,the applications and clinical trials of CRisPR/Cas9 in various illnesses are described.Due to its high precision and efficiency,CRISPR/Cas9 strategies may treat gene-related illnesses by deleting,inserting,modifying,or blocking the expression of specific genes.The most challenging barrier to the in vivo use of CRISPR/Cas9 like off-target effects will be discussed.The use of transfection vehicles for CRISPR/Cas9,including viral vectors(such as an Adeno-associated virus(AAV),and the development of non-viral vectors is also considered.

关键词： Clinical trials CRISPR/Cas9 gene therapy Non-viral vectors Viral vectors

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Intracellular RNA Labeling Technologies for the Analysis of RNA Biology

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Chinese Journal of Chemistry 2024年第7期42卷 790-801页

作者： Ruiqi Zhao Xin Fang Xiaocheng Weng department of Clinical Laboratory Center for Gene DiagnosisDepartment of NeurosurgeryZhongnan Hospital of Wuhan UniversityWuhanHubei 430071China College of Chemistryand Molecular Sciences Key Laboratory of Biomedical Polymers-Ministry of EducationWuhan UniversityWuhan Hubei 430072China

As a cornerstone of the central dogma of molecular biology,RNA plays vital roles in living organisms.Over the past few decades,many RNA labeling technologies have been developed to elucidate the biological function of RNA.These technologies have signifi-cantly advanced our understanding of RNA secondary structure,localization,and turnover.Additionally,taking advantage of these innovative RNA labeling approaches,plenty of tool kits have been devised for the regulation of RNA-related biological process,such as gene expression and gene editing.In this review,we primarily focus on an array of intracellular RNA labeling methods,encom-passing chemical probes-based labeling,metabolic labeling,and proximity-dependent labeling.We also provide a brief overview of their applications in the research of RNA biology.Finally,the perspectives of RNA labeling are also discussed.

关键词： RNA Chemical probes Metabolic labeling Proximity-dependent labeling RNA structures gene sequencing RNA recognition

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Roles of cancer-associated fibroblast functional heterogeneity in shaping the lymphatic metastatic landscape:new insights and therapeutic strategies

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Cancer Biology & Medicine 2024年第6期21卷 445-450页

作者： Hanhao Zheng Daiyin Liu Zhicong Liu Mingjie An Yuming Luo Changhao Chen Tianxin Lin department of Urology Sun Yat-sen Memorial Hospital Sun Yat-sen University Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and gene Regulation Sun Yat-sen Memorial Hospital State Key Laboratory of Oncology in South China department of general Surgery Guangdong Provincial People's Hospital Guangdong Academy of Medical Sciences

Lymph node (LN) metastasis is a process in which cancer cells travel from primary tumors to LNs via the lymphatic system,then proliferate and spread within the LNs. In most cancers,LN metastasis is a major mode of cancer dissemination,and a critical indicator of cancer progression and worsening prognosis1. The occurrence of LN metastasis indicates that the tumor has invaded the lymphatic system,

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The immune system: uncharted pathways between senses and the brain

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Neural Regeneration Research 2024年第6期19卷 1173-1174页

作者： Noelia Casares Mar Cuadrado-Tejedor Ana García-Osta Juan José Lasarte Immunology and Immunotherapy Program Centre for Applied Medical Research (CIMA) University of NavarraIDISNA Division of gene Therapy for Neurological Disorders Centre for Applied Medical Research (CIMA) University of NavarraIDISNA Pathology Anatomy and Physiology Department School of Medicine University of NavarraIDISNA

Humans and animals use the classic five senses-sight, hearing, touch, smell, and taste-to detect and monitor their environment, with the sense of position and movement often referred to as the sixth sense. The perception of external signals through the senses is essential to an organism’s survival, transmitting signals to the central nervous system(CNS) and prompting physiological changes in other biological systems. In addition to the direct effects of sense-induced mediators in the brain,

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Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

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Journal of Integrative Agriculture 2024年第7期23卷 2178-2195页

作者： Peng Liu Langlang Ma Siyi Jian Yao He Guangsheng Yuan Fei Ge Zhong Chen Chaoying Zou Guangtang Pan Thomas Lübberstedt Yaou Shen State Key Laboratory of Crop gene Exploration and Utilization in Southwest China/Maize Research Institute Sichuan Agricultural UniversityChengdu 611130China department of Agronomy Iowa State UniversityAmesIA 50011USA

genetic transformation has been an effective technology for improving the agronomic traits of maize.However,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype dependence.In this study,we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline(MQ2Gpipe).Based on the induction rate of EC(REC),these inbred lines were categorized into three subpopulations.The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.By integrating a genome-wide selective signature screen and region-based association analysis,we revealed 95.23 Mb of selective regions and 43 REC-associated variants.These variants had phenotypic variance explained values ranging between 21.46 and 49.46%.In total,103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated loci.These genes mainly participate in regulation of the cell cycle,regulation of cytokinesis,and other functions,among which MYB15 and EMB2745 were located within the previously reported QTL for EC induction.Numerous leaf area-associated variants with large effects were closely linked to several REC-related loci,implying a potential synergistic selection of REC and leaf size during modern maize breeding.

关键词： maize genetic transformation embryonic callus selective signal association analysis

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Method for the extraction of circulating nucleic acids based on MOF reveals cell-free RNA signatures in liver cancer

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National Science Review 2024年第1期11卷 94-106页

作者： Yuqing Sun Haixin Yu Shaoqing Han Ruoxi Ran Ying Yang Yongling Tang Yuhao Wang Wenhao Zhang Heng Tang Boqiao Fu Boshi Fu Xiaocheng Weng Song-Mei Liu Hexiang Deng Shuang Peng Xiang Zhou College of Chemistry and Molecular Sciences Key Laboratory of Biomedical Polymers-Ministry of Education Wuhan University department of Digestive Surgical Oncology Union Hospital Tongji Medical College Huazhong University of Science and Technology Cancer Center Union HospitalTongji Medical CollegeHuazhong University of Science and Technology department of Clinical Laboratory Center for Gene Diagnosis and Program of Clinical Laboratory Zhongnan Hospital of Wuhan University College of Chemistry and Materials Science Hubei Engineering University department of Pharmacology School of Pharmacy China Medical University Taikang Center for Life and Medical Sciences Wuhan University department of Hematology Zhongnan Hospital of Wuhan University

Cell-free RNA(cf RNA) allows assessment of health, status, and phenotype of a variety of human organs and is a potential biomarker to non-invasively diagnose numerous diseases. Nevertheless, there is a lack of highly efficient and bias-free cf RNA isolation technologies due to the low abundance and instability of cf RNA.Here, we developed a reproducible and high-efficiency isolation technology for different types of cell-free nucleic acids(containing cf RNA and viral RNA) in serum/plasma based on the inclusion of nucleic acids by metal-organic framework(MOF) materials, which greatly improved the isolation efficiency and was able to preserve RNA integrity compared with the most widely used research kit method. Importantly, the quality of cf RNA extracted by the MOF method is about 10-fold that of the kit method, and the MOF method isolates more than three times as many different RNA types as the kit method. The whole transcriptome mapping characteristics of cf RNA in serum from patients with liver cancer was described and a cf RNA signature with six cf RNAs was identified to diagnose liver cancer with high diagnostic efficiency(area under curve = 0.905 in the independent validation cohort) using this MOF method. Thus, this new MOF isolation technique will advance the field of liquid biopsy, with the potential to diagnose liver cancer.

关键词： MOF circulating cell-free RNA biomarker liver cancer diagnosis

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Elucidating and manipulating pressure-induced water intrusion–extrusion in tunable hydrophobic Co/Zn bimetallic ZIFs:Roles of pore size and hydrogen bond

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Nano Research 2024年第1期17卷 344-353页

作者： Diyi Fang Chuanlei Liu Yu Chen Qilong Peng Kongguo Wu Yuxiang Chen Hao Jiang Yuan Wu Benxian Shen Qiumin Wu Di Wu Hui Sun International Joint Research Center of Green Energy Chemical Engineering School of Chemical EngineeringEast China University of Science and TechnologyShanghai 200237China Alexandra Navrotsky Institute for Experimental Thermodynamics The Gene and Linda Voiland School of Chemical Engineering and BioengineeringMaterials Science and Engineeringand Department of ChemistryWashington State UniversityWashington 99163USA

Porous heterogeneous lyophobic systems(HLSs)find potential applications in energy restoring,dissipating,and absorbing.However,the development of controllable HLSs still lacks rational structure design of nanoporous materials matching the molecular sizes of adopted liquids.Besides that,thoroughly understanding the underlying transportation mechanism in the confined nano channels is greatly challenging.In this work,a series of Co/Zn bimetallic zeolitic imidazolate frameworks(ZIFs)with tunable structures were synthesized via regulating the Co to Zn ratios and employed to investigate the intrusion–extrusion of liquid water in confined nanopores.Structural characterizations confirm the heterometallic coordination in the Co/Zn-doped frameworks.Water intrusion–extrusion experiments unlock the relationship between the intrusion pressure and the nanopore size and realize the evolution of the HLSs between molecular spring and shock-absorber.In addition,cycling tests indicate the reversible structure change of Co/Zn ZIFs encountering pressure-induced water intrusion.In combination with molecular dynamics simulations,we present that the water multimers intrude into nanopores of ZIFs in chain-like forms along with dissociation of hydrogen bonds(HBs).Water molecules in the pre-intrusion state exhibit reduced HBs in response to the increase of pressure and linear structure with 1.6–3.0 HBs on average.After transition to the post-intrusion situation,the associative configuration of water tends to exhibit the tetrahedral structure.Herein,we highlight the roles of pore size and HB in synergically dominating the pressure-induced intrusion–extrusion of liquid water in hydrophobic nanopores.Furthermore,the present work can also guide the development of functional guest–host systems based on porous architectures.

关键词： heterometallic zeolitic imidazolate frameworks nanopore intrusion hydrogen bonds

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MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non-small cell lung cancer

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Cancer Innovation 2024年第3期3卷 33-48页

作者： Jing Chen Jing Yang Yufang Liu Xu Zhao Juanjuan Zhao Lin Tang Mengmeng Guo Ya Zhou Chao Chen Dongmei Li Zhenke Wen Guiyou Liang Lin Xu Special Key Laboratory of gene Detection&Therapy of Guizhou Province ZunyiGuizhouChina department of Immunology Zunyi Medical UniversityZunyiGuizhouChina department of Medical Physics Zunyi Medical UniversityZunyiGuizhouChina Institute of Biomedical Soochow UniversitySuzhouJiangsuChina department of Cardiovascular Surgery Affiliated Hospital of Guizhou Medical UniversityGuiyangGuizhouChina

Background:Angiogenesis plays an important role in the occurrence and development of non-small cell lung cancer(NSCLC).The atypical mitogen-activated protein kinase 4(MAPK4)has been shown to be involved in the pathogenesis of various diseases.However,the potential role of MAPK4 in the tumor angiogenesis of NSCLC remains unclear.Methods:Adult male C57BL/6 wild-type mice were randomly divided into the control group and p-siMAPK4 intervention group,respectively.The cell proliferation was analyzed with flow cytometry and immunofluorescence staining.The vascular density in tumor mass was analyzed by immuno-fluorescence staining.The expressions of MAPK4 and related signaling molecules were detected by western blot analysis and immunofluorescence staining,and so on.Results:We found that the expression of MAPK4,which was dominantly expressed in local endothelial cells(ECs),was correlated with tumor angiogenesis of NSCLC.Furthermore,MAPK4 silencing inhibited the proliferation and migration abilities of human umbilical vein ECs(HUVECs).QKHZC-2020-4Y156,QKH-JC-2018-1428,QKH-RC-2019-5612;Collaborative Innovation Center of Chinese Ministry of Education,Grant/Award Number:2020-39;Program for Science and Technology Joint Fund Project in Zunyi Science and Technology Bureau and Zunyi Medical University,Grant/Award Numbers:ZSKH-RPT-2020-6,ZSKH-HZ-2021-193;Graduate Research Fund of Zunyi Medical University,Grant/Award Number:2023-ZYK-171 Global gene analysis showed that MAPK4 silencing altered the expression of multiple genes related to cell cycle and angiogenesis pathways,and that MAPK4 silencing increased transduction of the extracellular regulated protein kinases 1/2(ERK1/2)pathway but not Akt and c-Jun n-terminal kinase pathways.Further analysis showed that MAPK4 silencing inhibited the proliferation and migration abilities of HUVECs cultured in tumor cell supernatant,which was accompanied with increased transduction of the ERK1/2 pathway.Clinical data analysis suggested that the higher expression of MAPK4 and CD34 were associa

关键词： angiogenesis endothelial cell MAPK4 NSCLC p-ERK1/2

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Proteomics analysis of coronary atherosclerotic heart disease with different Traditional Chinese Medicine syndrome types before and after percutaneous coronary intervention

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Journal of Traditional Chinese Medicine 2024年第3期44卷 554-563页

作者： WANG Zhibo LI Ying WANG Daoping MA Bo MIAO Lan REN Junguo LIU Jinghua LIU Jianxun Beijing Key Laboratory of Pharmacology of Chinese Materia Region Institute of Basic Medical SciencesXiyuan HospitalChina Academy of Chinese Medical SciencesNational Clinical Research Center of Cardiovascular Disease of Traditional Chinese Medicine the National Key Facility for Crop gene Resources and genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural Science department of Cardiology Beijing Anzhen HospitalCapital Medical University

OBJECTIVE: To investigate the underlying protein molecular mechanisms of "Qi stagnation and blood stasis syndrome"(QS) and "Qi deficiency and blood stasis syndrome"(QD), as two subtypes of coronary artery disease(CAD) in Traditional Chinese Medicine(TCM),following percutaneous coronary intervention(PCI).METHODS: In this study, a total of 227 CAD patients with QS and 211 CAD patients with QD were enrolled; all participants underwent PCI. Label-free quantification proteomics were employed to analyze the changes in serum in two subtypes of CAD patients before and 6 months after PCI, aiming to elucidate the intervention mechanism of PCI in treating CAD characterized by two different TCM syndromes.RESULTS: Biochemical analysis revealed significant changes in tumor necrosis factor-α, high density lipoprotein cholesterol, blood stasis clinical symptoms observation, and Gensini levels in both patient groups post-PCI; Proteomic analysis identified 79 and 95 differentially expressed proteins in the QS and QD patient groups, respectively, compared to their control groups.complement C8 alpha chain, complement factor H,apolipoprotein H, apolipoprotein B, plasminogen,carbonic anhydrase 2, and complement factor Ⅰ were altered in both comparison groups. Furthermore,enrichment analysis demonstrated that cell adhesion and connectivity-related processes underwent changes in QS patients post-PCI, whereas lipid metabolism-related pathways, including the peroxisome proliferator-activated receptor signaling pathway and extracellular matrix receptor interaction, underwent changes in the QD group.The protein-protein interaction network analysis further enriched 52 node proteins, including apolipoprotein B,lipoprotein(a), complement C5, apolipoprotein A4,complement C8 alpha chain, complement C8 beta chain,complement C8 gamma chain, apolipoprotein H,apolipoprotein A-Ⅱ, albumin, complement C4-B,apolipoprotein C3, among others. The functional network of these proteins is posited to contribute to the pathophysiology of CAD characterized by TC

关键词： Traditional Chinese Medicine syndrome coronary atherosclerotic heart disease peptide mapping percutaneous coronary intervention proteomics

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