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Multi-Omics and Its Clinical Application in Hepatocellular Carcinoma:Current Progress and Future Opportunities

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Chinese Medical Sciences Journal 2021年第3期36卷 173-186页

作者： Wanshui Yang Hanyu Jiang Chao Liu Jingwei Wei Yu Zhou Pengyun Gong Bin Song Jie Tian Department of Nutrition School of Public HealthAnhui Medical UniversityHefei 230032China Department of Radiology West China HospitalSichuan UniversityChengdu 610041China Beijing Advanced Innovation center for Big Data-Based Precision Medicine School of Medicine and EngineeringBeihang UniversityBeijing 100191China Key Laboratory of Big Data-Based Precision Medicine(Beihang University) Ministry of Industry and Information TechnologyBeijing 100191China Key Laboratory of Molecular Imaging Institute of AutomationChinese Academy of SciencesBeijing 100190China Beijing Key Laboratory of Molecular Imaging Beijing 100190China University of Chinese Academy of Sciences Beijing 100049China School of Life Science and Technology Xidian UniversityXi'an 710126China Engineering Research center of Molecular and Neuro Imaging of Ministry of Education School of Life Science and TechnologyXidian UniversityXi'an 710126China

Hepatocellular carcinoma(HCC)is the sixth most common malignancy and the fourth leading cause of cancer related death *** covers over half of cases,leading HCC to be a vital threaten to public *** advances in diagnosis and treatments,high recurrence rate remains a major obstacle in HCC ***-omics currently facilitates surveillance,precise diagnosis,and personalized treatment decision making in clinical ***-invasive radiomics utilizes preoperative radiological imaging to reflect subtle pixel-level pattern changes that correlate to specific clinical *** has been widely used in histopathological diagnosis prediction,treatment response evaluation,and prognosis ***-throughput sequencing and gene expression profiling enabled genomics and proteomics to identify distinct transcriptomic subclasses and recurrent genetic alterations in HCC,which would reveal the complex multistep process of the *** accumulation of big medical data and the development of artificial intelligence techniques are providing new insights for our better understanding of the mechanism of HCC via multi-omics,and show potential to convert surgical/intervention treatment into an antitumorigenic one,which would greatly advance precision medicine in HCC management.

关键词： hepatocellular carcinoma radiomics proteomics genomics multi-omics

Single-cell technologies:From research to application

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The Innovation 2022年第6期3卷 92-108页

作者： Lu Wen Guoqiang Li Tao Huang Wei Geng Hao Pei Jialiang Yang Miao Zhu Pengfei Zhang Rui Hou Geng Tian Wentao Su Jian Chen Dake Zhang Pingan Zhu Wei Zhang Xiuxin Zhang Ning Zhang Yunlong Zhao Xin Cao Guangdun Peng Xianwen Ren Nan Jiang Caihuan Tian Zi-Jiang Chen Biomedical Pioneering Innovation Centre(BIOPIC) Peking UniversityBeijing 100871China Bio-Med Big Data center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghai 200031China School of Chemical Engineering and Technology Sun Yat-Sen UniversityZhuhai 519082China Mozhuo Biotech(Zhejiang)Co. Ltd.TongxiangJiaxing 314500China Geneis(Beijing)Co. Ltd.Beijing 100102China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhou 510530China Department of Medical Oncology Zhongshan HospitalFudan UniversityShanghai 200032China School of Food Science and Technology Dalian Polytechnic UniversityDalian 116034China State Key Laboratory of Transducer Technology Aerospace Information Research InstituteChinese Academy of SciencesBeijing 100190China Key Laboratory of Biomechanics and Mechanobiology Ministry of EducationBeijing Advanced Innovation Center for Biomedical EngineeringSchool of Engineering MedicineBeihang UniversityBeijing 100083China Department of Mechanical Engineering City University of Hong KongHong Kong 999077China Chongqing Institute of Green and Intelligent Technology Chinese Academy of SciencesChongqing 400714China center of Peony Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Flower Crops(North China)Key Laboratory of Biology and Genetic Improvement of Horticultural CropsMinistry of Agriculture and Rural AffairsBeijing 100081China Department of Hepatic Surgery Fudan University Shanghai Cancer CenterShanghai 200032China Advanced Technology Institute University of SurreyGuildfordSurreyGU27XHUK National Physical Laboratory TeddingtonMiddlesex TW110LWUK Institute of Clinical Science Zhongshan HospitalFudan UniversityShanghai 200032China West China School of Basic Medical Sciences&Forensic Medicine Sichuan UniversityChengdu 610041China Jinfeng Laboratory Chongqing 401329China center for Reproduc

In recent years,more and more single-cell technologies have been developed.A vast amount of single-cell omics data has been generated by large projects,such as the Human Cell Atlas,the Mouse Cell Atlas,the Mouse RNA Atlas,the Mouse ATAC Atlas,and the Plant Cell *** on these single-cell big data,thousands of bioinformatics algorithms for quality control,clustering,cell-type annotation,developmental inference,cell-cell transition,cell-cell interaction,and spatial analysis are *** powerful experimental single-cell technology and state-of-the-art big data analysis methods based on artificial intelligence,the molecular landscape at the single-cell level can be revealed.

关键词： Atlas landscape application

Differential regulation of JAK1 expression by ETS1 associated with predisposition to primary biliary cholangitis

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Journal of Genetics and genomics 2023年第10期50卷 807-812页

作者： Peng Jiang Chan Wang Mingming Zhang Ye Tian Weifeng Zhao Junyi Xin Yexi Huang Zhibin Zhao Wenjuan Sun Jie Long Ruqi Tang Fang Qiu Xingjuan Shi Yi Zhao Li Zhu Na Dai Lei Liu Xudong Wu Jinshan Nie Bo Jiang Youlin Shao Yueqiu Gao Jianjiang Yu Zhigang Hu Zhidong Zang Yuhua Gong Yaping Dai Lan Wang Ningling Ding Ping Xu Sufang Chen Lu Wang Jing Xu Luyao Zhang Junyan Hong Ruonan Qian Hu Li Xuan Jiang Congwei Chen Wenyan Tian Jian Wu Yuzhang Jiang Chongxu Han Kui Zhang Hong Qiu Li Li Hong Fan Liming Chen Jianqiong Zhang Zhongsheng Sun Xiao Han Zhenhua Dai Erguang Li M.Eric Gershwin Zhexiong Lian Xiong Ma Michael F.Seldin Weichang Chen Meilin Wang Xiangdong Liu Key Laboratory of Developmental Genes and Human Diseases School of Life Science and TechnologySoutheast UniversityNanjingJiangsu 210096China Institute of Translational Medicine Yangzhou University Medical CollegeYangzhouJiangsu 225009China Department of Radiology&Oncology The Second Affiliated Hospital of Soochow UniversitySuzhouJiangsu 215004China The First Affiliated Hospital of Soochow University SuzhouJiangsu 215006China Department of bioinformatics School of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjingJiangsu 210029China Author links open overlay panelYexi Huang Guangdong Provincial People's Hospital Guangdong Academy of Medical SciencesGuangzhouGuangdong 510080China Department of Gastroenterology and Hepatology Shanghai Institute of Digestive DiseasesShanghai Jiao Tong University School of Medicine Affiliated Renji HospitalShanghai 200001China Department of Laboratory Medicine The Fourth Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsu 210031China Department of Gastrointestinal Endoscopy Eastern Hepatobiliary Surgery HospitalShanghai 201800China The Fifth People's Hospital Soochow UniversitySuzhouJiangsu 215007China Department of Gastroenterology Jiangsu University Affiliated Kunshan HospitalKunshanJiangsu 215300China Department of Gastroenterology Yixing People's HospitalYixinJiangsu 214200China Department of Gastroenterology Yancheng First People's HospitalYanchengJiangsu 224005China Department of Gastroenterology Taicang First People's HospitalSoochow UniversityTaicangJiangsu 215400China Department of Hepatology Jingjiang Second People's HospitalJingjiangJiangsu 214500China Department of Hepatology The Third People's Hospital of ChangzhouChangzhouJiangsu 213001China Department of Liver Diseases Shuguang HospitalShanghai University of Traditional Chinese MedicineShanghai 201203China Department of Laboratory Medicine Jiangyin People's HospitalSoutheast UniversityJiangyinJiangsu 214400China Department of Labora

Primary biliary cholangitis(PBC)is an autoimmune liver disease characterized by the destruction of intrahepatic small bile ducts and progressive cholestasis,eventually leading to liver cirrhosis and hepatic failure wi... 详细信息

关键词： cholangitis biliary

A comparative study on the genomes,transcriptomes,and metabolic properties of Escherichia coli strains Nissle 1917,BL21(DE3),and MG1655

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Engineering Microbiology 2022年第1期2卷 8-16页

作者： Linlin Zhao Guobin Yin Yonglin Zhang Chaofan Duan Yang Wang Zhen Kang The Key Laboratory of Carbohydrate Chemistry and Biotechnology Ministry of EducationJiangnan UniversityWuxi 214122China The Science center for Future Foods Jiangnan UniversityWuxi 214122China The Key Laboratory of Industrial Biotechnology Ministry of EducationSchool of BiotechnologyJiangnan UniversityWuxi 214122China

Escherichia coli is the most well-studied model prokaryote and has become an indispensable host for the biotech-nological production of proteins and *** particular,the probiotic status of one *** strain,*** Nissle 1917(EcN)has helped it become a new favorite amongst synthetic *** broaden its potential applications,here we assemble a comparative study on the genomes,transcriptomes,and metabolic properties of *** strains EcN,BL21(DE3),and *** genomics data suggests that EcN possesses 1404 unique *** particular,EcN has additional iron transport systems which endow EcN with a higher tolerance to iron scarcity when compared to two other *** *** transcriptome data demonstrates that *** strains EcN,BL21(DE3),and MG1655 all have comparable activities of the central metabolic pathway,however only EcN inherits the arginine deiminase ***,we found that EcN displayed a lower expres-sion of ribosomal proteins compared to BL21(DE3)and *** comparative study on *** strains EcN,BL21(DE3),and MG1655 aims to provide a reference for further engineering EcN as a biotechnological tool.

关键词： Escherichia coli Nissle 1917 probiotics comparative genomics transcriptome synthetic biology

Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis

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四川生理科学杂志 2020年第4期42卷 480-480页

作者： Carol C L Chen Department of Human Genetics McGill University Montreal QC H3A 0C7 Canada Canadian Centre for Computational genomics McGill University Montreal QC H3A 0E9 Canada Dana-Farber/Boston Children’s Cancer and Blood Disorders center Boston MA 02215 USA Department of Pathology Montreal Children’s Hospital McGill University Health Centre Montreal QC H4A 3J1 Canada UCL Queen Square Institute of Neurology London WC1N 3BG UK Department of Pediatrics McGill University and The Research Institute of the McGill University Health Centre Montreal QC H4A 3J1 Canada Samantha Dickson Brain Cancer Unit University College London Cancer Institute London United Kingdom Second Department of Paediatrics Semmelweis University Budapest 1094 Hungary Department of Neurosurgery University of Debrecen Debrecen 4032 Hungary Department of Paediatric Haematology and Oncology Second Faculty of Medicine Charles University and University Hospital Motol Prague 150 06 Czech Republic Department of Pathology and Molecular Medicine Second Faculty of Medicine Charles University and University Hospital Motol Prague 150 06 Czech Republic Children’s Cancer center The Royal Children’s Hospital Murdoch Children’s Research Institute Department of Pediatrics University of Melbourne Parkville VIC 3052 Australia Kids Cancer Centre Sydney Children’s Hospital Randwick NSW 2031 Australia Department of Pathology Centre Hospitalier Universitaire Sainte-Justine Université de Montréal Montréal QC H3T 1C5 Canada Department of Pediatric Oncology Dana-Farber Boston Children’s Cancer and Blood Disorders Center Boston MA 02215 USA School of Computer Science McGill University Montreal QC H3A 2A7 Canada and Murdoch Children’s Research Institute Parkville VIC 3052 Australia Department of Biochemistry McGill University Montreal QC H3A 1A3 Canada Department of Pediatric Neurosurgery Centre Hospitalier Universitaire Sainte-Justine Université de Montréal Montréal QC H3T 1C5 Canada Department of Biochemistry and

Histone H3.3 glycine 34 to arginine/valine(G34R/V)mutations drive deadly gliomas and show exquisite regional and temporal specificity,suggesting a developmental context permissive to their *** we show that 50%of G34R/V tumors(n=95)bear activating PDGFRA mutations that display strong selection pressure at *** considered gliomas,G34R/V tumors actually arise in GSX2/DLX-expressing interneuron progenitors,where G34R/V mutations impair neuronal *** lineage of origin may facilitate PDGFRA co-option through a chromatin loop connecting PDGFRA to GSX2 regulatory elements,promoting PDGFRA overexpression and *** the single-cell level,G34R/V tumors harbor dual neuronal/astroglial identity and lack oligodendroglial programs,actively repressed by GSX2/DLX-mediated cell fate specification.G34R/V may become dispensable for tumor maintenance,whereas mutant-PDGFRA is potently ***,our results open novel research avenues in deadly tumors.G34R/V gliomas are neuronal malignancies where interneuron progenitors are stalled in differentiation by G34R/V mutations and malignant gliogenesis is promoted by co-option of a potentially targetable pathway,PDGFRA signaling.

关键词： PDGFRA specificity connecting

genomics homologous polygenes analysis of cultivars of Ganoderma sinense for molecular identification and new member of FIPs exploration

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Genomics homologous polygenes analysis of cultivars of Ganod...

Competitive regulation of TNFSF13B by tRNA-Val-TAC-2-1 and miRNA-3182 in thyroid cancer:implications for tumor progression

第十二届药用真菌学术研讨会

作者： Ti-Qiang Chen Xiao-Lan Xu Chi Yang Lin Yang Zheng-He Ying Xiao-Kun Shi Meng-Guang Ding Institute of Edible Mushroom Fujian Academy of Agriculture Sciences National-Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Mushroom Department of traditional Chinese medicine resources and bee products College of Animal Science(College of Bee Science) Fujian Agriculture and Forestry University Chengdu Jinxu Biotechnology Co. Ltd

‘Zizhi S2' is a domesticated cultivar of Ganoderma sinense for commercial cultivation more than 18 years in southern China, which registered as Ganoderma sp. TQC-2021a strain Zizhi S2（NCBI: txid2816325）.Objectives To develop a genome-wide identification to verify the taxonomic status of this domesticated cultivars, and expect to explore novel gene（s） with important function. Methods The whole genome of Zizhi S2（56.76Mb, 16,681 genes） have been completed（DOI: 10.13560/***.1985.2021-1158）, and the assembled genome sequence and annotation information has been submitted to he Global Pharmacopoeia Herbal Genome Database with open download link（http://***/species/409）, 98.15% of complete BUSCOs were recovered in genome assembly, and the high-confidence annotation rate was accounted to 90.6%. Comparative genomics analysis and orthologous genes identification were analyzed by CD-HIT and OrthoMCL,collinearity analyses and Polygenetic sequence alignment were carry on by MUMmer and CLUSTAL *** software Phyml algorithm was applied to construct phylogenetic trees of 10 members of Ganoderma FIP gene family and two member of outgroup,3-D model were building on the SWISS-MODEL website together with the homologous FIPs. Results The collinearity exhibited the genome of ‘Zizhi S2' was 80.2% and 93.84% similar to reference genome of G. sinense ZZ0214-1 at the nucleotide and amino acid levels, respectively. And the core genes number between Zizhi S2 genome and reference genome of G. sinense ZZ0214-1 was 8,521 which presented 880 unique orthologous gene groups. Among that, at least seven highly conserved genes i.e. tef 1-α（translational elongation factor 1-alpha）, rpb2（RNA polymerase subunit 2）, β-tubulin（tubulin beta chain）, fip（fungal immunomodulatory protein）, CaM（Ca2+-binding protein）, Mn-SOD（manganese superoxide dismutase） and Ve A（velvet factor family protein）, which commonly used in phylogenetics) displaied high similarity to 99.27～100%.

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Competitive regulation of TNFSF13B by tRNA-Val-TAC-2-1 and m...

MET fusions and splicing variants convergently defne a subgroup of glioma sensitive to MET inhibitors

浙江省免疫学会第十三次学术大会

作者： Hongsheng Lu Guang Chen Yong Liang Yu Chen Yichao Wang Jie Zhu Jianguo Sun Qi Chen Department of Pathology Taizhou Central Hospital (Taizhou University Hospital) School of Medicine Taizhou University Department of Clinical Laboratory Medicine Taizhou Central Hospital (Taizhou Univesity Hospital) Department of Oncology Surgery Taizhou Central Hospital (Taizhou Univesity Hospital) Precision Medicine center Taizhou Central Hospital (Taizhou University Hospital)

Background:Thyroid cancer is one of the most frequently diagnosed endocrine malignancies,with a rapidly increasing incidence worldwide in recent *** and more studies have revealed that transform RNA-derived small RNAs(tsRNAs) play an important role in various biological processes,including ***,tsRNAs are rarely reported in the thyroid ***:This study aims to identify potential tsRNAs implicated in the development and progression of papillary thyroid cancer,and predicte its regulatory network by bioinformatics database,to further elucidate their underlying molecular *** and methods:The tsRNA sequencing was performed on both cancerous tissues and paracancerous tissues to identified papillary thyroid cancer-related ***,the effects of these tsRNAs on tumor cells were analyzed by examining cell proliferation,migration,invasion,angiogenesis,and the expression levels of cell cycle-related genes and ***,xenograft model in BALB/c nude mice was established to further validate the impact of tsRNAs on tumor growth in ***,mRNA sequencing was employed to uncover the target genes regulated by tsRNAs and database sequence alignments was conducted to identify mRNAs that are competitively regulated by ***:By comparing the tsRNA expression profiles between cancerous tissues and paracancerous tissues,we observed a significant differential expression of *** established human papillary thyroid cancer cells lines(TPC-1 and BCPAP cell) overexpressing tRNA-Val-TAC-2-1(Lenti-tRNA-Val-TAC-2-1) and found that both Lenti-tRNA-Val-TAC-2-1 TPC-1 and BCPAP cells exhibited higher colony formation,cell cycle-related protein expression levels,migration and invasion-related protein(E-cadherin,N-cadherin,and Vimentin) expression levels,and tube formation capabilities compared to their respective control cells(Lenti-control).Furthermore,the tumor-associated signaling pathways FAK,PI3 K-A

关键词： Thyroid cancer tRNA-derived small RNAs tRNA-Val-TAC-2-1 TNFSF13B miR-3182

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Holistic Integrative Oncology 2022年第1期1卷 244-254页

作者： Ke-Nan Zhang Zheng Zhao Jing Chen Zhaoshi Bao Rui-Chao Chai Zhiyan Sun Lingxiang Wu Zhiliang Wang Hanjie Liu Quanhua Mu Huimin Hu Fan Zeng Zheng Wang Guanzhang Li Yuanhao Chang Qiangwei Wang Fan Wu Ying Zhang Yuqing Liu Chunjie Jiang Ulf Dietrich Kahlert Do-Hyun Nam Wei Zhang Chunsheng Kang Jiguang Wang Rongjie Tao Qianghu Wang Tao Jiang Beijing Neurosurgical Institute Capital Medical UniversityBeijingChina Department of Neurosurgery Beijing Tiantan HospitalCapital Medical UniversityBeijingChina Department of bioinformatics Nanjing Medical UniversityNanjingJiangsuChina Department of Chemical and Biological Engineering Divison of Life ScienceCenter for Systems Biology and Human Healthand State Key Laboratory of Molecular NeuroscienceThe Hong Kong University of Science and TechnologyHong KongChina Division of Diabe‑tes Endocrinologyand MetabolismDepartment of MedicineBaylor College of MedicineHoustonTXUSA Molecular and Experimental Surgery Faculty of Medicine and University Medicine MagdeburgMagdeburgGermany Institute for Refractory Cancer Research Samsung Medical CenterSeoulRepublic of Korea Department of Health Science&Technology Samsung Advanced Institute for Health Sciences&Technology(SAIHST)Sungkyunkwan UniversitySeoulRepublic of Korea Department of Neurosurgery Samsung Medical CenterSungkyunkwan University School of MedicineSeoulRepublic of Korea Laboratory of Neuro‑Oncology Ministry of Education and Tianjin CityTianjin Neurological InstituteTianjin Medical University General HospitalKey Laboratory of PostNeuro Injury Neuro-Repair and Regeneration in Central Nervous SystemTianjinChina Departments of Neurosurgery Shandong Cancer Hospital and InstituteShandong UniversityJinanShandongChina center of Brain Tumor Beijing Institute for Brain DisordersBeijingChina China National Clinical Research center for Neurological Diseases BeijingChina Research Unit of Accurate Diagnosis Treatmentand Translational Medicine of Brain TumorsChinese Academy of Medical SciencesBeijingChina

Purpose:Our previous study has shown that PTPRZ1-MET(ZM)fusion is a viable target for MET inhibitors in ***,the diversity and prevalence of somatic MET alterations in difuse gliomas are still elusive and need to be extensively characterized for identifying novel therapeutic ***:Totally,1,350 glioma patients and 31 patient-derived cells were collected from the Chinese Glioma Genome Atlas(CGGA)and published *** kinds of MET fusions and/or splicing variants(MET F/SVs)were identifed by bioinformatical ***-cell RNA sequencing(scRNA-seq)were used for *** vitro experiments of drug resistance were conducted for the possibility of MET-targeted ***:MET F/SVs but not genomic amplifcation,were highly enriched in the secondary glioblastomas(sGBM)and marked worse *** molecular and scRNA-seq analysis revealed that MET F/SVs were induced in the course of glioma evolution and highly associated with MET *** in vitro and the clinical study showed that cells and patients harboring MET F/SVs have better response to MET ***:Our fndings expanded the percentage of gliomas with abnormal MET alterations and suggested that a subgroup of gliomas harboring MET F/SVs may beneft from MET-targeted therapy.

关键词： MET variation Secondary glioblastoma Biomarker MET inhibitor Precision neuro-oncology

The bioinformaticsanalyses reveal novel antigen epitopesin Major Outer Membrane Protein(MOMP) of Chlamydia trachomatis

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The bioinformaticsanalyses reveal novel antigen epitopesin M...