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Single-cell Transcriptome Study as Big Data

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Genomics, Proteomics & Bioinformatics 2016年第1期14卷 21-30页

作者： Pingjian Yu Wei Lin Genomics and Bioinformatics lab Baylor Institute for Immunology Research

The rapid growth of single-cell RNA-seq studies （scRNA-seq） demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing （NGS）-based studies, we propose a workflow that accounts for the unique characteris- tics of scRNA-seq data and primary objectives of single-cell studies.

关键词： Single-cell RNA -seq Big data TranscriptionaSingle-cell heterogenc-ity SignaSingle-cell normaSingle-cellization

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Gut microbiome,cognitive function and brain structure:a multi-omics integration analysis

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Translational Neurodegeneration 2022年第1期11卷 178-191页

作者： Xinxiu Liang Yuanqing Fu Wen-ting Cao Zhihong Wang Ke Zhang Zengliang Jiang Xiaofang Jia Chun-ying Liu Hong-rou Lin Haili Zhong Zelei Miao Wanglong Gou Menglei Shuai Yujing Huang Shengdi Chen Bing Zhang Yu-ming Chen Ju-Sheng Zheng College of Life Sciences Zhejiang UniversityHangzhou 310058China School of Life Sciences Westlake University18 Shilongshan RdCloud TownHangzhou 310024China Guangdong Provincial Key laboratory of Food Nutrition and HealthDepartment of Medical Statistics and EpidemiologySchool of Public HealthSun Yat-Sen UniversityGuangzhou 510080China Chinese Center for Disease Control and Prevention National Institute for Nutrition and HealthBeijing 100050China School of Public Health Hainan Medical UniversityHaikou 571199China Westlake Intelligent Biomarker discovery lab Westlake Laboratory of Life Sciences and BiomedicineHangzhou 310024China Department of Neurology and Institute of Neurology Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China Key laboratory of Trace Element Nutrition National Health CommissionBeijing 100050China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China.

Background:Microbiome-gut-brain axis may be involved in the progression of age-related cognitive impairment and relevant brain structure changes,but evidence from large human cohorts is lacking.This study was aimed to investigate the associations of gut microbiome with cognitive impairment and brain structure based on multi-omics from three independent populations.Methods:We included 1430 participants from the Guangzhou Nutrition and Health Study(GNHS)with both gut microbiome and cognitive assessment data available as a discovery cohort,of whom 272 individuals provided fecal samples twice before cognitive assessment.We selected 208 individuals with baseline microbiome data for brain magnetic resonance imaging during the follow-up visit.Fecal 16S rRNA and shotgun metagenomic sequencing,tar-geted serum metabolomics,and cytokine measurements were performed in the GNHS.The validation analyses were conducted in an Alzheimer’s disease case-control study(replication study 1,n=90)and another community-based cohort(replication study 2,n=1300)with cross-sectional dataset.Results:We found protective associations of specific gut microbial genera(Odoribacter,Butyricimonas,and Bac-teroides)with cognitive impairment in both the discovery cohort and the replication study 1.Result of Bacteroides was further validated in the replication study 2.Odoribacter was positively associated with hippocampal volume(β,0.16;95%CI 0.06-0.26,P=0.002),which might be mediated by acetic acids.Increased intra-individual alterations in gut microbial composition were found in participants with cognitive impairment.We also identified several serum metabolites and inflammation-associated metagenomic species and pathways linked to impaired cognition.Conclusions:Our findings reveal that specific gut microbial features are closely associated with cognitive impair-ment and decreased hippocampal volume,which may play an important role in dementia development.

关键词： Gut microbiome Cognitive impairment Brain structure Metagenomics Microbiome-gut-brain axis Cohort

Association of COVID- 19 with respiratory syncytial virus (RSV) infections in children aged 0-5 years in the USA in 2022: a multicentre retrospective cohort study

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Family Medicine and Community Health 2023年第4期11卷 45-55页

作者： Lindsey Wang Pamela B Davis Nathan Berger David C Kaelber Nora Volkow Rong Xu Center for Science Healthand SocietyCase Western Reserve UniversityClevelandOhioUSA Center for Community Health Integration Case Western Reserve University School of MedicineClevelandOhioUSA The Center for Clinical Informatics Research and Education and the Departments ofInternal Medicine Pediatricsand Population and Quantitative Health SciencesMetroHealth Medical CenterClevelandOhioUSA National Institute on Drug Abuse National Institute of HealthBethesdaMarylandUSA Center for AI in Drug discovery Case Western Reserve University School of MedicineClevelandOhioUSA

Objective To investigate whether COVID-19 infection was associated with increased risk for incident respiratory syncytial virus(RSV)infections and associated diseases among young children that might have contributed to the 2022 surge of severe paediatric RSV cases in the USA.Design This is a retrospective population-based cohort study.Five outcomes were examined,including overall RSV infection,positive lab test-confirmed RSV infection,clinically diagnosed RSV diseases,RSV-associated bronchiolitis and unspecified bronchiolitis.Risk ratio(RR)and 95%CI of the outcomes that occurred during the 2022 and 2021 RSV seasons were calculated by comparing propensity-score matched cohorts.Setting Nationwide multicentre database of electronic health records(EHRs)of 61.4million patients in the USA including 1.7million children 0–5 years of age,which was accessed through TriNetX Analytics that provides web-based and secure access to patient EHR data from hospitals,primary care and specialty treatment providers.Participants The study population consisted of 228940 children of 0–5 years with no prior RSV infection who had medical encounters in October 2022.Findings were replicated in a separate study population of 370919 children of 0–5 years with no prior RSV infection who had medical encounters in July 2021–August 2021 during a non-overlapping time period.Results For the 2022 study population(average age 2.4 years,46.8%girls,61%white,16%black),the risk for incident RSV infection during October 2022–December 2022 was 6.40%for children with prior COVID-19 infection,higher than 4.30%for the matched children without COVID-19(RR 1.40,95%CI 1.27 to 1.55);and among children aged 0–1year,the overall risk was 7.90%for those with prior COVID-19 infection,higher than 5.64%for matched children without(RR 1.40,95%CI 1.21 to 1.62).For the 2021 study population(average age 2.2 years,46%girls,57%white,20%black),the risk for incident RSV infection during July 2021–December 2021 was 4.85%for children with prior COVID-19 infection,higher than 3.68

关键词： infections matched centre

Impact of gene mutation in the development of Parkinson’s disease

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Genes & Diseases 2019年第2期6卷 120-128页

作者： Suganya Selvaraj Shanmughavel Piramanayagam Computational Biology lab Department of BioinformaticsBharathiar UniversityCoimbatore641046India Professor Computational Biology LabDepartment of BioinformaticsBharathiar UniversityCoimbatore641046India

Parkinson’s disease(PD)is the second most common age related neurodegenerative disorder worldwide and presents as a progressive movement disorder.Globally seven million to 10 million people have Parkinson’s disease.Parkinsonism is typically sporadic in nature.Loss of dopaminergic neurons from substantia nigra pars compacta(SNpc)and the neuronal intracellular Lewy body inclusions are the major cause of PD.Gene mutation and protein aggregation play a pivotal role in the degeneration of dopamine neurons.But the actual cause of dopamine degeneration remains unknown.However,several rare familial forms of PD are associated with genetic loci,and the recognition of causal mutations has provided insight into the disease process.Yet,the molecular pathways and gene transformation that trigger neuronal susceptibility are inadequately comprehended.The discovery of a mutation in new genes has provided a basis for much of the ongoing molecular work in the PD field and testing of targeted therapeutics.Single gene mutation in a dominantly or recessively inherited gene results a great impact in the development of Parkinson’s disease.In this review,we summarize the molecular genetics of PD.

关键词： Gene mutation Mitochondrial dysfunction Parkinson’s disease Protein aggregation Susceptibility genes

DeepNoise: Signal and Noise Disentanglement Based on Classifying Fluorescent Microscopy Images via Deep Learning

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 989-1001页

作者： Sen Yang Tao Shen Yuqi Fang Xiyue Wang Jun Zhang Wei Yang Junzhou Huang Xiao Han Tencent AI lab Shenzhen 518057China Department of Electronic Engineering The Chinese University of Hong KongHong Kong Special Administrative Region 999077China College of Computer Science Sichuan UniversityChengdu 610065China

The high-content image-based assay is commonly leveraged for identifying the phenotypic impact of genetic perturbations in biology field.However,a persistent issue remains unsolved during experiments:the interferential technical noises caused by systematic errors(e.g.,temperature,reagent concentration,and well location)are always mixed up with the real biological signals,leading to misinterpretation of any conclusion drawn.Here,we reported a mean teacher-based deep learning model(Deep Noise)that can disentangle biological signals from the experimental noises.Specifically,we aimed to classify the phenotypic impact of 1108 different genetic perturbations screened from 125,510 fluorescent microscopy images,which were totally unrecognizable by the human eye.We validated our model by participating in the Recursion Cellular Image Classification Challenge,and Deep Noise achieved an extremely high classification score(accuracy:99.596%),ranking the 2nd place among 866 participating groups.This promising result indicates the successful separation of biological and technical factors,which might help decrease the cost of treatment development and expedite the drug discovery process.The source code of Deep Noise is available at https://***/Scu-sen/Recursion-Cellular-Image-Classification-Challenge.

关键词： Fluorescent microscopy image Biological signal Classification Deep learning Genetic perturbation

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Identification of Bulbocodin D and C as novel STAT3 inhibitors and their anticancer activities in lung cancer cells

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Chinese Journal of Natural Medicines 2023年第11期21卷 842-851页

作者： HE Xinyu FU Jiarui LYU Wenyu HUANG Muyang MO Jianshan CHENG Yaxin XU Yulian ZHENG Lijun ZHANG Xiaolei QI Lu ZHANG Lele ZHENG Ying HUANG Mingqing NI Lin LU Jinjian State Key laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical SciencesUniversity of MacaoMacao 999078China College of Plant Protection Fujian Agriculture and Forestry UniversityFuzhou 350002China National-Local Joint Engineering laboratory of Druggability and New Drug Evaluation Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat-Sen UniversityGuangzhou 510006China College of Life Sciences China Jiliang UniversityHangzhou 310018China Department of Pharmacy Fujian Medical University Union HospitalFuzhou 350100China Department of Pathology School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China School of Basic Medical Sciences Chengdu UniversityChengdu 610106China College of Pharmacy Fujian University of Traditional Chinese MedicineFuzhou 350003China Department of Pharmaceutical Sciences Faculty of Health SciencesUniversity of MacaoMacao 999078China Guangdong-Hong Kong-Macao Joint lab on Chinese Medicine and Immune Disease Research University of MacaoMacao 999078China

Cancer stands as one of the predominant causes of mortality globally, necessitating ongoing efforts to develop innovative therapeutics. Historically, natural products have been foundational in the quest for anticancer agents. Bulbocodin D (BD) and Bulbocodin C (BC), two bibenzyls derived from Pleione bulbocodioides (Franch.) Rolfe, have demonstrated notable in vitro anticancer activity. In human lung cancer A549 cells, the IC50s for BD and BC were 11.63 and 11.71 μmol·L^(−1), respectively. BD triggered apoptosis, as evidenced by an upsurge in Annexin V-positive cells and elevated protein expression of cleaved-PARP in cancer cells. Furthermore, BD and BC markedly inhibited the migratory and invasive potentials of A549 cells. The altered genes identified through RNA-sequencing analysis were integrated into the CMap dataset, suggesting BD’s role as a potential signal transducer and activator of transcription 3 (STAT3) inhibitor. SwissDock and MOE analyses further revealed that both BD and BC exhibited a commendable binding affinity with STAT3. Additionally, a surface plasmon resonance assay confirmed the direct binding affinity between these compounds and STAT3. Notably, treatment with either BD or BC led to a significant reduction in p-STAT3 (Tyr 705) protein levels, regardless of interleukin-6 stimulation in A549 cells. In addition, the extracellular signal-regulated kinase (ERK) was activated after BD or BC treatment. An enhancement in cancer cell mortality was observed upon combined treatment of BD and U0126, the MEK1/2 inhibitor. In conclusion, BD and BC emerge as promising novel STAT3 inhibitors with potential implications in cancer therapy.

关键词： Cancer Natural products Bulbocodin D Bulbocodin C STAT3 ERK

Deep-ultraviolet nonlinear optical crystals: concept development and materials discovery

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Light(Science & Applications) 2022年第8期11卷 1718-1729页

作者： Lei Kang Zheshuai Lin Functional Crystals lab Technical Institute of Physics and ChemistryChinese Academy of SciencesBeijing100190China

Deep-ultraviolet (DUV, wavelength λ < 200 nm) nonlinear optical (NLO) crystal is the core component of frequency conversion to generate DUV laser, which plays an important role in cutting-edge laser technology and fundamental science. Significant progress has been made in both experimental exploration and theoretical design in the field of DUV NLO crystals over the past three decades. In-depth insight into “structure-property correlations”, in particular, allows for rigorous and precise identification of DUV NLO crystals. In this article, we reviewed the current experimental and theoretical research progress while elucidating the core concepts and stringent criteria of qualified DUV phase-matched second-harmonic generation crystals. We also discussed the development of the DUV NLO “structure-property correlations” from first principles and how it has sparked interest in related materials, as well as future directions for obtaining potential DUV NLO crystals.

关键词： optical ultraviolet Deep

Design, synthesis and antitumor evaluations of nucleoside base hydroxamic acid derivatives as DNMT and HDAC dual inhibitors

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Chinese Chemical Letters 2021年第8期32卷 2479-2483页

作者： Qinsheng Sun Qiuzi Dai Cunlong Zhang Yan Chen Lei Zhao Zigao Yuan Yuyang Jiang School of Life Science Tsinghua UniversityBeijing 100084China National&Local United Engineering lab for Personalized Anti-tumor Drugs The State Key Laboratory of Chemical OncogenomicsKey Laboratory of Chemical BiologyTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhen 518055China Institute of Biomedical Health Technology and Engineering Shenzhen Bay LaboratoryShenzhen 518055China National&Local United Engineering lab for Personalized Anti-tumor Drugs Shenzhen Kivita Innovative Drug Discovery InstituteShenzhen 518110China School of Pharmaceutical Sciences Tsinghua UniversityBeijing 100084China

DNA methyl transferase(DNMT) and histone deacetylase(HDAC) are well recognized epigenetic targets for discovery of antitumor agents.In this study,we designed and synthesized a series of nucleoside base hydroxamic acid derivatives as DNMT and HDAC dual inhibitors.MTT assays and enzymatic inhibitory activity tests indicated that compound 204 exhibited potent DNMT1 and HDAC1/6 inhibitory potency simultaneously in enzymatic levels and at cellular levels,inducing hypomethylation of p16 and hyperacetylation of histones H_(3) K9 and H4 K8.Besides,204 remarkably inhibited proliferation against cancer cells U937 by prompting G0/G1 cell cycle arrest.Molecular docking models explained the functional mechanism of 204 inhibiting DNMT1 and HDAC.Preliminary studies on metabolic profiles revealed that 204 showed desirable stability in liver microsomes.Our study suggested that 204 inhibiting DNMT and HDAC concurrently can be a potential lead compound for epigenetic cancer therapy.

关键词： Epigenetic DNMT HDAC Multitarget Antitumor bioactivity

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Progress in MXene-based catalysts for oxygen evolution reaction

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Electron 2024年第1期2卷 48-67页

作者： Jieli Chen Xiaohong Gao Jing Li Zhenye Kang Juan Bai Tianjiao Wang Yuliang Yuan Chenghang You Yu Chen Bao Yu Xia Xinlong Tian School of Marine Science and Engineering Hainan Provincial Key Lab of Fine ChemistrySchool of Chemistry and Chemical EngineeringHainan UniversityHaikouChina School of Chemistry and Physics Queensland University of TechnologyBrisbaneQueenslandAustralia Key laboratory of Macromolecular Science of Shaanxi Province School of Materials Science and EngineeringShaanxi Normal UniversityXi'anChina School of Chemistry and Chemical Engineering State Key Laboratory of Materials Processing and Die&Mould TechnologyKey Laboratory of Material Chemistry for Energy Conversion and Storage(Ministry of Education)Hubei Key Laboratory of Material Chemistry and Service FailureWuhan National Laboratory for OptoelectronicsHuazhong University of Science and Technology(HUST)WuhanChina

Electrochemical water splitting for hydrogen generation is considered one of the most promising strategies for reducing the use of fossil fuels and storing renewable electricity in hydrogen fuel.However,the anodic oxygen evolution process remains a bottleneck due to the remarkably high overpotential of about 300 mV to achieve a current density of 10 mA cm^(−2).The key to solving this dilemma is the development of highly efficient catalysts with minimized overpotential,long-term stability,and low cost.As a new 2D material,MXene has emerged as an intriguing material for future energy conversion technology due to its benefits,including superior conductivity,excellent hydrophilic properties,high surface area,versatile chemical composition,and ease of processing,which make it a potential constituent of the oxygen evolution catalyst layer.This review aims to summarize and discuss the recent development of oxygen evolution catalysts using MXene as a component,emphasizing the synthesis and synergistic effect of MXene-based composite catalysts.Based on the discussions summarized in this review,we also provide future research directions regarding electronic interaction,stability,and structural evolution of MXene-based oxygen evolution catalysts.We believe that a broader and deeper research in this area could accelerate the discovery of efficient catalysts for electrochemical oxygen evolution.

关键词： MXene-based catalysts oxygen evolution reaction water splitting