SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3′ tag-based RNA-seq of single cellsMethod Published on 2021-08-102022-11-01 Journal: Genome Biology [Category] COVID-19, MERS, SARS, [키워드] Accuracy Analysis APA Cell change cleavage de novo deep learning detect develop evaluate Gene Expression healthy individual identify identity information PAS PBMC Peak calling polyadenylation site profile RNA-Seq scRNA-seq scRNA-seq data sensitivity Single Cell single-cell supplementary material transcript Transcript quantification [DOI] 10.1186/s13059-021-02437-5 PMC 바로가기 [Article Type] Method
Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapyResearch Article Published on 2021-08-052022-10-31 Journal: eLife [Category] COVID-19, MERS, SARS, [키워드] Algorithm Analysis Cancer therapy CD4+ cell CD4+ T cell Cell cells changes in Chemotherapy clinical response comparable Complete COVID-19 COVID-19 patient Cytometry Disease progression emerging disease example homogeneous hotspot Human identify immune Immune cell immune changes Immune monitoring immune system immunology individual donor Infection inhibitor knowledge leukemia machine learning magnitude Melanoma MHCII Other Patient phenotype Post-infection provided reagent repeated reveal rhinovirus SARS-CoV-2 infections Single Cell subset Systems biology therapy trajectory virus virus-specific T cell [DOI] 10.7554/eLife.64653 PMC 바로가기 [Article Type] Research Article
Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanismSARS-CoV-2 감염 환자의 면역 특성 및 프로필은 잠재적인 숙주 치료 표적 및 SARS-CoV-2 종양 발생 메커니즘을 나타냅니다Article Published on 2021-08-012022-09-11 Journal: Virus research [Category] SARS, 변종, 유전자 메커니즘, [키워드] Analysis analyzed approved Bulk RNASeq analysis Cancer Cell Characteristics characterized clinical investigation contribute coronavirus COVID-19 COVID-19 infection COVID-19 pandemic COVID-19 patient COVID-19 patients COVID19 COVID19 patients Critical Cytokines develop differentially expressed disease pathogenesis disease severity E2F Emergency use expression FDA Gene expression analysis Host Host immune response host immune system human host identify immune Immune characterization of COVID19 patients immune factor immune profiling Immune profiling of COVID19 patients immunological immunological profile implicated Infection interferon Intervention investigated lymphopenia mechanism modulate modulated morbidity morbidity and mortality mortality rate NF-kB oncogenesis outbreak Outbreaks pandemic pathway Pathways Patient patients PKR Potential biomarker potential biomarkers Previous studies profile PROTECT protein targets Proteins RB1 reduce reveal RNAseq SARS-CoV-2 SARS-CoV-2 infected patient SARS-COV-2 infection scRNAseq severe COVID-19 patient severe COVID-19 patients severity of COVID-19 significant pathway significant pathways Single Cell Single cell scRNAseq analysis. Spread T cell T cell lymphopenia target the disease Therapeutic strategies therapeutic strategy therapeutic target therapeutic targets TNF transcription factor transcription factors treat upregulated Vaccine vaccine availability variant variants viral escape [DOI] 10.1016/j.virusres.2021.198464 PMC 바로가기 [Article Type] Article
Single-cell transcriptome of bronchoalveolar lavage fluid reveals sequential change of macrophages during SARS-CoV-2 infection in ferretsArticle Published on 2021-07-272022-10-29 Journal: Nature Communications [Category] COVID-19, [키워드] Activation Analysis approach Bronchoalveolar lavage fluid Cell change changes in Characteristics days post-infection downregulated drugs ferret ferrets Gene Expression Human identify immune microenvironment immune response infiltrating Inflammatory responses landscape longitudinal analysis lung M2 macrophage Macrophage macrophages Monocytes and macrophages proportion recruitment reveal RNA-sequencing SARS-CoV-2 SARS-COV-2 infection Single Cell Single-cell RNA sequencing subpopulation subset trajectory Transcriptome transcriptome change uninfected control viral infection [DOI] 10.1038/s41467-021-24807-0 PMC 바로가기 [Article Type] Article
Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’단일 세포 RNA 시퀀싱은 '역 표현형'을 통해 SARS-CoV-2 반응성 T 세포의 생체 외 서명을 밝힙니다.Article Published on 2021-07-262022-09-10 Journal: Nature Communications [Category] SARS, 진단, 치료기술, [키워드] absence activated Activation acute respiratory syndrome Antigen antigenic antigenic stimulation approach cellular cellular immunity characterisation cohorts Conventional coronavirus disease Coronavirus disease 2019 correspondence COVID-19 detect Ex vivo high resolution human leukocyte antigen identify immune response in vitro in vivo independent induce Infection introduced leukocyte Patient patients phenotype Phenotypes phenotypic phenotypic effect powerful tool presence or absence provide reactive respiratory respiratory tract reveal RNA sequencing SARS-CoV-2 sequence sequences Severe acute respiratory syndrome severe disease Single Cell Single-cell RNA sequencing Stimulation T cell T cell receptor T cell response T cells T-cell receptor TCR TCRs the SARS-CoV-2 tissue tissues transcriptional viral infection virus [DOI] 10.1038/s41467-021-24730-4 PMC 바로가기 [Article Type] Article
Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severityArticle Published on 2021-07-142022-10-04 Journal: Nature Communications [Category] SARS, 유전자 메커니즘, [키워드] accompanied Adaptive immune response Alter AT2 Cell cellular distribution changes in Characteristics chronic lung disease chronic lung diseases CLD Computational biology and bioinformatics Coronavirus disease-19 COVID-19 Efficiency Express Gene Expression healthy highlight identify Immunopathogenesis increased risk indicate Inflammation Inflammatory innate immune response lung lung cell Lung disease lung epithelium Lungs microenvironment molecular observé outcome outcomes Patient patients relative expression SARS-CoV-2 entry SARS-CoV-2 entry factor SARS-COV-2 infection severity Single Cell Transcriptome viral infection viral replication [DOI] 10.1038/s41467-021-24467-0 PMC 바로가기 [Article Type] Article
Distinct immunological signatures discriminate severe COVID-19 from non-SARS-CoV-2-driven critical pneumonia뚜렷한 면역학적 특징은 심각한 COVID-19를 SARS-CoV-2에 의해 유발되지 않은 치명적인 폐렴과 구별합니다.Comparative Study Published on 2021-07-132022-09-11 Journal: Immunity [Category] Fulltext, SARS, 바이오마커, 유전자 메커니즘, [키워드] adaptive alteration Analysis binding Biomarker cascade Cell change circulating ClinicalTrials COVID-19 COVID-19 patient Critical Cytometry driven by feature flow cytometry Frequency GM-CSF high-dimensional single cell analysis HLA HLA typing ICU patient ICU Patients immune Immune profile immune profiling immune signature Immunity immunological immunopathology Immunophenotyping Inflammatory response integration interfere longitudinal NKT outcome paralysis Patient peptide peptide binding strength peptides Pneumonia predicted Predictive SARS-CoV-2 SARS-CoV-2 peptide SARS-CoV-2 peptides severe COVID-19 Single Cell single-cell spectral flow cytometry. T cell the patient translation Treatment strategies treatment strategy virus recognition [DOI] 10.1016/j.immuni.2021.05.002 PMC 바로가기 [Article Type] Comparative Study
Endothelial cell infection and dysfunction, immune activation in severe COVID-19내피 세포 감염 및 기능 장애, 심한 Covid-19에서의 면역 활성화Research Paper Published on 2021-07-062022-09-10 Journal: Theranostics [Category] MERS, SARS, 진단, 치료기술, [키워드] Activation adhesion alveolar septa animals body weight Body weight loss Brain infection cadherin cause Cell circulation Coagulation collected complement conducted contribute correlated COVID-19 COVID-19 disease COVID-19 patients cytokine Deceased develop downregulation dysfunction edema electron microscopy endothelial Endothelial cell endothelial cells Endotheliitis Eosinopenia epithelial cells evidenced fatality hemorrhage ICAM1 immune activation Immune cell immune cells immunostaining infect Infection initial Injury interstitial inflammation K18 K18-hACE2 lung Lung epithelial cells Lungs lymphocytopenia mice Microscopy NHP NHP models organ organs Pathogenesis pathway Pathways Patient perivascular inflammation Platelet Platelets Pneumonia pulmonary PULMONARY VESSELS rationale Result RNA-seq analyses SARS-CoV-2 SARS-COV-2 infection serum severe COVID-19 severe COVID-19 disease severity Signaling Single Cell up-regulation upregulated Vascular VCAM1 VE-cadherin vessel weight loss while [DOI] 10.7150/thno.61810 PMC 바로가기 [Article Type] Research Paper
HLA-dependent heterogeneity and macrophage immunoproteasome activation during lung COVID-19 disease폐 COVID-19 질병 중 HLA 의존적 이질성 및 대식세포 면역프로테아좀 활성화Research Published on 2021-07-052022-09-10 Journal: Journal of Translational Medicine [Category] SARS, 치료기술, [키워드] A allele Activation addition allele alveolar alveolar clearance Analysis Antigen presentation Asian binding affinity bronchoalveolar caused CD68 Cell characterized clearance Cluster correlated COVID-19 COVID-19 disease COVID-19 patient COVID-19 patients COVID19 Defense disease effort ENCODE expression genomic heterogeneity HLA HLA-A Immunoproteasome impairment implication Integrative analysis less lung Macrophage macrophages mechanism MHC class MHC class I MHC class-I MHC-II mild case mild cases Peptidome populations positive positive relationship predict proteome PSMB8 Result SARS-CoV-2 SARS-CoV-2 RNA SARS-CoV-2 vaccine SARS-CoV-2 virus severe COVID-19 Single Cell single-cell transcriptome single-cell transcriptomes supplementary material Symptom the binding affinity the disease the SARS-CoV-2 the SARS-CoV-2 virus these cell These cells tissue trajectory Transcriptome transcriptomes widespread worldwide pandemic [DOI] 10.1186/s12967-021-02965-5 PMC 바로가기 [Article Type] Research
Integrated analysis of multimodal single-cell dataResource Published on 2021-06-242022-10-31 Journal: Cell [Category] COVID-19, MERS, SARS, [키워드] Abstract Analysis antibody applied approach Cell cellular circulating CITE-seq computational method coronavirus disease COVID-19 dataset heterogeneity Human immune system identification identify identity immune cell states immune populations immune response immune system IMPROVE Integrative analysis lymphoid mononuclear cell multimodal analysis PBMCs Peripheral blood reference mapping Single Cell single cell genomics single-cell single-cell genomics subpopulations T cell Transcriptome utility vaccination Vaccinations [DOI] 10.1016/j.cell.2021.04.048 PMC 바로가기 [Article Type] Resource