Evaluation of Stem-Cell Embryo Models by Integration with a Human Embryo Single-Cell Transcriptome Atlas DOI
San Kit To, Bradley P. Balaton, Vincent Pasque

и другие.

Methods in molecular biology, Год журнала: 2023, Номер unknown, С. 213 - 250

Опубликована: Янв. 1, 2023

Язык: Английский

Harnessing the Transcriptional Signatures of CAR-T-Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies DOI Open Access
Yu‐Mei Liao, Shih‐Hsien Hsu, Shyh‐Shin Chiou

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(4), С. 2416 - 2416

Опубликована: Фев. 19, 2024

Chimeric antigen receptor (CAR)-T-cell therapy has greatly improved outcomes for patients with relapsed or refractory hematological malignancies. However, challenges such as treatment resistance, relapse, and severe toxicity still hinder its widespread clinical application. Traditional transcriptome analysis provided limited insights into the complex transcriptional landscape of both leukemia cells engineered CAR-T-cells, well their interactions within tumor microenvironment. advent single-cell sequencing techniques, a paradigm shift occurred, providing robust tools to unravel complexities these factors. These techniques enable an unbiased cellular heterogeneity molecular patterns. are invaluable precise design, guiding gene-based T-cell modification, optimizing manufacturing conditions. Consequently, this review utilizes modern clarify intricacies CAR-Ts. The aim manuscript is discuss potential mechanisms that contribute failures CAR-T immunotherapy. We examine biological characteristics CAR-Ts, govern responses, adverse events. By exploring aspects, we hope gain deeper understanding therapy, which will ultimately lead broader therapeutic applications.

Язык: Английский

Процитировано

3

An Injectable Multifunctional Nanosweeper Eliminates Cardiac Mitochondrial DNA to Reduce Inflammation DOI Open Access

Yi‐Jing Li,

Xiumeng Hua, Yahui Zhao

и другие.

Advanced Healthcare Materials, Год журнала: 2025, Номер unknown

Опубликована: Янв. 15, 2025

Myocarditis, a leading cause of sudden cardiac death and heart transplantation, poses significant treatment challenges. The study clinical samples from myocarditis patients reveals correlation between the pathogenesis cardiomyocyte mitochondrial DNA (mtDNA). During inflammation, concentration mtDNA in cardiomyocytes increases. Hence, it is hypothesized that combined clearance its downstream STING pathway can treat myocarditis. However, clearing problematic. An innovative scavenger introduced, Nanosweeper (NS), which utilizes nanostructure to facilitate transport NS-mtDNA co-assemblies for degradation, achieving clearance. fluorescent probe on NS, bound functional peptides, enhances stability NS. NS also exhibits robust human plasma with half-life up 10 hours. In murine model, serves as drug delivery vehicle, targeting inhibitor C-176 myocardium. This approach synergistically modulates cGAS-STING axis effectively attenuating myocarditis- associated inflammatory cascade. evaluation porcine models corroborated superior biosafety profile capability. strategic targeted couple inhibition, significantly augments therapeutic efficacy against myocarditis, outperforming conventional C-176, indicating potential.

Язык: Английский

Процитировано

0

Application of Spatial Omics in the Cardiovascular System DOI Creative Commons
Yuhong Hu, Hao Jia, Hao Cui

и другие.

Research, Год журнала: 2025, Номер 8

Опубликована: Янв. 1, 2025

Cardiovascular diseases constitute a marked threat to global health, and the emergence of spatial omics technologies has revolutionized cardiovascular research. This review explores application omics, including transcriptomics, proteomics, metabolomics, genomics, epigenomics, providing more insight into molecular cellular foundations disease highlighting critical contributions science, discusses future prospects, technological advancements, integration multi-omics, clinical applications. These developments should contribute understanding guide progress precision medicine, targeted therapies, personalized treatments.

Язык: Английский

Процитировано

0

Deciphering immune cell heterogeneity in vascular diseases: Insights from single-cell sequencing DOI

Weirong Zeng,

Yu Zhang, Wen‐Zhao Zhong

и другие.

International Immunopharmacology, Год журнала: 2025, Номер 157, С. 114719 - 114719

Опубликована: Апрель 28, 2025

Язык: Английский

Процитировано

0

Navigating single-cell RNA-sequencing: protocols, tools, databases, and applications DOI Creative Commons

Ankish Arya,

Prabhat Tripathi, Nidhi Dubey

и другие.

Genomics & Informatics, Год журнала: 2025, Номер 23(1)

Опубликована: Май 17, 2025

Single-cell RNA-sequencing (scRNA-seq) technology brought about a revolutionary change in the transcriptomic world, paving way for comprehensive analysis of cellular heterogeneity complex biological systems. It enabled researchers to see how different cells behaved at single-cell levels, providing new insights into process. However, despite all these advancements, scRNA-seq also experiences challenges related complexity data analysis, interpretation, and multi-omics integration. In this review, complications were discussed detail, directly pointing optimization approaches understanding world its dynamics. Different protocols currently functional databases covered. This review highlights tools their methodologies, emphasizing innovative techniques that enhance resolution accuracy level. Various applications explored across domains including drug discovery, tumor microenvironment (TME), biomarker microbial profiling, case studies explain importance by uncovering novel rare cell types identification. underlines crucial aspect advancement personalized medicine potential understand

Язык: Английский

Процитировано

0

Transcriptomic profiling of immune cells in murine polymicrobial sepsis DOI Creative Commons

Atsushi Murao,

Alok Jha, Monowar Aziz

и другие.

Frontiers in Immunology, Год журнала: 2024, Номер 15

Опубликована: Янв. 26, 2024

Various immune cell types play critical roles in sepsis with numerous distinct subsets exhibiting unique phenotypes even within the same population. Single-cell RNA sequencing (scRNA-seq) enables comprehensive transcriptome profiling and unbiased classification. In this study, we have unveiled transcriptomic landscape of cells through scRNA-seq analysis. We induced mice by cecal ligation puncture. 20 h after surgery, spleen peritoneal lavage were collected. suspensions processed using a 10× Genomics pipeline sequenced on an Illumina platform. Count matrices generated Cell Ranger pipeline, which maps reads to mouse reference transcriptome, GRCm38/mm10. Subsequent analysis was performed R package Seurat. After quality control, subjected entire data set unsupervised Four major clusters identified as neutrophils, macrophages, B cells, T according their putative markers. Based differentially expressed genes, activated pathways for each type. related inflammatory signaling, such NF-κB responses pathogen-associated molecular patterns (PAMPs), cytokines, hypoxia activated. ones aging, PAMPs. endoplasmic reticulum stress PAMPs, acute lung injury. Next, further classified type into subsets. Neutrophils consisted four clusters. Some signaling or metabolism, whereas others possessed immunoregulatory aging properties. Macrophages clusters, namely, enhanced lymphocyte activation, extracellular matrix organization, cytokine activity. including possessing phenotype maturation aging. six whose include translocation activation. Transcriptomic has spectrum context sepsis. These findings are poised enhance our understanding pathophysiology, offering avenues targeting novel molecules, combat infectious diseases.

Язык: Английский

Процитировано

2

Unveiling aging dynamics in the hematopoietic system insights from single-cell technologies DOI

Xinrong Jin,

Ruohan Zhang,

Yunqi Fu

и другие.

Briefings in Functional Genomics, Год журнала: 2024, Номер 23(5), С. 639 - 650

Опубликована: Апрель 30, 2024

As the demographic structure shifts towards an aging society, strategies aimed at slowing down or reversing process become increasingly essential. Aging is a major predisposing factor for many chronic diseases in humans. The hematopoietic system, comprising blood cells and their associated bone marrow microenvironment, intricately participates hematopoiesis, coagulation, immune regulation other physiological phenomena. triggers various alterations within serving as spectrum of risk factors disorders, including clonal senescence, myeloproliferative neoplasms leukemia. emerging single-cell technologies provide novel insights into age-related changes system. In this review, we summarize recent studies dissecting system using technologies. We discuss cellular occurring during levels genomics, transcriptomics, epigenomics, proteomics, metabolomics spatial multi-omics. Finally, contemplate future prospects technologies, emphasizing impact they may bring to field research.

Язык: Английский

Процитировано

2

A new “single” era of biomedicine and implications in disease research DOI Creative Commons
Chunsong Hu

Journal of Bio-X Research, Год журнала: 2023, Номер 06(02), С. 37 - 48

Опубликована: Июнь 30, 2023

In recent decades, single-cell (SC) technologies and applications have been a very hot topics in the field of biology medicine. fact, early studies involving single cell were on malignant process acute nonlymphocytic leukemia inherited or sporadic genetic disease 1980s. And since RhD gene from maternal plasma was detected by fluorescence-based polymerase chain reaction (PCR) 1990s, "SC biopsies"[1] widely used for diagnosis clinical practice 2000s. Previous showed that SC RNA sequencing (scRNA-seq) to evaluate patterns allelic expression at allele-specific mRNA level, genome analysis can be diagnosis. Imprinted genes are linked etiology some syndromes common diseases, such as cardiovascular diseases (CVDs), diabetes, cancer. As powerful tool, there obvious advantages scRNA-seq identify imprinted human mouse models. Moreover, combination whole-genome genomic imprinting specific types different individuals. For example, comparative data helped disclose mechanisms Klinefelter syndrome understand causes infertility.[2] Recently, Zhang et al integrated >1.3 million chromatin profiles adult/fetal tissues[3] us interpret noncoding variants associated with complex traits diseases. Currently, heteroplasmy state assayed also standard control evaluation novel vascular Herein, this article thinks new "single" era biomedicine has come reviewed its application both CVDs coronavirus 2019 (COVID-19). A techniques essential studying understanding heterogeneity, differentiation, carcinogenesis, other important cellular processes, they become popular years. With development cellular, chemical, molecular techniques, SC, molecule, nucleus, chromosome, related biotechnologies, many breakthroughs life science It said come. First, single-molecule resolutions drug screening, study G protein–coupled receptor pharmacology, polymerases. However, tools (such transmission electron microscopy) amplification) necessary, strategies worthy development, meta-analysis multiomics COVID-19 studies[4,5] super-resolution microscopy optical imaging electrochemical reactions live cells.[6] Targeted implications cancer diagnosis, treatment, evolution,[7] omics successfully translated fields cancer, regenerative medicine, discovery immunology, well blueprints.[8] These include multiplex interactions, named chromatin-interaction via droplet-based barcode-linked (named ChIA-Drop),[9] assaying transcriptional activity.[10] Due technological advances, real-time is used, technologies, fluorescence situ hybridization (smFISH) SMOOTH-seq (a third-generation platform-based method, long fragments amplified through transposon insertion), viral infection fates living cells[11,12] opened chapter biomedicine.[13] To date, diabetes risk, origins potential therapeutic targets.[14–18] Second, single-chromosome after synthetic organisms Syn 1.0 3.0,[19,20] eukaryotic cells pair chromosomes lone-chromosome yeast strain artificially created clustered regularly interspaced short palindromic repeats (CRISPR) technology.[21,22] The 16 synthesized into just one two chromosomes, is, all vectors "in parallel" fused chimerized concatenated together (Fig. 1). Novel chimeric marked great success biological structure editing.Figure 1.: method chromosome. Here chromosome restructured CRISPR-based gene-editing technology. easy (16 C) only (1 C). This organism vector. author it's another classical example combinatorial biomedicine, which designed developed according previous done famous scientists.[ 21 , 22 ] CRISPR=clustered repeats.Chimeric therapy good idea beginning 2000s, promising direction. perfect vector system had not constructed time. Thus, CRISPR editing construction vectors. Even if current fusion therapy, it creates restructuring chimerizing still belongs therapy. methods conduction will help develop therapies artificial life. how assay, analyze, apply developing topic. cleavage under targets tagmentation (CUT&Tag) (scCUT&Tag) technology regions, research epigenomic landscapes tumor treatment central nervous improved more successful.[23,24] Hence, possible use scCUT&Tag Although rapid growth experimental studies, faces major challenges translation. believed breakthrough occur tackle unprecedented severe respiratory 2 (SARS-CoV-2). DNA base editors directly convert another, enabling efficient installation precise point mutations nondividing cells.[25] Recent found durable responses induction single-nucleotide, loss-of-function mutation. highlight adenine monogenic diseases.[26,27] When mass spectrometry machine learning approach) increased sensitivity, translational precisely measured.[28] Integrating spatial transcriptomics elucidate intercellular tissue dynamics.[13,29] bioinformatics, computational biology, information, (genomes, epigenomes, transcriptomes, proteomics) increasingly researchers.[30,31] Finally, biotechnologies biochemical strategies, C-H activation[32] functionalization,[33] platforms syntheses, landmark achievements expected biomedicine. Scientists open up medicine (Table 1)[34–41] brain heart.[42–44] Table 1 - biomedicine[34–41] Items Single-molecule Mass cytometryMass MC protocol organoid signaling networksLive scMS: direct metabolomic plant Massively parallel scRNA (MARS-seq2.0)An automated full-length sequencingSmall-RNA including miRNAs, tRNAs snoRNAs sequencingstRNA Omics scOmics analysis(a high-throughput platform) detection structural functional diversity Imaging scImaging: preclinical platformDFM imagingFM imagingSEM imagingFor nanoparticles nanomedicine dynamic nanomedicineFor pathways resolutionsFor mechanism RAD-51 nucleation filament RAD51 paralogue function Gene novoSpaRc algorithm: framework reconstruction sc expression(https://pypi.org/project/novosparc)Sc qRT–PCR combined arrays level Other seq scDNase-seq: detecting genome-wide DHSsG&T-seq: Separation genomes transcriptomes cellsscATAC-seq: CPCs Nkx2-5 Isl1 expression; immunophenotypic blood fetal liver bone marrow analyses Hi-C interactions: snapshots thousands interactions simultaneously cellSCRAMFACS-based genomics Western blotting western measurement proteins pH monitoring lung A549 CPCs=cardiac progenitor cells, DFM=dark-field microscopy, DHSs=DNase I hypersensitive sites, FACS=fluorescence-activated sorting, FM=fluorescence G&T-seq=genomes sequencing, MARS-seq2.0=massively MC=mass cytometry, miRNAs=microRNAs, MS=mass spectrometry, qRT–PCR=quantitative PCR, SC=single-cell, scDNase-seq=single-cell DNase scOmics=single-cell Omics, SCRAM=SC restriction methylation, SEM=scanning seq=sequencing, snoRNAs=small nucleolar RNAs, stRNA sequencing=spatial transcriptome tRNAs=transfer RNAs. role precision technique enables investigation entire cell, rapidly gained popularity over last few years profiling millions cells. now being analyze experiments designs, replication 2). intricate networks generate indices eventually enable targeted personalized medications. At same time, valuable analyzing heterogeneity. Cell composition accuracy critical cell–cell interaction data. high-sensitivity detection, factors/interleukins subsets, atlas level. set database secure management an activation sets basis.Figure 2.: Schematic workflow scRNA-seq. LCM=laser capture microdissection, MARS-Seq=massively SMART-Seq2=Switching Mechanism 5′ end Template Sequencing 2, PCR=polymerase reaction, UMIs=unique identifiers.With vital advances technology, provides opportunity accurately map architecture, characterize rare types, define perform detailed transcriptomic lymphoid-derived leukocytes better pathology compare primary cultures may serve target tissue. provided dissect distinct immune signatures, number samples draw systematic atlas. years, developed, massive parallel. comprehensive depiction heterogeneity definition clusters could design patients practice. importance highlighted systems, CVDs, COVID-19, system, exhibit significant currently, examined utility immunotherapy unmet goals contribute pathogenesis non-communicable resistance targets, make stratified informed decisions using approaches. design, collected multiple individuals find differentially expressed between groups Current offer unique opportunities exploring heterogeneous populations. in-depth characterization tissues often requires large numbers droplet- plate-based sampling bias affect datasets. type proportion estimates variable, shifts conditions due changes relative depletion enrichment particular type. Utilizing strategy based profiles, subtypes identified. flow cytometry delineate approaches diagnose decade. Intracellular determined integrating bulk-seq inhibitory experiments. Cell–cell (CCIs) play roles manipulating functions majority CCIs focus comparisons individual rather than "group-level" sample conditions. methods, we infer reveal previously inaccessible scale. Through joint compositions, genes, CCIs, pseudotime trajectories, factors, prognostic Applications CVD Research regarding resolution topic relatively independent scattered, limiting impact SARS-CoV-2 tissues. Here, briefly reviews status summarizes COVID-19. published Science Translational Medicine 2013 2021 2)[45–72] focused (Diamond-Blackfan anemia, myeloid leukemia, chronic lymphocytic myeloma), (Alzheimer disease, cognitive impairment, dementia), tumors (lethal childhood ependymomas); graft-vs-host disease; infectious (bacterial infection, hepatitis C virus HIV infection); retinal diseases; labor onset; nonalcoholic fatty cancers (malignant pleural effusions papillary renal carcinoma) inflammatory (rheumatoid arthritis). addition, inflammation, formation blood–brain barrier, NF-κB signals, cytokines, vaccines against employed 2021[45–72] "Single" Disease Mechanisms Targets Others Authors aGVHD controlling occupancy organs pathogenic donor CD8+ TRM Tkachev al[45] Single-cell proteomic Labor onset estimating time delivery Blood-based biomarkers delivery:Steroid hormone metabolites interleukin-1 4 Stelzer al[46] immunohistochemistry Lethal (H3.3G34R/V gliomas) LIF/STAT3 pathway key epigenetically driven druggable vulnerability Sweha al[47] ependymomas. Enhanced glycolysis tricarboxylic acid cycle metabolism Targeting metabolic/epigenetic Panwalkar al[48] RPL-DBA& RPS-DBA characterized erythroid differentiation arrest, whereas RPL-DBA preserved GATA1 activity Disordered ZFP36L2 corticosteroid response Iskander al[49] Phagocytosis infected debris Monocyte-derived macrophages dynamics host Speranza al[50] VCID AD cis P-tau might mediating Antibody targeting useful prevention, Qiu al[51] CLL relapse selection pressures graft-vs-leukemia bottleneck unlike those imposed chemotherapy; gain stem modules signature underlie, graft-vs-leukaemia posttransplant Bachireddy al[52] GVHD Cytokine-producing host-derived Trm local inflammation New markers skin Strobl al[53] HIV-1 Cellular factors supporting reactivation HIV-1–driven aberrant transcription Liu al[54] NAFLD Pathophysiology progressive fibrosing steatohepatitis Markers progression Govaere al[55] pRCC NOTCH1 overexpression worse outcomes pRCC. AKI Peired al[56] smFISH Severe pulmonary fibrosis transplantation Bharat al[57] HIV-specific T potently suppressed antiviral circulating Nguyen al[58] Inflammation CCR5 antagonists reduce processes antagonist maraviroc mucosal Woodward Davis al[59] reconstitute Inherited AAV blindness Tornabene al[60] Peritoneal Si al[61] RA Local macrophage phenotypes HBEGF+ Kuo al[62] MASC: reverse association significantly expanded population CD4+ identified CD27− HLA-DR+ effector memory Fonseka al[63] scDNA-seq AML Precision identification Saito al[64] MM CTCs Lohr al[65] Eliminate leukemic burden clonal evolution-induced Paguirigan al[66] Therapeutic efficacy kinetics MNP TNP distribution vivo Miller al[67] pharmacokinetic An anticancer drug: Eribulin mesylate assessment PK fluorescent analogue eribulin potent microtubule-targeting cytotoxic agent Laughney al[68] SCMA Bacterial Compared gold-standard broth microdilution test Single bacterial Rapid accurate antimicrobial susceptibility Choi al[69] Delayed recovery surgery Immune determine surgical trauma Gaudillière al[70] HCV High levels CD8(+) CD4(+) HCV-specific antigens. vaccine Swadling al[71] mechanophenotypes Malignant Label-free quantitative biophysical diagnoses algorithmic diagnostic scoring Tse al[72] AAV=adeno-associated viral, AD=Alzheimer aGVHD=acute AKI=acute kidney injury, AML=acute leukaemia, CLL=chronic CTCs=circulating HCV=hepatitis virus, LIF/STAT3=leukaemia factor/signal transducer activator 3, MASC=modeling associations MDM4 MDMX=mouse double minute homologue, MDM2=mouse MM=multiple myeloma, MNPs=magnetic nanoparticles, NAFLD=nonalcoholic PK=pharmacokinetic pRCC=papillary carcinoma, RA=rheumatoid arthritis, RPL RPS-DBA=ribosomal protein (RPL) small (RPS)-Diamond-Blackfan anemia (DBA), scDNA-seq=single-cell SCMA=single-cell morphological analysis, scRNA-seq=single-cell smFISH=single-molecule hybridization, TNPs=therapeutic VCID=vascular impairment dementia. transforming medical scRNA-seq, provide high-resolution insights covering systems,[73] atherosclerosis, myocardial infarction (AMI), arrhythmogenic cardiomyopathy (ACM), thoracic aortic aneurysm (iTAA) ascending (ATAA), calcific valve (CAVD), congenital heart tetralogy Fallot stenosis, failure, others, relevant 3).[74–98] progress made their research, endothelial cell–related (AMI, arterial hypertension, aging), markers, therapeutics.[75,99–101] 3 CVDs[74–98] Cardiovascular References notes CVDsASCVD Transcriptomic differences cardiac cellsOrgan-specific signatures heart-specific subpopulations markersA during smooth muscle phenotypic switching Cytoskeleton-associated modulator fibroblasts activationEndothelial lineTherapeutic SMC transitions Gladka al[74] Feng al[75] Pan al[76] scRNA-seqHigh-throughput analysisSC Epigenomics Functional Fine-MappingscRNA-seqSC accessibilityscRNA-seq ASExperimental ASLate-stage AS plaqueHuman PlaqueMouse Aortas connection atherosclerosis autoimmunity, ALDH4A1 increasedKlf4 Oct4 regulate plaque stabilityA pathophysiologyA strong atheroprotective innate lymphoid cells-2 cellsVSMCsALDH4A1 biomarker ASCVDGWAS LociStem pluripotency Klf4 Oct4Novel interventional relevanceInnate cell-2 cluster Iqbal al[77] Miano al[78] Lorenzo al[79] Örd al[80] Alencar al[81] Depuydt al[82] Zernecke al[83] scRNA-seqSC (molecular imaging) MIAMI Cardiac fibroblast ventricular remodelingCytokines basis attenuate adverse remodeling AMI CTHRC1 regulator healing scar processHuman iPSC–derived cardiomyocytes (iPSC-CMs) Ruiz-Villalba al[84] Ong al[85] ACMCardiac hypertrophy Mutations encoding desmosome (eg, DSP) Epicardial-derived cellsCell type– stage-specific intervention Yuan al[86] Ren al[87] Transcriptome Analysis LDS: iTAA dissectionATAA TGFBR1 variantDifferential Lineage-specific defectsHuman ATAA Zhou al[88] Li al[89] Multi-Omics Approaches CAVD Omics-based valvular (patho)biology Prioritized datasets Blaser al[90] Profiling CCS SN, AVN, His bundle, bundle branches, Purkinje fibers Goodyer al[91] Cytometry Inflammatory Regulated pMo pMo: Roberts al[92] CHD (ToF/PS) underlying cardiomyocyte cytokinesis failure repression ECT2, downstream β-ARs Inactivation β-AR administration β-blocker al[93] Heart Failure lymphocytes Circulating cellsCardiac these molecules, involved neutrophils, B NK mast Abplanalp al[94] Martini al[95] TranscriptomicsLarge-Scale CardiogenesisiPSC-ECs functionCardiac type-specific regulatory Differentiation processes: Chemotaxis-Mediated Intraorgan Cross talkMolecular Signatures Heterogeneous Populations human-iPSC-ECsGenetic cCRE KCNH2/HERG action repolarization cellHuman iPSC-ECDifferentiationCVD-associated Af variants) Xiong al[96] Paik al[97] Hocker al[98] ACM=arrhythmogenic cardiomyopathy, Af=atrial fibrillation, AMI=acute infarction, ASCVD=atherosclerotic ATAA=ascending aneurysm, AVN=atrioventricular node, β-ARs=β-adrenergic receptors, CAVD=calcific cCREs=candidate cis-regulatory elements, CCS=cardiac (ToF/PS)=congenital (tetralogy stenosis), CTHRC1=Collagen Triple Helix Repeat Containing 1, CVD=cardiovascular DSP=desmoplakin GWAS=genome-wide iPSC-ECs=induced pluripotent cell-derived iTAA=inherited LDS=Loeys–Dietz syndrome, NK=natural killer, pMo=patrolling monocytes, scRNA-seq=single SN=sinoatrial VSMCs=vascular 200 Advances, covers basic t

Язык: Английский

Процитировано

4

Harnessing the Transcriptional Signatures of Car-T Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies DOI Open Access
Yu‐Mei Liao, Shih‐Hsien Hsu, Shyh‐Shin Chiou

и другие.

Опубликована: Янв. 5, 2024

Chimeric antigen receptor (CAR) T-cell therapy has greatly improved outcomes for patients with relapsed or refractory hematological malignancies. However, challenges such as treatment resistance, relapse, and severe toxicity still hinder its widespread clinical application. Traditional transcriptome analysis provided limited insights into the complex transcriptional landscape of both leukemia cells engineered CAR-T cells, well their interactions within tumor microenvironment. advent single-cell sequencing techniques, a paradigm shift occurred, providing robust tools to unravel complexities these factors. These techniques enable unbiased cellular heterogeneity molecular patterns. are invaluable precise design, guiding gene-based T cell modification, optimizing manufacturing conditions. Consequently, this review utilizes modern clarify intricacies CAR-Ts. The aim manuscript is discuss potential mechanisms that contribute failures immunotherapy. We will examine biological characteristics CAR-Ts, govern responses, adverse events. By exploring aspects, we hope gain deeper understanding therapy, which ultimately lead broader therapeutic applications.

Язык: Английский

Процитировано

1

VICTOR: Validation and Inspection of Cell Type Annotation through Optimal Regression DOI Creative Commons

Chia-Jung Chang,

Chih–Yuan Hsu, Qi Liu

и другие.

Computational and Structural Biotechnology Journal, Год журнала: 2024, Номер 23, С. 3270 - 3280

Опубликована: Сен. 2, 2024

Single-cell RNA sequencing provides unprecedent opportunities to explore the heterogeneity and dynamics inherent in cellular biology. An essential step data analysis involves automatic annotation of cells. Despite development numerous tools for automated cell annotation, assessing reliability predicted annotations remains challenging, particularly rare unknown types. Here, we introduce VICTOR: Validation inspection type through optimal regression. VICTOR aims gauge confidence by an elastic-net regularized regression with thresholds. We demonstrated that performed well identifying inaccurate annotations, surpassing existing methods diagnostic ability across various single-cell datasets, including within-platform, cross-platform, cross-studies, cross-omics settings.

Язык: Английский

Процитировано

0