Single-cell RNA sequencing to identify cellular heterogeneity and targets in cardiovascular diseases: from bench to bedside

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

The complexity and diversity of vascular diseases highlight the urgent need to study their pathogenesis, particularly the key role of immune cell-mediated inflammatory responses in their development. While previous reviews have outlined the involvement of immune cells in vascular pathology, a comprehensive understanding of their dynamic changes, functional states, and intercellular interactions remains incomplete. Recent advances in single-cell sequencing (SCS) have provided unprecedented insights into immune cell heterogeneity, enabling the identification of novel subpopulations and their roles in disease progression.This review extends prior work by systematically summarizing the latest applications of SCS in vascular diseases, highlighting newly discovered immune cell subsets, their interactions, and their impact on vascular pathology. By addressing current gaps in the literature-such as the functional plasticity of immune cells and their temporal dynamics-this review offers new perspectives on immune-mediated mechanisms in vascular diseases and proposes novel therapeutic strategies for their prevention and treatment.

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

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

Cardiovascular diseases and depression: A meta-analysis and Mendelian randomization analysis

Depression is a common psychiatric symptom among patients with cardiovascular disease (CVD), adversely affecting their health. Despite the identification of various contributing factors, the precise mechanisms linking CVD and depression remain elusive. This study conducted a meta-analysis to investigate the association between CVD and depression. Furthermore, a bidirectional Mendelian randomization (MR) analysis was undertaken to clarify the causal relationship between the two conditions. The meta-analysis included 39 studies, encompassing 63,444 patients with CVD, 12,308 of whom were diagnosed with depression. The results revealed a significant association between CVD and depression or anxiety, with an estimated overall prevalence of depression in CVD patients of 20.8%. Subgroup analyses showed that the prevalence of depression in patients with coronary artery disease and heart failure was 19.8% and 24.7%, respectively. According to a random-effects model, depressive symptoms were linked to an increase in unadjusted all-cause mortality compared with non-depressed patients. The MR analysis, employing the inverse-variance weighted method as the primary tool for causality assessment, identified significant associations between various CVD types and depression or anxiety phenotypes. These findings underscore the significant relationship between CVD and depression or anxiety, leading to an elevated risk of all-cause mortality. Moreover, the MR analysis provides the first genetically-informed evidence suggesting that depression plays a critical role in the development and progression of certain CVD subtypes. This emphasizes the need for addressing depressive symptoms in CVD patients to prevent or reduce adverse cardiovascular outcomes.

An Injectable Multifunctional Nanosweeper Eliminates Cardiac Mitochondrial DNA to Reduce Inflammation

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

Exosomal miRNA reprogramming in pyroptotic macrophage drives silica-induced fibroblast-to-myofibroblast transition and pulmonary fibrosis

Silicosis is an occupational lung disease characterized by progressive pulmonary fibrosis, threatening millions of occupational workers worldwide due to a lack of effective treatments. To unveil mechanisms underlying silica-induced pulmonary fibrosis, we established in vitro and in vivo silicosis models, then employed scRNA-sequencing to profile the cellular landscape of lung tissues followed by characterization of macrophage pyroptosis and exosome therefrom in driving fibroblast-to-myofibroblast-transdifferentiation. Using hyperspectral imaging and artificial intelligence-powered pathological recognition, we found that silica nanoparticle (SiNP) triggered progressive lung fibrosis in vivo, and scRNA-seq implicated interstitial macrophage as pivotal regulators for fibroblast transdifferentiation. Mechanistically, SiNPs were demonstrated to induce macrophage pyroptosis and liberate exosomes, which upregulated pro-fibrotic markers and promoted myofibroblast transition. Subsequent high-throughput miR-sequencing revealed distinct exosomal miRNA signatures that modulated TGF-β signaling and induced fibroblast transdifferentiation. Lastly, we administered these exosomes into silicotic mice and found exacerbated inflammatory infiltration and pulmonary fibrosis. In conclusion, SiNPs exposure caused the remodeling of exosomal miRNAs by inducing interstitial macrophage pyroptosis, and exosomes derived from pyroptotic macrophage fuel fibroblast transdifferentiation by creating a pro-fibrotic microenvironment and promoting silicotic fibrosis. These findings provide critical insights into the pathogenesis of silicosis and the formulation of emerging therapeutic strategies.

KLF2-dependent transcriptional regulation safeguards the heart against pathological hypertrophy

BACKGROUND

Our previous single-cell RNA sequencing study in the adult human heart revealed that cardiomyocytes from both the atrium and ventricle display high activities of Krüppel-like factor 2 (KLF2) regulons. However, the role of the transcription factor KLF2 in cardiomyocyte biology remains largely unexplored.

METHODS AND RESULTS

We employed transverse aortic constriction surgery in male C57BL/6 J mice to develop an in vivo model of cardiac hypertrophy, and generated different in vitro cardiac hypertrophy models in neonatal rat ventricular myocytes and human embryonic stem cell-derived cardiomyocytes. Our results demonstrated a significant reduction in KLF2 expression during the progression of cardiac hypertrophy. In vitro, Klf2 deficiency exacerbates cardiac hypertrophy and enhances hypertrophic reprogramming, while KLF2 overexpression attenuates cardiac hypertrophy and reverses hypertrophic transcriptome reprogramming. Mechanistically, combined RNA-seq and cleavage under targets & tagmentation (CUT&Tag) analysis revealed that KLF2 exerts its protective effects by directly regulating a set of genes associated with cardiac hypertrophy. In vivo, KLF2 overexpression specifically in cardiomyocytes effectively prevents TAC-induced cardiac hypertrophy in mice. Additionally, we found that simvastatin elevates KLF2 expression in cardiomyocytes, which subsequently alleviates cardiomyocyte hypertrophy.

CONCLUSIONS

This study provides the first evidence that transcription factor KLF2 serves as a negative regulator of cardiac hypertrophy. Our findings highlight the therapeutic potential of enhancing KLF2 expression, particularly through simvastatin administration, as a promising strategy in the treatment of cardiac hypertrophy.

Multi-Omics Research on Angina Pectoris: A Novel Perspective

Angina pectoris (AP), a clinical syndrome characterized by paroxysmal chest pain, is caused by insufficient blood supply to the coronary arteries and sudden temporary myocardial ischemia and hypoxia. Long-term AP typically induces other cardiovascular events, including myocardial infarction and heart failure, posing a serious threat to patient safety. However, AP's complex pathological mechanisms and developmental processes introduce significant challenges in the rapid diagnosis and accurate treatment of its different subtypes, including stable angina pectoris (SAP), unstable angina pectoris (UAP), and variant angina pectoris (VAP). Omics research has contributed significantly to revealing the pathological mechanisms of various diseases with the rapid development of high-throughput sequencing approaches. The application of multi-omics approaches effectively interprets systematic information on diseases from the perspective of genes, RNAs, proteins, and metabolites. Integrating multi-omics research introduces novel avenues for identifying biomarkers to distinguish different AP subtypes. This study reviewed articles related to multi-omics and AP to elaborate on the research progress in multi-omics approaches (including genomics, transcriptomics, proteomics, and metabolomics), summarized their applications in screening biomarkers employed to discriminate multiple AP subtypes, and delineated integration methods for multi-omics approaches. Finally, we discussed the advantages and disadvantages of applying a single-omics approach in distinguishing diverse AP subtypes. Our review demonstrated that the integration of multi-omics technologies is preferable for quick and precise diagnosis of the three AP types, namely SAP, UAP, and VAP.

VICTOR: Validation and inspection of cell type annotation through optimal regression

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

Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction

Inflammation, fibrosis and metabolic stress critically promote heart failure with preserved ejection fraction (HFpEF). Exposure to high-fat diet and nitric oxide synthase inhibitor N[w]-nitro-l-arginine methyl ester (L-NAME) recapitulate features of HFpEF in mice. To identify disease-specific traits during adverse remodeling, we profiled interstitial cells in early murine HFpEF using single-cell RNAseq (scRNAseq). Diastolic dysfunction and perivascular fibrosis were accompanied by an activation of cardiac fibroblast and macrophage subsets. Integration of fibroblasts from HFpEF with two murine models for heart failure with reduced ejection fraction (HFrEF) identified a catalog of conserved fibroblast phenotypes across mouse models. Moreover, HFpEF-specific characteristics included induced metabolic, hypoxic and inflammatory transcription factors and pathways, including enhanced expression of Angiopoietin-like 4 (Angptl4) next to basement membrane compounds, such as collagen IV (Col4a1). Fibroblast activation was further dissected into transcriptional and compositional shifts and thereby highly responsive cell states for each HF model were identified. In contrast to HFrEF, where myofibroblast and matrifibrocyte activation were crucial features, we found that these cell states played a subsidiary role in early HFpEF. These disease-specific fibroblast signatures were corroborated in human myocardial bulk transcriptomes. Furthermore, we identified a potential cross-talk between macrophages and fibroblasts via SPP1 and TNFɑ with estimated fibroblast target genes including Col4a1 and Angptl4. Treatment with recombinant ANGPTL4 ameliorated the murine HFpEF phenotype and diastolic dysfunction by reducing collagen IV deposition from fibroblasts in vivo and in vitro. In line, ANGPTL4, was elevated in plasma samples of HFpEF patients and particularly high levels associated with a preserved global-longitudinal strain. Taken together, our study provides a comprehensive characterization of molecular fibroblast activation patterns in murine HFpEF, as well as the identification of Angiopoietin-like 4 as central mechanistic regulator with protective effects.

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

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

Revealing the crucial roles of suppressive immune microenvironment in cardiac myxoma progression

Cardiac myxoma is a commonly encountered tumor within the heart that has the potential to be life-threatening. However, the cellular composition of this condition is still not well understood. To fill this gap, we analyzed 75,641 cells from cardiac myxoma tissues based on single-cell sequencing. We defined a population of myxoma cells, which exhibited a resemblance to fibroblasts, yet they were distinguished by an increased expression of phosphodiesterases and genes associated with cell proliferation, differentiation, and adhesion. The clinical relevance of the cell populations indicated a higher proportion of myxoma cells and M2-like macrophage infiltration, along with their enhanced spatial interaction, were found to significantly contribute to the occurrence of embolism. The immune cells surrounding the myxoma exhibit inhibitory characteristics, with impaired function of T cells characterized by the expression of GZMK and TOX, along with a substantial infiltration of tumor-promoting macrophages expressed growth factors such as PDGFC. Furthermore, in vitro co-culture experiments showed that macrophages promoted the growth of myxoma cells significantly. In summary, this study presents a comprehensive single-cell atlas of cardiac myxoma, highlighting the heterogeneity of myxoma cells and their collaborative impact on immune cells. These findings shed light on the complex pathobiology of cardiac myxoma and present potential targets for intervention.

Paris saponin VII inhibits triple-negative breast cancer by targeting the MEK/ERK/STMN1 signaling axis

BACKGROUND

Triple-negative breast cancer (TNBC) is a category of breast cancer characterized with high molecular heterogeneity. Owing to the lack of effective therapeutic strategies, patients with TNBC have a poor prognosis. Paris saponin VII (PSⅦ), a steroidal saponin extracted from the rhizome of Trichillium tschonoskii Maxim, exhibits excellent anti-cancer activity in a variety of solid tumors. However, the role and potential mechanism of PSⅦ against TNBC remain unexplored.

PURPOSE

This study aimed to elucidate the therapeutic effects of PSⅦ against TNBC and explore the potential mechanism of action.

METHODS

We combined the analysis of public single-cell sequencing data with weighted gene co-expression network analysis (WGCNA) to identity differentially expressed genes (DEGs) that distinguished malignant and normal epithelial cells in TNBC. Subsequently, the biological features of DEGs in TNBC were evaluated. Gene set enrichment analysis (GSEA) was used to define potential pathways associated with the DEGs. The pharmacological activity of PSⅦ for TNBC was evidenced via in vitro and in vivo experiments, and molecular docking, molecular dynamics (MD), surface plasmon resonance (SPR) assay and western blotting were employed to confirm the relative mechanisms.

RESULTS

Single-cell sequencing and WGCNA revealed STMN1 as a pivotal biomarker of TNBC. STMN1 overexpression in TNBC was associated with poor patient prognosis. GSEA revealed a significant accumulation of STMN1 within the MAPK signaling pathway. Furthermore, In vitro experiments showed that PSⅦ showed significantly suppressive actions on the proliferation, migration and invasion abilities for TNBC cells, while inducing apoptosis. Molecular docking, MD analysis and SPR assay indicated a robust interaction between PSⅦ and the MEK protein. Western blotting revealed that PSⅦ may inhibit tumor progression by suppressing the phosphorylation of MEK1/2 and the downstream phosphorylation of ERK1/2 and STMN1. Intraperitoneal injection of PSⅦ (10 mg/kg) notably reduced tumor growth by 71.26 % in a 4T1 xenograft model.

CONCLUSION

In our study, the systems biology method was used to identify potential therapeutic targets for TNBC. In vitro and in vivo experiments demonstrated PSⅦ suppresses cancer progression by targeting the MEK/ERK/STMN1 signaling axis. For the first time, the inhibition of STMN1 phosphorylation has been indicated as a possible mechanism for the anticancer effects of PSⅦ. These results emphasize the potential value of PSⅦ as a promising anti-cancer drug candidate for further development in the field of TNBC therapeutics.

OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing

Single-cell sequencing is frequently affected by "omission" due to limitations in sequencing throughput, yet bulk RNA-seq may contain these ostensibly "omitted" cells. Here, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping communities. This approach effectively interpolates and restores the continuity of "omitted" cells within single-cell RNA sequencing datasets. Furthermore, OmicVerse provides an extensive toolkit for both bulk and single cell RNA-seq analysis, offering seamless access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of significant biological insights to advance scientific research.

Harnessing the Transcriptional Signatures of CAR-T-Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies

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

Macrophage profiling in atherosclerosis: understanding the unstable plaque

The development and rupture of atherosclerotic plaques is a major contributor to myocardial infarctions and ischemic strokes. The dynamic evolution of the plaque is largely attributed to monocyte/macrophage functions, which respond to various stimuli in the plaque microenvironment. To this end, macrophages play a central role in atherosclerotic lesions through the uptake of oxidized low-density lipoprotein that gets trapped in the artery wall, and the induction of an inflammatory response that can differentially affect the stability of the plaque in men and women. In this environment, macrophages can polarize towards pro-inflammatory M1 or anti-inflammatory M2 phenotypes, which represent the extremes of the polarization spectrum that include Mhem, M(Hb), Mox, and M4 populations. However, this traditional macrophage model paradigm has been redefined to include numerous immune and nonimmune cell clusters based on in-depth unbiased single-cell approaches. The goal of this review is to highlight (1) the phenotypic and functional properties of monocyte subsets in the circulation, and macrophage populations in atherosclerotic plaques, as well as their contribution towards stable or unstable phenotypes in men and women, and (2) single-cell RNA sequencing studies that have advanced our knowledge of immune, particularly macrophage signatures present in the atherosclerotic niche. We discuss the importance of performing high-dimensional approaches to facilitate the development of novel sex-specific immunotherapies that aim to reduce the risk of cardiovascular events.

Transcriptomic profiling of immune cells in murine polymicrobial sepsis

Introduction

Various immune cell types play critical roles in sepsis with numerous distinct subsets exhibiting unique phenotypes even within the same cell population. Single-cell RNA sequencing (scRNA-seq) enables comprehensive transcriptome profiling and unbiased cell classification. In this study, we have unveiled the transcriptomic landscape of immune cells in sepsis through scRNA-seq analysis.

Methods

We induced sepsis in mice by cecal ligation and puncture. 20 h after the surgery, the spleen and peritoneal lavage were collected. Single-cell suspensions were processed using a 10× Genomics pipeline and sequenced on an Illumina platform. Count matrices were generated using the Cell Ranger pipeline, which maps reads to the mouse reference transcriptome, GRCm38/mm10. Subsequent scRNA-seq analysis was performed using the R package Seurat.

Results

After quality control, we subjected the entire data set to unsupervised classification. Four major clusters were identified as neutrophils, macrophages, B cells, and T cells according to their putative markers. Based on the differentially expressed genes, we identified activated pathways in sepsis for each cell type. In neutrophils, pathways related to inflammatory signaling, such as NF-κB and responses to pathogen-associated molecular patterns (PAMPs), cytokines, and hypoxia were activated. In macrophages, activated pathways were the ones related to cell aging, inflammatory signaling, and responses to PAMPs. In B cells, pathways related to endoplasmic reticulum stress were activated. In T cells, activated pathways were the ones related to inflammatory signaling, responses to PAMPs, and acute lung injury. Next, we further classified each cell type into subsets. Neutrophils consisted of four clusters. Some subsets were activated in inflammatory signaling or cell metabolism, whereas others possessed immunoregulatory or aging properties. Macrophages consisted of four clusters, namely, the ones with enhanced aging, lymphocyte activation, extracellular matrix organization, or cytokine activity. B cells consisted of four clusters, including the ones possessing the phenotype of cell maturation or aging. T cells consisted of six clusters, whose phenotypes include molecular translocation or cell activation.

Conclusions

Transcriptomic analysis by scRNA-seq has unveiled a comprehensive spectrum of immune cell responses and distinct subsets in the context of sepsis. These findings are poised to enhance our understanding of sepsis pathophysiology, offering avenues for targeting novel molecules, cells, and pathways to combat infectious diseases.

A review of innovative electrochemical strategies for bioactive molecule detection and cell imaging: Current advances and challenges

Cellular heterogeneity poses a major challenge for tumor theranostics, requiring high-resolution intercellular bioanalysis strategies. Over the past decades, the advantages of electrochemical analysis, such as high sensitivity, good spatio-temporal resolution, and ease of use, have made it the preferred method to uncover cellular differences. To inspire more creative research, herein, we highlight seminal works in electrochemical techniques for biomolecule analysis and bioimaging. Specifically, micro/nano-electrode-based electrochemical techniques enable real-time quantitative analysis of electroactive substances relevant to life processes in the micro-nanostructure of cells and tissues. Nanopore-based technique plays a vital role in biosensing by utilizing nanoscale pores to achieve high-precision detection and analysis of biomolecules with exceptional sensitivity and single-molecule resolution. Electrochemiluminescence (ECL) technology is utilized for real-time monitoring of the behavior and features of individual cancer cells, enabling observation of their dynamic processes due to its capability of providing high-resolution and highly sensitive bioimaging of cells. Particularly, scanning electrochemical microscopy (SECM) and scanning ion conductance microscopy (SICM) which are widely used in real-time observation of cell surface biological processes and three-dimensional imaging of micro-nano structures, such as metabolic activity, ion channel activity, and cell morphology are introduced in this review. Furthermore, the expansion of the scope of cellular electrochemistry research by innovative functionalized electrodes and electrochemical imaging models and strategies to address future challenges and potential applications is also discussed in this review.

Deciphering and advancing CAR T-cell therapy with single-cell sequencing technologies

Chimeric antigen receptor (CAR) T-cell therapy has made remarkable progress in cancer immunotherapy, but several challenges with unclear mechanisms hinder its wide clinical application. Single-cell sequencing technologies, with the powerful unbiased analysis of cellular heterogeneity and molecular patterns at unprecedented resolution, have greatly advanced our understanding of immunology and oncology. In this review, we summarize the recent applications of single-cell sequencing technologies in CAR T-cell therapy, including the biological characteristics, the latest mechanisms of clinical response and adverse events, promising strategies that contribute to the development of CAR T-cell therapy and CAR target selection. Generally, we propose a multi-omics research mode to guide potential future research on CAR T-cell therapy.