Research progress on application of single-cell TCR/BCR sequencing technology to the tumor immune microenvironment, autoimmune diseases, and infectious diseases

He, Jian‐Jun; Shen, Jian; Luo, Wei; Han, Zeping; Xie, Fangmei; Liao, Liyin; Guo, Zhimou; Li, Jianhao; Li, Yuguang; Chen, Hanwei

doi:10.3389/fimmu.2022.969808

Cited by 9 publications

(4 citation statements)

References 43 publications

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“…To investigate intercellular communication, we utilized CellChat (version 1.6.1), an R package designed to facilitate the exploration of ligand-receptor interactions at the cell surface, thereby elucidating cell signaling across different cell types [13]. By leveraging gene expression data, we inferred protein expression and established a comprehensive cell interaction network.…”

Section: Cell-cell Communication Analysismentioning

confidence: 99%

“…They discern and adhere to antigens by means of TCR and BCR present on their respective surfaces, thereby facilitating the clearance of pathogens or neoplastic cells in vivo [13] . A computational approach named TRUST4 is employed to extract immune features from a vast amount of RNA-seq data, for the purpose of constructing TCR and BCR repertoires for SLE and HC samples [14] .…”

Section: Introductionmentioning

confidence: 99%

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Revealing the Immune Heterogeneity in Systemic Lupus Erythematosus Based on Multi-Omics Data Analysis

Liu,

Gong,

Liu

et al. 2024

Preprint

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Systemic lupus erythematosus is an autoimmune disorder characterized by a spectrum of clinical manifestations. With the progress of next-generation sequencing (NGS) technology, novel techniques for sequencing T cell receptors and B cell receptors have emerged. In this study, we employed the computational approach TRUST4 to construct TCR and BCR libraries using a substantial volume of RNA-seq data extracted from the peripheral blood of sepsis patients. Subsequently, we conducted an analysis to assess the clonality and diversity of the immune repertoire associated with this disease. A total of 30 distinct cell types were annotated and subsequently categorized into 12 clusters. SLE group demonstrated an increase in the innate immune responses of CD14 monocytes, CD16 monocytes, Megakaryocytes, NK cells, and Neutrophis in comparison to the HC group. The CellChat analysis findings unveiled four distinct patterns for input signals and four patterns for output signals. The results of trajectory analysis revealed that the majority of cell subsets are positioned in a single developmental stage. Our research results comprehensively demonstrate the dynamic changes of immune cells during the onset of SLE, and identify specific V and J genes in TCR and BCR that can be used to expand our understanding of SLE.

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Section: Cell-cell Communication Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Revealing the Immune Heterogeneity in Systemic Lupus Erythematosus Based on Multi-Omics Data Analysis

Liu,

Gong,

Liu

et al. 2024

Preprint

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“…The scRNA sequencing technology is an effective tool for analyzing immune infiltration (17)(18)(19) Therefore, two scRNA sequencing datasets (GSE140228_10X and GSE166635) were analyzed to investigate TXNL4A expression in each cell cluster using the TISCH2 database (20).…”

Section: Analysis Of Single-cell Sequencing Rna Materialsmentioning

confidence: 99%

Combined bulk RNA and single-cell RNA analyses reveal TXNL4A as a new biomarker for hepatocellular carcinoma

Zhu

Zhou

et al. 2023

Front. Oncol.

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IntroductionHepatocellular carcinoma (HCC) has a high mortality rate worldwide. The dysregulation of RNA splicing is a major event leading to the occurrence, progression, and drug resistance of cancer. Therefore, it is important to identify new biomarkers of HCC from the RNA splicing pathway.MethodsWe performed the differential expression and prognostic analyses of RNA splicing-related genes (RRGs) using The Cancer Genome Atlas-liver hepatocellular carcinoma (LIHC). The International Cancer Genome Consortium (ICGC)-LIHC dataset was used to construct and validate prognostic models, and the PubMed database was used to explore genes in the models to identify new markers. The screened genes were subjected to genomic analyses, including differential, prognostic, enrichment, and immunocorrelation analyses. Single-cell RNA (scRNA) data were used to further validate the immunogenetic relationship.ResultsOf 215 RRGs, we identified 75 differentially expressed prognosis-related genes, and a prognostic model incorporating thioredoxin like 4A (TXNL4A) was identified using least absolute shrinkage and selection operator regression analysis. ICGC-LIHC was used as a validation dataset to confirm the validity of the model. PubMed failed to retrieve HCC-related studies on TXNL4A. TXNL4A was highly expressed in most tumors and was associated with HCC survival. Chi-squared analyses indicated that TXNL4A expression positively correlated positively with the clinical features of HCC. Multivariate analyses revealed that high TXNL4A expression was an independent risk factor for HCC. Immunocorrelation and scRNA data analyses indicated that TXNL4A was correlated with CD8 T cell infiltration in HCC.ConclusionTherefore, we identified a prognostic and immune-related marker for HCC from the RNA splicing pathway.

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“…Single-cell sequencing, as a technique for analysis at the individual cellular level, overcomes the problem of cellular heterogeneity ( 5 ). It not only better reflects how the different cell populations that makeup TIME regulate different tumor states from a more microscopic perspective, but also has important implications for unraveling the mechanisms of cancer progression and immunotherapeutic response ( 6 , 7 ).…”

Section: Introductionmentioning

confidence: 99%

Development and validation of cuproptosis-related lncRNAs associated with pancreatic cancer immune microenvironment based on single-cell

Sun,

Yao,

Man

et al. 2023

Front. Immunol.

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BackgroundCuproptosis, a novel mode of cell death associated with the tricarboxylic acid (TCA) cycle, is relevant to the development of cancer. However, the impact of single-cell-based Cuproptosis-associated lncRNAs on the Tumor immune microenvironment (TIME) of Pancreatic adenocarcinoma (PAAD) and its potential value for individualized immunotherapy has not been clarified.Methods14 immune-related CRGs were screened by exploring the interaction between differentially expressed Immune-Related Genes (IRGs) and Cuproptosis-Related Genes (CRGs) in PAAD. Next, the expression amount and expression distribution of CRGs in single-cell samples were analyzed by focusing on 7-CRGs with significant expressions. On the one hand, MAP2K2, SOD1, and VEGFA, which were significantly differentially expressed between PAAD sites and normal tissues adjacent to them, were subjected to immunohistochemical validation and immune landscape analysis. On the other hand, from these 7-CRGs, prognostic signatures of lncRNAs were established by co-expression and LASSO-COX regression analysis, and their prognostic value and immune relevance were assessed. In addition, this study not only validated the hub CRGs and the lncRNAs constituting the signature in a PAAD animal model treated with immunotherapy-based combination therapy using immunohistochemistry and qRT-PCR but also explored the potential value of the combination of targeted, chemotherapy and immunotherapy.ResultsBased on the screening of 7-CRGs significantly expressed in a PAAD single-cell cohort and their co-expressed Cuproptosis-Related lncRNAs (CRIs), this study constructed a prognostic signature of 4-CRIs named CIR-score. A Nomogram integrating the CIR-score and clinical risk factors was constructed on this basis to predict the individualized survival of patients. Moreover, high and low-risk groups classified according to the median of signatures exhibited significant differences in clinical prognosis, immune landscape, bioenrichment, tumor burden, and drug sensitivity. And the immunohistochemical and qRT-PCR results of different mouse PAAD treatment strategies were consistent with the trend of inter-group variability in drug sensitivity of hub CRGs and CIR-score. The combination of immunotherapy, targeted therapy, and chemotherapy exhibited a better tumor suppression effect.ConclusionCIR-score, as a Cuproptosis-related TIME-specific prognostic signature based on PAAD single cells, not only predicts the prognosis and immune landscape of PAAD patients but also provides a new strategy for individualized immunotherapy-based combination therapy.

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Research progress on application of single-cell TCR/BCR sequencing technology to the tumor immune microenvironment, autoimmune diseases, and infectious diseases

Cited by 9 publications

References 43 publications

Revealing the Immune Heterogeneity in Systemic Lupus Erythematosus Based on Multi-Omics Data Analysis

Revealing the Immune Heterogeneity in Systemic Lupus Erythematosus Based on Multi-Omics Data Analysis

Combined bulk RNA and single-cell RNA analyses reveal TXNL4A as a new biomarker for hepatocellular carcinoma

Development and validation of cuproptosis-related lncRNAs associated with pancreatic cancer immune microenvironment based on single-cell

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