Single-cell RNA-Seq reveals CVI-mAb-induced Lyve1+ M2-like macrophages reduce atherosclerotic plaque area in Apoe-/- mice

Duan, Rui; Liu, Yan; Tang, Dongmei; Xiao, Sujun; Lin, Run; Zhao, Ming

doi:10.1016/j.intimp.2023.109794

Cited by 4 publications

(2 citation statements)

References 46 publications

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“…Another gene, TYROBP, is also a widely reported immune-associated gene. In accordance with recent publications, upregulation of TYROBP has been shown to be downregulated in a specific cell type, Lyve1 M2-like macrophage [74], corresponding with the quantitative rule generated on the MCFS feature list.…”

Section: B Cell Familysupporting

confidence: 88%

Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods

Yang,

Zhang,

Ren

et al. 2023

Life

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Immune cell infiltration that occurs at the site of colon tumors influences the course of cancer. Different immune cell compositions in the microenvironment lead to different immune responses and different therapeutic effects. This study analyzed single-cell RNA sequencing data in a normal colon with the aim of screening genetic markers of 25 candidate immune cell types and revealing quantitative differences between them. The dataset contains 25 classes of immune cells, 41,650 cells in total, and each cell is expressed by 22,164 genes at the expression level. They were fed into a machine learning-based stream. The five feature ranking algorithms (last absolute shrinkage and selection operator, light gradient boosting machine, Monte Carlo feature selection, minimum redundancy maximum relevance, and random forest) were first used to analyze the importance of gene features, yielding five feature lists. Then, incremental feature selection and two classification algorithms (decision tree and random forest) were combined to filter the most important genetic markers from each list. For different immune cell subtypes, their marker genes, such as KLRB1 in CD4 T cells, RPL30 in B cell IGA plasma cells, and JCHAIN in IgG producing B cells, were identified. They were confirmed to be differentially expressed in different immune cells and involved in immune processes. In addition, quantitative rules were summarized by using the decision tree algorithm to distinguish candidate immune cell types. These results provide a reference for exploring the cell composition of the colon cancer microenvironment and for clinical immunotherapy.

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Section: B Cell Familysupporting

confidence: 88%

Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods

Yang,

Zhang,

Ren

et al. 2023

Life

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“…The above genes were related to tissueresident macrophage. [25][26][27] Macrophage3 expressed a high level of ITGAX (Figure S5A), thus denoted a subset of proinflammatory macrophage. 28 HLA-DRA, which marked antigen-presenting cells, was found in macrophage5 (Figure S5A).…”

Section: Identifying Difference Of Macrophages In 3 Groupsmentioning

confidence: 99%

Overexpression of ATP5F1A in Cardiomyocytes Promotes Cardiac Reverse Remodeling

Xu,

Zhang,

Chang

et al. 2024

Circ: Heart Failure

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BACKGROUND: The mechanism of cardiac reverse remodeling (CRR) mediated by the left ventricular assist device remains unclear. This study aims to identify the specific cell type responsible for CRR and develop the therapeutic target that promotes CRR. METHODS: The nuclei were extracted from the left ventricular tissue of 4 normal controls, 4 CRR patients, and 4 no cardiac reverse remodeling patients and then subjected to single-nucleus RNA sequencing for identifying key cell types responsible for CRR. Gene overexpression in transverse aortic constriction and dilated cardiomyopathy heart failure mouse model (C57BL/6J background) and pathological staining were performed to validate the results of single-nucleus RNA sequencing. RESULTS: Ten cell types were identified among 126 156 nuclei. Cardiomyocytes in CRR patients expressed higher levels of ATP5F1A than the other 2 groups. The macrophages in CRR patients expressed more anti-inflammatory genes and functioned in angiogenesis. Endothelial cells that elevated in no cardiac reverse remodeling patients were involved in the inflammatory response. Echocardiography showed that overexpressing ATP5F1A through cardiomyocyte-specific adeno-associated virus 9 demonstrated an ability to improve heart function and morphology. Pathological staining showed that overexpressing ATP5F1A could reduce fibrosis and cardiomyocyte size in the heart failure mouse model. CONCLUSIONS: The present results of single-nucleus RNA sequencing and heart failure mouse model indicated that ATP5F1A could mediate CRR and supported the development of therapeutics for overexpressing ATP5F1A in promoting CRR.

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Tenofovir alters the immune microenvironment of pregnant women with hepatitis B virus infection: Evidence from single-cell RNA sequencing

Wang

Gao

et al. 2023

International Immunopharmacology

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Single-cell RNA-Seq reveals CVI-mAb-induced Lyve1+ M2-like macrophages reduce atherosclerotic plaque area in Apoe-/- mice

Cited by 4 publications

References 46 publications

Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods

Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods

Overexpression of ATP5F1A in Cardiomyocytes Promotes Cardiac Reverse Remodeling

Tenofovir alters the immune microenvironment of pregnant women with hepatitis B virus infection: Evidence from single-cell RNA sequencing

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