Molecular insights into the early stage of glomerular injury in IgA nephropathy using single-cell RNA sequencing

AbstractIn recent years, biomarkers have been integrated into the diagnostic process and have become increasingly indispensable for obtaining knowledge of the neurodegenerative processes in Alzheimer’s disease (AD). Peripheral blood mononuclear cells (PBMCs) in human blood have been reported to participate in a variety of neurodegenerative activities. Here, a single-cell RNA sequencing analysis of PBMCs from 4 AD patients (2 in the early stage, 2 in the late stage) and 2 normal controls was performed to explore the differential cell subpopulations in PBMCs of AD patients. A significant decrease in B cells was detected in the blood of AD patients. Furthermore, we further examined PBMCs from 43 AD patients and 41 normal subjects by fluorescence activated cell sorting (FACS), and combined with correlation analysis, we found that the reduction in B cells was closely correlated with the patients’ Clinical Dementia Rating (CDR) scores. To confirm the role of B cells in AD progression, functional experiments were performed in early-stage AD mice in which fibrous plaques were beginning to appear; the results demonstrated that B cell depletion in the early stage of AD markedly accelerated and aggravated cognitive dysfunction and augmented the Aβ burden in AD mice. Importantly, the experiments revealed 18 genes that were specifically upregulated and 7 genes that were specifically downregulated in B cells as the disease progressed, and several of these genes exhibited close correlation with AD. These findings identified possible B cell-based AD severity, which are anticipated to be conducive to the clinical identification of AD progression.

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Single-cell RNA sequencing reveals heterogeneous tumor and immune cell populations in early-stage lung adenocarcinomas harboring EGFR mutations

Oncogene ◽

10.1038/s41388-020-01528-0 ◽

2020 ◽

Cited By ~ 1

Author(s):

Di He ◽

Di Wang ◽

Ping Lu ◽

Nan Yang ◽

Zhigang Xue ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Single Cell ◽

Tumor Cells ◽

Rna Sequencing ◽

Early Stage ◽

Cell Types ◽

Egfr Mutations ◽

Advanced Tumor ◽

Single Cell Rna Sequencing

Abstract Lung adenocarcinoma (LUAD) harboring EGFR mutations prevails in Asian population. However, the inter-patient and intra-tumor heterogeneity has not been addressed at single-cell resolution. Here we performed single-cell RNA sequencing (scRNA-seq) of total 125,674 cells from seven stage-I/II LUAD samples harboring EGFR mutations and five tumor-adjacent lung tissues. We identified diverse cell types within the tumor microenvironment (TME) in which myeloid cells and T cells were the most abundant stromal cell types in tumors and adjacent lung tissues. Within tumors, accompanied by an increase in CD1C+ dendritic cells, the tumor-associated macrophages (TAMs) showed pro-tumoral functions without signature gene expression of defined M1 or M2 polarization. Tumor-infiltrating T cells mainly displayed exhausted and regulatory T-cell features. The adenocarcinoma cells can be categorized into different subtypes based on their gene expression signatures in distinct pathways such as hypoxia, glycolysis, cell metabolism, translation initiation, cell cycle, and antigen presentation. By performing pseudotime trajectory, we found that ELF3 was among the most upregulated genes in more advanced tumor cells. In response to secretion of inflammatory cytokines (e.g., IL1B) from immune infiltrates, ELF3 in tumor cells was upregulated to trigger the activation of PI3K/Akt/NF-κB pathway and elevated expression of proliferation and anti-apoptosis genes such as BCL2L1 and CCND1. Taken together, our study revealed substantial heterogeneity within early-stage LUAD harboring EGFR mutations, implicating complex interactions among tumor cells, stromal cells and immune infiltrates in the TME.

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Identification of silkworm hemocyte subsets and analysis of their response to BmNPV infection based on single-cell RNA sequencing

10.1101/2020.10.18.344127 ◽

2020 ◽

Author(s):

Min Feng ◽

Junming Xia ◽

Shigang Fei ◽

Xiong Wang ◽

Yaohong Zhou ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Rna Sequencing ◽

Current Knowledge ◽

Early Stage ◽

Expression Profiles ◽

Marker Genes ◽

Potential Marker ◽

Wide Range ◽

Single Cell Rna Sequencing

AbstractA wide range of hemocyte types exist in insects but a full definition of the different subclasses is not yet established. The current knowledge of the classification of silkworm hemocytes mainly comes from morphology rather than specific markers, so our understanding of the detailed classification, hemocyte lineage and functions of silkworm hemocytes is very incomplete. Bombyx mori nucleopolyhedrovirus (BmNPV) is a representative member of the baculoviruses, which are a major pathogens that specifically infects silkworms and cause serious loss in sericulture industry. Here, we performed single-cell RNA sequencing (scRNA-seq) of silkworm hemocytes in BmNPV and mock-infected larvae to comprehensively identify silkworm hemocyte subsets and determined specific molecular and cellular characteristics in each hemocyte subset before and after viral infection. A total of 19 cell clusters and their potential marker genes were identified in silkworm hemocytes. Among these hemocyte clusters, clusters 0, 1, 2, 5 and 9 might be granulocytes (GR); clusters 14 and 17 were predicted as plasmatocytes (PL); cluster 18 was tentatively identified as spherulocytes (SP); and clusters 7 and 11 could possibly correspond to oenocytoids (OE). In addition, all of the hemocyte clusters were infected by BmNPV and some infected cells carried high viral-load in silkworm larvae at 3 day post infection (dpi). Interestingly, BmNPV infection can cause severe and diverse changes in gene expression in hemocytes. Cells belonging to the infection group mainly located at the early stage of the pseudotime trajectories. Furthermore, we found that BmNPV infection suppresses the immune response in the major hemocyte types. In summary, our scRNA-seq analysis revealed the diversity of silkworm hemocytes and provided a rich resource of gene expression profiles for a systems-level understanding of their functions in the uninfected condition and as a response to BmNPV.

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Kidney pathological changes alter cell clustering features in single-cell RNA sequencing

10.1101/2021.10.08.463030 ◽

2021 ◽

Author(s):

Lijun Ma ◽

Mariana Murea ◽

Young A Choi ◽

Ashok K. Hemal ◽

Alexei V. Mikhailov ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Expression Profiles ◽

Kidney Tissue ◽

Human Kidney ◽

Cell Types ◽

Specific Gene ◽

Glomerular Injury ◽

Cell Clustering ◽

Single Cell Rna Sequencing

The kidney is composed of multiple cell types, each with specific physiological functions. Single-cell RNA sequencing (scRNA-Seq) is useful for classifying cell-specific gene expression profiles in kidney tissue. Because viable cells are critical in scRNA-Seq analyses, we report an optimized cell dissociation process and the necessity for histological screening of human kidney sections prior to performing scRNA-Seq. We show that glomerular injury can result in loss of select cell types during the cell clustering process. Subsequent fluorescence microscopy confirmed reductions in cell-specific markers among the injured cells seen on kidney sections and these changes need to be considered when interpreting results of scRNA-Seq.

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Single-cell RNA sequencing reveals markers of disease progression in primary cutaneous T-cell lymphoma

Molecular Cancer ◽

10.1186/s12943-021-01419-2 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Katharina Rindler ◽

Constanze Jonak ◽

Natalia Alkon ◽

Felix M. Thaler ◽

Harald Kurz ◽

...

Keyword(s):

T Cell ◽

Single Cell ◽

Disease Progression ◽

Rna Sequencing ◽

Cell Lymphoma ◽

Early Stage ◽

T Cell Lymphoma ◽

Advanced Stage ◽

Cutaneous T Cell Lymphoma ◽

Single Cell Rna Sequencing

Abstract Background In early-stage mycosis fungoides (MF), the most common primary cutaneous T-cell lymphoma, limited skin involvement with patches and plaques is associated with a favorable prognosis. Nevertheless, approximately 20–30% of cases progress to tumors or erythroderma, resulting in poor outcome. At present, factors contributing to this switch from indolent to aggressive disease are only insufficiently understood. Methods In patients with advanced-stage MF, we compared patches with longstanding history to newly developed plaques and tumors by using single-cell RNA sequencing, and compared results with early-stage MF as well as nonlesional MF and healthy control skin. Results Despite considerable inter-individual variability, lesion progression was uniformly associated with downregulation of the tissue residency markers CXCR4 and CD69, the heat shock protein HSPA1A, the tumor suppressors and immunoregulatory mediators ZFP36 and TXNIP, and the interleukin 7 receptor (IL7R) within the malignant clone, but not in benign T cells. This phenomenon was not only found in conventional TCR-αβ MF, but also in a case of TCR-γδ MF, suggesting a common mechanism across MF subtypes. Conversely, malignant cells in clinically unaffected skin from MF patients showed upregulation of these markers. Conclusions Our data reveal a specific panel of biomarkers that might be used for monitoring MF disease progression. Altered expression of these genes may underlie the switch in clinical phenotype observed in advanced-stage MF.

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Deciphering cell lineage specification of human lung adenocarcinoma with single-cell RNA sequencing

10.21203/rs.3.rs-127270/v1 ◽

2021 ◽

Author(s):

Zhoufeng Wang ◽

Zhe Li ◽

Kun Zhou ◽

Li Zhang ◽

Ying Yang ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Early Stage ◽

Precancerous Lesions ◽

Cell Types ◽

Marker Genes ◽

Adenocarcinoma In Situ ◽

Invasive Adenocarcinoma ◽

Single Cell Rna Sequencing ◽

Clinical Stages

Abstract Lung adenocarcinomas (LUAD) start as precancerous lesions such as atypical adenomatous hyperplasia (AAH), develop stepwise into adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA), then eventually progress toward invasive adenocarcinoma (IA). To date the cellular heterogeneity across these distinct clinical stages and the underlying molecular events driving tumor progression remain largely unclear. In this study, we performed single-cell RNA sequencing on 52 specimens from 25 patients spanning the four clinical stages. By assessing the expression pattern of marker genes among 268,471 cells, we identified 16 major cell types. We demonstrated that AT2 feature cell types (AT2-like cells) were associated with malignant composition. AT2-like subcluster emerged first in AAH and partially lost AT2 cell transcriptional identity, accompanied with a gain of stemness during cell transition. In addition, genes related to energy metabolism, ribosome synthesis were upregulated in the early stage of LUAD, leading us to identify new markers including miRNA10 and β-hydroxybutyric acid to diagnose early-stage LUAD noninvasively in the blood. We also identified MDK and TIMP1 as potential biomarkers to facilitate our understanding of LUAD pathogenesis. Taken together, our data identified a new mechanism in LUAD evolution, and provided a robust basis for diagnosis and treatment of LUAD.

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Single-cell RNA-sequencing reveals distinct immune cell subsets and signaling pathways in IgA nephropathy

Cell & Bioscience ◽

10.1186/s13578-021-00706-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Honghui Zeng ◽

Le Wang ◽

Jiajia Li ◽

Siweier Luo ◽

Qianqian Han ◽

...

Keyword(s):

Nk Cells ◽

Single Cell ◽

Iga Nephropathy ◽

Rna Sequencing ◽

Mononuclear Cells ◽

Cell Subset ◽

Clinical Severity ◽

Marker Genes ◽

Monocyte Subset ◽

Single Cell Rna Sequencing

Abstract Background IgA nephropathy (IgAN) is the most common primary glomerulonephritis globally. Increasing evidence suggests the importance of host immunity in the development of IgAN, but its dynamics during the early stage of IgAN are still largely unclear. Results Here we successfully resolved the early transcriptomic changes in immune cells of IgAN by conducting single-cell RNA-sequencing (scRNA-seq) with peripheral blood mononuclear cells. The differentially expressed genes (DEGs) between control and IgAN were predominantly enriched in NK cell-mediated cytotoxicity and cell killing pathways. Interestingly, we discovered that the number and cytotoxicity of NK cells are significantly reduced in IgAN patients, where both the number and marker genes of NK cells were negatively associated with the clinical parameters, including the levels of urine protein creatinine ratio (UPCR), serum galactose-deficient IgA1 and IgA. A distinctive B cell subset, which had suppressed NFκB signaling was predominantly in IgAN and positively associated with disease progression. Moreover, the DEGs of B cells were enriched in different viral infection pathways. Classical monocytes also significantly changed in IgAN and a monocyte subset expressing interferon-induced genes was positively associated with the clinical severity of IgAN. Finally, we identified vast dynamics in intercellular communications in IgAN. Conclusions We dissected the immune landscape of IgAN at the single-cell resolution, which provides new insights in developing novel biomarkers and immunotherapy against glomerulonephritis.

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Defining the variety of cell types in developing and adult human kidneys by single-cell RNA sequencing

npj Regenerative Medicine ◽

10.1038/s41536-021-00156-w ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

A. Schumacher ◽

M. B. Rookmaaker ◽

J. A. Joles ◽

R. Kramann ◽

T. Q. Nguyen ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Renal Cell ◽

Early Stage ◽

Kidney Tissue ◽

Cell Types ◽

Intermediate Cell ◽

Adult Human ◽

Single Cell Rna Sequencing

AbstractThe kidney is among the most complex organs in terms of the variety of cell types. The cellular complexity of human kidneys is not fully unraveled and this challenge is further complicated by the existence of multiple progenitor pools and differentiation pathways. Researchers disagree on the variety of renal cell types due to a lack of research providing a comprehensive picture and the challenge to translate findings between species. To find an answer to the number of human renal cell types, we discuss research that used single-cell RNA sequencing on developing and adult human kidney tissue and compares these findings to the literature of the pre-single-cell RNA sequencing era. We find that these publications show major steps towards the discovery of novel cell types and intermediate cell stages as well as complex molecular signatures and lineage pathways throughout development. The variety of cell types remains variable in the single-cell literature, which is due to the limitations of the technique. Nevertheless, our analysis approaches an accumulated number of 41 identified cell populations of renal lineage and 32 of non-renal lineage in the adult kidney, and there is certainly much more to discover. There is still a need for a consensus on a variety of definitions and standards in single-cell RNA sequencing research, such as the definition of what is a cell type. Nevertheless, this early-stage research already proves to be of significant impact for both clinical and regenerative medicine, and shows potential to enhance the generation of sophisticated in vitro kidney tissue.

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