scholarly journals Characterization of Organ-Specific Regulatory B Cells Using Single-Cell RNA Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Si-Yu Yang ◽  
Jie Long ◽  
Meng-Xing Huang ◽  
Pan-Yue Luo ◽  
Zhen-Hua Bian ◽  
...  
Keyword(s):  
Transcription Factor ◽  
B Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Receptor ◽  
Human Beings ◽  
Regulatory B Cells ◽  
Mesenteric Lymph Nodes ◽  
Single Cell Rna Sequencing ◽  
Organ Specific

Regulatory B cells (Breg) are considered as immunosuppressive cells. Different subsets of Breg cells have been identified both in human beings and in mice. However, there is a lack of unique markers to identify Breg cells, and the heterogeneity of Breg cells in different organs needs to be further illuminated. In this study, we performed high-throughput single-cell RNA sequencing (scRNA-seq) and single-cell B-cell receptor sequencing (scBCR-seq) of B cells from the murine spleen, liver, mesenteric lymph nodes, bone marrow, and peritoneal cavity to better define the phenotype of these cells. Breg cells were identified based on the expression of immunosuppressive genes and IL-10-producing B (B10) cell-related genes, to define B10 and non-B10 subsets in Breg cells based on the score of the B10 gene signatures. Moreover, we characterized 19 common genes significantly expressed in Breg cells, including Fcrl5, Zbtb20, Ccdc28b, Cd9, and Ptpn22, and further analyzed the transcription factor activity in defined Breg cells. Last, a BCR analysis was used to determine the clonally expanded clusters and the relationship of Breg cells across different organs. We demonstrated that Atf3 may potentially modulate the function of Breg cells as a transcription factor and that seven organ-specific subsets of Breg cells are found. Depending on gene expression and functional modules, non-B10 Breg cells exhibited activated the TGF-β pathway, thus suggesting that non-B10 Breg cells have specific immunosuppressive properties different from conventional B10 cells. In conclusion, our work provides new insights into Breg cells and illustrates their transcriptional profiles and BCR repertoire in different organs under physiological conditions.

scholarly journals Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David S. Fischer ◽  
Meshal Ansari ◽  
Karolin I. Wagner ◽  
Sebastian Jarosch ◽  
Yiqi Huang ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Ex Vivo ◽  
Severe Disease ◽  
Human Leukocyte ◽  
Cell Receptor ◽  
Single Cell Rna Sequencing

AbstractThe in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for ‘reverse phenotyping’. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.

scholarly journals Single-cell RNA sequencing reveals B cell–related molecular biomarkers for Alzheimer’s disease

2021 ◽  
Author(s):  
Liu-Lin Xiong ◽  
Lu-Lu Xue ◽  
Ruo-Lan Du ◽  
Rui-Ze Niu ◽  
Li Chen ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
B Cells ◽  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Early Stage ◽  
Diagnostic Process ◽  
Sequencing Analysis ◽  
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.

scholarly journals Single-Cell RNA Sequencing of Tumor-Infiltrating NK Cells Reveals that Inhibition of Transcription Factor HIF-1α Unleashes NK Cell Activity

Immunity ◽  
2020 ◽  
Vol 52 (6) ◽  
pp. 1075-1087.e8 ◽  
Author(s):  
Jing Ni ◽  
Xi Wang ◽  
Ana Stojanovic ◽  
Qin Zhang ◽  
Marian Wincher ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Nk Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Nk Cell ◽  
Cell Activity ◽  
Nk Cell Activity ◽  
Single Cell Rna Sequencing

scholarly journals EPCO-32. AN EPIGENETIC SINGLE-CELL ATLAS OF IDH-MUTANT GLIOMA REVEALS THE ROLE OF ATRX IN SHAPING TUMOR COMPOSITION

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii76-ii76
Author(s):  
Husam Babikir ◽  
Lin Wang ◽  
Karin Shamardani ◽  
Sweta Sudhir ◽  
Gary Kohanbash ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Rna Sequencing ◽  
Myeloid Cell ◽  
Cell Types ◽  
Open Chromatin ◽  
Helix Loop Helix ◽  
Local Immunosuppression ◽  
Single Cell Rna Sequencing

Abstract Recent single-cell RNA-sequencing studies have identified a hierarchy of cell types that is common to all isocitrate dehydrogenase (IDH) -mutant gliomas. This finding is somewhat paradoxical since the genetic differences between IDH-mutant astrocytomas and IDH-mutant oligodendrogliomas are prognostic, predictive of therapeutic response, and correlated with differences in immune infiltrates. To integrate these disparate findings, we constructed a single-cell atlas of 28 human IDH-mutant primary untreated grade-II/III gliomas. All specimens were profiled by single-cell assay for transposase-accessible chromatin, with additional cohorts profiled via single-cell RNA-sequencing and single-cell spatial proteomics. We determined the cell-type specific differences between IDH-mutant gliomas in transcription-factor utilization, associated targeting and cis-regulatory grammars. To elucidate the role of the chromatin remodeler ATRX (inactivated in over 86% of IDH-mutant astrocytomas) in shaping observed differences in open chromatin, we knocked out ATRX in an immunocompetent model of IDH-mutant glioma and subjected murine tumors to single-cell profiling. We found: 1. ATRX-deficient, IDH-mutant human and murine gliomas both upregulate an astrocytic regulatory program driven by Nuclear Factor I genes and downregulate an oligodendrocytic program driven by basic helix-loop-helix transcription factors. 2. Both human and mouse ATRX-deficient, IDH-mutant gliomas up-regulate genes that promote myeloid-cell chemotaxis and both have significantly higher percentages of myeloid-derived immune-suppressive cells than controls; 3. A transcription-factor program is conserved between human and murine ATRX-deficient tumors that shapes glial identity and promotes local immunosuppression. These studies elucidate how IDH-mutant gliomas from different subtypes can have distinct cellular morphologies and tumor micronenvironments despite a common lineage hierarchy.

scholarly journals Temporal single-cell transcriptomes of zebrafish spinal cord pMN progenitors reveal distinct neuronal and glial progenitor populations

2021 ◽  
Author(s):  
Kayt Scott ◽  
Rebecca O’Rourke ◽  
Caitlin C. Winkler ◽  
Christina A. Kearns ◽  
Bruce Appel
Keyword(s):  
Spinal Cord ◽  
Transcription Factor ◽  
Single Cell ◽  
Progenitor Cells ◽  
Rna Sequencing ◽  
Motor Neurons ◽  
Marker Genes ◽  
List Type ◽  
Fate Mapping ◽  
Single Cell Rna Sequencing

AbstractVentral spinal cord progenitor cells, which express the basic helix loop helix transcription factor Olig2, sequentially produce motor neurons and oligodendrocyte precursor cells (OPCs). Following specification some OPCs differentiate as myelinating oligodendrocytes while others persist as OPCs. Though a considerable amount of work has described the molecular profiles that define motor neurons, OPCs, and oligodendrocytes, less is known about the progenitors that produce them. To identify the developmental origins and transcriptional profiles of motor neurons and OPCs, we performed single-cell RNA sequencing on isolated pMN cells from embryonic zebrafish trunk tissue at stages that encompassed motor neurogenesis, OPC specification, and initiation of oligodendrocyte differentiation. Downstream analyses revealed two distinct pMN progenitor populations: one that appears to produce neurons and one that appears to produce OPCs. This latter population, called Pre-OPCs, is marked by expression of GS Homeobox 2 (gsx2), a gene that encodes a homeobox transcription factor. Using fluorescent in situ hybridizations, we identified gsx2-expressing Pre-OPCs in the spinal cord prior to expression of canonical OPC marker genes. Our data therefore reveal heterogeneous gene expression profiles among pMN progenitors, supporting prior fate mapping evidence.HighlightsSingle-cell RNA sequencing reveals the developmental trajectories of neurons and glia that arise from spinal cord pMN progenitor cells in zebrafish embryosTranscriptionally distinct subpopulations of pMN progenitors are the apparent sources of neurons or oligodendrocytes, consistent with fate mapping datagsx2 expression marks pMN progenitors that produce oligodendrocyte lineage cells

scholarly journals P13: CHARACTERISATION OF THE TUMOUR MICROENVIRONMENT IN MESENCHYMAL GASTRIC TUMOURS USING SINGLE-CELL RNA SEQUENCING

2021 ◽  
Vol 108 (Supplement_1) ◽  
Author(s):  
J Harrington ◽  
M Lloyd ◽  
N Mabrouk ◽  
R Walker ◽  
B Grace ◽  
...  
Keyword(s):  
B Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Therapeutic Targets ◽  
Tumour Microenvironment ◽  
Cell Populations ◽  
Limited Information ◽  
Single Cell Rna Sequencing ◽  
Mesenchymal Tumours

Abstract Introduction Gastric mesenchymal tumours are a rare group of neoplasms, which include gastrointestinal stromal tumours (GISTs) and leiomyomas. To date, there is limited information on the tumour microenvironment (TME) in these neoplasms, despite the TME widely known to influence the hallmarks of cancer. In this study we used single cell RNA sequencing (scRNAseq) to profile individual cells of the TME in GIST and leiomyoma. Method The two gastric mesenchymal tumours and two normal gastric samples were analysed using DropSeq, where single cell transcriptomes are captured onto barcoded beads using a microfluidic device before next generation sequencing. For comparison, we performed bulk RNA-sequencing and CIBERSORT to estimate the abundance of 22 immune cell populations. Furthermore, we used immunohistochemistry to elucidate the presence and location of several immune cells. Result Both neoplasms had diverse immune and stromal cell populations with a greater proportion of macrophages but less B cells than normal gastric tissue. ScRNAseq was able to identify subpopulations of B cells and T cells not detected with CIBERSORT. Interstitial cells of cajal, believed to be the pre-cursor to GISTs, were observed through scRNAseq and confirmed through immunohistochemistry. Conclusion To our knowledge, this is the first study to utilise scRNAseq on GISTs and leiomyomas, which enabled characterisation of the TME at a cellular level. Using this platform in future studies will enable better characterisation of the TME and may inform the discovery of therapeutic targets. Take-home message Single cell RNA sequencing enables the ability to explore the tumour microenvironment of mesenchymal tumours at an enhanced resolution, paving the way for potential future therapeutic targets.

Role of FOS transcription factor in diabetes associated atherosclerosis; insight from single cell RNA sequencing

2021 ◽  
Vol 331 ◽  
pp. e69-e70
Author(s):  
A.W. Khan ◽  
M.S.K. Lee ◽  
A.M. Watson ◽  
S. Maxwell ◽  
M.E. Cooper ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Rna Sequencing ◽  
Single Cell Rna Sequencing

scholarly journals Single-Cell RNA Sequencing Reveals Tissue Compartment-Specific Plasticity of Mycosis Fungoides Tumor Cells

2021 ◽  
Vol 12 ◽  
Author(s):  
Katharina Rindler ◽  
Wolfgang M. Bauer ◽  
Constanze Jonak ◽  
Matthias Wielscher ◽  
Lisa E. Shaw ◽  
...  
Keyword(s):  
T Cells ◽  
Lymph Node ◽  
T Cell ◽  
Single Cell ◽  
Tumor Cells ◽  
Rna Sequencing ◽  
Mycosis Fungoides ◽  
Cell Receptor ◽  
Skin Tumor ◽  
Single Cell Rna Sequencing

Mycosis fungoides (MF) is the most common primary cutaneous T-cell lymphoma. While initially restricted to the skin, malignant cells can appear in blood, bone marrow and secondary lymphoid organs in later disease stages. However, only little is known about phenotypic and functional properties of malignant T cells in relationship to tissue environments over the course of disease progression. We thus profiled the tumor micromilieu in skin, blood and lymph node in a patient with advanced MF using single-cell RNA sequencing combined with V-D-J T-cell receptor sequencing. In skin, we identified clonally expanded T-cells with characteristic features of tissue-resident memory T-cells (TRM, CD69+CD27-NR4A1+RGS1+AHR+). In blood and lymph node, the malignant clones displayed a transcriptional program reminiscent of a more central memory-like phenotype (KLF2+TCF7+S1PR1+SELL+CCR7+), while retaining tissue-homing receptors (CLA, CCR10). The skin tumor microenvironment contained potentially tumor-permissive myeloid cells producing regulatory (IDO1) and Th2-associated mediators (CCL13, CCL17, CCL22). Given their expression of PVR, TNFRSF14 and CD80/CD86, they might be under direct control by TIGIT+CTLA4+CSF2+TNFSF14+ tumor cells. In sum, this study highlights the adaptive phenotypic and functional plasticity of MF tumor cell clones. Thus, the TRM-like phenotype enables long-term skin residence of MF cells. Their switch to a TCM-like phenotype with persistent skin homing molecule expression in the circulation might explain the multi-focal nature of MF.

scholarly journals Single-Cell RNA Sequencing Reveals the Immunological Profiles of Renal Allograft Rejection in Mice

2021 ◽  
Vol 12 ◽  
Author(s):  
Qixia Shen ◽  
Yucheng Wang ◽  
Jiaoyi Chen ◽  
Lifeng Ma ◽  
Xiaoru Huang ◽  
...  
Keyword(s):  
T Cells ◽  
B Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Allograft Rejection ◽  
Renal Allograft ◽  
Immune Cell ◽  
Fold Increase ◽  
Renal Allograft Rejection ◽  
Single Cell Rna Sequencing

Allograft rejection is a common immunological feature in renal transplantation and is associated with reduced graft survival. A mouse renal allograft rejection model was induced and single-cell RNA sequencing (scRNA-seq) data of CD45+ leukocytes in kidney allografts on days 7 (D7) and 15 (D15) after operation was analyzed to reveal a full immunological profiling. We identified 20 immune cell types among 10,921 leukocytes. Macrophages and CD8+ T cells constituted the main populations on both timepoints. In the process from acute rejection (AR) towards chronic rejection (CR), the proportion of proliferating and naïve CD8+ T cells dropped significantly. Both B cells and neutrophils decreased by about 3 folds. On the contrary, the proportion of macrophages and dendritic cells (DCs) increased significantly, especially by about a 4.5-fold increase in Ly6cloMrc1+ macrophages and 2.6 folds increase in Ly6cloEar2+ macrophages. Moreover, myeloid cells harbored the richest ligand and receptor (LR) pairs with other cells, particularly for chemokine ligands such as Cxcl9, Cxcl10, Cxcl16 and Yars. However, macrophages with weak response to interferon gamma (IFNg) contributed to rejection chronicization. To conclude, reduction in CD8 T cells, B cells and neutrophils while increasing in Ly6cloMrc1+ macrophages and Ly6cloEar2+ macrophages, may contribute significantly to the progress from AR towards CR.

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