scholarly journals Cell subtypes and immune dysfunction in peritoneal fluid of endometriosis revealed by single-cell RNA-sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gen Zou ◽  
Jianzhang Wang ◽  
Xinxin Xu ◽  
Ping Xu ◽  
Libo Zhu ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Single Cell ◽  
Natural Killer ◽  
Rna Sequencing ◽  
Peritoneal Cavity ◽  
Immune Cells ◽  
Peritoneal Fluid ◽  
Control Sample ◽  
Immune Dysfunction ◽  
Single Cell Rna Sequencing

Abstract Background Endometriosis is a refractory and recurrent disease and it affects nearly 10% of reproductive-aged women and 40% of infertile patients. The commonly accepted theory for endometriosis is retrograde menstruation where endometrial tissues invade into peritoneal cavity and fail to be cleared due to immune dysfunction. Therefore, the comprehensive understanding of immunologic microenvironment of peritoneal cavity deserves further investigation for the previous studies mainly focus on one or several immune cells. Results High-quality transcriptomes were from peritoneal fluid samples of patients with endometriosis and control, and firstly subjected to 10 × genomics single-cell RNA-sequencing. We acquired the single-cell transcriptomes of 10,280 cells from endometriosis sample and 7250 cells from control sample with an average of approximately 63,000 reads per cell. A comprehensive map of overall cells in peritoneal fluid was first exhibited. We unveiled the heterogeneity of immune cells and discovered new cell subtypes including T cell receptor positive (TCR+) macrophages, proliferating macrophages and natural killer dendritic cells in peritoneal fluid, which was further verified by double immunofluorescence staining and flow cytometry. Pseudo-time analysis showed that the response of macrophages to the menstrual debris might follow the certain differentiation trajectory after endometrial tissues invaded into the peritoneal cavity, that is, from antigen presentation to pro-inflammation, then to chemotaxis and phagocytosis. Our analyses also mirrored the dysfunctions of immune cells including decreased phagocytosis and cytotoxic activity and elevated pro-inflammatory and chemotactic effects in endometriosis. Conclusion TCR+ macrophages, proliferating macrophages and natural killer dendritic cells are firstly reported in human peritoneal fluid. Our results also revealed that immune dysfunction happens in peritoneal fluid of endometriosis, which may be responsible for the residues of invaded menstrual debris. It provided a large-scale and high-dimensional characterization of peritoneal microenvironment and offered a useful resource for future development of immunotherapy.

scholarly journals A comprehensive cell profiling reveals new cell subtypes and immune dysfunction in peritoneal fluid of endometriosis

2020 ◽  
Author(s):  
Gen Zou ◽  
Jianzhang Wang ◽  
Xinxin Xu ◽  
Ping Xu ◽  
Libo Zhu ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Single Cell ◽  
Natural Killer ◽  
Peritoneal Cavity ◽  
Immune Cells ◽  
Peritoneal Fluid ◽  
Large Scale ◽  
Control Sample ◽  
Immune Dysfunction ◽  
Retrograde Menstruation

Abstract BackgroundEndometriosis is a refractory and recurrent disease and it affects nearly 10% of reproductive-aged women and 40% of infertile patients. The commonly accepted theory for endometriosis is retrograde menstruation where endometrial tissues invade into peritoneal cavity and fail to be cleared due to immune dysfunction. Therefore, the comprehensive understanding of immunologic microenvironment of peritoneal cavity deserves further investigation for the previous studies mainly focus on one or several immune cells.ResultsHigh-quality transcriptomes were from peritoneal fluid samples of patients with endometriosis and control, and firstly subjected to 10 × genomics single-cell RNA-sequencing. We acquired the single-cell transcriptomes of 10,280 cells from endometriosis sample and 7,250 cells from control sample with an average of approximately 63,000 reads per cell. A comprehensive map of overall cells in peritoneal fluid was first exhibited and it showed that immune cells predominated in peritoneal fluid. We unveiled the heterogeneity of immune cells and discovered new cell subtypes including TCR+ macrophages, proliferating macrophages and natural killer dendritic cells in peritoneal fluid, which was further verified by double immunofluorescence staining and flow cytometry. Pseudo-time analysis showed that the response of macrophages to the menstrual debris might follow the certain differentiation trajectory after endometrial tissues invaded into the peritoneal cavity. Our analyses also mirrored the dysfunctions of immune cells including decreased phagocytosis and cytotoxic activity and elevated pro-inflammatory and chemotactic effects in endometriosis.ConclusionTCR+ macrophages, proliferating macrophages and natural killer dendritic cells are firstly reported in peritoneal fluid. Our results also revealed that peritoneal cavity is an immune microenvironment and immune dysfunction happens in peritoneal fluid of endometriosis, which may be responsible for the residues of invaded menstrual debris. It provided a large-scale and high-dimensional characterization of peritoneal microenvironment and offered a useful resource for immunotherapy of endometriosis.

scholarly journals Sample processing and single cell RNA-sequencing of peripheral blood immune cells from COVID-19 patients

2021 ◽  
pp. 100582
Author(s):  
Changfu Yao ◽  
Stephanie A. Bora ◽  
Peter Chen ◽  
Helen S. Goodridge ◽  
Sina A. Gharib
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Peripheral Blood ◽  
Sample Processing ◽  
Single Cell Rna Sequencing

Multi tissue processing for single cell sequencing of human immune cells v1

2021 ◽  
Author(s):  
Daniel Rainbow ◽  
Sarah Howlett ◽  
Lorna Jarvis ◽  
Joanne Jones
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Human Tissues ◽  
Single Cell Sequencing ◽  
Tissue Processing ◽  
Simultaneous Processing ◽  
Single Cell Rna Sequencing ◽  
Human Immune

This protocol has been developed for the simultaneous processing of multiple human tissues to extract immune cells for single cell RNA sequencing using the 10X platform, and ideal for atlasing projects. Included in this protocol are the steps needed to go from tissue to loading the 10X Chromium for single cell RNA sequencing and includes the hashtag and CiteSeq labelling of cells as well as the details needed to stimulate cells with PMA+I.

scholarly journals Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Noa Bossel Ben-Moshe ◽  
Shelly Hen-Avivi ◽  
Natalia Levitin ◽  
Dror Yehezkel ◽  
Marije Oosting ◽  
...  
Keyword(s):  
Bacterial Infection ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Sequencing Analysis ◽  
Single Cell Rna Sequencing ◽  
Human Immune

scholarly journals Single-cell RNA sequencing of immune cells in gastric cancer patients

Aging ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 2747-2763 ◽  
Author(s):  
Kai Fu ◽  
Bingqing Hui ◽  
Qian Wang ◽  
Chen Lu ◽  
Weihong Shi ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Single Cell ◽  
Cancer Patients ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Single Cell Rna Sequencing ◽  
Gastric Cancer Patients

scholarly journals Clonal Hematopoiesis-Driver DNMT3A Mutations Alter Immune Cells in Heart Failure

2020 ◽  
Author(s):  
Wesley T Abplanalp ◽  
Sebastian Cremer ◽  
David John ◽  
Jedrzej Hoffmann ◽  
Bianca Schuhmacher ◽  
...  
Keyword(s):  
Heart Failure ◽  
T Cell ◽  
Chronic Heart Failure ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Driver Mutations ◽  
Clonal Hematopoiesis ◽  
Mutation Carriers ◽  
Single Cell Rna Sequencing

Rationale: Clonal hematopoiesis (CH) driven by mutations of DNA methyltransferase 3a (DNMT3A) is associated with increased incidence of cardiovascular disease and poor prognosis of patients with chronic heart failure (HF) and aortic stenosis. Although experimental studies suggest that DNMT3A CH-driver mutations may enhance inflammation, specific signatures of inflammatory cells in humans are missing. Objective: To define subsets of immune cells mediating inflammation in humans using single-cell RNA-sequencing. Methods and Results: Transcriptomic profiles of peripheral blood mononuclear cells were analysed in N=6 HF patients harboring DNMT3A CH-driver mutations and N=4 patients with HF and no DNMT3A mutations by single-cell RNA-sequencing. Monocytes of HF patients carrying DNMT3A mutations demonstrated a significantly increased expression of inflammatory genes compared to monocytes derived from HF patients without DNMT3A mutations. Among the specific up-regulated genes were the prototypic inflammatory interleukin (IL) IL1B, IL6, IL8, the inflammasome NLRP3, and the macrophage inflammatory proteins CCL3 and CCL4 as well as resistin, which augments monocyte-endothelial adhesion. Silencing of DNMT3A in monocytes induced a paracrine pro-inflammatory activation and increased adhesion to endothelial cells. Furthermore, the classical monocyte subset of DNMT3A mutation carriers showed increased expression of T-cell stimulating immunoglobulin superfamily members CD300LB, CD83, SIGLEC12, as well as the CD2 ligand and cell adhesion molecule CD58, all of which may be involved in monocyte-T cell interactions. DNMT3A mutation carriers were further characterized by increased expression of the T-cell alpha receptor constant chain and Th1, Th2, Th17, CD8+ effector, CD4+ memory and Treg specific signatures. Conclusions: This study demonstrates that circulating monocytes and T-cells of HF patients harboring CH-driver mutations in DNMT3A exhibit a highly inflamed transcriptome, which may contribute to the aggravation of chronic heart failure.

Single-cell RNA-sequencing reveals profound changes in circulating immune cells in patients with heart failure

2020 ◽  
Author(s):  
Wesley T Abplanalp ◽  
David John ◽  
Sebastian Cremer ◽  
Birgit Assmus ◽  
Lena Dorsheimer ◽  
...  
Keyword(s):  
Heart Failure ◽  
Flow Cytometry ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Healthy Subjects ◽  
Patients With Heart Failure ◽  
Single Cell Rna Sequencing ◽  
The Impact ◽  
Classical Monocytes

Abstract Aims Identification of signatures of immune cells at single-cell level may provide novel insights into changes of immune-related disorders. Therefore, we used single-cell RNA-sequencing to determine the impact of heart failure on circulating immune cells. Methods and results We demonstrate a significant change in monocyte to T-cell ratio in patients with heart failure, compared to healthy subjects, which were validated by flow cytometry analysis. Subclustering of monocytes and stratification of the clusters according to relative CD14 and FCGR3A (CD16) expression allowed annotation of classical, intermediate, and non-classical monocytes. Heart failure had a specific impact on the gene expression patterns in these subpopulations. Metabolically active genes such as FABP5 were highly enriched in classical monocytes of heart failure patients, whereas β-catenin expression was significantly higher in intermediate monocytes. The selective regulation of signatures in the monocyte subpopulations was validated by classical and multifactor dimensionality reduction flow cytometry analyses. Conclusion Together this study shows that circulating cells derived from patients with heart failure have altered phenotypes. These data provide a rich source for identification of signatures of immune cells in heart failure compared to healthy subjects. The observed increase in FABP5 and signatures of Wnt signalling may contribute to enhanced monocyte activation.

scholarly journals Single-cell profiling reveals the trajectories of natural killer cell differentiation in bone marrow and a stress signature induced by acute myeloid leukemia

2020 ◽  
Author(s):  
Adeline Crinier ◽  
Pierre-Yves Dumas ◽  
Bertrand Escalière ◽  
Christelle Piperoglou ◽  
Laurine Gil ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Acute Myeloid Leukemia ◽  
Nk Cells ◽  
Single Cell ◽  
Natural Killer ◽  
Rna Sequencing ◽  
Myeloid Leukemia ◽  
Nk Cell ◽  
Single Cell Rna Sequencing ◽  
Acute Myeloid

SummaryNatural killer (NK) cells are innate cytotoxic lymphoid cells (ILCs) involved in the killing of infected and tumor cells. Among human and mouse NK cells from the spleen and blood, we previously identified by single-cell RNA sequencing (scRNAseq) two similar major subsets, NK1 and NK2. Using the same technology, we report here the identification, by single-cell RNA sequencing (scRNAseq), of three NK cell subpopulations in human bone marrow. Pseudotime analysis identified a subset of resident CD56bright NK cells, NK0 cells, as the precursor of both circulating CD56dim NK1-like NK cells and CD56bright NK2-like NK cells in human bone marrow and spleen under physiological conditions. Transcriptomic profiles of bone marrow NK cells from patients with acute myeloid leukemia (AML) exhibited stress-induced repression of NK cell effector functions, highlighting the profound impact of this disease on NK cell heterogeneity. Bone marrow NK cells from AML patients exhibited reduced levels of CD160, but the CD160high group had a significantly higher survival rate.

scholarly journals Single-cell RNA sequencing shows the immunosuppressive landscape and tumor heterogeneity of HBV-associated hepatocellular carcinoma

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Daniel Wai-Hung Ho ◽  
Yu-Man Tsui ◽  
Lo-Kong Chan ◽  
Karen Man-Fong Sze ◽  
Xin Zhang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Single Cell ◽  
Tumor Cells ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Tumor Heterogeneity ◽  
Sequencing Analysis ◽  
T Cell Infiltration ◽  
Single Cell Rna Sequencing ◽  
Immune Oncology

AbstractInteraction between tumor cells and immune cells in the tumor microenvironment is important in cancer development. Immune cells interact with the tumor cells to shape this process. Here, we use single-cell RNA sequencing analysis to delineate the immune landscape and tumor heterogeneity in a cohort of patients with HBV-associated human hepatocellular carcinoma (HCC). We found that tumor-associated macrophages suppress tumor T cell infiltration and TIGIT-NECTIN2 interaction regulates the immunosuppressive environment. The cell state transition of immune cells towards a more immunosuppressive and exhaustive status exemplifies the overall cancer-promoting immunocellular landscape. Furthermore, the heterogeneity of global molecular profiles reveals co-existence of intra-tumoral and inter-tumoral heterogeneity, but is more apparent in the latter. This analysis of the immunosuppressive landscape and intercellular interactions provides mechanistic information for the design of efficacious immune-oncology treatments in hepatocellular carcinoma.

scholarly journals Unraveling the Heterogeneity and Ontogeny of Dendritic Cells Using Single-Cell RNA Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Binyao Chen ◽  
Lei Zhu ◽  
Shizhao Yang ◽  
Wenru Su
Keyword(s):  
Dendritic Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Adaptive Immunity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Future Trends ◽  
Innate And Adaptive Immunity ◽  
Sequencing Technologies ◽  
Single Cell Rna Sequencing

Dendritic cells (DCs) play essential roles in innate and adaptive immunity and show high heterogeneity and intricate ontogeny. Advances in high-throughput sequencing technologies, particularly single-cell RNA sequencing (scRNA-seq), have improved the understanding of DC subsets. In this review, we discuss in detail the remarkable perspectives in DC reclassification and ontogeny as revealed by scRNA-seq. Moreover, the heterogeneity and multifunction of DCs during diseases as determined by scRNA-seq are described. Finally, we provide insights into the challenges and future trends in scRNA-seq technologies and DC research.

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