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 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 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 ILDR1 Is a Prognostic Biomarker and Associated With Immune Infiltration in Gastric Cancer

2021 ◽  
Author(s):  
Yanling Ma ◽  
WenBo Qi ◽  
BaoHong Gu ◽  
XueMei Li ◽  
ZhenYu Yin ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
T Cells ◽  
Dendritic Cells ◽  
Cancer Patients ◽  
Cd8 T Cells ◽  
Immune Cells ◽  
Copy Number ◽  
Sequencing Data ◽  
Number Variation ◽  
Gastric Cancer Patients

Abstract Objective: To investigate the association between ILDR1 and prognosis and immune infiltration in gastric cancer. Methods: We analyzed the RNA sequencing data of 9736 tumor tissues and 8587 normal tissues in the TCGA and GTEx databases through the GEPIA2 platform. The expression of ILDR1 in gastric cancer and normal gastric mucosa tissues with GEPIA and TIMER. Clinical subgroup analysis was made through Kaplan-Meier analysis. Analyzed the correlation between ILDR1 and VEGFA expression in gastric cancer, through the gene sequencing data of gastric cancer in TCGA. Explored the relationship between ILDR1 methylation and the prognosis of gastric cancer patients through the MethSurv database. The correlation between ILDR1 and immune cells and the correlation of copy number variation were explored through the TIMER database. Results: ILDR1-high GC patients had a lower PFS and OS. High ILDR1 expression was significantly correlated with tumor grade. There was a negative correlation between the ILDR1 expression and the abundances of CD8+ T, Macrophages and DC and etc. The methylation level of ILDR1 is associated with a good prognosis of gastric cancer. ILDR1 copy number variation was correlated with immune cells, IDLR1 arm-loss was associated with the infiltration of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells, and arm-duplication was associated with the infiltration of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells. Conclusion: The increased expression of ILDR1 is associated with poor prognosis in patients with gastric cancer. ILDR1 can be used as a novel predictive biomarker to provide a new therapeutic target for gastric cancer patients.

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 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.

scholarly journals Prognostic Autophagy-Related Model Revealed by Integrating Single-Cell RNA Sequencing Data and Bulk Gene Profiles in Gastric Cancer

2022 ◽  
Vol 9 ◽  
Author(s):  
Tianying Tong ◽  
Jie Zhang ◽  
Xiaoqiang Zhu ◽  
Pingping Hui ◽  
Zhimin Wang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
High Risk ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Checkpoint ◽  
Risk Model ◽  
Risk Group ◽  
High Risk Group ◽  
Related Model ◽  
Single Cell Rna Sequencing

Autophagy has been associated with tumor progression, prognosis, and treatment response. However, an autophagy-related model and their clinical significance have not yet been fully elucidated. In the present study, through the integrative analysis of bulk RNA sequencing and single-cell RNA sequencing, an autophagy-related risk model was identified. The model was capable of distinguishing the worse prognosis of patients with gastric cancer (GC), which was validated in TCGA and two independent Gene Expression Omnibus cohorts utilizing the survival analysis, and was also independent of other clinical covariates evaluated by multivariable Cox regression. The clinical value of this model was further assessed using a receiver operating characteristic (ROC) and nomogram analysis. Investigation of single-cell RNA sequencing uncovered that this model might act as an indicator of the dysfunctional characteristics of T cells in the high-risk group. Moreover, the high-risk group exhibited the lower expression of immune checkpoint markers (PDCD1 and CTLA4) than the low-risk group, which indicated the potential predictive power to the current immunotherapy response in patients with GC. In conclusion, this autophagy-associated risk model may be a useful tool for prognostic evaluation and will facilitate the potential application of this model as an indicator of the predictive immune checkpoint biomarkers.

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.

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