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

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 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.

Integrative single cell RNA-sequencing descrambles a substantial divergence of adaptive immune cell identities and transcriptional programs in mouse and human atherosclerosis

2021 ◽  
Vol 42 (Supplement_1) ◽  
Author(s):  
H Horstmann ◽  
N Anto Michel ◽  
X S Sheng ◽  
S Hansen ◽  
A Lindau ◽  
...  
Keyword(s):  
T Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Immune Cell ◽  
Atherosclerotic Plaques ◽  
Cell Repertoire ◽  
Single Cell Rna Sequencing ◽  
Human Atherosclerosis ◽  
Human Immune

Abstract Aims The distinct function of immune cells in human atherosclerosis has been mostly defined by preclinical mouse studies. Contrastingly, the immune cell composition of human atherosclerotic plaques and their contribution to disease progression is only poorly understood. It remains uncertain whether genetic animal models allow for valuable translational approaches. Methods and results We performed single cell RNA-sequencing (scRNAseq) to define the immune cell landscape in human carotid atherosclerotic plaques. The human immune cell repertoire was dominated by T cells with a considerable inter-patient variability and an unexpected heterogeneity. We performed bioinformatical integration with 7 mouse data sets and discovered a total of 38 cellular identities, of which some were not conserved between species and exclusively found in mice or humans. Locations, frequencies, and transcriptional programs of immune cells in preclinical mouse models did not resemble the immune cell landscape in human atherosclerosis. In contrast to mice, human plaques were not myeloid- and B cell-dominated and instead contained several T cell phenotypes with hallmarks of T cell memory, dysregulation, exhaustion, and activation. Human immune cells were predominantly enriched for transcriptional programs of hypoxia, glucose, and autoimmunity. In a validation cohort of 43 patients activated immune cell subsets defined by multi-colour flow cytometry associated with cerebral ischemia and coronary artery disease. Conclusion Here, we uncover yet undefined immune cell types associating with clinical disease. This leukocyte atlas of human atherosclerosis builds the conceptual basis for subsequent identification of cellular targets for clinical immunomodulatory therapies and risk prediction. FUNDunding Acknowledgement Type of funding sources: Public grant(s) – National budget only. Main funding source(s): ERC Starting Grant

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

scholarly journals Single-cell RNA sequencing analysis of SARS-CoV-2 conventional and moonlighting receptors in human organoids

2020 ◽  
Author(s):  
Rajasekaran Mahalingam ◽  
Prakash Dharmalingam ◽  
Abirami Santhanam ◽  
Gangarao Davuluri ◽  
Harry Karmouty Quintana ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Sequencing Analysis ◽  
Single Cell Rna Sequencing

scholarly journals Single-Cell RNA Sequencing Analysis of the Immunometabolic Rewiring and Immunopathogenesis of Coronavirus Disease 2019

2021 ◽  
Vol 12 ◽  
Author(s):  
Furong Qi ◽  
Wenbo Zhang ◽  
Jialu Huang ◽  
Lili Fu ◽  
Jinfang Zhao
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Mononuclear Cells ◽  
Plasma Cells ◽  
Severe Disease ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Metabolic Remodeling ◽  
Single Cell Rna Sequencing ◽  
Antibody Secretion

Although immune dysfunction is a key feature of coronavirus disease 2019 (COVID-19), the metabolism-related mechanisms remain elusive. Here, by reanalyzing single-cell RNA sequencing data, we delineated metabolic remodeling in peripheral blood mononuclear cells (PBMCs) to elucidate the metabolic mechanisms that may lead to the progression of severe COVID-19. After scoring the metabolism-related biological processes and signaling pathways, we found that mono-CD14+ cells expressed higher levels of glycolysis-related genes (PKM, LDHA and PKM) and PPP-related genes (PGD and TKT) in severe patients than in mild patients. These genes may contribute to the hyperinflammation in mono-CD14+ cells of patients with severe COVID-19. The mono-CD16+ cell population in COVID-19 patients showed reduced transcription levels of genes related to lysine degradation (NSD1, KMT2E, and SETD2) and elevated transcription levels of genes involved in OXPHOS (ATP6V1B2, ATP5A1, ATP5E, and ATP5B), which may inhibit M2-like polarization. Plasma cells also expressed higher levels of the OXPHOS gene ATP13A3 in COVID-19 patients, which was positively associated with antibody secretion and survival of PCs. Moreover, enhanced glycolysis or OXPHOS was positively associated with the differentiation of memory B cells into plasmablasts or plasma cells. This study comprehensively investigated the metabolic features of peripheral immune cells and revealed that metabolic changes exacerbated inflammation in monocytes and promoted antibody secretion and cell survival in PCs in COVID-19 patients, especially those with severe disease.

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