scholarly journals An atlas of infiltrated B-lymphocytes in breast cancer revealed by paired single-cell RNA-sequencing and antigen receptor profiling

2019 ◽  
Author(s):  
Qingtao Hu ◽  
Yu Hong ◽  
Pan Qi ◽  
Guangqing Lu ◽  
Xueying Mai ◽  
...  
Keyword(s):  
Breast Cancer ◽  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
B Lymphocytes ◽  
Immune Cells ◽  
Breast Cancer Subtype ◽  
Antigen Receptor ◽  
Tumor Control ◽  
Single Cell Rna Sequencing

AbstractWhile it has been well-recognized that T-cell mediated adaptive cellular immunity plays important roles in cancer immune response and tumor control, the roles of B lymphocytes in tumor development and therapy have only been proposed until recently, and are still mostly controversial. To gain mechanistic insights into the origin and dynamics of tumor infiltrated immune cells, especially B lymphocytes, we combine single-cell RNA-sequencing and antigen receptor lineage analysis to characterize a large number of triple-negative breast cancer (TNBC) infiltrated immune cells and present a comprehensive atlas of infiltrated B-lymphocytes in TNBC, the most aggressive breast cancer subtype. We demonstrate that TNBC infiltrated B cells showed more mature and memory B cell characteristics, as well as high clonality and extensive IgH class switching recombination and somatic hypermutations. The B cell signatures based on single-cell RNA-seq results are significantly associated with improved survival for TNBC patients and provide better prognostication than classic single B cell markers (CD19 or CD20). Further dissection of the mechanisms regulating the functions and dynamic distribution of tumor infiltrated B cell populations will provide new clues for tumor immunotherapy.

scholarly journals Atlas of breast cancer infiltrated B-lymphocytes revealed by paired single-cell RNA-sequencing and antigen receptor profiling

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qingtao Hu ◽  
Yu Hong ◽  
Pan Qi ◽  
Guangqing Lu ◽  
Xueying Mai ◽  
...  
Keyword(s):  
Breast Cancer ◽  
B Cells ◽  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
B Lymphocytes ◽  
Immune Cells ◽  
Antigen Receptor ◽  
Cell Populations ◽  
Single Cell Rna Sequencing

AbstractTo gain mechanistic insights into the functions and developmental dynamics of tumor-infiltrated immune cells, especially B-lymphocytes, here we combine single-cell RNA-sequencing and antigen receptor lineage analysis to characterize a large number of triple-negative breast cancer infiltrated immune cells and report a comprehensive atlas of tumor-infiltrated B-lymphocytes. The single-cell transcriptional profiles reveal significant heterogeneity in tumor-infiltrated B-cell subgroups. The single-cell antigen receptor analyses demonstrate that compared with those in peripheral blood, tumor-infiltrated B-cells have more mature and memory B-cell characteristics, higher clonality, more class switching recombination and somatic hypermutations. Combined analyses suggest local differentiation of infiltrated memory B-cells within breast tumors. The B-cell signatures based on the single-cell RNA-sequencing results are significantly associated with improved survival in breast tumor patients. Functional analyses of tumor-infiltrated B-cell populations suggest that mechanistically, B-cell subgroups may contribute to immunosurveillance through various pathways. Further dissection of tumor-infiltrated B-cell populations will provide valuable clues for tumor immunotherapy.

scholarly journals BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing

2017 ◽  
Author(s):  
Ida Lindeman ◽  
Guy Emerton ◽  
Ludvig M. Sollid ◽  
Sarah A. Teichmann ◽  
Michael J.T. Stubbington
Keyword(s):  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
B Lymphocytes ◽  
Antigen Receptor ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Supplementary Note ◽  
Single Cell Rna Sequencing ◽  
Repertoire Sequencing

Reconstruction of antigen receptor sequences from single-cell RNA-sequencing (scRNA-seq) data allows the linking of antigen receptor usage to the full transcriptomic identity of individual B lymphocytes, without having to perform additional targeted repertoire sequencing (Rep-seq). Here we report BraCeR (freely available at https://github.com/teichlab/bracer/), an extension of TraCeR [1], for reconstruction of paired full-length B-cell receptor sequences and inference of clonality from scRNA-seq data (Supplementary Note 1).

Abstract 160: Identification of the carcinoma and immune cells in the breast cancer by single-cell RNA sequencing

2016 ◽  
Author(s):  
Woosung Chung ◽  
Hye Hyeon Eum ◽  
Kyu-Tae Kim ◽  
Kyung-Min Lee ◽  
Arum Jo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Single Cell Rna Sequencing

scholarly journals Single-Cell RNA Sequencing Reveals B Cells Are Important Regulators in Fracture Healing

2021 ◽  
Vol 12 ◽  
Author(s):  
Hao Zhang ◽  
Renkai Wang ◽  
Guangchao Wang ◽  
Bo Zhang ◽  
Chao Wang ◽  
...  
Keyword(s):  
Bone Marrow ◽  
B Cells ◽  
Fracture Healing ◽  
B Cell ◽  
Bone Regeneration ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cells ◽  
Bone Homeostasis ◽  
Single Cell Rna Sequencing

The bone marrow microenvironment is composed primarily of immune and stromal cells that play important roles in fracture healing. Although immune cells have been identified in mouse bone marrow, variations in their numbers and type during the fracture healing process remain poorly defined. In this study, single-cell RNA sequencing was used to identify immune cells in fracture tissues, including neutrophils, monocytes, T cells, B cells, and plasma cells. The number of B cells decreased significantly in the early stage of fracture healing. Furthermore, B cells in mice fracture models decreased significantly during the epiphyseal phase and then gradually returned to normal during the epiphyseal transformation phase of fracture healing. The B-cell pattern was opposite to that of bone formation and resorption activities. Notably, B-cell–derived exosomes inhibited bone homeostasis in fracture healing. In humans, a decrease in the number of B cells during the epiphyseal phase stimulated fracture healing. Then, as the numbers of osteoblasts increased during the callus reconstruction stage, the number of B cells gradually recovered, which reduced additional bone regeneration. Thus, B cells are key regulators of fracture healing and inhibit excessive bone regeneration by producing multiple osteoblast inhibitors.

scholarly journals Single-cell RNA-sequencing reveals distinct patterns of cell state heterogeneity in mouse models of breast cancer

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Syn Kok Yeo ◽  
Xiaoting Zhu ◽  
Takako Okamoto ◽  
Mingang Hao ◽  
Cailian Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Single Cell ◽  
Rna Sequencing ◽  
Breast Cancer Subtype ◽  
Mammary Epithelial ◽  
Cancer Subtypes ◽  
Specific Tumor ◽  
Cancer Subtype ◽  
Single Cell Rna Sequencing ◽  
Distinct Lineage

Breast cancer stem cells (BCSCs) contribute to intra-tumoral heterogeneity and therapeutic resistance. However, the binary concept of universal BCSCs co-existing with bulk tumor cells is over-simplified. Through single-cell RNA-sequencing, we found that Neu, PyMT and BRCA1-null mammary tumors each corresponded to a spectrum of minimally overlapping cell differentiation states without a universal BCSC population. Instead, our analyses revealed that these tumors contained distinct lineage-specific tumor propagating cells (TPCs) and this is reflective of the self-sustaining capabilities of lineage-specific stem/progenitor cells in the mammary epithelial hierarchy. By understanding the respective tumor hierarchies, we were able to identify CD14 as a TPC marker in the Neu tumor. Additionally, single-cell breast cancer subtype stratification revealed the co-existence of multiple breast cancer subtypes within tumors. Collectively, our findings emphasize the need to account for lineage-specific TPCs and the hierarchical composition within breast tumors, as these heterogenous sub-populations can have differential therapeutic susceptibilities.

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.

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