Single‐cell RNA‐sequencing atlas of bovine caudal intervertebral discs: Discovery of heterogeneous cell populations with distinct roles in homeostasis

2021 ◽  
Vol 35 (11) ◽  
Author(s):  
Christopher J. Panebianco ◽  
Arpit Dave ◽  
Daniel Charytonowicz ◽  
Robert Sebra ◽  
James C. Iatridis
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Intervertebral Discs ◽  
Cell Populations ◽  
Single Cell Rna Sequencing

scholarly journals Modeling cellular crosstalk and organotypic vasculature development with human iPSC-derived endothelial cells and cardiomyocytes

2020 ◽  
Author(s):  
Emmi Helle ◽  
Minna Ampuja ◽  
Alexandra Dainis ◽  
Laura Antola ◽  
Elina Temmes ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Shear Stress ◽  
Endothelial Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Tissue Growth ◽  
Cell Phenotype ◽  
Cell Populations ◽  
Pump System ◽  
Single Cell Rna Sequencing

AbstractRationaleCell-cell interactions are crucial for the development and function of the organs. Endothelial cells act as essential regulators of tissue growth and regeneration. In the heart, endothelial cells engage in delicate bidirectional communication with cardiomyocytes. The mechanisms and mediators of this crosstalk are still poorly known. Furthermore, endothelial cells in vivo are exposed to blood flow and their phenotype is greatly affected by shear stress.ObjectiveWe aimed to elucidate how cardiomyocytes regulate the development of organotypic phenotype in endothelial cells. In addition, the effects of flow-induced shear stress on endothelial cell phenotype were studied.Methods and resultsHuman induced pluripotent stem cell (hiPSC) -derived cardiomyocytes and endothelial cells were grown either as a monoculture or as a coculture. hiPS-endothelial cells were exposed to flow using the Ibidi-pump system. Single-cell RNA sequencing was performed to define cell populations and to uncover the effects on their transcriptomic phenotypes. The hiPS-cardiomyocyte differentiation resulted in two distinct populations; atrial and ventricular. Coculture had a more pronounced effect on hiPS-endothelial cells compared to hiPS-cardiomyocytes. Coculture increased hiPS-endothelial cell expression of transcripts related to vascular development and maturation, cardiac development, and the expression of cardiac endothelial cell -specific genes. Exposure to flow significantly reprogrammed the hiPS-endothelial cell transcriptome, and surprisingly, promoted the appearance of both venous and arterial clusters.ConclusionsSingle-cell RNA sequencing revealed distinct atrial and ventricular cell populations in hiPS-cardiomyocytes, and arterial and venous-like cell populations in flow exposed hiPS-endothelial cells. hiPS-endothelial cells acquired cardiac endothelial cell identity in coculture. Our study demonstrated that hiPS-cardiomoycytes and hiPS-endothelial cells readily adapt to coculture and flow in a consistent and relevant manner, indicating that the methods used represent improved physiological cell culturing conditions that potentially are more relevant in disease modelling. In addition, novel cardiomyocyte-endothelial cell crosstalk mediators were revealed.

scholarly journals Single-Cell RNA Sequencing in Human Retinal Degeneration Reveals Distinct Glial Cell Populations

Cells ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 438 ◽  
Author(s):  
Andrew P. Voigt ◽  
Elaine Binkley ◽  
Miles J. Flamme-Wiese ◽  
Shemin Zeng ◽  
Adam P. DeLuca ◽  
...  
Keyword(s):  
Single Cell ◽  
Retinal Degeneration ◽  
Rna Sequencing ◽  
Glial Cell ◽  
Glial Cells ◽  
Peripheral Retina ◽  
Cell Populations ◽  
Specific Gene ◽  
Autoimmune Retinopathy ◽  
Single Cell Rna Sequencing

Degenerative diseases affecting retinal photoreceptor cells have numerous etiologies and clinical presentations. We clinically and molecularly studied the retina of a 70-year-old patient with retinal degeneration attributed to autoimmune retinopathy. The patient was followed for 19 years for progressive peripheral visual field loss and pigmentary changes. Single-cell RNA sequencing was performed on foveal and peripheral retina from this patient and four control patients, and cell-specific gene expression differences were identified between healthy and degenerating retina. Distinct populations of glial cells, including astrocytes and Müller cells, were identified in the tissue from the retinal degeneration patient. The glial cell populations demonstrated an expression profile consistent with reactive gliosis. This report provides evidence that glial cells have a distinct transcriptome in the setting of human retinal degeneration and represents a complementary clinical and molecular investigation of a case of progressive retinal disease.

scholarly journals Single Cell RNA Sequencing of Rare Immune Cell Populations

2018 ◽  
Vol 9 ◽  
Author(s):  
Akira Nguyen ◽  
Weng Hua Khoo ◽  
Imogen Moran ◽  
Peter I. Croucher ◽  
Tri Giang Phan
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Cell Populations ◽  
Single Cell Rna Sequencing

scholarly journals COMP-16. COMPREHENSIVE TRANSCRIPTOMIC ANALYSIS OF SINGLE CELLS FROM RECURRENT AND PRIMARY GLIOBLASTOMA TO PREDICT CELL-TYPE SPECIFIC THERAPEUTICS

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi64-vi64
Author(s):  
Robert Suter ◽  
Vasileios Stathias ◽  
Anna Jermakowicz ◽  
Alexa Semonche ◽  
Michael Ivan ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Tumor Heterogeneity ◽  
Drug Response ◽  
Adult Brain ◽  
Cell Populations ◽  
Cell Type ◽  
Single Cell Rna Sequencing ◽  
Cell Type Specific ◽  
Recurrent Gbm

Abstract Glioblastoma (GBM) remains the most common adult brain tumor, with poor survival expectations, and no new therapeutic modalities approved in the last decade. Our laboratories have recently demonstrated that the integration of a transcriptional disease signature obtained from The Cancer Genome Atlas’ GBM dataset with transcriptional cell drug-response signatures in the LINCS L1000 dataset yields possible combinatorial therapeutics. Considering the extreme intra-tumor heterogeneity associated with the disease, we hypothesize that the utilization of single-cell RNA-sequencing (scRNA-seq) of patient tumors will further strengthen our predictive model by providing insight on the unique transcriptomes of the cellular niches present within these tumors, and into the transcriptional dynamics of these same cellular niches. By sequencing single-cell transcriptomes from recurrent GBM tumors resected from patients at the University of Miami, and integrating our datasets with previously published scRNA-seq data from primary GBM tumors, we are able to gain additional insight into the differences between these clinical distinctions. We have analyzed the differential expression of kinases both across and within distinct cell populations of primary and recurrent GBM tumors. This transcriptional map of kinase expression represents the heterogeneity of potential targets within individual tumors and between recurrent and primary GBM. Additionally, by generating disease signatures unique to each cellular population, and integrating these with transcriptional drug-response signatures from LINCS, we are able to predict compounds to target specific cell populations within GMB tumors. Additional computational techniques such as RNA velocity analysis and cell cycle scoring elucidate temporal insights to further prioritize these cell-type specific therapeutics, and reveal the intra-cellular dynamics present within these tumors. Collectively, our studies suggest that we have developed a novel omics pipeline based on the single cell RNA-sequencing of individual GBM cells that addresses intra-tumor heterogeneity, and may lead to novel therapeutic combinations for the treatment of this incurable disease.

scholarly journals Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma

Oncogene ◽  
2021 ◽  
Author(s):  
Philip Bischoff ◽  
Alexandra Trinks ◽  
Benedikt Obermayer ◽  
Jan Patrick Pett ◽  
Jennifer Wiederspahn ◽  
...  
Keyword(s):  
T Cells ◽  
Dendritic Cells ◽  
Tumor Microenvironment ◽  
Lung Adenocarcinoma ◽  
Single Cell ◽  
Rna Sequencing ◽  
Histological Grade ◽  
Cell Populations ◽  
Marker Genes ◽  
Single Cell Rna Sequencing

AbstractRecent developments in immuno-oncology demonstrate that not only cancer cells, but also the tumor microenvironment can guide precision medicine. A comprehensive and in-depth characterization of the tumor microenvironment is challenging since its cell populations are diverse and can be important even if scarce. To identify clinically relevant microenvironmental and cancer features, we applied single-cell RNA sequencing to ten human lung adenocarcinomas and ten normal control tissues. Our analyses revealed heterogeneous carcinoma cell transcriptomes reflecting histological grade and oncogenic pathway activities, and two distinct microenvironmental patterns. The immune-activated CP²E microenvironment was composed of cancer-associated myofibroblasts, proinflammatory monocyte-derived macrophages, plasmacytoid dendritic cells and exhausted CD8+ T cells, and was prognostically unfavorable. In contrast, the inert N³MC microenvironment was characterized by normal-like myofibroblasts, non-inflammatory monocyte-derived macrophages, NK cells, myeloid dendritic cells and conventional T cells, and was associated with a favorable prognosis. Microenvironmental marker genes and signatures identified in single-cell profiles had progonostic value in bulk tumor profiles. In summary, single-cell RNA profiling of lung adenocarcinoma provides additional prognostic information based on the microenvironment, and may help to predict therapy response and to reveal possible target cell populations for future therapeutic approaches.

scholarly journals Chicken peripheral blood lymphocyte response to ALV-J infection assessed by single-cell RNA sequencing

2021 ◽  
Author(s):  
Manman Dai ◽  
Min Feng ◽  
Ziwei Li ◽  
Weisan Chen ◽  
Ming Liao
Keyword(s):  
T Cells ◽  
T Cell ◽  
Viral Infection ◽  
Single Cell ◽  
Rna Sequencing ◽  
Peripheral Blood ◽  
Cell Populations ◽  
Control Group ◽  
Marker Genes ◽  
Single Cell Rna Sequencing

ABSTRACTChicken peripheral blood lymphocytes (PBLs) exhibit wide-ranging cell types, but current understanding of their subclasses, immune cell classification, and function is limited and incomplete. Previously, we found that viremia caused by avian leukosis virus subgroup J (ALV‐J) was eliminated by 21 days post infection (DPI), accompanied by increased CD8+ T cell ratio in PBLs and low antibody levels. Here we performed single-cell RNA sequencing (scRNA-seq) of PBLs in ALV-J infected and control chickens at 21 DPI to determine chicken PBL subsets and their specific molecular and cellular characteristics, before and after viral infection. Eight cell clusters and their potential marker genes were identified in chicken PBLs. T cell populations (clusters 6 and 7) had the strongest response to ALV-J infection at 21 DPI, based on detection of the largest number of differentially expressed genes (DEGs). T cell populations of clusters 6 and 7 could be further divided into four subsets: activated CD4+ T cells (cluster A0), Th1-like cells (cluster A2), Th2-like cells (cluster A1), and cytotoxic CD8+ T cells. Hallmark genes for each T cell subset response to viral infection were initially identified. Furthermore, pseudotime analysis results suggested that chicken CD4+ T cells could potentially differentiate into Th1-like and Th2-like cells. Moreover, ALV-J infection probably induced CD4+ T cell differentiation into Th1-like cells in which the most immune related DEGs were detected. With respect to the control group, ALV-J infection also had an obvious impact on PBL cell composition. B cells showed inconspicuous response and their numbers decreased in PBLs of the ALV-J infected chickens at 21 DPI. Percentages of cytotoxic Th1-like cells and CD8+ T cells were increased in the T cell population of PBLs from ALV-J infected chicken, which were potentially key mitigating factors against ALV-J infection. More importantly, our results provided a rich resource of gene expression profiles of chicken PBL subsets for a systems-level understanding of their function in homeostatic condition as well as in response to viral infection.

scholarly journals Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes

2020 ◽  
Vol 217 (6) ◽  
Author(s):  
Pavel N. Zakharov ◽  
Hao Hu ◽  
Xiaoxiao Wan ◽  
Emil R. Unanue
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Autoimmune Diabetes ◽  
Diabetic Mouse ◽  
Cell Populations ◽  
Target Organs ◽  
Distinct Cell ◽  
Single Cell Rna Sequencing ◽  
Macrophage Subpopulations

Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed an unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the nonobese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets, accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal proinflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions.

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.

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