Abstract 213: Single-Cell RNA Sequencing Reveals Pathways Dysregulation by a NFATc1 Mutation in Patient-Specific Cardiomyocytes Derived From Inducible Pluripotent Stem Cells

2019 ◽  
Vol 125 (Suppl_1) ◽  
Author(s):  
Natalia S Torres ◽  
Karissa Wang ◽  
Enrique Coca ◽  
Andrew Carey ◽  
Colin Maguire ◽  
...  
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Pluripotent Stem Cells ◽  
Patient Specific ◽  
Single Cell Rna Sequencing

scholarly journals Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations

2017 ◽  
Author(s):  
Quan H. Nguyen ◽  
Samuel W. Lukowski ◽  
Han Sheng Chiu ◽  
Anne Senabouth ◽  
Timothy J. C. Bruxner ◽  
...  
Keyword(s):  
Stem Cells ◽  
Induced Pluripotent Stem Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Pluripotent Stem Cells ◽  
Single Cells ◽  
State Transitions ◽  
Transcriptional Level ◽  
Single Cell Rna Sequencing ◽  
Induced Pluripotent

AbstractHeterogeneity of cell states represented in pluripotent cultures have not been described at the transcriptional level. Since gene expression is highly heterogeneous between cells, single-cell RNA sequencing can be used to identify how individual pluripotent cells function. Here, we present results from the analysis of single-cell RNA sequencing data from 18,787 individual WTC CRISPRi human induced pluripotent stem cells. We developed an unsupervised clustering method, and through this identified four subpopulations distinguishable on the basis of their pluripotent state including: a core pluripotent population (48.3%), proliferative (47.8%), early-primed for differentiation (2.8%) and late-primed for differentiation (1.1%). For each subpopulation we were able to identify the genes and pathways that define differences in pluripotent cell states. Our method identified four transcriptionally distinct predictor gene sets comprised of 165 unique genes that denote the specific pluripotency states; and using these sets, we developed a multigenic machine learning prediction method to accurately classify single cells into each of the subpopulations. Compared against a set of established pluripotency markers, our method increases prediction accuracy by 10%, specificity by 20%, and explains a substantially larger proportion of deviance (up to 3-fold) from the prediction model. Finally, we developed an innovative method to predict cells transitioning between subpopulations, and support our conclusions with results from two orthogonal pseudotime trajectory methods.

scholarly journals Canonical and early lineage-specific stem cell types identified in planarian SirNeoblasts

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kaimeng Niu ◽  
Hao Xu ◽  
Yuanyi Zhou Xiong ◽  
Yun Zhao ◽  
Chong Gao ◽  
...  
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Pluripotent Stem Cells ◽  
Expression Patterns ◽  
Cell Subpopulation ◽  
Functional Study ◽  
Sequencing Data ◽  
Single Cell Rna Sequencing

Abstract Background The pluripotent stem cells in planarians, a model for tissue and cellular regeneration, remain further identification. We recently developed a method to enrich piwi-1+ cells in Schmidtea mediterranea, by staining cells with SiR-DNA and Cell Tracker Green, named SirNeoblasts that permits their propagation and subsequent functional study in vivo. Since traditional enrichment for planarian neoblasts by Hoechst 33342 staining generates X1 cells, blocking the cell cycle and inducing cytotoxicity, this method by SiR-DNA and Cell Tracker Green represents a complementary technological advance for functional investigation of cell fate and regeneration. However, the similarities in heterogeneity of cell subtypes between SirNeoblasts and X1 remain unknown. Results In this work, we performed single cell RNA sequencing of SirNeoblasts for comparison with differential expression patterns in a publicly available X1 single cell RNA sequencing data. We found first that all of the lineage-specific progenitor cells in X1 were present in comparable proportions in SirNeoblasts. In addition, SirNeoblasts contain an early muscle progenitor that is unreported in X1. Analysis of new markers for putative pluripotent stem cells identified here, with subsequent sub-clustering analysis, revealed earlier lineages of epidermal, muscular, intestinal, and pharyngeal progenitors than have been observed in X1. Using the gcm as a marker, we also identified a cell subpopulation resided in previously identified tgs-1+ neoblasts. Knockdown of gcm impaired the neoblast repopulation, suggesting a function of gcm in neoblasts. Conclusions In summary, the use of SirNeoblasts will enable broad experimental advances in regeneration and cell fate specification, given the possibility for propagation and transplantation of recombinant and mutagenized pluripotent stem cells that are not previously afforded to this rapid and versatile model system.

scholarly journals Single-cell RNA sequencing of cultured human endometrial CD140b+CD146+ perivascular cells highlights the importance of in vivo microenvironment

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dandan Cao ◽  
Rachel W. S. Chan ◽  
Ernest H. Y. Ng ◽  
Kristina Gemzell-Danielsson ◽  
William S. B. Yeung
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Marker Gene ◽  
Cellular Heterogeneity ◽  
Stromal Fibroblast ◽  
Perivascular Cells ◽  
Endometrial Cells ◽  
Single Cell Rna Sequencing

Abstract Background Endometrial mesenchymal-like stromal/stem cells (eMSCs) have been proposed as adult stem cells contributing to endometrial regeneration. One set of perivascular markers (CD140b&CD146) has been widely used to enrich eMSCs. Although eMSCs are easily accessible for regenerative medicine and have long been studied, their cellular heterogeneity, relationship to primary counterpart, remains largely unclear. Methods In this study, we applied 10X genomics single-cell RNA sequencing (scRNA-seq) to cultured human CD140b+CD146+ endometrial perivascular cells (ePCs) from menstrual and secretory endometrium. We also analyzed publicly available scRNA-seq data of primary endometrium and performed transcriptome comparison between cultured ePCs and primary ePCs at single-cell level. Results Transcriptomic expression-based clustering revealed limited heterogeneity within cultured menstrual and secretory ePCs. A main subpopulation and a small stress-induced subpopulation were identified in secretory and menstrual ePCs. Cell identity analysis demonstrated the similar cellular composition in secretory and menstrual ePCs. Marker gene expression analysis showed that the main subpopulations identified from cultured secretory and menstrual ePCs simultaneously expressed genes marking mesenchymal stem cell (MSC), perivascular cell, smooth muscle cell, and stromal fibroblast. GO enrichment analysis revealed that genes upregulated in the main subpopulation enriched in actin filament organization, cellular division, etc., while genes upregulated in the small subpopulation enriched in extracellular matrix disassembly, stress response, etc. By comparing subpopulations of cultured ePCs to the publicly available primary endometrial cells, it was found that the main subpopulation identified from cultured ePCs was culture-unique which was unlike primary ePCs or primary endometrial stromal fibroblast cells. Conclusion In summary, these data for the first time provides a single-cell atlas of the cultured human CD140b+CD146+ ePCs. The identification of culture-unique relatively homogenous cell population of CD140b+CD146+ ePCs underscores the importance of in vivo microenvironment in maintaining cellular identity.

scholarly journals Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Amit Grover ◽  
Alejandra Sanjuan-Pla ◽  
Supat Thongjuea ◽  
Joana Carrelha ◽  
Alice Giustacchini ◽  
...  
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Haematopoietic Stem Cells ◽  
Single Cell Rna Sequencing

Novel Insights into the Stemness and Immune Privilege of Mesenchymal Stem Cells from Human Wharton Jelly by Single-Cell RNA Sequencing

2021 ◽  
Vol 28 ◽  
Author(s):  
Zikuan Leng ◽  
Longyu Li ◽  
Xiang Zhou ◽  
Guangyao Dong ◽  
Songfeng Chen ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Privilege ◽  
Single Cell Rna Sequencing

scholarly journals Mapping the biogenesis of forward programmed megakaryocytes from induced pluripotent stem cells

2021 ◽  
Author(s):  
Moyra Lawrence ◽  
Arash Shahsavari ◽  
Susanne Bornelöv ◽  
Thomas Moreau ◽  
Katarzyna Kania ◽  
...  
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Pluripotent Stem Cells ◽  
Surface Markers ◽  
Single Cell Rna Sequencing ◽  
Induced Pluripotent ◽  
Insight Into ◽  
Megakaryocyte Progenitors

SummaryPlatelet deficiency, known as thrombocytopenia, can cause haemorrhage and is treated with platelet transfusions. We developed a system for the production of platelet precursor cells, megakaryocytes, from pluripotent stem cells. These cultures can be maintained for >100 days, implying culture renewal by megakaryocyte progenitors (MKPs). However, it is unclear whether the MKP state in vitro mirrors the state in vivo, and MKPs cannot be purified using conventional surface markers. We performed single cell RNA sequencing throughout in vitro differentiation and mapped each state to its equivalent in vivo. This enabled the identification of 5 surface markers which reproducibly purify MKPs, allowing us an insight into their transcriptional and epigenetic profiles. Finally, we performed culture optimisation, increasing MKP production. Altogether, this study has mapped parallels between the MKP states in vivo and in vitro and allowed the purification of MKPs, accelerating the progress of in vitro-derived transfusion products towards the clinic.

Sign in / Sign up

Export Citation Format

Share Document