scholarly journals Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs

2015 ◽  
Author(s):  
Courtney L Kagan ◽  
Nicholas E Banovich ◽  
Bryan J Pavlovic ◽  
Kristen Patterson ◽  
Irene Gallego Romero ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Pluripotent Stem Cells ◽  
Paradigm Shift ◽  
Human Genetics ◽  
Cell Type ◽  
Pluripotent Cells ◽  
Somatic Tissues ◽  
Main Driver ◽  
Induced Pluripotent ◽  
Gene Expression Levels

The advent of induced pluripotent stem cells (iPSCs) revolutionized Human Genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues. This technology can have immense implications for regenerative medicine, but iPSCs also represent a paradigm shift in the study of complex human phenotypes, including gene regulation and disease. Yet, an unresolved caveat of the iPSC model system is the extent to which reprogrammed iPSCs retain residual phenotypes from their precursor somatic cells. To directly address this issue, we used an effective study design to compare regulatory phenotypes between iPSCs derived from two types of commonly used somatic precursor cells. We show that the cell type of origin only minimally affects gene expression levels and DNA methylation in iPSCs. Instead, genetic variation is the main driver of regulatory differences between iPSCs of different donors.

scholarly journals Discovery and characterization of variance QTLs in human induced pluripotent stem cells

2018 ◽  
Author(s):  
Abhishek K. Sarkar ◽  
Po-Yuan Tung ◽  
John D. Blischak ◽  
Jonathan E. Burnett ◽  
Yang I. Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Genetic Variation ◽  
Single Cell ◽  
Pluripotent Stem Cells ◽  
Human Tissues ◽  
Rna Seq ◽  
Induced Pluripotent ◽  
Expression Variance ◽  
Gene Expression Levels

AbstractQuantification of gene expression levels at the single cell level has revealed that gene expression can vary substantially even across a population of homogeneous cells. However, it is currently unclear what genomic features control variation in gene expression levels, and whether common genetic variants may impact gene expression variation. Here, we take a genome-wide approach to identify expression variance quantitative trait loci (vQTLs). To this end, we generated single cell RNA-seq (scRNA-seq) data from induced pluripotent stem cells (iPSCs) derived from 53 Yoruba individuals. We collected data for a median of 95 cells per individual and a total of 5,447 single cells, and identified 241 mean expression QTLs (eQTLs) at 10% FDR, of which 82% replicate in bulk RNA-seq data from the same individuals. We further identified 14 vQTLs at 10% FDR, but demonstrate that these can also be explained as effects on mean expression. Our study suggests that dispersion QTLs (dQTLs) which could alter the variance of expression independently of the mean can have larger fold changes, but explain less phenotypic variance than eQTLs. We estimate 424 individuals as a lower bound to achieve 80% power to detect the strongest dQTLs in iPSCs. These results will guide the design of future studies on understanding the genetic control of gene expression variance.Author summaryCommon genetic variation can alter the level of average gene expression in human tissues, and through changes in gene expression have downstream consequences on cell function, human development, and human disease. However, human tissues are composed of many cells, each with its own level of gene expression. With advances in single cell sequencing technologies, we can now go beyond simply measuring the average level of gene expression in a tissue sample and directly measure cell-to-cell variance in gene expression. We hypothesized that genetic variation could also alter gene expression variance, potentially revealing new insights into human development and disease. To test this hypothesis, we used single cell RNA sequencing to directly measure gene expression variance in multiple individuals, and then associated the gene expression variance with genetic variation in those same individuals. Our results suggest that effects on gene expression variance are smaller than effects on mean expression, relative to how much the phenotypes vary between individuals, and will require much larger studies than previously thought to detect.

scholarly journals Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Drew Neavin ◽  
Quan Nguyen ◽  
Maciej S. Daniszewski ◽  
Helena H. Liang ◽  
Han Sheng Chiu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Population Genetics ◽  
Genetic Variation ◽  
Single Cell ◽  
Pluripotent Stem Cells ◽  
Individual Cell ◽  
Cell Type ◽  
Cell Type Specific ◽  
Induced Pluripotent

Abstract Background The discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) has provided a foundation for in vitro human disease modelling, drug development and population genetics studies. Gene expression plays a critical role in complex disease risk and therapeutic response. However, while the genetic background of reprogrammed cell lines has been shown to strongly influence gene expression, the effect has not been evaluated at the level of individual cells which would provide significant resolution. By integrating single cell RNA-sequencing (scRNA-seq) and population genetics, we apply a framework in which to evaluate cell type-specific effects of genetic variation on gene expression. Results Here, we perform scRNA-seq on 64,018 fibroblasts from 79 donors and map expression quantitative trait loci (eQTLs) at the level of individual cell types. We demonstrate that the majority of eQTLs detected in fibroblasts are specific to an individual cell subtype. To address if the allelic effects on gene expression are maintained following cell reprogramming, we generate scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type-specific eQTLs in iPSCs and show that the eQTLs in fibroblasts almost entirely disappear during reprogramming. Conclusions This work provides an atlas of how genetic variation influences gene expression across cell subtypes and provides evidence for patterns of genetic architecture that lead to cell type-specific eQTL effects.

scholarly journals Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells

2020 ◽  
Author(s):  
Drew Neavin ◽  
Quan Nguyen ◽  
Maciej S. Daniszewski ◽  
Helena H. Liang ◽  
Han Sheng Chiu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Single Cell ◽  
Pluripotent Stem Cells ◽  
Cell Types ◽  
Cell Type ◽  
Single Cell Rna Sequencing ◽  
Cell Type Specific ◽  
Induced Pluripotent

AbstractThe discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) - cells that can be differentiated into any cell type of the three germ layers - has provided a foundation for in vitro human disease modelling1,2, drug development1,2, and population genetics studies3,4. In the majority of instances, the expression levels of genes, plays a critical role in contributing to disease risk, or the ability to identify therapeutic targets. However, while the effect of the genetic background of cell lines has been shown to strongly influence gene expression, the effect has not been evaluated at the level of individual cells. Differences in the effect of genetic variation on the gene expression of different cell-types, would provide significant resolution for in vitro research using preprogramed cells. By bringing together single cell RNA sequencing15–21 and population genetics, we now have a framework in which to evaluate the cell-types specific effects of genetic variation on gene expression. Here, we performed single cell RNA-sequencing on 64,018 fibroblasts from 79 donors and we mapped expression quantitative trait loci (eQTL) at the level of individual cell types. We demonstrate that the large majority of eQTL detected in fibroblasts are specific to an individual sub-type of cells. To address if the allelic effects on gene expression are dynamic across cell reprogramming, we generated scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type specific eQTL in iPSCs, and show that that the eQTL in fibroblasts are almost entirely disappear during reprogramming. This work provides an atlas of how genetic variation influences gene expression across cell subtypes, and provided evidence for patterns of genetic architecture that lead to cell-types specific eQTL effects.

scholarly journals Induced pluripotent stem cells are Japanese brand sources for therapeutic cells to pretrial clinical research

2020 ◽  
Vol 7 (1) ◽  
pp. 296-303
Author(s):  
Rupendra Shrestha
Keyword(s):  
Pluripotent Stem Cells ◽  
Clinical Studies ◽  
Immune Cell ◽  
Government Support ◽  
Cardiac Cell ◽  
Pluripotent Cells ◽  
Cell Lineages ◽  
Research Institution ◽  
Potential Benefits ◽  
Induced Pluripotent

iPSCs are promising and have potential benefits for medical use, understanding human organogenesis, and cell therapy for advanced diseases. iPSCs are derived pluripotent cells which can further differentiate into functional human cell-lineages, such as neuronal, epithelial cells, cardiac cell, immune cell, and blood cells, etc. Thirteen years on, the discovery of iPSC has revolutionized the field of regenerative medicine, and also the number of clinical studies using iPSC has been growing rapidly worldwide. However, Japan is leading the race of iPSC-based studies and clinical trials due to government support. The Japanese government implemented the world’s fastest approval system and set to host first pretrial clinical studies using iPSC derived therapeutic products. Also, multinational companies of Japan are investing enormously in iPSC-based research for mobilization of iPSC-derived regenerative products to the research institution globally. This review presents an overview of iPSCs, potential benefits, commercialization of iPSC, iPSC-based pretrial clinical studies, and iPSC biobanking in Japan.

GENERATION OF RABBIT PLURIPOTENT STEM CELL LINES

2012 ◽  
Vol 24 (1) ◽  
pp. 286
Author(s):  
A. Dinnyes ◽  
M. K. Pirity ◽  
E. Gocza ◽  
P. Osteil ◽  
N. Daniel ◽  
...  
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Pluripotent Stem Cells ◽  
Pluripotent Stem Cell ◽  
Pluripotent Cells ◽  
Domestic Species ◽  
Isolation And Characterization ◽  
Induced Pluripotent ◽  
Pluripotency Genes

Pluripotent stem cells have the capacity to divide indefinitely and to differentiate to all the somatic tissues. They can be genetically manipulated in vitro by knocking in and out genes, therefore they serve as an excellent tool for gene-function studies and for the generation of models for human diseases. Since 1981, when the first mouse embryonic stem cell (ESC) line was generated, several attempts have been made to generate pluripotent stem cells from other species as it would help us to understand the differences and similarities of signaling pathways involved in pluripotency and differentiation, and would reveal whether the fundamental mechanism controlling self-renewal of pluripotent cells is conserved among different species. This review gives an overlook of embryonic and induced pluripotent stem cell (iPSCs) research in the rabbit which is one of the most relevant non-rodent species for animal models. To date, several lines of putative ESCs and iPSCs have been described in the rabbit. All expressed stem cell-associated markers and exhibited longevity and pluripotency in vitro, but none have been proven to exhibit full pluripotency in vivo. Moreover, similarly to several domestic species, markers used to characterize the putative ESCs are not fully adequate because studies in domestic species have revealed that they are not specific to the pluripotent inner cell mass. Future validation of rabbit pluripotent stem cells would benefit greatly from a reliable panel of molecular markers specific to pluripotent cells of the developing rabbit embryo. The status of isolation and characterization of the putative pluripotency genes in rabbit will be discussed. Using rabbit specific pluripotency genes we might be able to reprogram somatic cells and generate induced pluripotent stem cells more efficiently thus overcome some of the challenges towards harnessing the potential of this technology. This study was financed by EU FP7 (PartnErS, PIAP-GA-2008-218205; InduHeart, PEOPLE-IRG-2008-234390; InduVir, PEOPLE-IRG-2009-245808; RabPstem, PERG07-GA-2010-268422; PluriSys, HEALTH-2007-B-223485; AniStem, PIAP-GA-2011-286264), NKTH-OTKA-EU-7KP HUMAN-MB08-C-80-205; Plurabbit, OMFB-00130-00131/2010 ANR-NKTH/09-GENM-010-01.

Red blood cell generation from human induced pluripotent stem cells of different donor cell type origin

2013 ◽  
Vol 41 (8) ◽  
pp. S27
Author(s):  
Isabel Dorn ◽  
Katharina Klich ◽  
Martina Radstaak ◽  
Katherina Psathaki ◽  
Marcos Arauzo-Bravo ◽  
...  
Keyword(s):  
Stem Cells ◽  
Blood Cell ◽  
Induced Pluripotent Stem Cells ◽  
Red Blood Cell ◽  
Pluripotent Stem Cells ◽  
Donor Cell ◽  
Cell Generation ◽  
Cell Type ◽  
Induced Pluripotent ◽  
Donor Cell Type

scholarly journals Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell types

2017 ◽  
Author(s):  
Jingqi QX Gong ◽  
Eric A Sobie
Keyword(s):  
Pluripotent Stem Cells ◽  
Cardiac Electrophysiology ◽  
Cell Types ◽  
Population Based ◽  
Experimental Models ◽  
Mechanistic Modeling ◽  
Type Model ◽  
Cell Type ◽  
Drug Responses ◽  
Induced Pluripotent

ABSTRACTQuantitative mismatches between human physiology and experimental models can present serious limitations for the development of effective therapeutics. We addressed this issue, in the context of cardiac electrophysiology, through mechanistic mathematical modeling combined with statistical analyses. Physiological metrics were simulated in heterogeneous populations describing cardiac myocytes from adult ventricles and those derived from induced pluripotent stem cells (iPSC-CMs). These simulated measures were used to construct a cross-cell type regression model that predicts adult myocyte drug responses from iPSC-CM behaviors. We found that quantitatively accurate predictions of responses to selective or non-selective drugs could be generated based on iPSC-CM responses and that the method can be extended to predict drug responses in diseased as well as healthy cells. This cross-cell type model can be of great value in drug development, and the approach, which can be applied to other fields, represents an important strategy for overcoming experimental model limitations.

scholarly journals 188 MicroRNA characterization in equine induced pluripotent stem cells

2019 ◽  
Vol 31 (1) ◽  
pp. 218
Author(s):  
L. N. Moro ◽  
G. Amin ◽  
V. Furmento ◽  
A. Waisman ◽  
G. Neiman ◽  
...  
Keyword(s):  
Stem Cells ◽  
Induced Pluripotent Stem Cells ◽  
Pluripotent Stem Cells ◽  
Seed Region ◽  
Seed Sequence ◽  
Rt Pcr ◽  
Pluripotent Cells ◽  
Mesenchymal Transition ◽  
Mrna Targets ◽  
Induced Pluripotent

Cell reprogramming has been well described in mouse and human cells. The expression of specific microRNAs has demonstrated to be essential for pluripotent maintenance and cell differentiation, but not much information is available in domestic species. A single microRNA can regulate the expression of hundreds of mRNA targets, a property given by a short sequence (called “seed”) in positions 2 to 8 from the 5′ end that is complementary to the 3′ untranslated region (UTR) tail of specific mRNAs. We aimed to generate horse induced pluripotent stem cells (iPSC), characterise them, and evaluate the expression of different microRNAs (miR-302a, b, c, d, miR-205, miR-145, miR-9, miR-96, miR-125b, and miR-296) in pluripotency and differentiation. Both cell states were evaluated (pluripotency and differentiation) in order to understand more deeply the complex network of transcriptional regulation in different contexts but with the same genomic background. Two equine iPSC lines (named L2 and L3) were characterised after the reprogramming of equine fibroblasts with the 4 human Yamanaka factors (OCT-4, SOX-2, c-MYC, KLF4). The pluripotency of both lines was assessed by phosphatase alkaline activity, expression of OCT-4, NANOG, and REX1 by RT-PCR, and by immunofluorescence of OCT-4, SOX-2, and c-MYC. In vitro differentiation to embryo bodies (EB) showed the capacity of the iPSC to differentiate into ectodermal, endodermal, and mesodermal phenotypes. MicroRNA expression was analysed by quantitative RT-PCR and resulted in higher expression of the miR-302 family, miR-9, and miR-96 in L2 and L3v. fibroblasts (P ≤ 0.05), as previously shown in human pluripotent cells. Moreover, down-regulation of miR-145 and miR-205 was observed. After differentiation to EB, greater expression of miR-96 was observed in the EB compared with iPSC, and the expression of miR-205 was induced but only in the EB-L2. In addition, we performed in silico analysis of horse and human microRNAs. First, we compared the horse-miR-302/367 cluster with the human-miR-302/367 cluster and determined a 75% homology between them. Moreover, the seed region of the horse-miR-302 family resulted complementary to the 3′ UTR of horse cell cycle regulator genes CDK2, CYCLIN D1, and E2F1, and to the 3′ UTR of the RHOC gene, which is involved in the epithelial-mesenchymal transition. The miR-145 seed sequence was complementary to the 3′ UTR region of the OCT-4 and KLF-4 horse genes. With respect to miR-9 and miR-96, the seed sequence of these genes were complementary to the HES1 and PAX-6 genes. In all cases, the same gene targets were previously demonstrated in humans. In conclusion, we report the generation and characterization of equine iPSC and determined for the first time the expression of microRNAs in equine pluripotent cells. Moreover, several results led us to think that the horse microRNAs evaluated herein are highly conserved in sequence and function with respect to the human species. It will now be necessary to generate directed differentiations to derivatives of the 3 germ layers in order to strengthen our results. This is the first report to evaluate the expression and possible targets of microRNAs in pluripotent cells from domestic animals.

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