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Farbehi N, Neavin DR, Cuomo ASE, Studer L, MacArthur DG, Powell JE. Integrating population genetics, stem cell biology and cellular genomics to study complex human diseases. Nat Genet 2024; 56:758-766. [PMID: 38741017 DOI: 10.1038/s41588-024-01731-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/20/2024] [Indexed: 05/16/2024]
Abstract
Human pluripotent stem (hPS) cells can, in theory, be differentiated into any cell type, making them a powerful in vitro model for human biology. Recent technological advances have facilitated large-scale hPS cell studies that allow investigation of the genetic regulation of molecular phenotypes and their contribution to high-order phenotypes such as human disease. Integrating hPS cells with single-cell sequencing makes identifying context-dependent genetic effects during cell development or upon experimental manipulation possible. Here we discuss how the intersection of stem cell biology, population genetics and cellular genomics can help resolve the functional consequences of human genetic variation. We examine the critical challenges of integrating these fields and approaches to scaling them cost-effectively and practically. We highlight two areas of human biology that can particularly benefit from population-scale hPS cell studies, elucidating mechanisms underlying complex disease risk loci and evaluating relationships between common genetic variation and pharmacotherapeutic phenotypes.
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Affiliation(s)
- Nona Farbehi
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Drew R Neavin
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anna S E Cuomo
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Lorenz Studer
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
- The Center for Stem Cell Biology and Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, University of New South Wales, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Joseph E Powell
- Garvan Weizmann Center for Cellular Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia.
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2
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Caudal A, Snyder MP, Wu JC. Harnessing human genetics and stem cells for precision cardiovascular medicine. CELL GENOMICS 2024; 4:100445. [PMID: 38359791 PMCID: PMC10879032 DOI: 10.1016/j.xgen.2023.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/22/2023] [Accepted: 10/25/2023] [Indexed: 02/17/2024]
Abstract
Human induced pluripotent stem cell (iPSC) platforms are valuable for biomedical and pharmaceutical research by providing tissue-specific human cells that retain patients' genetic integrity and display disease phenotypes in a dish. Looking forward, combining iPSC phenotyping platforms with genomic and screening technologies will continue to pave new directions for precision medicine, including genetic prediction, visualization, and treatment of heart disease. This review summarizes the recent use of iPSC technology to unpack the influence of genetic variants in cardiovascular pathology. We focus on various state-of-the-art genomic tools for cardiovascular therapies-including the expansion of genetic toolkits for molecular interrogation, in vitro population studies, and function-based drug screening-and their current applications in patient- and genome-edited iPSC platforms that are heralding new avenues for cardiovascular research.
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Affiliation(s)
- Arianne Caudal
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Greenstone Biosciences, Palo Alto, CA 94304, USA.
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3
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Brooks IR, Garrone CM, Kerins C, Kiar CS, Syntaka S, Xu JZ, Spagnoli FM, Watt FM. Functional genomics and the future of iPSCs in disease modeling. Stem Cell Reports 2022; 17:1033-1047. [PMID: 35487213 PMCID: PMC9133703 DOI: 10.1016/j.stemcr.2022.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 10/28/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are valuable in disease modeling because of their potential to expand and differentiate into virtually any cell type and recapitulate key aspects of human biology. Functional genomics are genome-wide studies that aim to discover genotype-phenotype relationships, thereby revealing the impact of human genetic diversity on normal and pathophysiology. In this review, we make the case that human iPSCs (hiPSCs) are a powerful tool for functional genomics, since they provide an in vitro platform for the study of population genetics. We describe cutting-edge tools and strategies now available to researchers, including multi-omics technologies, advances in hiPSC culture techniques, and innovations in drug development. Functional genomics approaches based on hiPSCs hold great promise for advancing drug discovery, disease etiology, and the impact of genetic variation on human biology.
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Affiliation(s)
- Imogen R Brooks
- St John's Institute of Dermatology, King's College London, London, SE1 9RT, UK
| | - Cristina M Garrone
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Caoimhe Kerins
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Cher Shen Kiar
- Peter Gorer Department of Immunobiology, King's College London, London, SE1 9RT, UK
| | - Sofia Syntaka
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Jessie Z Xu
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK
| | - Francesca M Spagnoli
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK.
| | - Fiona M Watt
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, SE1 9RT, UK; Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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4
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Mullin NK, Voigt AP, Cooke JA, Bohrer LR, Burnight ER, Stone EM, Mullins RF, Tucker BA. Patient derived stem cells for discovery and validation of novel pathogenic variants in inherited retinal disease. Prog Retin Eye Res 2021; 83:100918. [PMID: 33130253 PMCID: PMC8559964 DOI: 10.1016/j.preteyeres.2020.100918] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of inherited retinal disease has benefited immensely from molecular genetic analysis over the past several decades. New technologies that allow for increasingly detailed examination of a patient's DNA have expanded the catalog of genes and specific variants that cause retinal disease. In turn, the identification of pathogenic variants has allowed the development of gene therapies and low-cost, clinically focused genetic testing. Despite this progress, a relatively large fraction (at least 20%) of patients with clinical features suggestive of an inherited retinal disease still do not have a molecular diagnosis today. Variants that are not obviously disruptive to the codon sequence of exons can be difficult to distinguish from the background of benign human genetic variations. Some of these variants exert their pathogenic effect not by altering the primary amino acid sequence, but by modulating gene expression, isoform splicing, or other transcript-level mechanisms. While not discoverable by DNA sequencing methods alone, these variants are excellent targets for studies of the retinal transcriptome. In this review, we present an overview of the current state of pathogenic variant discovery in retinal disease and identify some of the remaining barriers. We also explore the utility of new technologies, specifically patient-derived induced pluripotent stem cell (iPSC)-based modeling, in further expanding the catalog of disease-causing variants using transcriptome-focused methods. Finally, we outline bioinformatic analysis techniques that will allow this new method of variant discovery in retinal disease. As the knowledge gleaned from previous technologies is informing targets for therapies today, we believe that integrating new technologies, such as iPSC-based modeling, into the molecular diagnosis pipeline will enable a new wave of variant discovery and expanded treatment of inherited retinal disease.
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Affiliation(s)
- Nathaniel K Mullin
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Andrew P Voigt
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jessica A Cooke
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Laura R Bohrer
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Erin R Burnight
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Edwin M Stone
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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5
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Abstract
The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium's plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled-along with validated datasets-into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit-and the knowledge generated by its applications-as a means to accelerate the clinical development of new therapies for a wide range of conditions.
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6
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Stojkovic M, Han D, Jeong M, Stojkovic P, Stankovic KM. Human induced pluripotent stem cells and CRISPR/Cas-mediated targeted genome editing: Platforms to tackle sensorineural hearing loss. STEM CELLS (DAYTON, OHIO) 2021; 39:673-696. [PMID: 33586253 DOI: 10.1002/stem.3353] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/13/2020] [Indexed: 11/09/2022]
Abstract
Hearing loss (HL) is a major global health problem of pandemic proportions. The most common type of HL is sensorineural hearing loss (SNHL) which typically occurs when cells within the inner ear are damaged. Human induced pluripotent stem cells (hiPSCs) can be generated from any individual including those who suffer from different types of HL. The development of new differentiation protocols to obtain cells of the inner ear including hair cells (HCs) and spiral ganglion neurons (SGNs) promises to expedite cell-based therapy and screening of potential pharmacologic and genetic therapies using human models. Considering age-related, acoustic, ototoxic, and genetic insults which are the most frequent causes of irreversible damage of HCs and SGNs, new methods of genome editing (GE), especially the CRISPR/Cas9 technology, could bring additional opportunities to understand the pathogenesis of human SNHL and identify novel therapies. However, important challenges associated with both hiPSCs and GE need to be overcome before scientific discoveries are correctly translated to effective and patient-safe applications. The purpose of the present review is (a) to summarize the findings from published reports utilizing hiPSCs for studies of SNHL, hence complementing recent reviews focused on animal studies, and (b) to outline promising future directions for deciphering SNHL using disruptive molecular and genomic technologies.
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Affiliation(s)
- Miodrag Stojkovic
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Dongjun Han
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Minjin Jeong
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Petra Stojkovic
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Konstantina M Stankovic
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard University, Cambridge, Massachusetts, USA.,Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
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7
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Lago SG, Tomasik J, Bahn S. Functional patient-derived cellular models for neuropsychiatric drug discovery. Transl Psychiatry 2021; 11:128. [PMID: 33597511 PMCID: PMC7888004 DOI: 10.1038/s41398-021-01243-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Mental health disorders are a leading cause of disability worldwide. Challenges such as disease heterogeneity, incomplete characterization of the targets of existing drugs and a limited understanding of functional interactions of complex genetic risk loci and environmental factors have compromised the identification of novel drug candidates. There is a pressing clinical need for drugs with new mechanisms of action which address the lack of efficacy and debilitating side effects of current medications. Here we discuss a novel strategy for neuropsychiatric drug discovery which aims to address these limitations by identifying disease-related functional responses ('functional cellular endophenotypes') in a variety of patient-derived cells, such as induced pluripotent stem cell (iPSC)-derived neurons and organoids or peripheral blood mononuclear cells (PBMCs). Disease-specific alterations in cellular responses can subsequently yield novel drug screening targets and drug candidates. We discuss the potential of this approach in the context of recent advances in patient-derived cellular models, high-content single-cell screening of cellular networks and changes in the diagnostic framework of neuropsychiatric disorders.
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Affiliation(s)
- Santiago G. Lago
- grid.5335.00000000121885934Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Jakub Tomasik
- grid.5335.00000000121885934Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom.
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8
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Cashman JR. Small Molecule Regulation of Stem Cells that Generate Bone, Chondrocyte, and Cardiac Cells. Curr Top Med Chem 2020; 20:2344-2361. [PMID: 32819246 DOI: 10.2174/1568026620666200820143912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/20/2020] [Accepted: 08/13/2020] [Indexed: 11/22/2022]
Abstract
Embryonic stem cells (ESCs) are stem cells (SCs) that can self-renew and differentiate into a myriad of cell types. The process of developing stemness is determined by signaling molecules that drive stem cells to a specific lineage. For example, ESCs can differentiate into mature cells (e.g., cardiomyocytes) and mature cardiomyocytes can be characterized for cell beating, action potential, and ion channel function. A goal of this Perspective is to show how small molecules can be used to differentiate ESCs into cardiomyocytes and how this can reveal novel aspects of SC biology. This approach can also lead to the discovery of new molecules of use in cardiovascular disease. Human induced pluripotent stem cells (hiPSCs) afford the ability to produce unlimited numbers of normal human cells. The creation of patient-specific hiPSCs provides an opportunity to study cell models of human disease. The second goal is to show that small molecules can stimulate hiPSC commitment to cardiomyocytes. How iPSCs can be used in an approach to discover new molecules of use in cardiovascular disease will also be shown in this study. Adult SCs, including mesenchymal stem cells (MSCs), can likewise participate in self-renewal and multilineage differentiation. MSCs are capable of differentiating into osteoblasts, adipocytes or chondrocytes. A third goal of this Perspective is to describe differentiation of MSCs into chondrogenic and osteogenic lineages. Small molecules can stimulate MSCs to specific cell fate both in vitro and in vivo. In this Perspective, some recent examples of applying small molecules for osteogenic and chondrogenic cell fate determination are summarized. Underlying molecular mechanisms and signaling pathways involved are described. Small molecule-based modulation of stem cells shows insight into cell regulation and potential approaches to therapeutic strategies for MSC-related diseases.
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Affiliation(s)
- John R Cashman
- Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, United States
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9
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Patient hiPSCs Identify Vascular Smooth Muscle Arylacetamide Deacetylase as Protective against Atherosclerosis. Cell Stem Cell 2020; 27:147-157.e7. [DOI: 10.1016/j.stem.2020.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/15/2019] [Accepted: 04/23/2020] [Indexed: 12/19/2022]
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10
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Kanchan K, Iyer K, Yanek LR, Carcamo-Orive I, Taub MA, Malley C, Baldwin K, Becker LC, Broeckel U, Cheng L, Cowan C, D'Antonio M, Frazer KA, Quertermous T, Mostoslavsky G, Murphy G, Rabinovitch M, Rader DJ, Steinberg MH, Topol E, Yang W, Knowles JW, Jaquish CE, Ruczinski I, Mathias RA. Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program. Stem Cell Res 2020; 46:101803. [PMID: 32442913 PMCID: PMC7575060 DOI: 10.1016/j.scr.2020.101803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 03/11/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Human induced pluripotent stem cell (hiPSC) lines have previously been generated through the NHLBI sponsored NextGen program at nine individual study sites. Here, we examined the structural integrity of 506 hiPSC lines as determined by copy number variations (CNVs). We observed that 149 hiPSC lines acquired 258 CNVs relative to donor DNA. We identified six recurrent regions of CNVs on chromosomes 1, 2, 3, 16 and 20 that overlapped with cancer associated genes. Furthermore, the genes mapping to regions of acquired CNVs show an enrichment in cancer related biological processes (IL6 production) and signaling cascades (JNK cascade & NFκB cascade). The genomic region of instability on chr20 (chr20q11.2) includes transcriptomic signatures for cancer associated genes such as ID1, BCL2L1, TPX2, PDRG1 and HCK. Of these HCK shows statistically significant differential expression between carrier and non-carrier hiPSC lines. Overall, while a low level of genomic instability was observed in the NextGen generated hiPSC lines, the observation of structural instability in regions with known cancer associated genes substantiates the importance of systematic evaluation of genetic variations in hiPSCs before using them as disease/research models.
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Affiliation(s)
- Kanika Kanchan
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kruthika Iyer
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa R Yanek
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ivan Carcamo-Orive
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public health, Johns Hopkins University, Baltimore, MD, USA
| | - Claire Malley
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kristin Baldwin
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Lewis C Becker
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ulrich Broeckel
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Linzhao Cheng
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Chad Cowan
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Thomas Quertermous
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Gustavo Mostoslavsky
- The Center for Regenerative Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - George Murphy
- The Center for Regenerative Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Marlene Rabinovitch
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Daniel J Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martin H Steinberg
- Department of Medicine, Section of Hematology-Oncology, Boston University School of Medicine, Boston, MA, USA
| | - Eric Topol
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Wenli Yang
- Penn Center for Pulmonary Biology and Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua W Knowles
- Department of Medicine, Cardiovascular Institute and Diabetes Research Center, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public health, Johns Hopkins University, Baltimore, MD, USA
| | - Rasika A Mathias
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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11
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Hnatiuk A, Mercola M. Stars in the Night Sky: iPSC-Cardiomyocytes Return the Patient Context to Drug Screening. Cell Stem Cell 2020; 24:506-507. [PMID: 30951657 DOI: 10.1016/j.stem.2019.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
iPSC-derived cardiomyocytes have the potential to revolutionize the discovery of new medicines for serious heart conditions; however, heart failure remains a major cause of mortality worldwide. In this issue of Cell Stem Cell, Fiedler et al. (2019) describe using iPSC-derived cardiomyocytes to screen new chemical entities, discovering a small molecule for ischemic injury.
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Affiliation(s)
- Anna Hnatiuk
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, 1651 Page Mill Road, Palo Alto, CA 94305, USA
| | - Mark Mercola
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, 1651 Page Mill Road, Palo Alto, CA 94305, USA.
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12
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Chen Z, Yu H, Shi X, Warren CR, Lotta LA, Friesen M, Meissner TB, Langenberg C, Wabitsch M, Wareham N, Benson MD, Gerszten RE, Cowan CA. Functional Screening of Candidate Causal Genes for Insulin Resistance in Human Preadipocytes and Adipocytes. Circ Res 2019; 126:330-346. [PMID: 31739742 DOI: 10.1161/circresaha.119.315246] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Rationale: Genome-wide association studies have identified genetic loci associated with insulin resistance (IR) but pinpointing the causal genes of a risk locus has been challenging. Objective: To identify candidate causal genes for IR, we screened regional and biologically plausible genes (16 in total) near the top 10 IR-loci in risk-relevant cell types, namely preadipocytes and adipocytes. Methods and Results: We generated 16 human Simpson-Golabi-Behmel syndrome preadipocyte knockout lines each with a single IR-gene knocked out by lentivirus-mediated CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system. We evaluated each gene knockout by screening IR-relevant phenotypes in the 3 insulin-sensitizing mechanisms, including adipogenesis, lipid metabolism, and insulin signaling. We performed genetic analyses using data on the genotype-tissue expression portal expression quantitative trait loci database and accelerating medicines partnership type 2 diabetes mellitus Knowledge Portal to evaluate whether candidate genes prioritized by our in vitro studies were expression quantitative trait loci genes in human subcutaneous adipose tissue, and whether expression of these genes is associated with risk of IR, type 2 diabetes mellitus, and cardiovascular diseases. We further validated the functions of 3 new adipose IR genes by overexpression-based phenotypic rescue in the Simpson-Golabi-Behmel syndrome preadipocyte knockout lines. Twelve genes, PPARG, IRS-1, FST, PEPD, PDGFC, MAP3K1, GRB14, ARL15, ANKRD55, RSPO3, COBLL1, and LYPLAL1, showed diverse phenotypes in the 3 insulin-sensitizing mechanisms, and the first 7 of these genes could affect all the 3 mechanisms. Five out of 6 expression quantitative trait loci genes are among the top candidate causal genes and the abnormal expression levels of these genes (IRS-1, GRB14, FST, PEPD, and PDGFC) in human subcutaneous adipose tissue could be associated with increased risk of IR, type 2 diabetes mellitus, and cardiovascular disease. Phenotypic rescue by overexpression of the candidate causal genes (FST, PEPD, and PDGFC) in the Simpson-Golabi-Behmel syndrome preadipocyte knockout lines confirmed their function in adipose IR. Conclusions: Twelve genes showed diverse phenotypes indicating differential roles in insulin sensitization, suggesting mechanisms bridging the association of their genomic loci with IR. We prioritized PPARG, IRS-1, GRB14, MAP3K1, FST, PEPD, and PDGFC as top candidate genes. Our work points to novel roles for FST, PEPD, and PDGFC in adipose tissue, with consequences for cardiometabolic diseases.
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Affiliation(s)
- Zhifen Chen
- From the Beth Israel Deaconess Medical Center, Cardiovascular Institute, Harvard Medical School, Boston, MA (Z.C., H.Y., X.S., M.F., T.B.M., M.D.B., R.E.G, C.A.C.).,Harvard Stem Cell Institute, Harvard University, Cambridge, MA (Z.C., H.Y., M.F., C.R.W., T.B.M., C.A.C.)
| | - Haojie Yu
- From the Beth Israel Deaconess Medical Center, Cardiovascular Institute, Harvard Medical School, Boston, MA (Z.C., H.Y., X.S., M.F., T.B.M., M.D.B., R.E.G, C.A.C.).,Harvard Stem Cell Institute, Harvard University, Cambridge, MA (Z.C., H.Y., M.F., C.R.W., T.B.M., C.A.C.)
| | - Xu Shi
- From the Beth Israel Deaconess Medical Center, Cardiovascular Institute, Harvard Medical School, Boston, MA (Z.C., H.Y., X.S., M.F., T.B.M., M.D.B., R.E.G, C.A.C.)
| | - Curtis R Warren
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA (Z.C., H.Y., M.F., C.R.W., T.B.M., C.A.C.).,Cardiometabolic Disease Research, Boehringer-Ingelheim Pharmaceuticals, Inc, Ridgefield, CT (C.R.W.)
| | - Luca A Lotta
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom (L.A.L., C.L., N.W.)
| | - Max Friesen
- From the Beth Israel Deaconess Medical Center, Cardiovascular Institute, Harvard Medical School, Boston, MA (Z.C., H.Y., X.S., M.F., T.B.M., M.D.B., R.E.G, C.A.C.).,Harvard Stem Cell Institute, Harvard University, Cambridge, MA (Z.C., H.Y., M.F., C.R.W., T.B.M., C.A.C.)
| | - Torsten B Meissner
- From the Beth Israel Deaconess Medical Center, Cardiovascular Institute, Harvard Medical School, Boston, MA (Z.C., H.Y., X.S., M.F., T.B.M., M.D.B., R.E.G, C.A.C.).,Harvard Stem Cell Institute, Harvard University, Cambridge, MA (Z.C., H.Y., M.F., C.R.W., T.B.M., C.A.C.)
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom (L.A.L., C.L., N.W.)
| | - Martin Wabitsch
- Pediatrics and Adolescent Medicine, Ulm University Hospital, Germany (M.W.)
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom (L.A.L., C.L., N.W.)
| | - Mark D Benson
- From the Beth Israel Deaconess Medical Center, Cardiovascular Institute, Harvard Medical School, Boston, MA (Z.C., H.Y., X.S., M.F., T.B.M., M.D.B., R.E.G, C.A.C.)
| | - Rob E Gerszten
- From the Beth Israel Deaconess Medical Center, Cardiovascular Institute, Harvard Medical School, Boston, MA (Z.C., H.Y., X.S., M.F., T.B.M., M.D.B., R.E.G, C.A.C.)
| | - Chad A Cowan
- From the Beth Israel Deaconess Medical Center, Cardiovascular Institute, Harvard Medical School, Boston, MA (Z.C., H.Y., X.S., M.F., T.B.M., M.D.B., R.E.G, C.A.C.).,Harvard Stem Cell Institute, Harvard University, Cambridge, MA (Z.C., H.Y., M.F., C.R.W., T.B.M., C.A.C.)
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13
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Human Pluripotent Stem Cell-Derived Endoderm for Modeling Development and Clinical Applications. Cell Stem Cell 2019; 22:485-499. [PMID: 29625066 DOI: 10.1016/j.stem.2018.03.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The liver, lung, pancreas, and digestive tract all originate from the endoderm germ layer, and these vital organs are subject to many life-threatening diseases affecting millions of patients. However, primary cells from endodermal organs are often difficult to grow in vitro. Human pluripotent stem cells thus hold great promise for generating endoderm cells and their derivatives as tools for the development of new therapeutics against a variety of global healthcare challenges. Here we describe recent advances in methods for generating endodermal cell types from human pluripotent stem cells and their use for disease modeling and cell-based therapy.
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14
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Hoffman GE, Schrode N, Flaherty E, Brennand KJ. New considerations for hiPSC-based models of neuropsychiatric disorders. Mol Psychiatry 2019; 24:49-66. [PMID: 29483625 PMCID: PMC6109625 DOI: 10.1038/s41380-018-0029-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/17/2017] [Accepted: 11/27/2017] [Indexed: 02/06/2023]
Abstract
The development of human-induced pluripotent stem cells (hiPSCs) has made possible patient-specific modeling across the spectrum of human disease. Here, we discuss recent advances in psychiatric genomics and post-mortem studies that provide critical insights concerning cell-type composition and sample size that should be considered when designing hiPSC-based studies of complex genetic disease. We review recent hiPSC-based models of SZ, in light of our new understanding of critical power limitations in the design of hiPSC-based studies of complex genetic disorders. Three possible solutions are a movement towards genetically stratified cohorts of rare variant patients, application of CRISPR technologies to engineer isogenic neural cells to study the impact of common variants, and integration of advanced genetics and hiPSC-based datasets in future studies. Overall, we emphasize that to advance the reproducibility and relevance of hiPSC-based studies, stem cell biologists must contemplate statistical and biological considerations that are already well accepted in the field of genetics. We conclude with a discussion of the hypothesis of biological convergence of disease-through molecular, cellular, circuit, and patient level phenotypes-and how this might emerge through hiPSC-based studies.
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Affiliation(s)
- Gabriel E Hoffman
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nadine Schrode
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erin Flaherty
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kristen J Brennand
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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15
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Lau E, Paik DT, Wu JC. Systems-Wide Approaches in Induced Pluripotent Stem Cell Models. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:395-419. [PMID: 30379619 DOI: 10.1146/annurev-pathmechdis-012418-013046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human induced pluripotent stem cells (iPSCs) provide a renewable supply of patient-specific and tissue-specific cells for cellular and molecular studies of disease mechanisms. Combined with advances in various omics technologies, iPSC models can be used to profile the expression of genes, transcripts, proteins, and metabolites in relevant tissues. In the past 2 years, large panels of iPSC lines have been derived from hundreds of genetically heterogeneous individuals, further enabling genome-wide mapping to identify coexpression networks and elucidate gene regulatory networks. Here, we review recent developments in omics profiling of various molecular phenotypes and the emergence of human iPSCs as a systems biology model of human diseases.
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Affiliation(s)
- Edward Lau
- Stanford Cardiovascular Institute, and Department of Medicine, Division of Cardiology, Stanford University, Stanford, California 94305, USA;
| | - David T Paik
- Stanford Cardiovascular Institute, and Department of Medicine, Division of Cardiology, Stanford University, Stanford, California 94305, USA;
| | - Joseph C Wu
- Stanford Cardiovascular Institute, and Department of Medicine, Division of Cardiology, Stanford University, Stanford, California 94305, USA; .,Department of Radiology, Stanford University, Stanford, California 94305, USA
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16
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Soldner F, Jaenisch R. Stem Cells, Genome Editing, and the Path to Translational Medicine. Cell 2018; 175:615-632. [PMID: 30340033 PMCID: PMC6461399 DOI: 10.1016/j.cell.2018.09.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/31/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
Abstract
The derivation of human embryonic stem cells (hESCs) and the stunning discovery that somatic cells can be reprogrammed into human induced pluripotent stem cells (hiPSCs) holds the promise to revolutionize biomedical research and regenerative medicine. In this Review, we focus on disorders of the central nervous system and explore how advances in human pluripotent stem cells (hPSCs) coincide with evolutions in genome engineering and genomic technologies to provide realistic opportunities to tackle some of the most devastating complex disorders.
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Affiliation(s)
- Frank Soldner
- The Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA.
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17
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Zhang J, Li H, Trounson A, Wu JC, Nioi P. Combining hiPSCs and Human Genetics: Major Applications in Drug Development. Cell Stem Cell 2018; 21:161-165. [PMID: 28777942 DOI: 10.1016/j.stem.2017.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Merging iPSC models and human genetic research has opened up new avenues in understanding disease mechanisms and target biology, which facilitate exciting translation of this research to many areas of drug development. We highlight recent applications of these combined disciplines and discuss remaining challenges and potential solutions.
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Affiliation(s)
- Jin Zhang
- The First Affiliated Hospital and Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Translational Systems Biology Group, Department of Comparative Biology and Safety Sciences, Amgen Inc., Cambridge, MA 02141, USA.
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Alan Trounson
- Monash University and Hudson Institute for Medical Research, Clayton, VIC 3168, Australia
| | - Joseph C Wu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul Nioi
- Translational Systems Biology Group, Department of Comparative Biology and Safety Sciences, Amgen Inc., Cambridge, MA 02141, USA.
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18
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Sarafian R, Morato-Marques M, Borsoi J, Pereira LV. Monitoring cell line identity in collections of human induced pluripotent stem cells. Stem Cell Res 2018; 28:66-70. [PMID: 29433076 DOI: 10.1016/j.scr.2018.01.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 01/07/2023] Open
Abstract
The ability to reprogram somatic cells into induced pluripotent stem cells (hiPSCs) has led to the generation of large collections of cell lines from thousands of individuals with specific phenotypes, many of which will be shared among different research groups as invaluable tools for biomedical research. As hiPSC-based research involves extensive culture of many cell lines, the issue periodic cell line identification is particularly important to ensure that cell line identity remains accurate. Here we analyzed the different commercially available genotyping methods considering ease of in-house genotyping, cost and informativeness, and applied one of them in our workflow for hiPSC generation. We show that the chosen STR method was able to establish a unique DNA profile for each of the 35 individuals/hiPSC lines at the examined sites, as well as identify two discrepancies resulting from inadvertently exchanged samples. Our results highlight the importance of hiPSC line genotyping by an in-house method that allows periodic cell line identification and demonstrate that STR is a useful approach to supplement less frequent karyotyping and epigenetic evaluations.
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Affiliation(s)
- Raquel Sarafian
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Mariana Morato-Marques
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Juliana Borsoi
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil
| | - Lygia Veiga Pereira
- National Laboratory for Embryonic Stem Cells (LaNCE), Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, SP 05508-900, Brazil.
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19
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Park E, Pan Z, Zhang Z, Lin L, Xing Y. The Expanding Landscape of Alternative Splicing Variation in Human Populations. Am J Hum Genet 2018; 102:11-26. [PMID: 29304370 PMCID: PMC5777382 DOI: 10.1016/j.ajhg.2017.11.002] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing is a tightly regulated biological process by which the number of gene products for any given gene can be greatly expanded. Genomic variants in splicing regulatory sequences can disrupt splicing and cause disease. Recent developments in sequencing technologies and computational biology have allowed researchers to investigate alternative splicing at an unprecedented scale and resolution. Population-scale transcriptome studies have revealed many naturally occurring genetic variants that modulate alternative splicing and consequently influence phenotypic variability and disease susceptibility in human populations. Innovations in experimental and computational tools such as massively parallel reporter assays and deep learning have enabled the rapid screening of genomic variants for their causal impacts on splicing. In this review, we describe technological advances that have greatly increased the speed and scale at which discoveries are made about the genetic variation of alternative splicing. We summarize major findings from population transcriptomic studies of alternative splicing and discuss the implications of these findings for human genetics and medicine.
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Affiliation(s)
- Eddie Park
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhicheng Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zijun Zhang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lan Lin
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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20
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Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, Gutteridge A, Gaffney DJ. Molecular and functional variation in iPSC-derived sensory neurons. Nat Genet 2018; 50:54-61. [PMID: 29229984 PMCID: PMC5742539 DOI: 10.1038/s41588-017-0005-8] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 11/06/2017] [Indexed: 12/20/2022]
Abstract
Induced pluripotent stem cells (iPSCs), and cells derived from them, have become key tools for modeling biological processes, particularly in cell types that are difficult to obtain from living donors. Here we present a map of regulatory variants in iPSC-derived neurons, based on 123 differentiations of iPSCs to a sensory neuronal fate. Gene expression was more variable across cultures than in primary dorsal root ganglion, particularly for genes related to nervous system development. Using single-cell RNA-sequencing, we found that the number of neuronal versus contaminating cells was influenced by iPSC culture conditions before differentiation. Despite high differentiation-induced variability, our allele-specific method detected thousands of quantitative trait loci (QTLs) that influenced gene expression, chromatin accessibility, and RNA splicing. On the basis of these detected QTLs, we estimate that recall-by-genotype studies that use iPSC-derived cells will require cells from at least 20-80 individuals to detect the effects of regulatory variants with moderately large effect sizes.
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Affiliation(s)
- Jeremy Schwartzentruber
- Wellcome Trust Sanger Institute, Hinxton, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Stefanie Foskolou
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK
| | - Helena Kilpinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Kaur Alasoo
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Minal Patel
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Rita Ferreira
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK
| | | | - Anna Wilbrey
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK
| | - Magda Bictash
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK
| | - Emma Impey
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK
| | - Lishuang Cao
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK
| | - Sergio Lainez
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK
| | | | - Paul John Whiting
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK
- AR-UK Drug Discovery Institute, Institute of Neurology, University College London, London, UK
| | - Alex Gutteridge
- Pfizer Neuroscience and Pain Research Unit, Pfizer Ltd., Cambridge, UK.
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21
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Humanity in a Dish: Population Genetics with iPSCs. Trends Cell Biol 2017; 28:46-57. [PMID: 29054332 DOI: 10.1016/j.tcb.2017.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/26/2017] [Accepted: 09/28/2017] [Indexed: 12/17/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are powerful tools for investigating the relationship between genotype and phenotype. Recent publications have described iPSC cohort studies of common genetic variants and their effects on gene expression and cellular phenotypes. These in vitro quantitative trait locus (QTL) studies are the first experiments in a new paradigm with great potential: iPSC-based functional population genetic studies. iPSC collections from large cohorts are currently under development to facilitate the next wave of these studies, which have the potential to discover the effects of common genetic variants on cellular phenotypes and to uncover the molecular basis of common genetic diseases. Here, we describe the recent advances in this developing field, and provide a road map for future in vitro functional population genetic studies and trial-in-a-dish experiments.
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22
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Noh H, Shao Z, Coyle JT, Chung S. Modeling schizophrenia pathogenesis using patient-derived induced pluripotent stem cells (iPSCs). Biochim Biophys Acta Mol Basis Dis 2017; 1863:2382-2387. [PMID: 28668333 PMCID: PMC5737829 DOI: 10.1016/j.bbadis.2017.06.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/07/2017] [Accepted: 06/23/2017] [Indexed: 12/24/2022]
Abstract
Schizophrenia is a chronic disabling mental disorder that affects about 1% population world-wide, for which there is a desperate need to develop more effective treatments. In this minireview, we summarize the findings from recent studies using induced pluripotent stem cells to model the developmental pathogenesis of schizophrenia and discuss what we have learned from these studies. We also discuss what are the important next steps and key issues to be addressed to move the field forward.
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Affiliation(s)
- Haneul Noh
- Translational Stem Cell Neurobiology Lab, McLean Hospital/Harvard Medical School, Belmont, MA 02478, United States
| | - Zhicheng Shao
- Translational Stem Cell Neurobiology Lab, McLean Hospital/Harvard Medical School, Belmont, MA 02478, United States
| | - Joseph T Coyle
- Laboratory for Psychiatric and Molecular Neuroscience, McLean Hospital/Harvard Medical School, Belmont, MA 02478, United States
| | - Sangmi Chung
- Translational Stem Cell Neurobiology Lab, McLean Hospital/Harvard Medical School, Belmont, MA 02478, United States.
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23
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Yamasaki AE, Panopoulos AD, Belmonte JCI. Understanding the genetics behind complex human disease with large-scale iPSC collections. Genome Biol 2017; 18:135. [PMID: 28728561 PMCID: PMC5520285 DOI: 10.1186/s13059-017-1276-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Three recent studies analyzing large-scale collections of human induced pluripotent stem cell lines provide valuable insight into how genetic regulatory variation affects cellular and molecular traits.
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Affiliation(s)
- Amanda E Yamasaki
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Athanasia D Panopoulos
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
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