Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models
Genetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlyin...
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2020-06-01
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doaj-051c6b7b3fc94f27b8244d1722c52ff22020-11-25T03:18:07ZengMDPI AGCells2073-44092020-06-0191406140610.3390/cells9061406Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural ModelsJames A. Gregory0Emily Hoelzli1Rawan Abdelaal2Catherine Braine3Miguel Cuevas4Madeline Halpern5Natalie Barretto6Nadine Schrode7Güney Akbalik8Kristy Kang9Esther Cheng10Kathryn Bowles11Steven Lotz12Susan Goderie13Celeste M. Karch14Sally Temple15Alison Goate16Kristen J. Brennand17Hemali Phatnani18Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USACenter for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USACenter for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USADepartment of Neurology, Columbia University Medical Center, New York, NY 10068, USADepartment of Neurology, Columbia University Medical Center, New York, NY 10068, USAPamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USAPamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USAPamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USACenter for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USACenter for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USAPamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USARonald M. Loeb Center for Alzheimer’s Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USANeural Stem Cell Institute, One Discovery Drive, Rensselaer, NY 12144, USANeural Stem Cell Institute, One Discovery Drive, Rensselaer, NY 12144, USADepartment of Psychiatry, Washington University in St. Louis, St. Louis, MO 63110, USANeural Stem Cell Institute, One Discovery Drive, Rensselaer, NY 12144, USARonald M. Loeb Center for Alzheimer’s Disease, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USAPamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USACenter for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY 10013, USAGenetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease but also challenge our ability to resolve cell type-specific perturbations. Here, we report an extension of the RiboTag system, first developed to achieve cell type-restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety of in vitro applications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables depletion of up to 87 percent of off-target RNA in mixed species co-cultures. Nonetheless, depletion efficiency varies across independent experimental replicates, particularly for hiPSC-derived motor neurons. The challenges and potential of implementing RiboTags in complex in vitro cultures are discussed.https://www.mdpi.com/2073-4409/9/6/1406hiPSCneurongliaRiboTagbacTRAPgenomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
James A. Gregory Emily Hoelzli Rawan Abdelaal Catherine Braine Miguel Cuevas Madeline Halpern Natalie Barretto Nadine Schrode Güney Akbalik Kristy Kang Esther Cheng Kathryn Bowles Steven Lotz Susan Goderie Celeste M. Karch Sally Temple Alison Goate Kristen J. Brennand Hemali Phatnani |
spellingShingle |
James A. Gregory Emily Hoelzli Rawan Abdelaal Catherine Braine Miguel Cuevas Madeline Halpern Natalie Barretto Nadine Schrode Güney Akbalik Kristy Kang Esther Cheng Kathryn Bowles Steven Lotz Susan Goderie Celeste M. Karch Sally Temple Alison Goate Kristen J. Brennand Hemali Phatnani Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models Cells hiPSC neuron glia RiboTag bacTRAP genomics |
author_facet |
James A. Gregory Emily Hoelzli Rawan Abdelaal Catherine Braine Miguel Cuevas Madeline Halpern Natalie Barretto Nadine Schrode Güney Akbalik Kristy Kang Esther Cheng Kathryn Bowles Steven Lotz Susan Goderie Celeste M. Karch Sally Temple Alison Goate Kristen J. Brennand Hemali Phatnani |
author_sort |
James A. Gregory |
title |
Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models |
title_short |
Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models |
title_full |
Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models |
title_fullStr |
Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models |
title_full_unstemmed |
Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models |
title_sort |
cell type-specific in vitro gene expression profiling of stem cell-derived neural models |
publisher |
MDPI AG |
series |
Cells |
issn |
2073-4409 |
publishDate |
2020-06-01 |
description |
Genetic and genomic studies of brain disease increasingly demonstrate disease-associated interactions between the cell types of the brain. Increasingly complex and more physiologically relevant human-induced pluripotent stem cell (hiPSC)-based models better explore the molecular mechanisms underlying disease but also challenge our ability to resolve cell type-specific perturbations. Here, we report an extension of the RiboTag system, first developed to achieve cell type-restricted expression of epitope-tagged ribosomal protein (RPL22) in mouse tissue, to a variety of in vitro applications, including immortalized cell lines, primary mouse astrocytes, and hiPSC-derived neurons. RiboTag expression enables depletion of up to 87 percent of off-target RNA in mixed species co-cultures. Nonetheless, depletion efficiency varies across independent experimental replicates, particularly for hiPSC-derived motor neurons. The challenges and potential of implementing RiboTags in complex in vitro cultures are discussed. |
topic |
hiPSC neuron glia RiboTag bacTRAP genomics |
url |
https://www.mdpi.com/2073-4409/9/6/1406 |
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