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Hertz E, Perez G, Hao Y, Rytel K, Ma C, Kirby M, Anderson S, Wincovitch S, Andersh K, Ahfeldt T, Blanchard J, Qi YA, Lopez G, Tayebi N, Sidransky E, Chen Y. Comparative study of enriched dopaminergic neurons from siblings with Gaucher disease discordant for parkinsonism. bioRxiv 2024:2024.02.25.581985. [PMID: 38529501 PMCID: PMC10962709 DOI: 10.1101/2024.02.25.581985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Inducible pluripotent stem cells (iPSCs) derived from patient samples have significantly enhanced our ability to model neurological diseases. Comparative studies of dopaminergic (DA) neurons differentiated from iPSCs derived from siblings with Gaucher disease discordant for parkinsonism provides a valuable avenue to explore genetic modifiers contributing to GBA1 -associated parkinsonism in disease-relevant cells. However, such studies are often complicated by the inherent heterogeneity in differentiation efficiency among iPSC lines derived from different individuals. To address this technical challenge, we devised a selection strategy to enrich dopaminergic (DA) neurons expressing tyrosine hydroxylase (TH). A neomycin resistance gene (neo) was inserted at the C-terminus of the TH gene following a T2A self-cleavage peptide, placing its expression under the control of the TH promoter. This allows for TH+ DA neuron enrichment through geneticin selection. This method enabled us to generate comparable, high-purity DA neuron cultures from iPSC lines derived from three sisters that we followed for over a decade: one sibling is a healthy individual, and the other two have Gaucher disease (GD) with GBA1 genotype N370S/c.203delC+R257X (p.N409S/c.203delC+p.R296X). Notably, the younger sister with GD later developed Parkinson disease (PD). A comprehensive analysis of these high-purity DA neurons revealed that although GD DA neurons exhibited decreased levels of glucocerebrosidase (GCase), there was no substantial difference in GCase protein levels or lipid substrate accumulation between DA neurons from the GD and GD/PD sisters, suggesting that the PD discordance is related to of other genetic modifiers.
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2
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Wang Q, Wang M, Choi I, Sarrafha L, Liang M, Ho L, Farrell K, Beaumont KG, Sebra R, De Sanctis C, Crary JF, Ahfeldt T, Blanchard J, Neavin D, Powell J, Davis DA, Sun X, Zhang B, Yue Z. Molecular profiling of human substantia nigra identifies diverse neuron types associated with vulnerability in Parkinson's disease. Sci Adv 2024; 10:eadi8287. [PMID: 38198537 PMCID: PMC10780895 DOI: 10.1126/sciadv.adi8287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Parkinson's disease (PD) is characterized pathologically by the loss of dopaminergic (DA) neurons in the substantia nigra (SN). Whether cell types beyond DA neurons in the SN show vulnerability in PD remains unclear. Through transcriptomic profiling of 315,867 high-quality single nuclei in the SN from individuals with and without PD, we identified cell clusters representing various neuron types, glia, endothelial cells, pericytes, fibroblasts, and T cells and investigated cell type-dependent alterations in gene expression in PD. Notably, a unique neuron cluster marked by the expression of RIT2, a PD risk gene, also displayed vulnerability in PD. We validated RIT2-enriched neurons in midbrain organoids and the mouse SN. Our results demonstrated distinct transcriptomic signatures of the RIT2-enriched neurons in the human SN and implicated reduced RIT2 expression in the pathogenesis of PD. Our study sheds light on the diversity of cell types, including DA neurons, in the SN and the complexity of molecular and cellular changes associated with PD pathogenesis.
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Affiliation(s)
- Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Insup Choi
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Lily Sarrafha
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Marianna Liang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Kurt Farrell
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Kristin G. Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Claudia De Sanctis
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - John F. Crary
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, NY 10029, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Ronald Loeb Alzheimer’s Disease Center, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Joel Blanchard
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Ronald Loeb Alzheimer’s Disease Center, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Drew Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, 384 Victoria Street, Sydney 2010, Australia
| | - Joseph Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, 384 Victoria Street, Sydney 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Kensington, Sydney 2052, Australia
| | - David A. Davis
- Department of Neurology, Evelyn F. McKnight Brain Institute, Brain Endowment Bank, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xiaoyan Sun
- Department of Neurology, Evelyn F. McKnight Brain Institute, Brain Endowment Bank, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Zhenyu Yue
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- The Center for Parkinson’s Disease Neurobiology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
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3
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Morrone Parfitt G, Coccia E, Goldman C, Whitney K, Reyes R, Sarrafha L, Nam KH, Sohail S, Jones DR, Crary JF, Ordureau A, Blanchard J, Ahfeldt T. Disruption of lysosomal proteolysis in astrocytes facilitates midbrain organoid proteostasis failure in an early-onset Parkinson's disease model. Nat Commun 2024; 15:447. [PMID: 38200091 PMCID: PMC10781970 DOI: 10.1038/s41467-024-44732-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Accumulation of advanced glycation end products (AGEs) on biopolymers accompanies cellular aging and drives poorly understood disease processes. Here, we studied how AGEs contribute to development of early onset Parkinson's Disease (PD) caused by loss-of-function of DJ1, a protein deglycase. In induced pluripotent stem cell (iPSC)-derived midbrain organoid models deficient for DJ1 activity, we find that lysosomal proteolysis is impaired, causing AGEs to accumulate, α-synuclein (α-syn) phosphorylation to increase, and proteins to aggregate. We demonstrated these processes are at least partly driven by astrocytes, as DJ1 loss reduces their capacity to provide metabolic support and triggers acquisition of a pro-inflammatory phenotype. Consistently, in co-cultures, we find that DJ1-expressing astrocytes are able to reverse the proteolysis deficits of DJ1 knockout midbrain neurons. In conclusion, astrocytes' capacity to clear toxic damaged proteins is critical to preserve neuronal function and their dysfunction contributes to the neurodegeneration observed in a DJ1 loss-of-function PD model.
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Affiliation(s)
- Gustavo Morrone Parfitt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA.
| | - Elena Coccia
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Camille Goldman
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Kristen Whitney
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular, and Cell-Based Medicine at Mount Sinai, New York, NY, USA
| | - Ricardo Reyes
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soha Sohail
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Drew R Jones
- Metabolomics Core Resource Laboratory, NYU Langone Health, New York, NY, USA
| | - John F Crary
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
- Friedman Brain Institute at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence & Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular, and Cell-Based Medicine at Mount Sinai, New York, NY, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel Blanchard
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA.
- Recursion Pharmaceuticals, Salt Lake City, UT, USA.
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4
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Sarrafha L, Neavin DR, Parfitt GM, Kruglikov IA, Whitney K, Reyes R, Coccia E, Kareva T, Goldman C, Tipon R, Croft G, Crary JF, Powell JE, Blanchard J, Ahfeldt T. Novel human pluripotent stem cell-derived hypothalamus organoids demonstrate cellular diversity. iScience 2023; 26:107525. [PMID: 37646018 PMCID: PMC10460991 DOI: 10.1016/j.isci.2023.107525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/19/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023] Open
Abstract
The hypothalamus is a region of the brain that plays an important role in regulating body functions and behaviors. There is a growing interest in human pluripotent stem cells (hPSCs) for modeling diseases that affect the hypothalamus. Here, we established an hPSC-derived hypothalamus organoid differentiation protocol to model the cellular diversity of this brain region. Using an hPSC line with a tyrosine hydroxylase (TH)-TdTomato reporter for dopaminergic neurons (DNs) and other TH-expressing cells, we interrogated DN-specific pathways and functions in electrophysiologically active hypothalamus organoids. Single-cell RNA sequencing (scRNA-seq) revealed diverse neuronal and non-neuronal cell types in mature hypothalamus organoids. We identified several molecularly distinct hypothalamic DN subtypes that demonstrated different developmental maturities. Our in vitro 3D hypothalamus differentiation protocol can be used to study the development of this critical brain structure and can be applied to disease modeling to generate novel therapeutic approaches for disorders centered around the hypothalamus.
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Affiliation(s)
- Lily Sarrafha
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Drew R. Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Gustavo M. Parfitt
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | | | - Kristen Whitney
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Mount Sinai, New York, NY 10029, USA
| | - Ricardo Reyes
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Elena Coccia
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Tatyana Kareva
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Camille Goldman
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Regine Tipon
- New York Stem Cell Foundation, New York, NY 10019, USA
| | - Gist Croft
- New York Stem Cell Foundation, New York, NY 10019, USA
| | - John F. Crary
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Mount Sinai, New York, NY 10029, USA
- Windreich Department of Artificial Intelligence and Human Health, Mount Sinai, New York, NY 10029, USA
| | - Joseph E. Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | - Joel Blanchard
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY 10029, USA
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5
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Ferreira AC, Hemmer BM, Philippi SM, Grau-Perales AB, Rosenstadt JL, Liu H, Zhu JD, Kareva T, Ahfeldt T, Varghese M, Hof PR, Castellano JM. Neuronal TIMP2 regulates hippocampus-dependent plasticity and extracellular matrix complexity. Mol Psychiatry 2023; 28:3943-3954. [PMID: 37914840 PMCID: PMC10730400 DOI: 10.1038/s41380-023-02296-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/27/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Functional output of the hippocampus, a brain region subserving memory function, depends on highly orchestrated cellular and molecular processes that regulate synaptic plasticity throughout life. The structural requirements of such plasticity and molecular events involved in this regulation are poorly understood. Specific molecules, including tissue inhibitor of metalloproteinases-2 (TIMP2) have been implicated in plasticity processes in the hippocampus, a role that decreases with brain aging as expression is lost. Here, we report that TIMP2 is highly expressed by neurons within the hippocampus and its loss drives changes in cellular programs related to adult neurogenesis and dendritic spine turnover with corresponding impairments in hippocampus-dependent memory. Consistent with the accumulation of extracellular matrix (ECM) in the hippocampus we observe with aging, we find that TIMP2 acts to reduce accumulation of ECM around synapses in the hippocampus. Moreover, its deletion results in hindrance of newborn neuron migration through a denser ECM network. A novel conditional TIMP2 knockout (KO) model reveals that neuronal TIMP2 regulates adult neurogenesis, accumulation of ECM, and ultimately hippocampus-dependent memory. Our results define a mechanism whereby hippocampus-dependent function is regulated by TIMP2 and its interactions with the ECM to regulate diverse processes associated with synaptic plasticity.
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Affiliation(s)
- Ana Catarina Ferreira
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brittany M Hemmer
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah M Philippi
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alejandro B Grau-Perales
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacob L Rosenstadt
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hanxiao Liu
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey D Zhu
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tatyana Kareva
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Merina Varghese
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph M Castellano
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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Paul KC, Krolewski RC, Lucumi Moreno E, Blank J, Holton KM, Ahfeldt T, Furlong M, Yu Y, Cockburn M, Thompson LK, Kreymerman A, Ricci-Blair EM, Li YJ, Patel HB, Lee RT, Bronstein J, Rubin LL, Khurana V, Ritz B. Publisher Correction: A pesticide and iPSC dopaminergic neuron screen identifies and classifies Parkinson-relevant pesticides. Nat Commun 2023; 14:3747. [PMID: 37353544 PMCID: PMC10290090 DOI: 10.1038/s41467-023-39001-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023] Open
Affiliation(s)
- Kimberly C Paul
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA.
| | - Richard C Krolewski
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Edinson Lucumi Moreno
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Kristina M Holton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tim Ahfeldt
- Recursion Pharmaceuticals, Salt Lake City, UT, USA
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
| | - Melissa Furlong
- University of Arizona, Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA
| | - Yu Yu
- UCLA Center for Health Policy Research, Los Angeles, CA, USA
| | - Myles Cockburn
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Laura K Thompson
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alexander Kreymerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Yu Jun Li
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Heer B Patel
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Richard T Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis St, Boston, MA, 02115, USA
| | - Jeff Bronstein
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Vikram Khurana
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Beate Ritz
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA.
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7
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Paul KC, Krolewski RC, Lucumi Moreno E, Blank J, Holton KM, Ahfeldt T, Furlong M, Yu Y, Cockburn M, Thompson LK, Kreymerman A, Ricci-Blair EM, Li YJ, Patel HB, Lee RT, Bronstein J, Rubin LL, Khurana V, Ritz B. A pesticide and iPSC dopaminergic neuron screen identifies and classifies Parkinson-relevant pesticides. Nat Commun 2023; 14:2803. [PMID: 37193692 PMCID: PMC10188516 DOI: 10.1038/s41467-023-38215-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/20/2023] [Indexed: 05/18/2023] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease with etiology rooted in genetic vulnerability and environmental factors. Here we combine quantitative epidemiologic study of pesticide exposures and PD with toxicity screening in dopaminergic neurons derived from PD patient induced pluripotent stem cells (iPSCs) to identify Parkinson's-relevant pesticides. Agricultural records enable investigation of 288 specific pesticides and PD risk in a comprehensive, pesticide-wide association study. We associate long-term exposure to 53 pesticides with PD and identify co-exposure profiles. We then employ a live-cell imaging screening paradigm exposing dopaminergic neurons to 39 PD-associated pesticides. We find that 10 pesticides are directly toxic to these neurons. Further, we analyze pesticides typically used in combinations in cotton farming, demonstrating that co-exposures result in greater toxicity than any single pesticide. We find trifluralin is a driver of toxicity to dopaminergic neurons and leads to mitochondrial dysfunction. Our paradigm may prove useful to mechanistically dissect pesticide exposures implicated in PD risk and guide agricultural policy.
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Affiliation(s)
- Kimberly C Paul
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA.
| | - Richard C Krolewski
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Edinson Lucumi Moreno
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Kristina M Holton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tim Ahfeldt
- Recursion Pharmaceuticals, Salt Lake City, UT, USA
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY, USA
| | - Melissa Furlong
- University of Arizona, Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA
| | - Yu Yu
- UCLA Center for Health Policy Research, Los Angeles, CA, USA
| | - Myles Cockburn
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Laura K Thompson
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alexander Kreymerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Yu Jun Li
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Heer B Patel
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Richard T Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis St, Boston, MA, 02115, USA
| | - Jeff Bronstein
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Vikram Khurana
- Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Beate Ritz
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA.
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8
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Pantazis CB, Yang A, Lara E, McDonough JA, Blauwendraat C, Peng L, Oguro H, Kanaujiya J, Zou J, Sebesta D, Pratt G, Cross E, Blockwick J, Buxton P, Kinner-Bibeau L, Medura C, Tompkins C, Hughes S, Santiana M, Faghri F, Nalls MA, Vitale D, Ballard S, Qi YA, Ramos DM, Anderson KM, Stadler J, Narayan P, Papademetriou J, Reilly L, Nelson MP, Aggarwal S, Rosen LU, Kirwan P, Pisupati V, Coon SL, Scholz SW, Priebe T, Öttl M, Dong J, Meijer M, Janssen LJM, Lourenco VS, van der Kant R, Crusius D, Paquet D, Raulin AC, Bu G, Held A, Wainger BJ, Gabriele RMC, Casey JM, Wray S, Abu-Bonsrah D, Parish CL, Beccari MS, Cleveland DW, Li E, Rose IVL, Kampmann M, Calatayud Aristoy C, Verstreken P, Heinrich L, Chen MY, Schüle B, Dou D, Holzbaur ELF, Zanellati MC, Basundra R, Deshmukh M, Cohen S, Khanna R, Raman M, Nevin ZS, Matia M, Van Lent J, Timmerman V, Conklin BR, Johnson Chase K, Zhang K, Funes S, Bosco DA, Erlebach L, Welzer M, Kronenberg-Versteeg D, Lyu G, Arenas E, Coccia E, Sarrafha L, Ahfeldt T, Marioni JC, Skarnes WC, Cookson MR, Ward ME, Merkle FT. A reference human induced pluripotent stem cell line for large-scale collaborative studies. Cell Stem Cell 2022; 29:1685-1702.e22. [PMID: 36459969 PMCID: PMC9782786 DOI: 10.1016/j.stem.2022.11.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 10/07/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.
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Affiliation(s)
- Caroline B Pantazis
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Andrian Yang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Erika Lara
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lirong Peng
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA; Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Hideyuki Oguro
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jitendra Kanaujiya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jizhong Zou
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | | | - Marianita Santiana
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Daniel Vitale
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Shannon Ballard
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kailyn M Anderson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Julia Stadler
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Priyanka Narayan
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Genetics and Biochemistry Branch, NIDDK, NINDS, National Institutes of Health, Bethesda, MD 20814, USA
| | - Jason Papademetriou
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Luke Reilly
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sanya Aggarwal
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Leah U Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Kirwan
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Venkat Pisupati
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Steven L Coon
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Theresa Priebe
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Miriam Öttl
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Jian Dong
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Marieke Meijer
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Lara J M Janssen
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Vanessa S Lourenco
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Rik van der Kant
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands; Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, the Netherlands
| | - Dennis Crusius
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | | | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Aaron Held
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian J Wainger
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rebecca M C Gabriele
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Jackie M Casey
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Selina Wray
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Dad Abu-Bonsrah
- The Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Pediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Clare L Parish
- The Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine and Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine and Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Emmy Li
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Carles Calatayud Aristoy
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven, Belgium
| | - Laurin Heinrich
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Max Y Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dan Dou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria Clara Zanellati
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richa Basundra
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mohanish Deshmukh
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richa Khanna
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | | | | | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | | | | | - Ke Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Salome Funes
- Department of Neurology, UMass Chan Medical School, Worcester, MA, USA
| | - Daryl A Bosco
- Department of Neurology, UMass Chan Medical School, Worcester, MA, USA
| | - Lena Erlebach
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Marc Welzer
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Deborah Kronenberg-Versteeg
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Guochang Lyu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ernest Arenas
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elena Coccia
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Mark R Cookson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Michael E Ward
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Florian T Merkle
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
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9
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Ordureau A, Kraus F, Zhang J, An H, Park S, Ahfeldt T, Paulo JA, Harper JW. Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy. Mol Cell 2021; 81:5082-5098.e11. [PMID: 34699746 DOI: 10.1016/j.molcel.2021.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/23/2021] [Accepted: 10/01/2021] [Indexed: 12/18/2022]
Abstract
Cell state changes are associated with proteome remodeling to serve newly emergent cell functions. Here, we show that NGN2-driven conversion of human embryonic stem cells to induced neurons (iNeurons) is associated with increased PINK1-independent mitophagic flux that is temporally correlated with metabolic reprogramming to support oxidative phosphorylation. Global multiplex proteomics during neurogenesis revealed large-scale remodeling of functional modules linked with pluripotency, mitochondrial metabolism, and proteostasis. Differentiation-dependent mitophagic flux required BNIP3L and its LC3-interacting region (LIR) motif, and BNIP3L also promoted mitophagy in dopaminergic neurons. Proteomic analysis of ATG12-/- iNeurons revealed accumulation of endoplasmic reticulum, Golgi, and mitochondria during differentiation, indicative of widespread organelle remodeling during neurogenesis. This work reveals broad organelle remodeling of membrane-bound organelles during NGN2-driven neurogenesis via autophagy, identifies BNIP3L's central role in programmed mitophagic flux, and provides a proteomic resource for elucidating how organelle remodeling and autophagy alter the proteome during changes in cell state.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
| | - Felix Kraus
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Heeseon An
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sookhee Park
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA; Department of Neurology at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA; Ronald M. Loeb Center for Alzheimer's Disease at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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10
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Navarro E, Udine E, de Paiva Lopes K, Parks M, Riboldi G, Schilder BM, Humphrey J, Snijders GJL, Vialle RA, Zhuang M, Sikder T, Argyrou C, Allan A, Chao MJ, Farrell K, Henderson B, Simon S, Raymond D, Elango S, Ortega RA, Shanker V, Swan M, Zhu CW, Ramdhani R, Walker RH, Tse W, Sano M, Pereira AC, Ahfeldt T, Goate AM, Bressman S, Crary JF, de Witte L, Frucht S, Saunders-Pullman R, Raj T. Dysregulation of mitochondrial and proteolysosomal genes in Parkinson's disease myeloid cells. Nat Aging 2021; 1:850-863. [PMID: 35005630 PMCID: PMC8728893 DOI: 10.1038/s43587-021-00110-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
An increasing number of identified Parkinson's disease (PD) risk loci contain genes highly expressed in innate immune cells, yet their role in pathology is not understood. We hypothesize that PD susceptibility genes modulate disease risk by influencing gene expression within immune cells. To address this, we have generated transcriptomic profiles of monocytes from 230 individuals with sporadic PD and healthy subjects. We observed a dysregulation of mitochondrial and proteasomal pathways. We also generated transcriptomic profiles of primary microglia from brains of 55 subjects and observed discordant transcriptomic signatures of mitochondrial genes in PD monocytes and microglia. We further identified 17 PD susceptibility genes whose expression, relative to each risk allele, is altered in monocytes. These findings reveal widespread transcriptomic alterations in PD monocytes, with some being distinct from microglia, and facilitate efforts to understand the roles of myeloid cells in PD as well as the development of biomarkers.
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Affiliation(s)
- Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Evan Udine
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Madison Parks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Giulietta Riboldi
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
- Universita degli Studi di Milano, Molecular and Translational Medicine, Milan, Italy
| | - Brian M. Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gijsje J. L. Snijders
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Mental Illness Research Education Clinical, Centers of Excellence, VA, Mental Health, Veterans, Bronx, United States of America
| | - Ricardo A. Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Maojuan Zhuang
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Tamjeed Sikder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Charalambos Argyrou
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Amanda Allan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Michael J. Chao
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Kurt Farrell
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Brooklyn Henderson
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
| | - Sarah Simon
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Deborah Raymond
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Sonya Elango
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Roberto A. Ortega
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Vicki Shanker
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Matthew Swan
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Carolyn W. Zhu
- Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Geriatric Research, Education and Clinical Centers (GRECC), James J. Peters VA Medical Center, Bronx, New York, NY, United States of America
- Alzheimer's Disease Research Center (ADRC), Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ritesh Ramdhani
- Department of Neurology, Zucker School of Medicine at Hofstra Northwell, New York, NY, United States of America
| | - Ruth H. Walker
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, James J. Peters VA Medical Center, Bronx, NY, United States of America
| | - Winona Tse
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Mary Sano
- Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Geriatric Research, Education and Clinical Centers (GRECC), James J. Peters VA Medical Center, Bronx, New York, NY, United States of America
- Alzheimer's Disease Research Center (ADRC), Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ana C. Pereira
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alison M. Goate
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Susan Bressman
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - John F. Crary
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Lotje de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Mental Illness Research Education Clinical, Centers of Excellence, VA, Mental Health, Veterans, Bronx, United States of America
| | - Steven Frucht
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
| | - Rachel Saunders-Pullman
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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11
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Sarrafha L, Parfitt GM, Reyes R, Goldman C, Coccia E, Kareva T, Ahfeldt T. High-throughput generation of midbrain dopaminergic neuron organoids from reporter human pluripotent stem cells. STAR Protoc 2021; 2:100463. [PMID: 33997803 PMCID: PMC8086141 DOI: 10.1016/j.xpro.2021.100463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Here, we describe a high-throughput 3D differentiation protocol for deriving midbrain dopaminergic neurons from human pluripotent stem cells. The use of organoids has become prevalent in disease modeling, but there is a high demand for more homogeneous cultures. Our approach is advantageous for large-scale production of uniform midbrain organoids that can be maintained in diverse formats, and our reporters allow for sorting of dopaminergic neurons. The maturing long-term organoid cultures can be used as a model for the entire midbrain. For complete details on the use and execution of this protocol, please refer to Ahfeldt et al. (2020).
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Affiliation(s)
- Lily Sarrafha
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA
- Department of Neurology at Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Gustavo M. Parfitt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA
- Department of Neurology at Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Ricardo Reyes
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA
- Department of Neurology at Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Camille Goldman
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA
- Department of Neurology at Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Elena Coccia
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA
- Department of Neurology at Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Tatyana Kareva
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA
- Department of Neurology at Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience at Mount Sinai, New York, NY 10029, USA
- Department of Neurology at Mount Sinai, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology at Mount Sinai, New York, NY 10029, USA
- Ronald M. Loeb Center for Alzheimer’s Disease at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute at Mount Sinai, New York, NY 10029, USA
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12
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Coccia E, Ahfeldt T. Towards physiologically relevant human pluripotent stem cell (hPSC) models of Parkinson's disease. Stem Cell Res Ther 2021; 12:253. [PMID: 33926571 PMCID: PMC8082939 DOI: 10.1186/s13287-021-02326-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/05/2021] [Indexed: 02/06/2023] Open
Abstract
The derivation of human embryonic stem cells followed by the discovery of induced pluripotent stem cells and leaps in genome editing approaches have continuously fueled enthusiasm for the development of new models of neurodegenerative diseases such as Parkinson's disease (PD). PD is characterized by the relative selective loss of dopaminergic neurons (DNs) in specific areas of substantia nigra pars compacta (SNpc). While degeneration in late stages can be widespread, there is stereotypic early degeneration of these uniquely vulnerable neurons. Various causes of selective vulnerability have been investigated but much remains unclear. Most studies have sought to identify cell autonomous properties of the most vulnerable neurons. However, recent findings from genetic studies and model systems have added to our understanding of non-cell autonomous contributions including regional-specific neuro-immune interactions with astrocytes, resident or damage-activated microglia, neuro-glia cell metabolic interactions, involvement of endothelial cells, and damage to the vascular system. All of these contribute to specific vulnerability and, along with aging and environmental factors, might be integrated in a complex stressor-threshold model of neurodegeneration. In this forward-looking review, we synthesize recent advances in the field of PD modeling using human pluripotent stem cells, with an emphasis on organoid and complex co-culture models of the nigrostriatal niche, with emerging CRISPR applications to edit or perturb expression of causal PD genes and associated risk factors, such as GBA, to understand the impact of these genes on relevant phenotypes.
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Affiliation(s)
- Elena Coccia
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
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13
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Abstract
The genetic architecture of each individual comprises common and rare variants that, acting alone and in combination, confer risk of disease. The cell-type-specific and/or context-dependent functional consequences of the risk variants linked to brain disease must be resolved. Coupling human induced pluripotent stem cell (hiPSC)-based technology with CRISPR-based genome engineering facilitates precise isogenic comparisons of variants across genetic backgrounds. Although functional-validation studies are typically performed on one variant in isolation and in one cell type at a time, complex genetic diseases require multiplexed gene perturbations to interrogate combinations of genes and resolve physiologically relevant disease biology. Our aim is to discuss advances at the intersection of genomics, hiPSCs and CRISPR. A better understanding of the molecular mechanisms underlying disease risk will improve genetic diagnosis, drive phenotypic drug discovery and pave the way toward precision medicine.
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Affiliation(s)
- Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Alper Neural Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Alper Neural Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Alper Neural Stem Cell Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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14
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Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, Hou Z, Heo JM, Rubin LL, Sidhu SS, Gygi SP, Harper JW. Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell 2018; 70:211-227.e8. [PMID: 29656925 DOI: 10.1016/j.molcel.2018.03.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/21/2018] [Accepted: 03/08/2018] [Indexed: 11/24/2022]
Abstract
Flux through kinase and ubiquitin-driven signaling systems depends on the modification kinetics, stoichiometry, primary site specificity, and target abundance within the pathway, yet we rarely understand these parameters and their spatial organization within cells. Here we develop temporal digital snapshots of ubiquitin signaling on the mitochondrial outer membrane in embryonic stem cell-derived neurons, and we model HeLa cell systems upon activation of the PINK1 kinase and PARKIN ubiquitin ligase by proteomic counting of ubiquitylation and phosphorylation events. We define the kinetics and site specificity of PARKIN-dependent target ubiquitylation, and we demonstrate the power of this approach to quantify pathway modulators and to mechanistically define the role of PARKIN UBL phosphorylation in pathway activation in induced neurons. Finally, through modulation of pS65-Ub on mitochondria, we demonstrate that Ub hyper-phosphorylation is inhibitory to mitophagy receptor recruitment, indicating that pS65-Ub stoichiometry in vivo is optimized to coordinate PARKIN recruitment via pS65-Ub and mitophagy receptors via unphosphorylated chains.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Tim Ahfeldt
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02132, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Erin F Cohn
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhonggang Hou
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02132, USA
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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15
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Abstract
Utilizing patient derived cells has enormous promise for discovering new drugs for diseases of the nervous system, a goal that has been historically quite challenging. In this review, we will outline the potential of human stem cell derived neuron models for assessing therapeutics and high-throughput screening and compare to more traditional drug discovery strategies. We summarize recent successes of the approach and discuss special considerations for developing human stem cell based assays. New technologies, such as genome editing, offer improvements to help overcome the challenges that remain. Finally, human neurons derived from patient cells have advantages for translational research beyond drug screening as they can also be used to identify individual efficacy and safety prior to clinical testing and for dissecting disease mechanisms. This article is part of a Special Issue entitled SI: Exploiting human neurons.
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Affiliation(s)
- Tim Ahfeldt
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
| | - Nadia K. Litterman
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
| | - Lee L. Rubin
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
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16
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Madison JM, Zhou F, Nigam A, Hussain A, Barker DD, Nehme R, van der Ven K, Hsu J, Wolf P, Fleishman M, O’Dushlaine C, Rose S, Chambert K, Lau FH, Ahfeldt T, Rueckert EH, Sheridan SD, Fass DM, Nemesh J, Mullen TE, Daheron L, McCarroll S, Sklar P, Perlis RH, Haggarty SJ. Characterization of bipolar disorder patient-specific induced pluripotent stem cells from a family reveals neurodevelopmental and mRNA expression abnormalities. Mol Psychiatry 2015; 20:703-17. [PMID: 25733313 PMCID: PMC4440839 DOI: 10.1038/mp.2015.7] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 10/29/2014] [Accepted: 12/19/2014] [Indexed: 02/07/2023]
Abstract
Bipolar disorder (BD) is a common neuropsychiatric disorder characterized by chronic recurrent episodes of depression and mania. Despite evidence for high heritability of BD, little is known about its underlying pathophysiology. To develop new tools for investigating the molecular and cellular basis of BD, we applied a family-based paradigm to derive and characterize a set of 12 induced pluripotent stem cell (iPSC) lines from a quartet consisting of two BD-affected brothers and their two unaffected parents. Initially, no significant phenotypic differences were observed between iPSCs derived from the different family members. However, upon directed neural differentiation, we observed that CXCR4 (CXC chemokine receptor-4) expressing central nervous system (CNS) neural progenitor cells (NPCs) from both BD patients compared with their unaffected parents exhibited multiple phenotypic differences at the level of neurogenesis and expression of genes critical for neuroplasticity, including WNT pathway components and ion channel subunits. Treatment of the CXCR4(+) NPCs with a pharmacological inhibitor of glycogen synthase kinase 3, a known regulator of WNT signaling, was found to rescue a progenitor proliferation deficit in the BD patient NPCs. Taken together, these studies provide new cellular tools for dissecting the pathophysiology of BD and evidence for dysregulation of key pathways involved in neurodevelopment and neuroplasticity. Future generation of additional iPSCs following a family-based paradigm for modeling complex neuropsychiatric disorders in conjunction with in-depth phenotyping holds promise for providing insights into the pathophysiological substrates of BD and is likely to inform the development of targeted therapeutics for its treatment and ideally prevention.
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Affiliation(s)
- Jon M. Madison
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA,Correspondence: (JM), (SJH)
| | - Fen Zhou
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aparna Nigam
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ali Hussain
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Douglas D. Barker
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA,Department of Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, MA 02114, USA
| | - Karlijn van der Ven
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jenny Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Pavlina Wolf
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, MA 02114, USA
| | - Morgan Fleishman
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Colm O’Dushlaine
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Sam Rose
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Kimberly Chambert
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Frank H. Lau
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA
| | - Tim Ahfeldt
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA
| | - Erroll H. Rueckert
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA,Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Steven D. Sheridan
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel M. Fass
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Department of Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, MA 02114, USA,Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas E. Mullen
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Laurence Daheron
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA
| | - Steve McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela Sklar
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Roy H. Perlis
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA,Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephen J. Haggarty
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA,Psychiatric & Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Neurology, Massachusetts General Hospital & Harvard Medical School, Boston, MA 02114, USA,Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA,Correspondence: (JM), (SJH)
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17
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Ding Q, Lee YK, Schaefer EAK, Peters DT, Veres A, Kim K, Kuperwasser N, Motola DL, Meissner TB, Hendriks WT, Trevisan M, Gupta RM, Moisan A, Banks E, Friesen M, Schinzel RT, Xia F, Tang A, Xia Y, Figueroa E, Wann A, Ahfeldt T, Daheron L, Zhang F, Rubin LL, Peng LF, Chung RT, Musunuru K, Cowan CA. A TALEN genome-editing system for generating human stem cell-based disease models. Cell Stem Cell 2012; 12:238-51. [PMID: 23246482 DOI: 10.1016/j.stem.2012.11.011] [Citation(s) in RCA: 376] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 10/19/2012] [Accepted: 11/12/2012] [Indexed: 10/27/2022]
Abstract
Transcription activator-like effector nucleases (TALENs) are a new class of engineered nucleases that are easier to design to cleave at desired sites in a genome than previous types of nucleases. We report here the use of TALENs to rapidly and efficiently generate mutant alleles of 15 genes in cultured somatic cells or human pluripotent stem cells, the latter for which we differentiated both the targeted lines and isogenic control lines into various metabolic cell types. We demonstrate cell-autonomous phenotypes directly linked to disease-dyslipidemia, insulin resistance, hypoglycemia, lipodystrophy, motor-neuron death, and hepatitis C infection. We found little evidence of TALEN off-target effects, but each clonal line nevertheless harbors a significant number of unique mutations. Given the speed and ease with which we were able to derive and characterize these cell lines, we anticipate TALEN-mediated genome editing of human cells becoming a mainstay for the investigation of human biology and disease.
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Affiliation(s)
- Qiurong Ding
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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18
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Mou H, Zhao R, Sherwood R, Ahfeldt T, Lapey A, Wain J, Sicilian L, Izvolsky K, Musunuru K, Cowan C, Rajagopal J. Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs. Cell Stem Cell 2012; 10:385-97. [PMID: 22482504 DOI: 10.1016/j.stem.2012.01.018] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 12/15/2011] [Accepted: 01/19/2012] [Indexed: 12/15/2022]
Abstract
Deriving lung progenitors from patient-specific pluripotent cells is a key step in producing differentiated lung epithelium for disease modeling and transplantation. By mimicking the signaling events that occur during mouse lung development, we generated murine lung progenitors in a series of discrete steps. Definitive endoderm derived from mouse embryonic stem cells (ESCs) was converted into foregut endoderm, then into replicating Nkx2.1+ lung endoderm, and finally into multipotent embryonic lung progenitor and airway progenitor cells. We demonstrated that precisely-timed BMP, FGF, and WNT signaling are required for NKX2.1 induction. Mouse ESC-derived Nkx2.1+ progenitor cells formed respiratory epithelium (tracheospheres) when transplanted subcutaneously into mice. We then adapted this strategy to produce disease-specific lung progenitor cells from human Cystic Fibrosis induced pluripotent stem cells (iPSCs), creating a platform for dissecting human lung disease. These disease-specific human lung progenitors formed respiratory epithelium when subcutaneously engrafted into immunodeficient mice.
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Affiliation(s)
- Hongmei Mou
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, 02114, USA
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19
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Schinzel RT, Ahfeldt T, Lau FH, Lee YK, Cowley A, Shen T, Peters D, Lum DH, Cowan CA. Efficient culturing and genetic manipulation of human pluripotent stem cells. PLoS One 2011; 6:e27495. [PMID: 22194785 PMCID: PMC3240614 DOI: 10.1371/journal.pone.0027495] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 10/18/2011] [Indexed: 11/19/2022] Open
Abstract
Human pluripotent stem cells (hPSC) hold great promise as models for understanding disease and as a source of cells for transplantation therapies. However, the lack of simple, robust and efficient culture methods remains a significant obstacle for realizing the utility of hPSCs. Here we describe a platform for the culture of hPSCs that 1) allows for dissociation and replating of single cells, 2) significantly increases viability and replating efficiency, 3) improves freeze/thaw viability 4) improves cloning efficiency and 5) colony size variation. When combined with standard methodologies for genetic manipulation, we found that the enhanced culture platform allowed for lentiviral transduction rates of up to 95% and electroporation efficiencies of up to 25%, with a significant increase in the total number of antibiotic-selected colonies for screening for homologous recombination. We further demonstrated the utility of the enhanced culture platform by successfully targeting the ISL1 locus. We conclude that many of the difficulties associated with culturing and genetic manipulation of hPSCs can be addressed with optimized culture conditions, and we suggest that the use of the enhanced culture platform could greatly improve the ease of handling and general utility of hPSCs.
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Affiliation(s)
- Robert T. Schinzel
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Institut für Biologie - Mikrobiologie, Fachbereich Biologie, Chemie, Pharmazie, Freie Universität Berlin, Berlin, Germany
| | - Tim Ahfeldt
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Frank H. Lau
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Youn-Kyoung Lee
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Alicia Cowley
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard College, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tony Shen
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard College, Harvard University, Cambridge, Massachusetts, United States of America
| | - Derek Peters
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - David H. Lum
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States of America
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Chad A. Cowan
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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20
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Lau FH, Deo RC, Mowrer G, Caplin J, Ahfeldt T, Kaplan A, Ptaszek L, Walker JD, Rosengard BR, Cowan CA. Pattern specification and immune response transcriptional signatures of pericardial and subcutaneous adipose tissue. PLoS One 2011; 6:e26092. [PMID: 22022522 PMCID: PMC3191160 DOI: 10.1371/journal.pone.0026092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 09/19/2011] [Indexed: 11/18/2022] Open
Abstract
Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality in the United States. Recent studies suggest that pericardial adipose tissue (PCAT) secretes inflammatory factors that contribute to the development of CVD. To better characterize the role of PCAT in the pathogenesis of disease, we performed a large-scale unbiased analysis of the transcriptional differences between PCAT and subcutaneous adipose tissue, analysing 53 microarrays across 19 individuals. As it was unknown whether PCAT-secreted factors are produced by adipocytes or cells in the supporting stromal fraction, we also sought to identify differentially expressed genes in isolated pericardial adipocytes vs. isolated subcutaneous adipocytes. Using microarray analysis, we found that: 1) pericardial adipose tissue and isolated pericardial adipocytes both overexpress atherosclerosis-promoting chemokines and 2) pericardial and subcutaneous fat depots, as well as isolated pericardial adipocytes and subcutaneous adipocytes, express specific patterns of homeobox genes. In contrast, a core set of lipid processing genes showed no significant overlap with differentially expressed transcripts. These depot-specific homeobox signatures and transcriptional profiles strongly suggest different functional roles for the pericardial and subcutaneous adipose depots. Further characterization of these inter-depot differences should be a research priority.
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Affiliation(s)
- Frank H. Lau
- Center for Regenerative Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Rahul C. Deo
- Center for Regenerative Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Gregory Mowrer
- Center for Regenerative Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Joshua Caplin
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Tim Ahfeldt
- Center for Regenerative Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Adam Kaplan
- Center for Regenerative Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Leon Ptaszek
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jennifer D. Walker
- Division of Cardiac Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Bruce R. Rosengard
- Division of Cardiac Surgery, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Chad A. Cowan
- Center for Regenerative Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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21
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Musunuru K, Strong A, Frank-Kamenetsky M, Lee NE, Ahfeldt T, Sachs KV, Li X, Li H, Kuperwasser N, Ruda VM, Pirruccello JP, Muchmore B, Prokunina-Olsson L, Hall JL, Schadt EE, Morales CR, Lund-Katz S, Phillips MC, Wong J, Cantley W, Racie T, Ejebe KG, Orho-Melander M, Melander O, Koteliansky V, Fitzgerald K, Krauss RM, Cowan CA, Kathiresan S, Rader DJ. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 2010; 466:714-9. [PMID: 20686566 DOI: 10.1038/nature09266] [Citation(s) in RCA: 825] [Impact Index Per Article: 58.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 06/09/2010] [Indexed: 12/27/2022]
Abstract
Recent genome-wide association studies (GWASs) have identified a locus on chromosome 1p13 strongly associated with both plasma low-density lipoprotein cholesterol (LDL-C) and myocardial infarction (MI) in humans. Here we show through a series of studies in human cohorts and human-derived hepatocytes that a common noncoding polymorphism at the 1p13 locus, rs12740374, creates a C/EBP (CCAAT/enhancer binding protein) transcription factor binding site and alters the hepatic expression of the SORT1 gene. With small interfering RNA (siRNA) knockdown and viral overexpression in mouse liver, we demonstrate that Sort1 alters plasma LDL-C and very low-density lipoprotein (VLDL) particle levels by modulating hepatic VLDL secretion. Thus, we provide functional evidence for a novel regulatory pathway for lipoprotein metabolism and suggest that modulation of this pathway may alter risk for MI in humans. We also demonstrate that common noncoding DNA variants identified by GWASs can directly contribute to clinical phenotypes.
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Affiliation(s)
- Kiran Musunuru
- Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
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22
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Abstract
Recent advances in nuclear reprogramming technology allow the transformation of terminally differentiated, adult cells into induced pluripotent stem cells whose phenotype is indistinguishable from that of embryonic stem cells. This leap forward enables the creation of patient-specific pluripotent cell lines that carry disease genotypes. These cell lines could be used both as in vitro models for the study of disease and as potential sources of material for cell replacement therapy. Ultimately, a greater understanding of the process by which cellular identity is shaped and altered may allow the generation of particular cell types for the treatment of degenerative disease.
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Affiliation(s)
- Frank Lau
- Stowers Medical Institute and Harvard Stem Cell Institute, Harvard University, Department of Stem Cell and Regenerative Biology, 185 Cambridge Street CPZN 4234, Boston, MA 02114, USA.
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23
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Maherali N, Ahfeldt T, Rigamonti A, Utikal J, Cowan C, Hochedlinger K. A high-efficiency system for the generation and study of human induced pluripotent stem cells. Cell Stem Cell 2008; 3:340-5. [PMID: 18786420 DOI: 10.1016/j.stem.2008.08.003] [Citation(s) in RCA: 347] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 08/07/2008] [Accepted: 08/12/2008] [Indexed: 12/28/2022]
Abstract
Direct reprogramming of human fibroblasts to a pluripotent state has been achieved through ectopic expression of the transcription factors OCT4, SOX2, and either cMYC and KLF4 or NANOG and LIN28. Little is known, however, about the mechanisms by which reprogramming occurs, which is in part limited by the low efficiency of conversion. To this end, we sought to create a doxycycline-inducible lentiviral system to convert primary human fibroblasts and keratinocytes into human induced pluripotent stem cells (hiPSCs). hiPSCs generated with this system were molecularly and functionally similar to human embryonic stem cells (hESCs), demonstrated by gene expression profiles, DNA methylation status, and differentiation potential. While expression of the viral transgenes was required for several weeks in fibroblasts, we found that 10 days was sufficient for the reprogramming of keratinocytes. Using our inducible system, we developed a strategy to induce hiPSC formation at high frequency. Upon addition of doxycycline to hiPSC-derived differentiated cells, we obtained "secondary" hiPSCs at a frequency at least 100-fold greater than the initial conversion. The ability to reprogram cells at high efficiency provides a unique platform to dissect the underlying molecular and biochemical processes that accompany nuclear reprogramming.
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Affiliation(s)
- Nimet Maherali
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Massachusetts General Hospital Center for Regenerative Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
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24
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Park IH, Arora N, Huo H, Maherali N, Ahfeldt T, Shimamura A, Lensch MW, Cowan C, Hochedlinger K, Daley GQ. Disease-specific induced pluripotent stem cells. Cell 2008; 134:877-86. [PMID: 18691744 DOI: 10.1016/j.cell.2008.07.041] [Citation(s) in RCA: 1577] [Impact Index Per Article: 98.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 07/14/2008] [Accepted: 07/30/2008] [Indexed: 12/16/2022]
Abstract
Tissue culture of immortal cell strains from diseased patients is an invaluable resource for medical research but is largely limited to tumor cell lines or transformed derivatives of native tissues. Here we describe the generation of induced pluripotent stem (iPS) cells from patients with a variety of genetic diseases with either Mendelian or complex inheritance; these diseases include adenosine deaminase deficiency-related severe combined immunodeficiency (ADA-SCID), Shwachman-Bodian-Diamond syndrome (SBDS), Gaucher disease (GD) type III, Duchenne (DMD) and Becker muscular dystrophy (BMD), Parkinson disease (PD), Huntington disease (HD), juvenile-onset, type 1 diabetes mellitus (JDM), Down syndrome (DS)/trisomy 21, and the carrier state of Lesch-Nyhan syndrome. Such disease-specific stem cells offer an unprecedented opportunity to recapitulate both normal and pathologic human tissue formation in vitro, thereby enabling disease investigation and drug development.
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Affiliation(s)
- In-Hyun Park
- Department of Medicine, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute, Boston, MA 02115, USA
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