1
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Workman MJ, Lim RG, Wu J, Frank A, Ornelas L, Panther L, Galvez E, Perez D, Meepe I, Lei S, Valencia V, Gomez E, Liu C, Moran R, Pinedo L, Tsitkov S, Ho R, Kaye JA, Thompson T, Rothstein JD, Finkbeiner S, Fraenkel E, Sareen D, Thompson LM, Svendsen CN. Large-scale differentiation of iPSC-derived motor neurons from ALS and control subjects. Neuron 2023; 111:1191-1204.e5. [PMID: 36764301 PMCID: PMC10557526 DOI: 10.1016/j.neuron.2023.01.010] [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: 08/03/2022] [Revised: 11/29/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023]
Abstract
Using induced pluripotent stem cells (iPSCs) to understand the mechanisms of neurological disease holds great promise; however, there is a lack of well-curated lines from a large array of participants. Answer ALS has generated over 1,000 iPSC lines from control and amyotrophic lateral sclerosis (ALS) patients along with clinical and whole-genome sequencing data. The current report summarizes cell marker and gene expression in motor neuron cultures derived from 92 healthy control and 341 ALS participants using a 32-day differentiation protocol. This is the largest set of iPSCs to be differentiated into motor neurons, and characterization suggests that cell composition and sex are significant sources of variability that need to be carefully controlled for in future studies. These data are reported as a resource for the scientific community that will utilize Answer ALS data for disease modeling using a wider array of omics being made available for these samples.
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Affiliation(s)
- Michael J Workman
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ryan G Lim
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Aaron Frank
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Loren Ornelas
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lindsay Panther
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Erick Galvez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Daniel Perez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Imara Meepe
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Lei
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Viviana Valencia
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emilda Gomez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chunyan Liu
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ruby Moran
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Louis Pinedo
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stanislav Tsitkov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ritchie Ho
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Neural Science and Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Julia A Kaye
- Center for Systems and Therapeutics, Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA; Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dhruv Sareen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Leslie M Thompson
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA; Department of Biological Chemistry, University of California, Irvine, CA, USA; Department of Neurobiology and Behavior, University of California, Irvine, CA, USA; Department of Psychiatry and Human Behavior and Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA, USA.
| | - Clive N Svendsen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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2
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Baxi EG, Thompson T, Li J, Kaye JA, Lim RG, Wu J, Ramamoorthy D, Lima L, Vaibhav V, Matlock A, Frank A, Coyne AN, Landin B, Ornelas L, Mosmiller E, Thrower S, Farr SM, Panther L, Gomez E, Galvez E, Perez D, Meepe I, Lei S, Mandefro B, Trost H, Pinedo L, Banuelos MG, Liu C, Moran R, Garcia V, Workman M, Ho R, Wyman S, Roggenbuck J, Harms MB, Stocksdale J, Miramontes R, Wang K, Venkatraman V, Holewenski R, Sundararaman N, Pandey R, Manalo DM, Donde A, Huynh N, Adam M, Wassie BT, Vertudes E, Amirani N, Raja K, Thomas R, Hayes L, Lenail A, Cerezo A, Luppino S, Farrar A, Pothier L, Prina C, Morgan T, Jamil A, Heintzman S, Jockel-Balsarotti J, Karanja E, Markway J, McCallum M, Joslin B, Alibazoglu D, Kolb S, Ajroud-Driss S, Baloh R, Heitzman D, Miller T, Glass JD, Patel-Murray NL, Yu H, Sinani E, Vigneswaran P, Sherman AV, Ahmad O, Roy P, Beavers JC, Zeiler S, Krakauer JW, Agurto C, Cecchi G, Bellard M, Raghav Y, Sachs K, Ehrenberger T, Bruce E, Cudkowicz ME, Maragakis N, Norel R, Van Eyk JE, Finkbeiner S, Berry J, Sareen D, Thompson LM, Fraenkel E, Svendsen CN, Rothstein JD. Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines. Nat Neurosci 2022; 25:226-237. [PMID: 35115730 PMCID: PMC8825283 DOI: 10.1038/s41593-021-01006-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [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: 05/20/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022]
Abstract
Answer ALS is a biological and clinical resource of patient-derived, induced pluripotent stem (iPS) cell lines, multi-omic data derived from iPS neurons and longitudinal clinical and smartphone data from over 1,000 patients with ALS. This resource provides population-level biological and clinical data that may be employed to identify clinical-molecular-biochemical subtypes of amyotrophic lateral sclerosis (ALS). A unique smartphone-based system was employed to collect deep clinical data, including fine motor activity, speech, breathing and linguistics/cognition. The iPS spinal neurons were blood derived from each patient and these cells underwent multi-omic analytics including whole-genome sequencing, RNA transcriptomics, ATAC-sequencing and proteomics. The intent of these data is for the generation of integrated clinical and biological signatures using bioinformatics, statistics and computational biology to establish patterns that may lead to a better understanding of the underlying mechanisms of disease, including subgroup identification. A web portal for open-source sharing of all data was developed for widespread community-based data analytics.
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Affiliation(s)
- Emily G Baxi
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jonathan Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia A Kaye
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan G Lim
- UCI MIND, University of California, Irvine, CA, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Divya Ramamoorthy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leandro Lima
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Vineet Vaibhav
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrea Matlock
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Aaron Frank
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alyssa N Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Barry Landin
- Computational Biology Center, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Loren Ornelas
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Elizabeth Mosmiller
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sara Thrower
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Lindsey Panther
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emilda Gomez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Erick Galvez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Daniel Perez
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Imara Meepe
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Lei
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Berhan Mandefro
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hannah Trost
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Louis Pinedo
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Maria G Banuelos
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chunyan Liu
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ruby Moran
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Veronica Garcia
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael Workman
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richie Ho
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stacia Wyman
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Harms
- Department of Neurology and Genetics, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jennifer Stocksdale
- Department of Psychiatry and Human Behavior and Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA, USA
| | | | - Keona Wang
- Department of Psychiatry and Human Behavior and Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA, USA
| | - Vidya Venkatraman
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ronald Holewenski
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Niveda Sundararaman
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rakhi Pandey
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Danica-Mae Manalo
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Aneesh Donde
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nhan Huynh
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brook T Wassie
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Edward Vertudes
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Naufa Amirani
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Krishna Raja
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben Thomas
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Lindsey Hayes
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alex Lenail
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aianna Cerezo
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Luppino
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alanna Farrar
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lindsay Pothier
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carolyn Prina
- Department of Neurology and Genetics, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Arish Jamil
- Department of Neurology, Emory University, Atlanta, GA, USA
| | - Sarah Heintzman
- Department of Neurology and Genetics, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | | | - Jesse Markway
- Department of Neurology, Washington University, St. Louis, MO, USA
| | - Molly McCallum
- Department of Neurology, Washington University, St. Louis, MO, USA
| | - Ben Joslin
- Department of Neurology, Northwestern University, Chicago, IL, USA
| | - Deniz Alibazoglu
- Department of Neurology, Northwestern University, Chicago, IL, USA
| | - Stephen Kolb
- Department of Neurology and Genetics, Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Robert Baloh
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Tim Miller
- Department of Neurology, Washington University, St. Louis, MO, USA
| | | | | | - Hong Yu
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ervin Sinani
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Prasha Vigneswaran
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander V Sherman
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Omar Ahmad
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Promit Roy
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jay C Beavers
- Microsoft Research, Microsoft Corporation, Redmond, WA, USA
| | - Steven Zeiler
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John W Krakauer
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carla Agurto
- Computational Biology Center, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Guillermo Cecchi
- Computational Biology Center, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Mary Bellard
- Microsoft University Relations, Microsoft Corporation, Redmond, WA, USA
| | - Yogindra Raghav
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Karen Sachs
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tobias Ehrenberger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elizabeth Bruce
- Microsoft University Relations, Microsoft Corporation, Redmond, WA, USA
| | - Merit E Cudkowicz
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicholas Maragakis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Raquel Norel
- Computational Biology Center, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - James Berry
- Department of Neurology, Healey Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dhruv Sareen
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Leslie M Thompson
- UCI MIND, University of California, Irvine, CA, USA
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- Department of Psychiatry and Human Behavior and Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Clive N Svendsen
- Cedars-Sinai Biomanufacturing Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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3
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Walters R, Dee A, Storry P, Ornelas L, Davies A. Body reprogramming. Service improvement analysis of a new group-based therapy for fibromyalgia. Physiotherapy 2021. [DOI: 10.1016/j.physio.2021.10.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Li J, Lim RG, Kaye JA, Dardov V, Coyne AN, Wu J, Milani P, Cheng A, Thompson TG, Ornelas L, Frank A, Adam M, Banuelos MG, Casale M, Cox V, Escalante-Chong R, Daigle JG, Gomez E, Hayes L, Holewenski R, Lei S, Lenail A, Lima L, Mandefro B, Matlock A, Panther L, Patel-Murray NL, Pham J, Ramamoorthy D, Sachs K, Shelley B, Stocksdale J, Trost H, Wilhelm M, Venkatraman V, Wassie BT, Wyman S, Yang S, Van Eyk JE, Lloyd TE, Finkbeiner S, Fraenkel E, Rothstein JD, Sareen D, Svendsen CN, Thompson LM. An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients. iScience 2021; 24:103221. [PMID: 34746695 PMCID: PMC8554488 DOI: 10.1016/j.isci.2021.103221] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/29/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases are challenging for systems biology because of the lack of reliable animal models or patient samples at early disease stages. Induced pluripotent stem cells (iPSCs) could address these challenges. We investigated DNA, RNA, epigenetics, and proteins in iPSC-derived motor neurons from patients with ALS carrying hexanucleotide expansions in C9ORF72. Using integrative computational methods combining all omics datasets, we identified novel and known dysregulated pathways. We used a C9ORF72 Drosophila model to distinguish pathways contributing to disease phenotypes from compensatory ones and confirmed alterations in some pathways in postmortem spinal cord tissue of patients with ALS. A different differentiation protocol was used to derive a separate set of C9ORF72 and control motor neurons. Many individual -omics differed by protocol, but some core dysregulated pathways were consistent. This strategy of analyzing patient-specific neurons provides disease-related outcomes with small numbers of heterogeneous lines and reduces variation from single-omics to elucidate network-based signatures. Multi-omic analysis of differentiated C9ORF72 iPSC-derived motor neurons Network-based integrative computational analysis Pathogenic versus compensatory pathways elucidated using C9ORF72 Drosophila model Pathways confirmed with alternative differentiation protocol and postmortem data
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Affiliation(s)
| | - Jonathan Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan G Lim
- UCI MIND, University of California, Irvine, CA 92697, USA
| | - Julia A Kaye
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Victoria Dardov
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA.,Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alyssa N Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA.,Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Pamela Milani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrew Cheng
- Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | | | - Loren Ornelas
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Aaron Frank
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maria G Banuelos
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Malcolm Casale
- UCI MIND, University of California, Irvine, CA 92697, USA.,Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Veerle Cox
- Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Renan Escalante-Chong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - J Gavin Daigle
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA.,Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Emilda Gomez
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Lindsey Hayes
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Ronald Holewenski
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Lei
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Alex Lenail
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leandro Lima
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Berhan Mandefro
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Andrea Matlock
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lindsay Panther
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | | | - Jacqueline Pham
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Divya Ramamoorthy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karen Sachs
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brandon Shelley
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Jennifer Stocksdale
- UCI MIND, University of California, Irvine, CA 92697, USA.,Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Hannah Trost
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Mark Wilhelm
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Vidya Venkatraman
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brook T Wassie
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stacia Wyman
- Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA 92697, USA
| | - Stephanie Yang
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | | | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Thomas E Lloyd
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA.,Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA.,Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA.,Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Dhruv Sareen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Clive N Svendsen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Leslie M Thompson
- UCI MIND, University of California, Irvine, CA 92697, USA.,Department of Biological Chemistry, University of California, Irvine, CA 92697, USA.,Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA.,Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697, USA.,Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA 92697, USA
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5
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Toombs J, Panther L, Ornelas L, Liu C, Gomez E, Martín-Ibáñez R, Cox SR, Ritchie SJ, Harris SE, Taylor A, Redmond P, Russ TC, Murphy L, Cooper JD, Burr K, Selvaraj BT, Browne C, Svendsen CN, Cowley SA, Deary IJ, Chandran S, Spires-Jones TL, Sareen D. Generation of twenty four induced pluripotent stem cell lines from twenty four members of the Lothian Birth Cohort 1936. Stem Cell Res 2020; 46:101851. [PMID: 32450543 PMCID: PMC7347008 DOI: 10.1016/j.scr.2020.101851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/01/2020] [Accepted: 05/13/2020] [Indexed: 11/19/2022] Open
Abstract
Cognitive decline is among the most feared aspects of ageing. We have generated induced pluripotent stem cells (iPSCs) from 24 people from the Lothian Birth Cohort 1936, whose cognitive ability was tested in childhood and in older age. Peripheral blood mononuclear cells (PBMCs) were reprogrammed using non-integrating oriP/EBNA1 backbone plasmids expressing six iPSC reprogramming factors (OCT3/4 (POU5F1), SOX2, KLF4, L-Myc, shp53, Lin28, SV40LT). All lines demonstrated STR matched karyotype and pluripotency was validated by multiple methods. These iPSC lines are a valuable resource to study molecular mechanisms underlying individual differences in cognitive ageing and resilience to age-related neurodegenerative diseases.
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Affiliation(s)
- Jamie Toombs
- Centre for Discovery Brain Sciences, UK Dementia Research Institute, The University of Edinburgh, UK
| | - Lindsay Panther
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | - Loren Ornelas
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | - Chunyan Liu
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | - Emilda Gomez
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | | | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Stuart J Ritchie
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Adele Taylor
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tom C Russ
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK; Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - James D Cooper
- Dementia Research Institute at the University of Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Karen Burr
- Dementia Research Institute at the University of Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Bhuvaneish T Selvaraj
- Dementia Research Institute at the University of Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Cathy Browne
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Clive N Svendsen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Sally A Cowley
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; Oxford Parkinson's Disease Centre, Oxford, UK
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- Dementia Research Institute at the University of Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Tara L Spires-Jones
- Centre for Discovery Brain Sciences, UK Dementia Research Institute, The University of Edinburgh, UK.
| | - Dhruv Sareen
- iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA; Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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6
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Das Sharma S, Pal R, Reddy BK, Selvaraj BT, Raj N, Samaga KK, Srinivasan DJ, Ornelas L, Sareen D, Livesey MR, Bassell GJ, Svendsen CN, Kind PC, Chandran S, Chattarji S, Wyllie DJA. Cortical neurons derived from human pluripotent stem cells lacking FMRP display altered spontaneous firing patterns. Mol Autism 2020; 11:52. [PMID: 32560741 PMCID: PMC7304215 DOI: 10.1186/s13229-020-00351-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/11/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Fragile X syndrome (FXS), a neurodevelopmental disorder, is a leading monogenetic cause of intellectual disability and autism spectrum disorder. Notwithstanding the extensive studies using rodent and other pre-clinical models of FXS, which have provided detailed mechanistic insights into the pathophysiology of this disorder, it is only relatively recently that human stem cell-derived neurons have been employed as a model system to further our understanding of the pathophysiological events that may underlie FXS. Our study assesses the physiological properties of human pluripotent stem cell-derived cortical neurons lacking fragile X mental retardation protein (FMRP). METHODS Electrophysiological whole-cell voltage- and current-clamp recordings were performed on two control and three FXS patient lines of human cortical neurons derived from induced pluripotent stem cells. In addition, we also describe the properties of an isogenic pair of lines in one of which FMR1 gene expression has been silenced. RESULTS Neurons lacking FMRP displayed bursts of spontaneous action potential firing that were more frequent but shorter in duration compared to those recorded from neurons expressing FMRP. Inhibition of large conductance Ca2+-activated K+ currents and the persistent Na+ current in control neurons phenocopies action potential bursting observed in neurons lacking FMRP, while in neurons lacking FMRP pharmacological potentiation of voltage-dependent Na+ channels phenocopies action potential bursting observed in control neurons. Notwithstanding the changes in spontaneous action potential firing, we did not observe any differences in the intrinsic properties of neurons in any of the lines examined. Moreover, we did not detect any differences in the properties of miniature excitatory postsynaptic currents in any of the lines. CONCLUSIONS Pharmacological manipulations can alter the action potential burst profiles in both control and FMRP-null human cortical neurons, making them appear like their genetic counterpart. Our studies indicate that FMRP targets that have been found in rodent models of FXS are also potential targets in a human-based model system, and we suggest potential mechanisms by which activity is altered.
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Affiliation(s)
- Shreya Das Sharma
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India.,The University of Trans-Displinary Health Sciences and Technology, Bangalore, 560064, India
| | - Rakhi Pal
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India
| | - Bharath Kumar Reddy
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India
| | - Bhuvaneish T Selvaraj
- Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, Edinburgh, EH16 4SB, UK.,UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh, EH16 4SB, UK
| | - Nisha Raj
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Krishna Kumar Samaga
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India
| | - Durga J Srinivasan
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India.,The University of Trans-Displinary Health Sciences and Technology, Bangalore, 560064, India
| | - Loren Ornelas
- The Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.,iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.,Cedars-Sinai Biomanufacturing Center, West Hollywood, CA, 90069, USA
| | - Dhruv Sareen
- The Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.,iPSC Core, The David Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.,Cedars-Sinai Biomanufacturing Center, West Hollywood, CA, 90069, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Matthew R Livesey
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK
| | - Gary J Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Clive N Svendsen
- The Board of Governors Regenerative Medicine Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Peter C Kind
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India.,Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK.,Patrick Wild Centre, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK
| | - Siddharthan Chandran
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India.,Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, Edinburgh, EH16 4SB, UK.,UK Dementia Research Institute at the University of Edinburgh, Edinburgh Medical School, Chancellor's Building, Edinburgh, EH16 4SB, UK.,Patrick Wild Centre, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK
| | - Sumantra Chattarji
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India. .,Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK. .,Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK. .,National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, 560065, India.
| | - David J A Wyllie
- Centre for Brain Development and Repair, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, 560065, India. .,Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK. .,Patrick Wild Centre, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK. .,Simons Initiative for the Developing Brain, University of Edinburgh, Hugh Robson Building, Edinburgh, EH8 9XD, UK.
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7
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Zhao W, Beers DR, Thonhoff JR, Thome AD, Faridar A, Wang J, Wen S, Ornelas L, Sareen D, Goodridge HS, Svendsen CN, Appel SH. Immunosuppressive Functions of M2 Macrophages Derived from iPSCs of Patients with ALS and Healthy Controls. iScience 2020; 23:101192. [PMID: 32521508 PMCID: PMC7286967 DOI: 10.1016/j.isci.2020.101192] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a disorder with immune alterations that augment disease severity. M2 macrophages benefit diabetic and nephrotic mice by suppressing the pro-inflammatory state. However, neither have M2 cells been investigated in ALS nor have human induced pluripotent stem cell (iPSC)-derived M2 cells been thoroughly studied for immunosuppressive potentials. Here, iPSCs of C9orf72 mutated or sporadic ALS patients were differentiated into M2 macrophages, which suppressed activation of pro-inflammatory M1 macrophages as well as proliferation of ALS CD4+CD25- Tc (Teffs). M2 cells converted ALS Teffs into CD4+CD25+Foxp3+ regulatory T cells (Tregs) and rescued Tregs of ALS patients from losing CD25 and Foxp3. Furthermore, Tregs induced or rescued by iPSC-derived M2 had strong suppressive functions. ALS iPSC-derived M2 cells including those with C9orf72 mutation had similar immunomodulatory activity as control iPSC-derived M2 cells. This study demonstrates that M2 cells differentiated from iPSCs of ALS patients are immunosuppressive, boost ALS Tregs, and may serve as a candidate for immune-cell-based therapy to mitigate inflammation in ALS.
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Affiliation(s)
- Weihua Zhao
- Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, 6560 Fannin Street, Suite ST-802, Houston, TX 77030, USA
| | - David R Beers
- Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, 6560 Fannin Street, Suite ST-802, Houston, TX 77030, USA
| | - Jason R Thonhoff
- Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, 6560 Fannin Street, Suite ST-802, Houston, TX 77030, USA
| | - Aaron D Thome
- Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, 6560 Fannin Street, Suite ST-802, Houston, TX 77030, USA
| | - Alireza Faridar
- Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, 6560 Fannin Street, Suite ST-802, Houston, TX 77030, USA
| | - Jinghong Wang
- Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, 6560 Fannin Street, Suite ST-802, Houston, TX 77030, USA
| | - Shixiang Wen
- Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, 6560 Fannin Street, Suite ST-802, Houston, TX 77030, USA
| | - Loren Ornelas
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | - Dhruv Sareen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Cedars-Sinai Biomanufacturing Center, West Hollywood, CA 90069, USA
| | - Helen S Goodridge
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Clive N Svendsen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stanley H Appel
- Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, 6560 Fannin Street, Suite ST-802, Houston, TX 77030, USA.
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8
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Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst 2018; 6:13-24. [PMID: 29199020 PMCID: PMC5799026 DOI: 10.1016/j.cels.2017.11.001] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [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: 07/27/2017] [Revised: 09/13/2017] [Accepted: 11/01/2017] [Indexed: 12/19/2022]
Abstract
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.
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Affiliation(s)
- Alexandra B Keenan
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L Jenkins
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M Jagodnik
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simon Koplev
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Edward He
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Denis Torre
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anders B Dohlman
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Moshe C Silverstein
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maxim V Kuleshov
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- BD2K-LINCS DCIC, Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Vasileios Stathias
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Raymond Terryn
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Daniel Cooper
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Michele Forlin
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Amar Koleti
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Dusica Vidovic
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Caty Chung
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Stephan C Schürer
- BD2K-LINCS DCIC, Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL 33146, USA
| | - Jouzas Vasiliauskas
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Marcin Pilarczyk
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Behrouz Shamsaei
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Mehdi Fazel
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Yan Ren
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Wen Niu
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Nicholas A Clark
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Shana White
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Naim Mahi
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Lixia Zhang
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Michal Kouril
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - John F Reichard
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Siva Sivaganesan
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Mario Medvedovic
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Jaroslaw Meller
- BD2K-LINCS DCIC, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45220, USA
| | - Rick J Koch
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marc R Birtwistle
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ravi Iyengar
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric A Sobie
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Evren U Azeloglu
- DToxS, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Julia Kaye
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jeannette Osterloh
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kelly Haston
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jaslin Kalra
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Steve Finkbiener
- NeuroLINCS, Gladstone Institute of Neurological Disease and the Departments of Neurology and Physiology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jonathan Li
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Pamela Milani
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Miriam Adam
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | | | - Karen Sachs
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Alex Lenail
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Divya Ramamoorthy
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Ernest Fraenkel
- NeuroLINCS, Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Gavin Daigle
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Uzma Hussain
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Alyssa Coye
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey Rothstein
- NeuroLINCS, Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Dhruv Sareen
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Loren Ornelas
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Maria Banuelos
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Berhan Mandefro
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ritchie Ho
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Clive N Svendsen
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ryan G Lim
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Jennifer Stocksdale
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Malcolm S Casale
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Terri G Thompson
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Jie Wu
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Leslie M Thompson
- NeuroLINCS, Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Victoria Dardov
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Andrea Matlock
- NeuroLINCS, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Jacob D Jaffe
- LINCS PCCSE, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Aravind Subramanian
- LINCS Center for Transcriptomics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Todd R Golub
- LINCS Center for Transcriptomics, The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sean D Erickson
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Marc Hafner
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jia-Ren Lin
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Niepel
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - David Wrobel
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Peter K Sorger
- HMS LINCS Center, Harvard Medical School, Boston, MA 02115, USA
| | - Laura M Heiser
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joe W Gray
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - James E Korkola
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gordon B Mills
- MEP-LINCS Center, Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark LaBarge
- MEP-LINCS Center, Department of Population Sciences, Beckman Research Institute at City of Hope, Duarte, CA 91011, USA; MEP-LINCS Center, Center for Cancer Biomarkers Research, University of Bergen, Bergen 5009, Norway
| | - Heidi S Feiler
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark A Dane
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elmar Bucher
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michel Nederlof
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA; MEP-LINCS Center, Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Damir Sudar
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA; MEP-LINCS Center, Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Sean Gross
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - David F Kilburn
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rebecca Smith
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kaylyn Devlin
- MEP-LINCS Center, Oregon Health & Science University, Portland, OR 97239, USA
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9
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Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR. A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries. Sci Rep 2017; 7:14626. [PMID: 29116112 PMCID: PMC5676863 DOI: 10.1038/s41598-017-14892-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 02/14/2017] [Accepted: 10/18/2017] [Indexed: 11/26/2022] Open
Abstract
Creating a cDNA library for deep mRNA sequencing (mRNAseq) is generally done by random priming, creating multiple sequencing fragments along each transcript. A 3'-end-focused library approach cannot detect differential splicing, but has potentially higher throughput at a lower cost, along with the ability to improve quantification by using transcript molecule counting with unique molecular identifiers (UMI) that correct PCR bias. Here, we compare an implementation of such a 3'-digital gene expression (3'-DGE) approach with "conventional" random primed mRNAseq. Given our particular datasets on cultured human cardiomyocyte cell lines, we find that, while conventional mRNAseq detects ~15% more genes and needs ~500,000 fewer reads per sample for equivalent statistical power, the resulting differentially expressed genes, biological conclusions, and gene signatures are highly concordant between two techniques. We also find good quantitative agreement at the level of individual genes between two techniques for both read counts and fold changes between given conditions. We conclude that, for high-throughput applications, the potential cost savings associated with 3'-DGE approach are likely a reasonable tradeoff for modest reduction in sensitivity and inability to observe alternative splicing, and should enable many larger scale studies focusing on not only differential expression analysis, but also quantitative transcriptome profiling.
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Affiliation(s)
- Yuguang Xiong
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magali Soumillon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Berkeley Lights, Inc. 5858 Horton St., Emeryville, CA, 94608, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
| | - Jens Hansen
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Hu
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan G C van Hasselt
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gomathi Jayaraman
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Lim
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
| | - Mehdi Bouhaddou
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Loren Ornelas
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | | | - Lindsay Lenaeus
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | | | - Jaehee Shim
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilda Gomez
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | - Dhruv Sareen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Clive Svendsen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Leslie M Thompson
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
- Department of Psychiatry and Human Behavior, Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Milind Mahajan
- Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric A Sobie
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evren U Azeloglu
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Marc R Birtwistle
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
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10
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Yucer N, Holzapfel M, Jenkins Vogel T, Lenaeus L, Ornelas L, Laury A, Sareen D, Barrett R, Karlan BY, Svendsen CN. Directed Differentiation of Human Induced Pluripotent Stem Cells into Fallopian Tube Epithelium. Sci Rep 2017; 7:10741. [PMID: 28878359 PMCID: PMC5587694 DOI: 10.1038/s41598-017-05519-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/30/2017] [Indexed: 01/20/2023] Open
Abstract
The fallopian tube epithelium (FTE) has been recognized as a site of origin of high-grade serous ovarian cancer (HGSC). However, the absence of relevant in vitro human models that can recapitulate tissue-specific architecture has hindered our understanding of FTE transformation and initiation of HGSC. Here, induced pluripotent stem cells (iPSCs) were used to establish a novel 3-dimensional (3D) human FTE organoid in vitro model containing the relevant cell types of the human fallopian tube as well as a luminal architecture that closely reflects the organization of fallopian tissues in vivo. Modulation of Wnt and BMP signaling directed iPSC differentiation into Müllerian cells and subsequent use of pro-Müllerian growth factors promoted FTE precursors. The expression and localization of Müllerian markers verified correct cellular differentiation. An innovative 3D growth platform, which enabled the FTE organoid to self-organize into a convoluted luminal structure, permitted matured differentiation to a FTE lineage. This powerful human-derived FTE organoid model can be used to study the earliest stages of HGSC development and to identify novel and specific biomarkers of early fallopian tube epithelial cell transformation.
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Affiliation(s)
- Nur Yucer
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.,Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Marie Holzapfel
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Tilley Jenkins Vogel
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Lindsay Lenaeus
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Loren Ornelas
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Anna Laury
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Dhruv Sareen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Robert Barrett
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Beth Y Karlan
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA. .,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| | - Clive N Svendsen
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA. .,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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11
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Sheyn D, Ben-David S, Shapiro G, De Mel S, Bez M, Ornelas L, Sahabian A, Sareen D, Da X, Pelled G, Tawackoli W, Liu Z, Gazit D, Gazit Z. Human Induced Pluripotent Stem Cells Differentiate Into Functional Mesenchymal Stem Cells and Repair Bone Defects. Stem Cells Transl Med 2016; 5:1447-1460. [PMID: 27400789 PMCID: PMC5070500 DOI: 10.5966/sctm.2015-0311] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/08/2016] [Indexed: 12/19/2022] Open
Abstract
Using short-term exposure of embryoid bodies to transforming growth factor-β, the authors directed induced pluripotent stem cells (iPSCs) toward mesenchymal stem cell (MSC) differentiation. Two types of iPSC-derived MSCs were identified: early (aiMSCs) and late (tiMSCs) outgrowing cells. Both types differentiated in vitro in response to osteogenic or adipogenic supplements; aiMSCs demonstrated higher osteogenic potential than tiMSCs. Upon orthotopic injection into radial defects, both types regenerated bone and contributed to defect repair. Mesenchymal stem cells (MSCs) are currently the most established cells for skeletal tissue engineering and regeneration; however, their availability and capability of self-renewal are limited. Recent discoveries of somatic cell reprogramming may be used to overcome these challenges. We hypothesized that induced pluripotent stem cells (iPSCs) that were differentiated into MSCs could be used for bone regeneration. Short-term exposure of embryoid bodies to transforming growth factor-β was used to direct iPSCs toward MSC differentiation. During this process, two types of iPSC-derived MSCs (iMSCs) were identified: early (aiMSCs) and late (tiMSCs) outgrowing cells. The transition of iPSCs toward MSCs was documented using MSC marker flow cytometry. Both types of iMSCs differentiated in vitro in response to osteogenic or adipogenic supplements. The results of quantitative assays showed that both cell types retained their multidifferentiation potential, although aiMSCs demonstrated higher osteogenic potential than tiMSCs and bone marrow-derived MSCs (BM-MSCs). Ectopic injections of BMP6-overexpressing tiMSCs produced no or limited bone formation, whereas similar injections of BMP6-overexpressing aiMSCs resulted in substantial bone formation. Upon orthotopic injection into radial defects, all three cell types regenerated bone and contributed to defect repair. In conclusion, MSCs can be derived from iPSCs and exhibit self-renewal without tumorigenic ability. Compared with BM-MSCs, aiMSCs acquire more of a stem cell phenotype, whereas tiMSCs acquire more of a differentiated osteoblast phenotype, which aids bone regeneration but does not allow the cells to induce ectopic bone formation (even when triggered by bone morphogenetic proteins), unless in an orthotopic site of bone fracture. Significance Mesenchymal stem cells (MSCs) are currently the most established cells for skeletal tissue engineering and regeneration of various skeletal conditions; however, availability of autologous MSCs is very limited. This study demonstrates a new method to differentiate human fibroblast-derived induced pluripotent stem cells (iPSCs) to cells with MSC properties, which we comprehensively characterized including differentiation potential and transcriptomic analysis. We showed that these iPS-derived MSCs are able to regenerate nonunion bone defects in mice more efficiently than bone marrow-derived human MSCs when overexpressing BMP6 using a nonviral transfection method.
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Affiliation(s)
- Dmitriy Sheyn
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shiran Ben-David
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Galina Shapiro
- Skeletal Biotech Laboratory, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sandra De Mel
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Maxim Bez
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Skeletal Biotech Laboratory, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Loren Ornelas
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- iPSC Core Facility, The David and Janet Polak Stem Cell Laboratory, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Anais Sahabian
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- iPSC Core Facility, The David and Janet Polak Stem Cell Laboratory, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dhruv Sareen
- Skeletal Biotech Laboratory, Hebrew University of Jerusalem, Jerusalem, Israel
- iPSC Core Facility, The David and Janet Polak Stem Cell Laboratory, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Xiaoyu Da
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gadi Pelled
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Skeletal Biotech Laboratory, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Wafa Tawackoli
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Zhenqiu Liu
- Biostatistics and Bioinformatics Core, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dan Gazit
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Skeletal Biotech Laboratory, Hebrew University of Jerusalem, Jerusalem, Israel
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Zulma Gazit
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Skeletal Biotech Laboratory, Hebrew University of Jerusalem, Jerusalem, Israel
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12
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Mattis VB, Tom C, Akimov S, Saeedian J, Østergaard ME, Southwell AL, Doty CN, Ornelas L, Sahabian A, Lenaeus L, Mandefro B, Sareen D, Arjomand J, Hayden MR, Ross CA, Svendsen CN. HD iPSC-derived neural progenitors accumulate in culture and are susceptible to BDNF withdrawal due to glutamate toxicity. Hum Mol Genet 2015; 24:3257-71. [PMID: 25740845 DOI: 10.1093/hmg/ddv080] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/02/2015] [Indexed: 12/12/2022] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disease, caused by expansion of polyglutamine repeats in the Huntingtin gene, with longer expansions leading to earlier ages of onset. The HD iPSC Consortium has recently reported a new in vitro model of HD based on the generation of induced pluripotent stem cells (iPSCs) from HD patients and controls. The current study has furthered the disease in a dish model of HD by generating new non-integrating HD and control iPSC lines. Both HD and control iPSC lines can be efficiently differentiated into neurons/glia; however, the HD-derived cells maintained a significantly greater number of nestin-expressing neural progenitor cells compared with control cells. This cell population showed enhanced vulnerability to brain-derived neurotrophic factor (BDNF) withdrawal in the juvenile-onset HD (JHD) lines, which appeared to be CAG repeat-dependent and mediated by the loss of signaling from the TrkB receptor. It was postulated that this increased death following BDNF withdrawal may be due to glutamate toxicity, as the N-methyl-d-aspartate (NMDA) receptor subunit NR2B was up-regulated in the cultures. Indeed, blocking glutamate signaling, not just through the NMDA but also mGlu and AMPA/Kainate receptors, completely reversed the cell death phenotype. This study suggests that the pathogenesis of JHD may involve in part a population of 'persistent' neural progenitors that are selectively vulnerable to BDNF withdrawal. Similar results were seen in adult hippocampal-derived neural progenitors isolated from the BACHD model mouse. Together, these results provide important insight into HD mechanisms at early developmental time points, which may suggest novel approaches to HD therapeutics.
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Affiliation(s)
- Virginia B Mattis
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
| | - Colton Tom
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
| | - Sergey Akimov
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jasmine Saeedian
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
| | | | - Amber L Southwell
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada and
| | - Crystal N Doty
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada and
| | - Loren Ornelas
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
| | - Anais Sahabian
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
| | - Lindsay Lenaeus
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
| | - Berhan Mandefro
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
| | - Dhruv Sareen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
| | | | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada and
| | - Christopher A Ross
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Clive N Svendsen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Blvd, 8400 AHSP, Los Angeles, CA 90048, USA
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13
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Barrett R, Ornelas L, Yeager N, Mandefro B, Sahabian A, Lenaeus L, Targan SR, Svendsen CN, Sareen D. Reliable generation of induced pluripotent stem cells from human lymphoblastoid cell lines. Stem Cells Transl Med 2014; 3:1429-34. [PMID: 25298370 DOI: 10.5966/sctm.2014-0121] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [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] [Indexed: 12/12/2022] Open
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) hold great promise for many applications, including disease modeling to elucidate mechanisms involved in disease pathogenesis, drug screening, and ultimately regenerative medicine therapies. A frequently used starting source of cells for reprogramming has been dermal fibroblasts isolated from skin biopsies. However, numerous repositories containing lymphoblastoid cell lines (LCLs) generated from a wide array of patients also exist in abundance. To date, this rich bioresource has been severely underused for iPSC generation. We first attempted to create iPSCs from LCLs using two existing methods but were unsuccessful. Here we report a new and more reliable method for LCL reprogramming using episomal plasmids expressing pluripotency factors and p53 shRNA in combination with small molecules. The LCL-derived iPSCs (LCL-iPSCs) exhibited identical characteristics to fibroblast-derived iPSCs (fib-iPSCs), wherein they retained their genotype, exhibited a normal pluripotency profile, and readily differentiated into all three germ-layer cell types. As expected, they also maintained rearrangement of the heavy chain immunoglobulin locus. Importantly, we also show efficient iPSC generation from LCLs of patients with spinal muscular atrophy and inflammatory bowel disease. These LCL-iPSCs retained the disease mutation and could differentiate into neurons, spinal motor neurons, and intestinal organoids, all of which were virtually indistinguishable from differentiated cells derived from fib-iPSCs. This method for reliably deriving iPSCs from patient LCLs paves the way for using invaluable worldwide LCL repositories to generate new human iPSC lines, thus providing an enormous bioresource for disease modeling, drug discovery, and regenerative medicine applications.
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Affiliation(s)
- Robert Barrett
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Loren Ornelas
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nicole Yeager
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Berhan Mandefro
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Anais Sahabian
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lindsay Lenaeus
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Clive N Svendsen
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dhruv Sareen
- Regenerative Medicine Institute, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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14
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Sareen D, Saghizadeh M, Ornelas L, Winkler MA, Narwani K, Sahabian A, Funari VA, Tang J, Spurka L, Punj V, Maguen E, Rabinowitz YS, Svendsen CN, Ljubimov AV. Differentiation of human limbal-derived induced pluripotent stem cells into limbal-like epithelium. Stem Cells Transl Med 2014; 3:1002-12. [PMID: 25069777 DOI: 10.5966/sctm.2014-0076] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [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] [Indexed: 12/12/2022] Open
Abstract
Limbal epithelial stem cell (LESC) deficiency (LSCD) leads to corneal abnormalities resulting in compromised vision and blindness. LSCD can be potentially treated by transplantation of appropriate cells, which should be easily expandable and bankable. Induced pluripotent stem cells (iPSCs) are a promising source of transplantable LESCs. The purpose of this study was to generate human iPSCs and direct them to limbal differentiation by maintaining them on natural substrata mimicking the native LESC niche, including feederless denuded human amniotic membrane (HAM) and de-epithelialized corneas. These iPSCs were generated with nonintegrating vectors from human primary limbal epithelial cells. This choice of parent cells was supposed to enhance limbal cell differentiation from iPSCs by partial retention of parental epigenetic signatures in iPSCs. When the gene methylation patterns were compared in iPSCs to parental LESCs using Illumina global methylation arrays, limbal-derived iPSCs had fewer unique methylation changes than fibroblast-derived iPSCs, suggesting retention of epigenetic memory during reprogramming. Limbal iPSCs cultured for 2 weeks on HAM developed markedly higher expression of putative LESC markers ABCG2, ΔNp63α, keratins 14, 15, and 17, N-cadherin, and TrkA than did fibroblast iPSCs. On HAM culture, the methylation profiles of select limbal iPSC genes (including NTRK1, coding for TrkA protein) became closer to the parental cells, but fibroblast iPSCs remained closer to parental fibroblasts. On denuded air-lifted corneas, limbal iPSCs even upregulated differentiated corneal keratins 3 and 12. These data emphasize the importance of the natural niche and limbal tissue of origin in generating iPSCs as a LESC source with translational potential for LSCD treatment.
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Affiliation(s)
- Dhruv Sareen
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Mehrnoosh Saghizadeh
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Loren Ornelas
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Michael A Winkler
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Kavita Narwani
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Anais Sahabian
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Vincent A Funari
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Jie Tang
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Lindsay Spurka
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Vasu Punj
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Ezra Maguen
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Yaron S Rabinowitz
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Clive N Svendsen
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Alexander V Ljubimov
- Regenerative Medicine Institute, Eye Program, and Departments of Biomedical Sciences, Neurosurgery, Genomics Core, and Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA; Norris Comprehensive Cancer Center Bioinformatics Core and Division of Hematology, University of Southern California, Los Angeles, California, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
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15
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Sareen D, O'Rourke JG, Meera P, Muhammad AKMG, Grant S, Simpkinson M, Bell S, Carmona S, Ornelas L, Sahabian A, Gendron T, Petrucelli L, Baughn M, Ravits J, Harms MB, Rigo F, Bennett CF, Otis TS, Svendsen CN, Baloh RH. Targeting RNA foci in iPSC-derived motor neurons from ALS patients with a C9ORF72 repeat expansion. Sci Transl Med 2014; 5:208ra149. [PMID: 24154603 DOI: 10.1126/scitranslmed.3007529] [Citation(s) in RCA: 507] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative condition characterized by loss of motor neurons in the brain and spinal cord. Expansions of a hexanucleotide repeat (GGGGCC) in the noncoding region of the C9ORF72 gene are the most common cause of the familial form of ALS (C9-ALS), as well as frontotemporal lobar degeneration and other neurological diseases. How the repeat expansion causes disease remains unclear, with both loss of function (haploinsufficiency) and gain of function (either toxic RNA or protein products) proposed. We report a cellular model of C9-ALS with motor neurons differentiated from induced pluripotent stem cells (iPSCs) derived from ALS patients carrying the C9ORF72 repeat expansion. No significant loss of C9ORF72 expression was observed, and knockdown of the transcript was not toxic to cultured human motor neurons. Transcription of the repeat was increased, leading to accumulation of GGGGCC repeat-containing RNA foci selectively in C9-ALS iPSC-derived motor neurons. Repeat-containing RNA foci colocalized with hnRNPA1 and Pur-α, suggesting that they may be able to alter RNA metabolism. C9-ALS motor neurons showed altered expression of genes involved in membrane excitability including DPP6, and demonstrated a diminished capacity to fire continuous spikes upon depolarization compared to control motor neurons. Antisense oligonucleotides targeting the C9ORF72 transcript suppressed RNA foci formation and reversed gene expression alterations in C9-ALS motor neurons. These data show that patient-derived motor neurons can be used to delineate pathogenic events in ALS.
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Affiliation(s)
- Dhruv Sareen
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
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16
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Sareen D, Gowing G, Sahabian A, Staggenborg K, Paradis R, Avalos P, Latter J, Ornelas L, Garcia L, Svendsen CN. Human induced pluripotent stem cells are a novel source of neural progenitor cells (iNPCs) that migrate and integrate in the rodent spinal cord. J Comp Neurol 2014; 522:2707-28. [PMID: 24610630 DOI: 10.1002/cne.23578] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 12/14/2022]
Abstract
Transplantation of human neural progenitor cells (NPCs) into the brain or spinal cord to replace lost cells, modulate the injury environment, or create a permissive milieu to protect and regenerate host neurons is a promising therapeutic strategy for neurological diseases. Deriving NPCs from human fetal tissue is feasible, although problematic issues include limited sources and ethical concerns. Here we describe a new and abundant source of NPCs derived from human induced pluripotent stem cells (iPSCs). A novel chopping technique was used to transform adherent iPSCs into free-floating spheres that were easy to maintain and were expandable (EZ spheres) (Ebert et al. [2013] Stem Cell Res 10:417-427). These EZ spheres could be differentiated towards NPC spheres with a spinal cord phenotype using a combination of all-trans retinoic acid (RA) and epidermal growth factor (EGF) and fibroblast growth factor-2 (FGF-2) mitogens. Suspension cultures of NPCs derived from human iPSCs or fetal tissue have similar characteristics, although they were not similar when grown as adherent cells. In addition, iPSC-derived NPCs (iNPCs) survived grafting into the spinal cord of athymic nude rats with no signs of overgrowth and with a very similar profile to human fetal-derived NPCs (fNPCs). These results suggest that human iNPCs behave like fNPCs and could thus be a valuable alternative for cellular regenerative therapies of neurological diseases.
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Affiliation(s)
- Dhruv Sareen
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048
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17
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Saitta B, Passarini J, Sareen D, Ornelas L, Sahabian A, Argade S, Krakow D, Cohn DH, Svendsen CN, Rimoin DL. Patient-derived skeletal dysplasia induced pluripotent stem cells display abnormal chondrogenic marker expression and regulation by BMP2 and TGFβ1. Stem Cells Dev 2014; 23:1464-78. [PMID: 24559391 DOI: 10.1089/scd.2014.0014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Skeletal dysplasias (SDs) are caused by abnormal chondrogenesis during cartilage growth plate differentiation. To study early stages of aberrant cartilage formation in vitro, we generated the first induced pluripotent stem cells (iPSCs) from fibroblasts of an SD patient with a lethal form of metatropic dysplasia, caused by a dominant mutation (I604M) in the calcium channel gene TRPV4. When micromasses were grown in chondrogenic differentiation conditions and compared with control iPSCs, mutant TRPV4-iPSCs showed significantly (P<0.05) decreased expression by quantitative real-time polymerase chain reaction of COL2A1 (IIA and IIB forms), SOX9, Aggrecan, COL10A1, and RUNX2, all of which are cartilage growth plate markers. We found that stimulation with BMP2, but not TGFβ1, up-regulated COL2A1 (IIA and IIB) and SOX9 gene expression, only in control iPSCs. COL2A1 (Collagen II) expression data were confirmed at the protein level by western blot and immunofluorescence microscopy. TRPV4-iPSCs showed only focal areas of Alcian blue stain for proteoglycans, while in control iPSCs the stain was seen throughout the micromass sample. Similar staining patterns were found in neonatal cartilage from control and patient samples. We also found that COL1A1 (Collagen I), a marker of osteogenic differentiation, was significantly (P<0.05) up-regulated at the mRNA level in TRPV4-iPSCs when compared with the control, and confirmed at the protein level. Collagen I expression in the TRPV4 model also may correlate with abnormal staining patterns seen in patient tissues. This study demonstrates that an iPSC model can recapitulate normal chondrogenesis and that mutant TRPV4-iPSCs reflect molecular evidence of aberrant chondrogenic developmental processes, which could be used to design therapeutic approaches for disorders of cartilage.
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Affiliation(s)
- Biagio Saitta
- 1 Department of Biomedical Sciences, Cedars-Sinai Medical Center , Los Angeles, California
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18
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Mattis VB, Wakeman DR, Tom C, Dodiya HB, Yeung SY, Tran AH, Bernau K, Ornelas L, Sahabian A, Reidling J, Sareen D, Thompson LM, Kordower JH, Svendsen CN. Neonatal immune-tolerance in mice does not prevent xenograft rejection. Exp Neurol 2014; 254:90-8. [PMID: 24440640 DOI: 10.1016/j.expneurol.2014.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 09/18/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 12/24/2022]
Abstract
Assessing the efficacy of human stem cell transplantation in rodent models is complicated by the significant immune rejection that occurs. Two recent reports have shown conflicting results using neonatal tolerance to xenografts in rats. Here we extend this approach to mice and assess whether neonatal tolerance can prevent the rapid rejection of xenografts. In three strains of neonatal immune-intact mice, using two different brain transplant regimes and three independent stem cell types, we conclusively show that there is rapid rejection of the implanted cells. We also address specific challenges associated with the generation of humanized mouse models of disease.
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Affiliation(s)
- Virginia B Mattis
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Colton Tom
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | | | - Loren Ornelas
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anais Sahabian
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Dhruv Sareen
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | - Clive N Svendsen
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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19
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Saghizadeh M, Winkler MA, Kramerov AA, Hemmati DM, Ghiam CA, Dimitrijevich SD, Sareen D, Ornelas L, Ghiasi H, Brunken WJ, Maguen E, Rabinowitz YS, Svendsen CN, Jirsova K, Ljubimov AV. A simple alkaline method for decellularizing human amniotic membrane for cell culture. PLoS One 2013; 8:e79632. [PMID: 24236148 PMCID: PMC3827346 DOI: 10.1371/journal.pone.0079632] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [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: 08/28/2013] [Accepted: 10/03/2013] [Indexed: 12/18/2022] Open
Abstract
Human amniotic membrane is a standard substratum used to culture limbal epithelial stem cells for transplantation to patients with limbal stem cell deficiency. Various methods were developed to decellularize amniotic membrane, because denuded membrane is poorly immunogenic and better supports repopulation by dissociated limbal epithelial cells. Amniotic membrane denuding usually involves treatment with EDTA and/or proteolytic enzymes; in many cases additional mechanical scraping is required. Although ensuring limbal cell proliferation, these methods are not standardized, require relatively long treatment times and can result in membrane damage. We propose to use 0.5 M NaOH to reliably remove amniotic cells from the membrane. This method was used before to lyse cells for DNA isolation and radioactivity counting. Gently rubbing a cotton swab soaked in NaOH over the epithelial side of amniotic membrane leads to nearly complete and easy removal of adherent cells in less than a minute. The denuded membrane is subsequently washed in a neutral buffer. Cell removal was more thorough and uniform than with EDTA, or EDTA plus mechanical scraping with an electric toothbrush, or n-heptanol plus EDTA treatment. NaOH-denuded amniotic membrane did not show any perforations compared with mechanical or thermolysin denuding, and showed excellent preservation of immunoreactivity for major basement membrane components including laminin α2, γ1-γ3 chains, α1/α2 and α6 type IV collagen chains, fibronectin, nidogen-2, and perlecan. Sodium hydroxide treatment was efficient with fresh or cryopreserved (10% dimethyl sulfoxide or 50% glycerol) amniotic membrane. The latter method is a common way of membrane storage for subsequent grafting in the European Union. NaOH-denuded amniotic membrane supported growth of human limbal epithelial cells, immortalized corneal epithelial cells, and induced pluripotent stem cells. This simple, fast and reliable method can be used to standardize decellularized amniotic membrane preparations for expansion of limbal stem cells in vitro before transplantation to patients.
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Affiliation(s)
- Mehrnoosh Saghizadeh
- Eye Program, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Departments of Biomedical Sciences, Surgery, and Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Michael A. Winkler
- Eye Program, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Departments of Biomedical Sciences, Surgery, and Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Andrei A. Kramerov
- Eye Program, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Departments of Biomedical Sciences, Surgery, and Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - David M. Hemmati
- Eye Program, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- University of California Los Angeles, Los Angeles, California, United States of America
| | - Chantelle A. Ghiam
- Eye Program, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- University of California Los Angeles, Los Angeles, California, United States of America
| | - Slobodan D. Dimitrijevich
- Department of Integrative Physiology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Dhruv Sareen
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Loren Ornelas
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Homayon Ghiasi
- Departments of Biomedical Sciences, Surgery, and Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - William J. Brunken
- Departments of Ophthalmology and Cell Biology, State University of New York, Downstate Medical Center, Brooklyn, New York, New York, United States of America
| | - Ezra Maguen
- Departments of Biomedical Sciences, Surgery, and Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- American Eye Institute, Los Angeles, California, United States of America
| | - Yaron S. Rabinowitz
- Eye Program, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Departments of Biomedical Sciences, Surgery, and Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Clive N. Svendsen
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Departments of Biomedical Sciences, Surgery, and Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- University of California Los Angeles, Los Angeles, California, United States of America
| | - Katerina Jirsova
- Laboratory of the Biology and Pathology of the Eye, Institute of Inherited Metabolic Disorders, 1 Faculty of Medicine and General Teaching Hospital, Charles University, Prague, Czech Republic
| | - Alexander V. Ljubimov
- Eye Program, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- Departments of Biomedical Sciences, Surgery, and Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
- University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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20
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MacLennan NK, Dong J, Aten JE, Horvath S, Rahib L, Ornelas L, Dipple KM, McCabe ERB. Weighted gene co-expression network analysis identifies biomarkers in glycerol kinase deficient mice. Mol Genet Metab 2009; 98:203-14. [PMID: 19546021 DOI: 10.1016/j.ymgme.2009.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Accepted: 05/19/2009] [Indexed: 11/19/2022]
Abstract
Symptomatic glycerol kinase deficiency (GKD) is associated with episodic metabolic and central nervous system deterioration. We report here the first application of weighted gene co-expression network analysis (WGCNA) to investigate a knockout (KO) murine model of a human genetic disease. WGCNA identified networks and key hub transcripts from liver mRNA of glycerol kinase (Gyk) KO and wild-type (WT) mice. Day of life 1 (dol1) samples from KO mice contained a network module enriched for organic acid metabolism before Gyk KO mice develop organic acidemia and die on dol3-4. Furthermore, the module containing Gyk was enriched with apoptotic genes. We used causal testing to elucidate the causal relationships between intramodular hub genes Acot, Psat and Plk3. Important causal relationships are confirmed in cell cultures. We provide evidence that GK may have an apoptotic moonlighting role that is lost in GKD. This first application of WGCNA to mouse knockout data provides insights into the molecular mechanisms of GKD pathogenesis. The resulting systems-genetic gene screening method identifies candidate biomarkers for GKD.
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Affiliation(s)
- Nicole K MacLennan
- Department of Pediatrics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1752, USA
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