1
|
Throesch BT, Bin Imtiaz MK, Muñoz-Castañeda R, Sakurai M, Hartzell AL, James KN, Rodriguez AR, Martin G, Lippi G, Kupriyanov S, Wu Z, Osten P, Izpisua Belmonte JC, Wu J, Baldwin KK. Functional sensory circuits built from neurons of two species. Cell 2024; 187:2143-2157.e15. [PMID: 38670072 DOI: 10.1016/j.cell.2024.03.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/18/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
A central question for regenerative neuroscience is whether synthetic neural circuits, such as those built from two species, can function in an intact brain. Here, we apply blastocyst complementation to selectively build and test interspecies neural circuits. Despite approximately 10-20 million years of evolution, and prominent species differences in brain size, rat pluripotent stem cells injected into mouse blastocysts develop and persist throughout the mouse brain. Unexpectedly, the mouse niche reprograms the birth dates of rat neurons in the cortex and hippocampus, supporting rat-mouse synaptic activity. When mouse olfactory neurons are genetically silenced or killed, rat neurons restore information flow to odor processing circuits. Moreover, they rescue the primal behavior of food seeking, although less well than mouse neurons. By revealing that a mouse can sense the world using neurons from another species, we establish neural blastocyst complementation as a powerful tool to identify conserved mechanisms of brain development, plasticity, and repair.
Collapse
Affiliation(s)
- Benjamin T Throesch
- Department of Neuroscience, The Scripps Research Institute, La Jolla, San Diego, CA, USA; Neuroscience Graduate Program, University of California, San Diego, La Jolla, San Diego, CA, USA
| | - Muhammad Khadeesh Bin Imtiaz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Masahiro Sakurai
- Salk Institute for Biological Studies, La Jolla, San Diego, CA, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrea L Hartzell
- Department of Neuroscience, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Kiely N James
- Department of Neuroscience, The Scripps Research Institute, La Jolla, San Diego, CA, USA; Neuroscience Graduate Program, University of California, San Diego, La Jolla, San Diego, CA, USA
| | - Alberto R Rodriguez
- Mouse Genetics Core, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Greg Martin
- Mouse Genetics Core, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Giordano Lippi
- Department of Neuroscience, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Sergey Kupriyanov
- Mouse Genetics Core, The Scripps Research Institute, La Jolla, San Diego, CA, USA
| | - Zhuhao Wu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Juan Carlos Izpisua Belmonte
- Salk Institute for Biological Studies, La Jolla, San Diego, CA, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, San Diego, CA, USA; Altos Labs, San Diego, CA, USA
| | - Jun Wu
- Salk Institute for Biological Studies, La Jolla, San Diego, CA, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Kristin K Baldwin
- Department of Neuroscience, The Scripps Research Institute, La Jolla, San Diego, CA, USA; Neuroscience Graduate Program, University of California, San Diego, La Jolla, San Diego, CA, USA; Department of Genetics and Development, Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY, USA.
| |
Collapse
|
2
|
Yoon S, Munoz A, Yamrom B, Lee YH, Andrews P, Marks S, Wang Z, Reeves C, Winterkorn L, Krieger AM, Buja A, Pradhan K, Ronemus M, Baldwin KK, Levy D, Wigler M, Iossifov I. Rates of contributory de novo mutation in high and low-risk autism families. Commun Biol 2021; 4:1026. [PMID: 34471188 PMCID: PMC8410909 DOI: 10.1038/s42003-021-02533-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
Autism arises in high and low-risk families. De novo mutation contributes to autism incidence in low-risk families as there is a higher incidence in the affected of the simplex families than in their unaffected siblings. But the extent of contribution in low-risk families cannot be determined solely from simplex families as they are a mixture of low and high-risk. The rate of de novo mutation in nearly pure populations of high-risk families, the multiplex families, has not previously been rigorously determined. Moreover, rates of de novo mutation have been underestimated from studies based on low resolution microarrays and whole exome sequencing. Here we report on findings from whole genome sequence (WGS) of both simplex families from the Simons Simplex Collection (SSC) and multiplex families from the Autism Genetic Resource Exchange (AGRE). After removing the multiplex samples with excessive cell-line genetic drift, we find that the contribution of de novo mutation in multiplex is significantly smaller than the contribution in simplex. We use WGS to provide high resolution CNV profiles and to analyze more than coding regions, and revise upward the rate in simplex autism due to an excess of de novo events targeting introns. Based on this study, we now estimate that de novo events contribute to 52-67% of cases of autism arising from low risk families, and 30-39% of cases of all autism.
Collapse
Affiliation(s)
- Seungtai Yoon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Adriana Munoz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Yoon-Ha Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Steven Marks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | | | - Abba M Krieger
- Statistics Department, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Andreas Buja
- Statistics Department, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Kith Pradhan
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Kristin K Baldwin
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA, USA.,Department of Genetics and Development, Columbia University, New York, NY, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA. .,New York Genome Center, New York, NY, USA.
| |
Collapse
|
3
|
Lai JI, Nachun D, Petrosyan L, Throesch B, Campau E, Gao F, Baldwin KK, Coppola G, Gottesfeld JM, Soragni E. Transcriptional profiling of isogenic Friedreich ataxia neurons and effect of an HDAC inhibitor on disease signatures. J Biol Chem 2019; 294:1846-1859. [PMID: 30552117 PMCID: PMC6369281 DOI: 10.1074/jbc.ra118.006515] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 11/02/2018] [Revised: 12/12/2018] [Indexed: 12/16/2022] Open
Abstract
Friedreich ataxia (FRDA) is a neurodegenerative disorder caused by transcriptional silencing of the frataxin (FXN) gene, resulting in loss of the essential mitochondrial protein frataxin. Based on the knowledge that a GAA·TTC repeat expansion in the first intron of FXN induces heterochromatin, we previously showed that 2-aminobenzamide-type histone deacetylase inhibitors (HDACi) increase FXN mRNA levels in induced pluripotent stem cell (iPSC)-derived FRDA neurons and in circulating lymphocytes from patients after HDACi oral administration. How the reduced expression of frataxin leads to neurological and other systemic symptoms in FRDA patients remains unclear. Similar to other triplet-repeat disorders, it is unknown why FRDA affects only specific cell types, primarily the large sensory neurons of the dorsal root ganglia and cardiomyocytes. The combination of iPSC technology and genome-editing techniques offers the unique possibility to address these questions in a relevant cell model of FRDA, obviating confounding effects of variable genetic backgrounds. Here, using "scarless" gene-editing methods, we created isogenic iPSC lines that differ only in the length of the GAA·TTC repeats. To uncover the gene expression signatures due to the GAA·TTC repeat expansion in FRDA neuronal cells and the effect of HDACi on these changes, we performed RNA-seq-based transcriptomic analysis of iPSC-derived central nervous system (CNS) and isogenic sensory neurons. We found that cellular pathways related to neuronal function, regulation of transcription, extracellular matrix organization, and apoptosis are affected by frataxin loss in neurons of the CNS and peripheral nervous system and that these changes are partially restored by HDACi treatment.
Collapse
Affiliation(s)
- Jiun-I Lai
- From the Departments of Molecular Medicine and
| | - Daniel Nachun
- the Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | | | - Benjamin Throesch
- Neuroscience, The Scripps Research Institute, La Jolla, California 92037 and
| | | | - Fuying Gao
- the Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Kristin K Baldwin
- Neuroscience, The Scripps Research Institute, La Jolla, California 92037 and
| | - Giovanni Coppola
- the Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | | | | |
Collapse
|
4
|
Kumar A, Thomas SK, Wong KC, Lo Sardo V, Cheah DS, Hou YH, Placone JK, Tenerelli KP, Ferguson WC, Torkamani A, Topol EJ, Baldwin KK, Engler AJ. Mechanical activation of noncoding-RNA-mediated regulation of disease-associated phenotypes in human cardiomyocytes. Nat Biomed Eng 2019; 3:137-146. [PMID: 30911429 PMCID: PMC6430136 DOI: 10.1038/s41551-018-0344-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 12/07/2018] [Indexed: 12/24/2022]
Abstract
How common polymorphisms in noncoding genome regions can regulate cellular function remains largely unknown. Here we show that cardiac fibrosis, mimicked using a hydrogel with controllable stiffness, affects the regulation of the phenotypes of human cardiomyocytes by a portion of the long noncoding RNA ANRIL, the gene of which is located in the disease-associated 9p21 locus. In a physiological environment, cultured cardiomyocytes derived from induced pluripotent stem cells obtained from patients who are homozygous for cardiovascular-risk alleles (R/R cardiomyocytes) or from healthy individuals who are homozygous for nonrisk alleles contracted synchronously, independently of genotype. After hydrogel stiffening to mimic fibrosis, only the R/R cardiomyocytes exhibited asynchronous contractions. These effects were associated with increased expression of the short ANRIL isoform in R/R cardiomyocytes, which induced a c-Jun N-terminal kinase (JNK) phosphorylation-based mechanism that impaired gap junctions (particularly, loss of connexin-43 expression) following stiffening. Deletion of the risk locus or treatment with a JNK antagonist was sufficient to maintain gap junctions and prevent asynchronous contraction of cardiomyocytes. Our findings suggest that mechanical changes in the microenvironment of cardiomyocytes can activate the regulation of their function by noncoding loci.
Collapse
Affiliation(s)
- Aditya Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Stephanie K Thomas
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Kirsten C Wong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Valentina Lo Sardo
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel S Cheah
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Yang-Hsun Hou
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jesse K Placone
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Kevin P Tenerelli
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - William C Ferguson
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA, USA
| | - Eric J Topol
- Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristin K Baldwin
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Adam J Engler
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
| |
Collapse
|
5
|
Lo Sardo V, Chubukov P, Ferguson W, Kumar A, Teng EL, Duran M, Zhang L, Cost G, Engler AJ, Urnov F, Topol EJ, Torkamani A, Baldwin KK. Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing. Cell 2018; 175:1796-1810.e20. [PMID: 30528432 DOI: 10.1016/j.cell.2018.11.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [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: 09/19/2017] [Revised: 04/24/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023]
Abstract
The 9p21.3 cardiovascular disease locus is the most influential common genetic risk factor for coronary artery disease (CAD), accounting for ∼10%-15% of disease in non-African populations. The ∼60 kb risk haplotype is human-specific and lacks coding genes, hindering efforts to decipher its function. Here, we produce induced pluripotent stem cells (iPSCs) from risk and non-risk individuals, delete each haplotype using genome editing, and generate vascular smooth muscle cells (VSMCs). Risk VSMCs exhibit globally altered transcriptional networks that intersect with previously identified CAD risk genes and pathways, concomitant with aberrant adhesion, contraction, and proliferation. Unexpectedly, deleting the risk haplotype rescues VSMC stability, while expressing the 9p21.3-associated long non-coding RNA ANRIL induces risk phenotypes in non-risk VSMCs. This study shows that the risk haplotype selectively predisposes VSMCs to adopt a cell state associated with CAD phenotypes, defines new VSMC-based networks of CAD risk genes, and establishes haplotype-edited iPSCs as powerful tools for functionally annotating the human genome.
Collapse
Affiliation(s)
- Valentina Lo Sardo
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pavel Chubukov
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William Ferguson
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aditya Kumar
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA
| | - Evan L Teng
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA
| | - Michael Duran
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lei Zhang
- Sangamo BioSciences, Inc., Richmond, CA 94804-3517, USA
| | - Gregory Cost
- Sangamo BioSciences, Inc., Richmond, CA 94804-3517, USA
| | - Adam J Engler
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Fyodor Urnov
- Sangamo BioSciences, Inc., Richmond, CA 94804-3517, USA
| | - Eric J Topol
- Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, CA
| | - Ali Torkamani
- Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kristin K Baldwin
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
6
|
Sardo VL, Ferguson W, Erikson GA, Topol EJ, Baldwin KK, Torkamani A. Influence of donor age on induced pluripotent stem cells. Nat Biotechnol 2017; 35:69-74. [PMID: 27941802 PMCID: PMC5505172 DOI: 10.1038/nbt.3749] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 11/14/2016] [Indexed: 12/14/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are being pursued as a source of cells for autologous therapies, many of which will be aimed at aged patients. To explore the impact of age on iPSC quality, we produced iPSCs from blood cells of 16 donors aged 21-100. We find that iPSCs from older donors retain an epigenetic signature of age, which can be reduced through passaging. Clonal expansion via reprogramming also enables the discovery of somatic mutations present in individual donor cells, which are missed by bulk sequencing methods. We show that exomic mutations in iPSCs increase linearly with age, and all iPSC lines analyzed carry at least one gene-disrupting mutation, several of which have been associated with cancer or dysfunction. Unexpectedly, elderly donors (>90 yrs) harbor fewer mutations than predicted, likely due to a contracted blood progenitor pool. These studies establish that donor age is associated with an increased risk of abnormalities in iPSCs and will inform clinical development of reprogramming technology.
Collapse
Affiliation(s)
- Valentina Lo Sardo
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California
| | - William Ferguson
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Galina A. Erikson
- The Scripps Translational Science Institute, Scripps Health and The Scripps Research Institute, La Jolla, California
| | - Eric J Topol
- The Scripps Translational Science Institute, Scripps Health and The Scripps Research Institute, La Jolla, California
| | - Kristin K Baldwin
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Ali Torkamani
- The Scripps Translational Science Institute, Scripps Health and The Scripps Research Institute, La Jolla, California
| |
Collapse
|
7
|
Hazen JL, Faust GG, Rodriguez AR, Ferguson WC, Shumilina S, Clark RA, Boland MJ, Martin G, Chubukov P, Tsunemoto RK, Torkamani A, Kupriyanov S, Hall IM, Baldwin KK. The Complete Genome Sequences, Unique Mutational Spectra, and Developmental Potency of Adult Neurons Revealed by Cloning. Neuron 2016; 89:1223-1236. [PMID: 26948891 DOI: 10.1016/j.neuron.2016.02.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/14/2015] [Accepted: 01/13/2016] [Indexed: 02/07/2023]
Abstract
Somatic mutation in neurons is linked to neurologic disease and implicated in cell-type diversification. However, the origin, extent, and patterns of genomic mutation in neurons remain unknown. We established a nuclear transfer method to clonally amplify the genomes of neurons from adult mice for whole-genome sequencing. Comprehensive mutation detection and independent validation revealed that individual neurons harbor ∼100 unique mutations from all classes but lack recurrent rearrangements. Most neurons contain at least one gene-disrupting mutation and rare (0-2) mobile element insertions. The frequency and gene bias of neuronal mutations differ from other lineages, potentially due to novel mechanisms governing postmitotic mutation. Fertile mice were cloned from several neurons, establishing the compatibility of mutated adult neuronal genomes with reprogramming to pluripotency and development.
Collapse
Affiliation(s)
- Jennifer L Hazen
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla CA 92037, USA
| | - Gregory G Faust
- Department of Biochemistry and Molecular Genetics, 1340 Jefferson Park Ave, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Alberto R Rodriguez
- Mouse Genetics Core Facility, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - William C Ferguson
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla CA 92037, USA
| | - Svetlana Shumilina
- Department of Biochemistry and Molecular Genetics, 1340 Jefferson Park Ave, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Royden A Clark
- Department of Biochemistry and Molecular Genetics, 1340 Jefferson Park Ave, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Michael J Boland
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla CA 92037, USA
| | - Greg Martin
- Mouse Genetics Core Facility, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Pavel Chubukov
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rachel K Tsunemoto
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla CA 92037, USA.,Neuroscience Graduate Program, 9500 Gilman Drive, University of California San Diego, La Jolla, California, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sergey Kupriyanov
- Mouse Genetics Core Facility, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ira M Hall
- McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO 63108, USA.,Department of Medicine, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, USA
| | - Kristin K Baldwin
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla CA 92037, USA.,Neuroscience Graduate Program, 9500 Gilman Drive, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
8
|
Tsunemoto RK, Eade KT, Blanchard JW, Baldwin KK. Forward engineering neuronal diversity using direct reprogramming. EMBO J 2015; 34:1445-55. [PMID: 25908841 PMCID: PMC4474523 DOI: 10.15252/embj.201591402] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 03/24/2015] [Indexed: 01/03/2023] Open
Abstract
The nervous system is comprised of a vast diversity of distinct neural cell types. Differences between neuronal subtypes drive the assembly of neuronal circuits and underlie the subtype specificity of many neurological diseases. Yet, because neurons are irreversibly post-mitotic and not readily available from patients, it has not been feasible to study specific subtypes of human neurons in larger numbers. A powerful means to study neuronal diversity and neurological disease is to establish methods to produce desired neuronal subtypes in vitro. Traditionally this has been accomplished by treating pluripotent or neural stem cells with growth factors and morphogens that recapitulate exogenous developmental signals. These approaches often require extended periods of culture, which can limit their utility. However, more recently, it has become possible to produce neurons directly from fibroblasts using transcription factors and/or microRNAs. This technique referred to as direct reprogramming or transdifferentiation has proven to be a rapid, robust, and reproducible method to generate mature neurons of many different subtypes from multiple cell sources. Here, we highlight recent advances in generating neurons of specific subtypes using direct reprogramming and outline various scenarios in which induced neurons may be applied to studies of neuronal function and neurological disease.
Collapse
Affiliation(s)
| | - Kevin T Eade
- The Scripps Research Institute, La Jolla, CA, USA
| | | | | |
Collapse
|
9
|
Abstract
The technology to convert adult human non-neural cells into neural lineages, through induced pluripotent stem cells (iPSCs), somatic cell nuclear transfer, and direct lineage reprogramming or transdifferentiation has progressed tremendously in recent years. Reprogramming-based approaches aimed at manipulating cellular identity have enormous potential for disease modeling, high-throughput drug screening, cell therapy, and personalized medicine. Human iPSC (hiPSC)-based cellular disease models have provided proof of principle evidence of the validity of this system. However, several challenges remain before patient-specific neurons produced by reprogramming can provide reliable insights into disease mechanisms or be efficiently applied to drug discovery and transplantation therapy. This review will first discuss limitations of currently available reprogramming-based methods in faithfully and reproducibly recapitulating disease pathology. Specifically, we will address issues such as culture heterogeneity, interline and inter-individual variability, and limitations of two-dimensional differentiation paradigms. Second, we will assess recent progress and the future prospects of reprogramming-based neurologic disease modeling. This includes three-dimensional disease modeling, advances in reprogramming technology, prescreening of hiPSCs and creating isogenic disease models using gene editing.
Collapse
Affiliation(s)
- Anjana Nityanandam
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California
| | - Kristin K Baldwin
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California
| |
Collapse
|
10
|
Boland MJ, Hazen JL, Nazor KL, Rodriguez AR, Martin G, Kupriyanov S, Baldwin KK. Generation of mice derived from induced pluripotent stem cells. J Vis Exp 2012:e4003. [PMID: 23222420 PMCID: PMC3565852 DOI: 10.3791/4003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [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] [Indexed: 01/06/2023] Open
Abstract
The production of induced pluripotent stem cells (iPSCs) from somatic cells provides a means to create valuable tools for basic research and may also produce a source of patient-matched cells for regenerative therapies. iPSCs may be generated using multiple protocols and derived from multiple cell sources. Once generated, iPSCs are tested using a variety of assays including immunostaining for pluripotency markers, generation of three germ layers in embryoid bodies and teratomas, comparisons of gene expression with embryonic stem cells (ESCs) and production of chimeric mice with or without germline contribution(2). Importantly, iPSC lines that pass these tests still vary in their capacity to produce different differentiated cell types(2). This has made it difficult to establish which iPSC derivation protocols, donor cell sources or selection methods are most useful for different applications. The most stringent test of whether a stem cell line has sufficient developmental potential to generate all tissues required for survival of an organism (termed full pluripotency) is tetraploid embryo complementation (TEC)(3-5). Technically, TEC involves electrofusion of two-cell embryos to generate tetraploid (4n) one-cell embryos that can be cultured in vitro to the blastocyst stage(6). Diploid (2n) pluripotent stem cells (e.g. ESCs or iPSCs) are then injected into the blastocoel cavity of the tetraploid blastocyst and transferred to a recipient female for gestation (see Figure 1). The tetraploid component of the complemented embryo contributes almost exclusively to the extraembryonic tissues (placenta, yolk sac), whereas the diploid cells constitute the embryo proper, resulting in a fetus derived entirely from the injected stem cell line. Recently, we reported the derivation of iPSC lines that reproducibly generate adult mice via TEC(1). These iPSC lines give rise to viable pups with efficiencies of 5-13%, which is comparable to ESCs(3,4,7) and higher than that reported for most other iPSC lines(8-12). These reports show that direct reprogramming can produce fully pluripotent iPSCs that match ESCs in their developmental potential and efficiency of generating pups in TEC tests. At present, it is not clear what distinguishes between fully pluripotent iPSCs and less potent lines(13-15). Nor is it clear which reprogramming methods will produce these lines with the highest efficiency. Here we describe one method that produces fully pluripotent iPSCs and "all- iPSC" mice, which may be helpful for investigators wishing to compare the pluripotency of iPSC lines or establish the equivalence of different reprogramming methods.
Collapse
Affiliation(s)
- Michael J Boland
- Dorris Neuroscience Center & Department of Cell Biology, The Scripps Research Institute, USA
| | | | | | | | | | | | | |
Collapse
|
11
|
Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM. Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. Cell Stem Cell 2012; 9:366-73. [PMID: 21982236 DOI: 10.1016/j.stem.2011.07.018] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 06/21/2011] [Accepted: 07/29/2011] [Indexed: 12/31/2022]
Abstract
The biomedical utility of induced pluripotent stem cells (iPSCs) will be diminished if most iPSC lines harbor deleterious genetic mutations. Recent microarray studies have shown that human iPSCs carry elevated levels of DNA copy number variation compared with those in embryonic stem cells, suggesting that these and other classes of genomic structural variation (SV), including inversions, smaller duplications and deletions, complex rearrangements, and retroelement transpositions, may frequently arise as a consequence of reprogramming. Here we employ whole-genome paired-end DNA sequencing and sensitive mapping algorithms to identify all classes of SV in three fully pluripotent mouse iPSC lines. Despite the improved scope and resolution of this study, we find few spontaneous mutations per line (one or two) and no evidence for endogenous retroelement transposition. These results show that genome stability can persist throughout reprogramming, and argue that it is possible to generate iPSCs lacking gene-disrupting mutations using current reprogramming methods.
Collapse
Affiliation(s)
- Aaron R Quinlan
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | | | | | | | | | | | | |
Collapse
|
12
|
Ghosh S, Larson SD, Hefzi H, Marnoy Z, Cutforth T, Dokka K, Baldwin KK. Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons. Nature 2011; 472:217-20. [PMID: 21451523 DOI: 10.1038/nature09945] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 02/18/2011] [Indexed: 11/09/2022]
Abstract
Sensory information may be represented in the brain by stereotyped mapping of axonal inputs or by patterning that varies between individuals. In olfaction, a stereotyped map is evident in the first sensory processing centre, the olfactory bulb (OB), where different odours elicit activity in unique combinatorial patterns of spatially invariant glomeruli. Activation of each glomerulus is relayed to higher cortical processing centres by a set of ∼20-50 'homotypic' mitral and tufted (MT) neurons. In the cortex, target neurons integrate information from multiple glomeruli to detect distinct features of chemically diverse odours. How this is accomplished remains unclear, perhaps because the cortical mapping of glomerular information by individual MT neurons has not been described. Here we use new viral tracing and three-dimensional brain reconstruction methods to compare the cortical projections of defined sets of MT neurons. We show that the gross-scale organization of the OB is preserved in the patterns of axonal projections to one processing centre yet reordered in another, suggesting that distinct coding strategies may operate in different targets. However, at the level of individual neurons neither glomerular order nor stereotypy is preserved in either region. Rather, homotypic MT neurons from the same glomerulus innervate broad regions that differ between individuals. Strikingly, even in the same animal, MT neurons exhibit extensive diversity in wiring; axons of homotypic MT pairs diverge from each other, emit primary branches at distinct locations and 70-90% of branches of homotypic and heterotypic pairs are non-overlapping. This pronounced reorganization of sensory maps in the cortex offers an anatomic substrate for expanded combinatorial integration of information from spatially distinct glomeruli and predicts an unanticipated role for diversification of otherwise similar output neurons.
Collapse
Affiliation(s)
- Sulagna Ghosh
- Department of Cell Biology, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California 92037, USA
| | | | | | | | | | | | | |
Collapse
|
13
|
Boland MJ, Hazen JL, Nazor KL, Rodriguez AR, Gifford W, Martin G, Kupriyanov S, Baldwin KK. Adult mice generated from induced pluripotent stem cells. Nature 2009; 461:91-4. [PMID: 19672243 DOI: 10.1038/nature08310] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 07/23/2009] [Indexed: 02/07/2023]
Abstract
Recent landmark experiments have shown that transient overexpression of a small number of transcription factors can reprogram differentiated cells into induced pluripotent stem (iPS) cells that resemble embryonic stem (ES) cells. These iPS cells hold great promise for medicine because they have the potential to generate patient-specific cell types for cell replacement therapy and produce in vitro models of disease, without requiring embryonic tissues or oocytes. Although current iPS cell lines resemble ES cells, they have not passed the most stringent test of pluripotency by generating full-term or adult mice in tetraploid complementation assays, raising questions as to whether they are sufficiently potent to generate all of the cell types in an organism. Whether this difference between iPS and ES cells reflects intrinsic limitations of direct reprogramming is not known. Here we report fertile adult mice derived entirely from iPS cells that we generated by inducible genetic reprogramming of mouse embryonic fibroblasts. Producing adult mice derived entirely from a reprogrammed fibroblast shows that all features of a differentiated cell can be restored to an embryonic level of pluripotency without exposure to unknown ooplasmic factors. Comparing these fully pluripotent iPS cell lines to less developmentally potent lines may reveal molecular markers of different pluripotent states. Furthermore, mice derived entirely from iPS cells will provide a new resource to assess the functional and genomic stability of cells and tissues derived from iPS cells, which is important to validate their utility in cell replacement therapy and research applications.
Collapse
Affiliation(s)
- Michael J Boland
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Tasic B, Nabholz CE, Baldwin KK, Kim Y, Rueckert EH, Ribich SA, Cramer P, Wu Q, Axel R, Maniatis T. Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing. Mol Cell 2002; 10:21-33. [PMID: 12150904 DOI: 10.1016/s1097-2765(02)00578-6] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A family of mammalian protocadherin (Pcdh) proteins is encoded by three closely linked gene clusters (alpha, beta, and gamma). Multiple alpha and gamma Pcdh mRNAs are expressed in distinct patterns in the nervous system and are generated by alternative pre-mRNA splicing between different "variable" exons and three "constant" exons within each cluster. We show that each Pcdh variable exon is preceded by a promoter and that promoter choice determines which variable exon is included in a Pcdh mRNA. In addition, we provide evidence that alternative splicing of variable exons within a gene cluster occurs via a cis-splicing mechanism. However, virtually every variable exon can engage in trans-splicing with constant exons from another cluster, albeit at a far lower level.
Collapse
Affiliation(s)
- Bosiljka Tasic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Baldwin KK, Trenchak BP, Altman JD, Davis3 MM. Negative Selection of T Cells Occurs Throughout Thymic Development. The Journal of Immunology 1999. [DOI: 10.4049/jimmunol.163.2.689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Thymic positive and negative selections govern the development of a self-MHC-reactive, yet self-tolerant, T cell repertoire. Whether these processes occur independently or sequentially remains controversial. To investigate these issues, we have employed tetrameric peptide-MHC complexes to fluorescently label and monitor polyclonal populations of thymocytes that are specific for moth cytochrome c (MCC)/I-Ek. In TCR β mice tetramer-positive thymocytes are detectable even in the most immature TCR-expressing cells. In the presence of MCC peptide, thymocytes that bind strongly to MCC/I-Ek tetramers are deleted earlier in development and more extensively than cells that bind weakly. This negative selection of the MCC/I-Ek-specific cells occurs continuously throughout development and before any evidence of positive selection. Thus, positive and negative selections are independent processes that need not occur sequentially.
Collapse
Affiliation(s)
| | - Brian P. Trenchak
- †Department of Microbiology and Immunology, and
- ‡Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305; and
| | - John D. Altman
- §Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322
| | - Mark M. Davis3
- †Department of Microbiology and Immunology, and
- ‡Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305; and
| |
Collapse
|
16
|
Baldwin KK, Trenchak BP, Altman JD, Davis MM. Negative selection of T cells occurs throughout thymic development. J Immunol 1999; 163:689-98. [PMID: 10395659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Thymic positive and negative selections govern the development of a self-MHC-reactive, yet self-tolerant, T cell repertoire. Whether these processes occur independently or sequentially remains controversial. To investigate these issues, we have employed tetrameric peptide-MHC complexes to fluorescently label and monitor polyclonal populations of thymocytes that are specific for moth cytochrome c (MCC)/I-Ek. In TCR beta mice tetramer-positive thymocytes are detectable even in the most immature TCR-expressing cells. In the presence of MCC peptide, thymocytes that bind strongly to MCC/I-Ek tetramers are deleted earlier in development and more extensively than cells that bind weakly. This negative selection of the MCC/I-Ek-specific cells occurs continuously throughout development and before any evidence of positive selection. Thus, positive and negative selections are independent processes that need not occur sequentially.
Collapse
Affiliation(s)
- K K Baldwin
- Program in Immunology, Department of Microbiology and Immunology, Howard Hughes Medical Institute, Stanford University, CA 94305, USA
| | | | | | | |
Collapse
|
17
|
Abstract
To investigate the influence of endogenous peptides on the developmental processes that occur during thymocyte selection, we have used monoclonal antibodies that preferentially recognize the major histocompatibility complex (MHC) molecule I-Ek when it is bound to the moth cytochrome c peptide (88-103). One of these antibodies (G35) specifically blocks the positive selection of transgenic thymocytes expressing a T cell receptor that is reactive to this peptide- MHC complex. Furthermore, G35 does not block the differentiation of transgenic T cells bearing receptors for a different I-Ek-peptide complex. This antibody recognizes a subset of endogenous I-Ek-peptide complexes found on a significant fraction of thymic antigen-presenting cells, including cortical and medullary epithelial cells. The sensitivity of G35 to minor alterations in peptide sequence suggests that the thymic peptide-MHC complexes that mediate the positive selection of a particular class II MHC-restricted thymocyte are structurally related to the complexes that can activate it in the periphery.
Collapse
Affiliation(s)
- K K Baldwin
- Howard Hughes Medical Institute, and the Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | | | | | | | | |
Collapse
|
18
|
Bennett CB, Lewis AL, Baldwin KK, Resnick MA. Lethality induced by a single site-specific double-strand break in a dispensable yeast plasmid. Proc Natl Acad Sci U S A 1993; 90:5613-7. [PMID: 8516308 PMCID: PMC46771 DOI: 10.1073/pnas.90.12.5613] [Citation(s) in RCA: 212] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Cells of the yeast Saccharomyces cerevisiae are delayed in the G2 phase of the cell cycle following chromosomal DNA damage. This arrest is RAD9-dependent and suggests a signaling mechanism(s) between chromosomal lesions and cell cycling. We examined the global nature of growth inhibition caused by an HO endonuclease-induced double-strand break (DSB) at a 45-bp YZ sequence (from MAT YZ) in a non-yeast region of a dispensable single-copy plasmid. The presence of an unrepaired DSB results in cellular death even though the plasmid is dispensable. Loss of cell viability is partially dependent on the RAD9 gene product. Following induction of the DSB, 40% of RAD+ and 49% of rad9 delta cells [including both unbudded (G1) and budded (S plus G2) cells] did not progress further in the cell cycle. The remaining RAD+ cells progressed to form microcolonies (< 30 cells) containing aberrantly shaped inviable cells. For the rad9 delta mutant, the majority of the remaining cells produced viable colonies accounting for the greater survival of the rad9 delta strain. Based on the profound effects of a single nonchromosomal DNA lesion, this system provides a convenient means for studying the signaling effects of a DNA lesion, as well as for designing strategies for modulating cell proliferation.
Collapse
Affiliation(s)
- C B Bennett
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | | | | | | |
Collapse
|