1
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Fowler JL, Zheng SL, Nguyen A, Chen A, Xiong X, Chai T, Chen JY, Karigane D, Banuelos AM, Niizuma K, Kayamori K, Nishimura T, Cromer MK, Gonzalez-Perez D, Mason C, Liu DD, Yilmaz L, Miquerol L, Porteus MH, Luca VC, Majeti R, Nakauchi H, Red-Horse K, Weissman IL, Ang LT, Loh KM. Lineage-tracing hematopoietic stem cell origins in vivo to efficiently make human HLF+ HOXA+ hematopoietic progenitors from pluripotent stem cells. Dev Cell 2024:S1534-5807(24)00143-6. [PMID: 38569552 DOI: 10.1016/j.devcel.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/05/2023] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
The developmental origin of blood-forming hematopoietic stem cells (HSCs) is a longstanding question. Here, our non-invasive genetic lineage tracing in mouse embryos pinpoints that artery endothelial cells generate HSCs. Arteries are transiently competent to generate HSCs for 2.5 days (∼E8.5-E11) but subsequently cease, delimiting a narrow time frame for HSC formation in vivo. Guided by the arterial origins of blood, we efficiently and rapidly differentiate human pluripotent stem cells (hPSCs) into posterior primitive streak, lateral mesoderm, artery endothelium, hemogenic endothelium, and >90% pure hematopoietic progenitors within 10 days. hPSC-derived hematopoietic progenitors generate T, B, NK, erythroid, and myeloid cells in vitro and, critically, express hallmark HSC transcription factors HLF and HOXA5-HOXA10, which were previously challenging to upregulate. We differentiated hPSCs into highly enriched HLF+ HOXA+ hematopoietic progenitors with near-stoichiometric efficiency by blocking formation of unwanted lineages at each differentiation step. hPSC-derived HLF+ HOXA+ hematopoietic progenitors could avail both basic research and cellular therapies.
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Affiliation(s)
- Jonas L Fowler
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Sherry Li Zheng
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Alana Nguyen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Angela Chen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Xiaochen Xiong
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Timothy Chai
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Julie Y Chen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Daiki Karigane
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Allison M Banuelos
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kouta Niizuma
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kensuke Kayamori
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Toshinobu Nishimura
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Charlotte Mason
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Leyla Yilmaz
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Lucile Miquerol
- Aix-Marseille Université, CNRS UMR 7288, IBDM, Marseille 13288, France
| | - Matthew H Porteus
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Vincent C Luca
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kristy Red-Horse
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Lay Teng Ang
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
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2
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Loh KM, Ang LT. Building human artery and vein endothelial cells from pluripotent stem cells, and enduring mysteries surrounding arteriovenous development. Semin Cell Dev Biol 2024; 155:62-75. [PMID: 37393122 DOI: 10.1016/j.semcdb.2023.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/07/2023] [Indexed: 07/03/2023]
Abstract
Owing to their manifold roles in health and disease, there have been intense efforts to synthetically generate blood vessels in vitro from human pluripotent stem cells (hPSCs). However, there are multiple types of blood vessel, including arteries and veins, which are molecularly and functionally different. How can we specifically generate either arterial or venous endothelial cells (ECs) from hPSCs in vitro? Here, we summarize how arterial or venous ECs arise during embryonic development. VEGF and NOTCH arbitrate the bifurcation of arterial vs. venous ECs in vivo. While manipulating these two signaling pathways biases hPSC differentiation towards arterial and venous identities, efficiently generating these two subtypes of ECs has remained challenging until recently. Numerous questions remain to be fully addressed. What is the complete identity, timing and combination of extracellular signals that specify arterial vs. venous identities? How do these extracellular signals intersect with fluid flow to modulate arteriovenous fate? What is a unified definition for endothelial progenitors or angioblasts, and when do arterial vs. venous potentials segregate? How can we regulate hPSC-derived arterial and venous ECs in vitro, and generate organ-specific ECs? In turn, answers to these questions could avail the production of arterial and venous ECs from hPSCs, accelerating vascular research, tissue engineering, and regenerative medicine.
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Affiliation(s)
- Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Lay Teng Ang
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
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3
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Vijayakumar S, Sala R, Kang G, Chen A, Pablo MA, Adebayo AI, Cipriano A, Fowler JL, Gomes DL, Ang LT, Loh KM, Sebastiano V. Monolayer platform to generate and purify primordial germ-like cells in vitro provides insights into human germline specification. Nat Commun 2023; 14:5690. [PMID: 37709760 PMCID: PMC10502105 DOI: 10.1038/s41467-023-41302-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Generating primordial germ cell-like cells (PGCLCs) from human pluripotent stem cells (hPSCs) advances studies of human reproduction and development of infertility treatments, but often entails complex 3D aggregates. Here we develop a simplified, monolayer method to differentiate hPSCs into PGCs within 3.5 days. We use our simplified differentiation platform and single-cell RNA-sequencing to achieve further insights into PGCLC specification. Transient WNT activation for 12 h followed by WNT inhibition specified PGCLCs; by contrast, sustained WNT induced primitive streak. Thus, somatic cells (primitive streak) and PGCLCs are related-yet distinct-lineages segregated by temporally-dynamic signaling. Pluripotency factors including NANOG are continuously expressed during the transition from pluripotency to posterior epiblast to PGCs, thus bridging pluripotent and germline states. Finally, hPSC-derived PGCLCs can be easily purified by virtue of their CXCR4+PDGFRA-GARP- surface-marker profile and single-cell RNA-sequencing reveals that they harbor transcriptional similarities with fetal PGCs.
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Affiliation(s)
- Sivakamasundari Vijayakumar
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Roberta Sala
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gugene Kang
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Angela Chen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michelle Ann Pablo
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Abidemi Ismail Adebayo
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Andrea Cipriano
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jonas L Fowler
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Danielle L Gomes
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lay Teng Ang
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Vittorio Sebastiano
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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4
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Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R. An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biol 2023; 24:16. [PMID: 36691074 PMCID: PMC9869549 DOI: 10.1186/s13059-023-02849-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/05/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Association of chromatin with lamin proteins at the nuclear periphery has emerged as a potential mechanism to coordinate cell type-specific gene expression and maintain cellular identity via gene silencing. Unlike many histone modifications and chromatin-associated proteins, lamina-associated domains (LADs) are mapped genome-wide in relatively few genetically normal human cell types, which limits our understanding of the role peripheral chromatin plays in development and disease. RESULTS To address this gap, we map LAMIN B1 occupancy across twelve human cell types encompassing pluripotent stem cells, intermediate progenitors, and differentiated cells from all three germ layers. Integrative analyses of this atlas with gene expression and repressive histone modification maps reveal that lamina-associated chromatin in all twelve cell types is organized into at least two subtypes defined by differences in LAMIN B1 occupancy, gene expression, chromatin accessibility, transposable elements, replication timing, and radial positioning. Imaging of fluorescently labeled DNA in single cells validates these subtypes and shows radial positioning of LADs with higher LAMIN B1 occupancy and heterochromatic histone modifications primarily embedded within the lamina. In contrast, the second subtype of lamina-associated chromatin is relatively gene dense, accessible, dynamic across development, and positioned adjacent to the lamina. Most genes gain or lose LAMIN B1 occupancy consistent with cell types along developmental trajectories; however, we also identify examples where the enhancer, but not the gene body and promoter, changes LAD state. CONCLUSIONS Altogether, this atlas represents the largest resource to date for peripheral chromatin organization studies and reveals an intermediate chromatin subtype.
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Affiliation(s)
- Parisha P. Shah
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Kathleen C. Keough
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Ketrin Gjoni
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Garrett T. Santini
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Richard J. Abdill
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Nadeera M. Wickramasinghe
- grid.59734.3c0000 0001 0670 2351Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Carolyn E. Dundes
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Ashley Karnay
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Angela Chen
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Rachel E. A. Salomon
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Patrick J. Walsh
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Son C. Nguyen
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sean Whalen
- grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Eric F. Joyce
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kyle M. Loh
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Nicole Dubois
- grid.59734.3c0000 0001 0670 2351Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Katherine S. Pollard
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA ,grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
| | - Rajan Jain
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA ,Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
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5
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Gonzalez-Perez D, Das S, Antfolk D, Ahsan HS, Medina E, Dundes CE, Jokhai RT, Egan ED, Blacklow SC, Loh KM, Rodriguez PC, Luca VC. Affinity-matured DLL4 ligands as broad-spectrum modulators of Notch signaling. Nat Chem Biol 2023; 19:9-17. [PMID: 36050494 PMCID: PMC10132381 DOI: 10.1038/s41589-022-01113-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/14/2022] [Indexed: 12/31/2022]
Abstract
The Notch pathway regulates cell fate decisions and is an emerging target for regenerative and cancer therapies. Recombinant Notch ligands are attractive candidates for modulating Notch signaling; however, their intrinsically low receptor-binding affinity restricts their utility in biomedical applications. To overcome this limitation, we evolved variants of the ligand Delta-like 4 with enhanced affinity and cross-reactivity. A consensus variant with maximized binding affinity, DeltaMAX, binds human and murine Notch receptors with 500- to 1,000-fold increased affinity compared with wild-type human Delta-like 4. DeltaMAX also potently activates Notch in plate-bound, bead-bound and cellular formats. When administered as a soluble decoy, DeltaMAX inhibits Notch in reporter and neuronal differentiation assays, highlighting its dual utility as an agonist or antagonist. Finally, we demonstrate that DeltaMAX stimulates increased proliferation and expression of effector mediators in T cells. Taken together, our data define DeltaMAX as a versatile tool for broad-spectrum activation or inhibition of Notch signaling.
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Affiliation(s)
| | - Satyajit Das
- Department of Immunology, Moffitt Cancer Center, Tampa, FL, USA
| | - Daniel Antfolk
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL, USA
| | - Hadia S Ahsan
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elliot Medina
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL, USA
| | - Carolyn E Dundes
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rayyan T Jokhai
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Emily D Egan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Vincent C Luca
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL, USA.
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6
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Genuth NR, Shi Z, Kunimoto K, Hung V, Xu AF, Kerr CH, Tiu GC, Oses-Prieto JA, Salomon-Shulman REA, Axelrod JD, Burlingame AL, Loh KM, Barna M. A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production. Nat Commun 2022; 13:5491. [PMID: 36123354 PMCID: PMC9485161 DOI: 10.1038/s41467-022-33263-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 03/09/2022] [Accepted: 09/09/2022] [Indexed: 02/05/2023] Open
Abstract
Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control cell fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem cell differentiation, we identify dozens of ribosome composition changes underlying cell fate specification. We observe upregulation of RPL10A/uL1-containing ribosomes in the primitive streak followed by progressive decreases during mesoderm differentiation. An Rpl10a loss-of-function allele in mice causes striking early mesodermal phenotypes, including posterior trunk truncations, and inhibits paraxial mesoderm production in culture. Ribosome profiling in Rpl10a loss-of-function mice reveals decreased translation of mesoderm regulators, including Wnt pathway mRNAs, which are also enriched on RPL10A/uL1-containing ribosomes. We further show that RPL10A/uL1 regulates canonical and non-canonical Wnt signaling during stem cell differentiation and in the developing embryo. These findings reveal unexpected ribosome composition modularity that controls differentiation and development through the specialized translation of key signaling networks.
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Affiliation(s)
- Naomi R Genuth
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Zhen Shi
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Genentech Inc, South San Francisco, CA, 94080, USA
| | - Koshi Kunimoto
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Victoria Hung
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Adele F Xu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gerald C Tiu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | | | - Jeffrey D Axelrod
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Kyle M Loh
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA
| | - Maria Barna
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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7
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Roodgar M, Suchy FP, Nguyen LH, Bajpai VK, Sinha R, Vilches-Moure JG, Van Bortle K, Bhadury J, Metwally A, Jiang L, Jian R, Chiang R, Oikonomopoulos A, Wu JC, Weissman IL, Mankowski JL, Holmes S, Loh KM, Nakauchi H, VandeVoort CA, Snyder MP. Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos. Cell Rep 2022; 40:111264. [PMID: 36044843 PMCID: PMC10075238 DOI: 10.1016/j.celrep.2022.111264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Received: 11/01/2020] [Revised: 01/06/2022] [Accepted: 08/04/2022] [Indexed: 12/26/2022] Open
Abstract
As our closest living relatives, non-human primates uniquely enable explorations of human health, disease, development, and evolution. Considerable effort has thus been devoted to generating induced pluripotent stem cells (iPSCs) from multiple non-human primate species. Here, we establish improved culture methods for chimpanzee (Pan troglodytes) and pig-tailed macaque (Macaca nemestrina) iPSCs. Such iPSCs spontaneously differentiate in conventional culture conditions, but can be readily propagated by inhibiting endogenous WNT signaling. As a unique functional test of these iPSCs, we injected them into the pre-implantation embryos of another non-human species, rhesus macaques (Macaca mulatta). Ectopic expression of gene BCL2 enhances the survival and proliferation of chimpanzee and pig-tailed macaque iPSCs within the pre-implantation embryo, although the identity and long-term contribution of the transplanted cells warrants further investigation. In summary, we disclose transcriptomic and proteomic data, cell lines, and cell culture resources that may be broadly enabling for non-human primate iPSCs research.
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Affiliation(s)
- Morteza Roodgar
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Fabian P Suchy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lan H Nguyen
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Vivek K Bajpai
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jose G Vilches-Moure
- Department of Comparative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kevin Van Bortle
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joydeep Bhadury
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Biomedicine, Sahlgrenska University Hospital, University of Gothenburg, SE 413 45 Gothenburg, Sweden
| | - Ahmed Metwally
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Rosaria Chiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Angelos Oikonomopoulos
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph L Mankowski
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, Davis, CA, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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8
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Ang LT, Nguyen AT, Liu KJ, Chen A, Xiong X, Curtis M, Martin RM, Raftry BC, Ng CY, Vogel U, Lander A, Lesch BJ, Fowler JL, Holman AR, Chai T, Vijayakumar S, Suchy FP, Nishimura T, Bhadury J, Porteus MH, Nakauchi H, Cheung C, George SC, Red-Horse K, Prescott JB, Loh KM. Generating human artery and vein cells from pluripotent stem cells highlights the arterial tropism of Nipah and Hendra viruses. Cell 2022; 185:2523-2541.e30. [PMID: 35738284 DOI: 10.1016/j.cell.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Received: 08/18/2021] [Revised: 03/26/2022] [Accepted: 05/26/2022] [Indexed: 02/07/2023]
Abstract
Stem cell research endeavors to generate specific subtypes of classically defined "cell types." Here, we generate >90% pure human artery or vein endothelial cells from pluripotent stem cells within 3-4 days. We specified artery cells by inhibiting vein-specifying signals and vice versa. These cells modeled viral infection of human vasculature by Nipah and Hendra viruses, which are extraordinarily deadly (∼57%-59% fatality rate) and require biosafety-level-4 containment. Generating pure populations of artery and vein cells highlighted that Nipah and Hendra viruses preferentially infected arteries; arteries expressed higher levels of their viral-entry receptor. Virally infected artery cells fused into syncytia containing up to 23 nuclei, which rapidly died. Despite infecting arteries and occupying ∼6%-17% of their transcriptome, Nipah and Hendra largely eluded innate immune detection, minimally eliciting interferon signaling. We thus efficiently generate artery and vein cells, introduce stem-cell-based toolkits for biosafety-level-4 virology, and explore the arterial tropism and cellular effects of Nipah and Hendra viruses.
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Affiliation(s)
- Lay Teng Ang
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Alana T Nguyen
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Kevin J Liu
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela Chen
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Xiaochen Xiong
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Matthew Curtis
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | - Renata M Martin
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Brian C Raftry
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Chun Yi Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Uwe Vogel
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Angelika Lander
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Benjamin J Lesch
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Jonas L Fowler
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Alyssa R Holman
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Timothy Chai
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Siva Vijayakumar
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Fabian P Suchy
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Toshinobu Nishimura
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joydeep Bhadury
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Steven C George
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | - Kristy Red-Horse
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Prescott
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany.
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA.
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9
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Chang CY, Shipony Z, Lin SG, Kuo A, Xiong X, Loh KM, Greenleaf WJ, Crabtree GR. Increased ACTL6A occupancy within mSWI/SNF chromatin remodelers drives human squamous cell carcinoma. Mol Cell 2021; 81:4964-4978.e8. [PMID: 34687603 PMCID: PMC8761479 DOI: 10.1016/j.molcel.2021.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 03/03/2021] [Revised: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022]
Abstract
Mammalian SWI/SNF (BAF) chromatin remodelers play dosage-sensitive roles in many human malignancies and neurologic disorders. The gene encoding the BAF subunit actin-like 6a (ACTL6A) is amplified early in the development of many squamous cell carcinomas (SCCs), but its oncogenic role remains unclear. Here we demonstrate that ACTL6A overexpression leads to its stoichiometric assembly into BAF complexes and drives their interaction and engagement with specific regulatory regions in the genome. In normal epithelial cells, ACTL6A was substoichiometric to other BAF subunits. However, increased ACTL6A levels by ectopic expression or in SCC cells led to near saturation of ACTL6A within BAF complexes. Increased ACTL6A occupancy enhanced polycomb opposition genome-wide to activate SCC genes and facilitated the co-dependent loading of BAF and TEAD-YAP complexes on chromatin. Both mechanisms appeared to be critical and function as a molecular AND gate for SCC initiation and maintenance, thereby explaining the specificity of the role of ACTL6A amplification in SCCs.
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Affiliation(s)
- Chiung-Ying Chang
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sherry G Lin
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ann Kuo
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiaochen Xiong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Gerald R Crabtree
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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10
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Roth JG, Muench KL, Asokan A, Mallett VM, Gai H, Verma Y, Weber S, Charlton C, Fowler JL, Loh KM, Dolmetsch RE, Palmer TD. 16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development. eLife 2020; 9:58178. [PMID: 33169669 PMCID: PMC7695459 DOI: 10.7554/elife.58178] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 04/22/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Microdeletions and microduplications of the 16p11.2 chromosomal locus are associated with syndromic neurodevelopmental disorders and reciprocal physiological conditions such as macro/microcephaly and high/low body mass index. To facilitate cellular and molecular investigations into these phenotypes, 65 clones of human induced pluripotent stem cells (hiPSCs) were generated from 13 individuals with 16p11.2 copy number variations (CNVs). To ensure these cell lines were suitable for downstream mechanistic investigations, a customizable bioinformatic strategy for the detection of random integration and expression of reprogramming vectors was developed and leveraged towards identifying a subset of ‘footprint’-free hiPSC clones. Transcriptomic profiling of cortical neural progenitor cells derived from these hiPSCs identified alterations in gene expression patterns which precede morphological abnormalities reported at later neurodevelopmental stages. Interpreting clinical information—available with the cell lines by request from the Simons Foundation Autism Research Initiative—with this transcriptional data revealed disruptions in gene programs related to both nervous system function and cellular metabolism. As demonstrated by these analyses, this publicly available resource has the potential to serve as a powerful medium for probing the etiology of developmental disorders associated with 16p11.2 CNVs.
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Affiliation(s)
- Julien G Roth
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Kristin L Muench
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Aditya Asokan
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Victoria M Mallett
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Hui Gai
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Neurobiology, Stanford University School of Medicine, Stanford, United States
| | - Yogendra Verma
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Stephen Weber
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Carol Charlton
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Jonas L Fowler
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Kyle M Loh
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Ricardo E Dolmetsch
- Department of Neurobiology, Stanford University School of Medicine, Stanford, United States
| | - Theo D Palmer
- Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
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11
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Martin RM, Fowler JL, Cromer MK, Lesch BJ, Ponce E, Uchida N, Nishimura T, Porteus MH, Loh KM. Improving the safety of human pluripotent stem cell therapies using genome-edited orthogonal safeguards. Nat Commun 2020; 11:2713. [PMID: 32483127 PMCID: PMC7264334 DOI: 10.1038/s41467-020-16455-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [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: 11/25/2019] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
Despite their rapidly-expanding therapeutic potential, human pluripotent stem cell (hPSC)-derived cell therapies continue to have serious safety risks. Transplantation of hPSC-derived cell populations into preclinical models has generated teratomas (tumors arising from undifferentiated hPSCs), unwanted tissues, and other types of adverse events. Mitigating these risks is important to increase the safety of such therapies. Here we use genome editing to engineer a general platform to improve the safety of future hPSC-derived cell transplantation therapies. Specifically, we develop hPSC lines bearing two drug-inducible safeguards, which have distinct functionalities and address separate safety concerns. In vitro administration of one small molecule depletes undifferentiated hPSCs >106-fold, thus preventing teratoma formation in vivo. Administration of a second small molecule kills all hPSC-derived cell-types, thus providing an option to eliminate the entire hPSC-derived cell product in vivo if adverse events arise. These orthogonal safety switches address major safety concerns with pluripotent cell-derived therapies. Human pluripotent stem cell derived therapies can have serious safety risks. Here the authors design two drug inducible genetic safeguards to deplete undifferentiated hPSCs and hPSC-derived cell types.
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Affiliation(s)
- Renata M Martin
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jonas L Fowler
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - M Kyle Cromer
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Benjamin J Lesch
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ezequiel Ponce
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nobuko Uchida
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA.,ReGen Med Division, BOCO Silicon Valley, Palo Alto, CA, 94303, USA
| | - Toshinobu Nishimura
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Matthew H Porteus
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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12
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Affiliation(s)
- Carolyn E Dundes
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyle M Loh
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Cui KW, Engel L, Dundes CE, Nguyen TC, Loh KM, Dunn AR. Spatially controlled stem cell differentiation via morphogen gradients: A comparison of static and dynamic microfluidic platforms. J Vac Sci Technol A 2020; 38:033205. [PMID: 32255900 PMCID: PMC7093209 DOI: 10.1116/1.5142012#suppl] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 05/30/2023]
Abstract
The ability to harness the processes by which complex tissues arise during embryonic development would improve the ability to engineer complex tissuelike constructs in vitro-a longstanding goal of tissue engineering and regenerative medicine. In embryos, uniform populations of stem cells are exposed to spatial gradients of diffusible extracellular signaling proteins, known as morphogens. Varying levels of these signaling proteins induce stem cells to differentiate into distinct cell types at different positions along the gradient, thus creating spatially patterned tissues. Here, the authors describe two straightforward and easy-to-adopt microfluidic strategies to expose human pluripotent stem cells in vitro to spatial gradients of desired differentiation-inducing extracellular signals. Both approaches afford a high degree of control over the distribution of extracellular signals, while preserving the viability of the cultured stem cells. The first microfluidic platform is commercially available and entails static culture, whereas the second microfluidic platform requires fabrication and dynamic fluid exchange. In each platform, the authors first computationally modeled the spatial distribution of differentiation-inducing extracellular signals. Then, the authors used each platform to expose human pluripotent stem cells to a gradient of these signals (in this case, inducing a cell type known as the primitive streak), resulting in a regionalized culture with differentiated primitive streak cells predominately localized on one side and undifferentiated stem cells at the other side of the device. By combining this approach with a fluorescent reporter for differentiated cells and live-cell fluorescence imaging, the authors characterized the spatial and temporal dynamics of primitive streak differentiation within the induced signaling gradients. Microfluidic approaches to create precisely controlled morphogen gradients will add to the stem cell and developmental biology toolkit, and may eventually pave the way to create increasingly spatially patterned tissuelike constructs in vitro.
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Affiliation(s)
- Kiara W Cui
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Leeya Engel
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Carolyn E Dundes
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305
| | - Tina C Nguyen
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Kyle M Loh
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
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14
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Cui KW, Engel L, Dundes CE, Nguyen TC, Loh KM, Dunn AR. Spatially controlled stem cell differentiation via morphogen gradients: A comparison of static and dynamic microfluidic platforms. J Vac Sci Technol A 2020; 38:033205. [PMID: 32255900 PMCID: PMC7093209 DOI: 10.1116/1.5142012] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 05/21/2023]
Abstract
The ability to harness the processes by which complex tissues arise during embryonic development would improve the ability to engineer complex tissuelike constructs in vitro-a longstanding goal of tissue engineering and regenerative medicine. In embryos, uniform populations of stem cells are exposed to spatial gradients of diffusible extracellular signaling proteins, known as morphogens. Varying levels of these signaling proteins induce stem cells to differentiate into distinct cell types at different positions along the gradient, thus creating spatially patterned tissues. Here, the authors describe two straightforward and easy-to-adopt microfluidic strategies to expose human pluripotent stem cells in vitro to spatial gradients of desired differentiation-inducing extracellular signals. Both approaches afford a high degree of control over the distribution of extracellular signals, while preserving the viability of the cultured stem cells. The first microfluidic platform is commercially available and entails static culture, whereas the second microfluidic platform requires fabrication and dynamic fluid exchange. In each platform, the authors first computationally modeled the spatial distribution of differentiation-inducing extracellular signals. Then, the authors used each platform to expose human pluripotent stem cells to a gradient of these signals (in this case, inducing a cell type known as the primitive streak), resulting in a regionalized culture with differentiated primitive streak cells predominately localized on one side and undifferentiated stem cells at the other side of the device. By combining this approach with a fluorescent reporter for differentiated cells and live-cell fluorescence imaging, the authors characterized the spatial and temporal dynamics of primitive streak differentiation within the induced signaling gradients. Microfluidic approaches to create precisely controlled morphogen gradients will add to the stem cell and developmental biology toolkit, and may eventually pave the way to create increasingly spatially patterned tissuelike constructs in vitro.
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Affiliation(s)
- Kiara W Cui
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Leeya Engel
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Carolyn E Dundes
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305
| | - Tina C Nguyen
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Kyle M Loh
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
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15
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Fowler JL, Ang LT, Loh KM. A critical look: Challenges in differentiating human pluripotent stem cells into desired cell types and organoids. Wiley Interdiscip Rev Dev Biol 2019; 9:e368. [PMID: 31746148 DOI: 10.1002/wdev.368] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/17/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022]
Abstract
Too many choices can be problematic. This is certainly the case for human pluripotent stem cells (hPSCs): they harbor the potential to differentiate into hundreds of cell types; yet it is highly challenging to exclusively differentiate hPSCs into a single desired cell type. This review focuses on unresolved and fundamental questions regarding hPSC differentiation and critiquing the identity and purity of the resultant cell populations. These are timely issues in view of the fact that hPSC-derived cell populations have or are being transplanted into patients in over 30 ongoing clinical trials. While many in vitro differentiation protocols purport to "mimic development," the exact number and identity of intermediate steps that a pluripotent cell takes to differentiate into a given cell type in vivo remains largely unknown. Consequently, most differentiation efforts inevitably generate a heterogeneous cellular population, as revealed by single-cell RNA-sequencing and other analyses. The presence of unwanted cell types in differentiated hPSC populations does not portend well for transplantation therapies. This provides an impetus to precisely control differentiation to desired ends-for instance, by logically blocking the formation of unwanted cell types or by overexpressing lineage-specifying transcription factors-or by harnessing technologies to selectively purify desired cell types. Conversely, approaches to differentiate three-dimensional "organoids" from hPSCs intentionally generate heterogeneous cell populations. While this is intended to mimic the rich cellular diversity of developing tissues, whether all such organoids are spatially organized in a manner akin to native organs (and thus, whether they fully qualify as organoids) remains to be fully resolved. This article is categorized under: Adult Stem Cells > Tissue Renewal > Regeneration: Stem Cell Differentiation and Reversion Gene Expression > Transcriptional Hierarchies: Cellular Differentiation Early Embryonic Development: Gastrulation and Neurulation.
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Affiliation(s)
- Jonas L Fowler
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, California.,Department of Developmental Biology, Bio-X, Cancer Institute, Cardiovascular Institute, ChEM-H, Diabetes Research Center, Maternal & Child Health Research Institute, Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California
| | - Lay Teng Ang
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, California
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, California.,Department of Developmental Biology, Bio-X, Cancer Institute, Cardiovascular Institute, ChEM-H, Diabetes Research Center, Maternal & Child Health Research Institute, Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California
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16
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Nichane M, Loh KM. Obliterating Obstacles to an Odyssey. Cell Stem Cell 2019; 23:313-315. [PMID: 30193127 DOI: 10.1016/j.stem.2018.08.013] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Why is reprogramming to generate induced pluripotent stem cells (iPSCs) a protracted and inefficient odyssey? In this issue of Cell Stem Cell, Mor et al. (2018) hypothesize that reprogramming factors paradoxically activate and inhibit pluripotency gene expression and show that eliminating Gatad2a (a NuRD corepressor complex subcomponent) rapidly and efficiently reprograms multiple cell types into iPSCs.
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Affiliation(s)
- Massimo Nichane
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Kyle M Loh
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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17
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Wilkinson AC, Ishida R, Kikuchi M, Sudo K, Morita M, Crisostomo RV, Yamamoto R, Loh KM, Nakamura Y, Watanabe M, Nakauchi H, Yamazaki S. Author Correction: Long-term ex vivo haematopoietic-stem-cell expansion allows nonconditioned transplantation. Nature 2019; 571:E12. [PMID: 31289376 DOI: 10.1038/s41586-019-1395-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Misako Kikuchi
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Sudo
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Maiko Morita
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ralph Valentine Crisostomo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryo Yamamoto
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Motoo Watanabe
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamazaki
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. .,Division of Stem Cell Biology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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18
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George BM, Kao KS, Kwon HS, Velasco BJ, Poyser J, Chen A, Le AC, Chhabra A, Burnett CE, Cajuste D, Hoover M, Loh KM, Shizuru JA, Weissman IL. Antibody Conditioning Enables MHC-Mismatched Hematopoietic Stem Cell Transplants and Organ Graft Tolerance. Cell Stem Cell 2019; 25:185-192.e3. [PMID: 31204177 DOI: 10.1016/j.stem.2019.05.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 06/04/2018] [Revised: 12/14/2018] [Accepted: 05/20/2019] [Indexed: 02/07/2023]
Abstract
Hematopoietic cell transplantation can correct hematological and immunological disorders by replacing a diseased blood system with a healthy one, but this currently requires depleting a patient's existing hematopoietic system with toxic and non-specific chemotherapy, radiation, or both. Here we report an antibody-based conditioning protocol with reduced toxicity and enhanced specificity for robust hematopoietic stem cell (HSC) transplantation and engraftment in recipient mice. Host pre-treatment with six monoclonal antibodies targeting CD47, T cells, NK cells, and HSCs followed by donor HSC transplantation enabled stable hematopoietic system reconstitution in recipients with mismatches at half (haploidentical) or all major histocompatibility complex (MHC) genes. This approach allowed tolerance to heart tissue from HSC donor strains in haploidentical recipients, showing potential applications for solid organ transplantation without immune suppression. Fully mismatched chimeric mice developed antibody responses to nominal antigens, showing preserved functional immunity. These findings suggest approaches for transplanting immunologically mismatched HSCs and solid organs with limited toxicity.
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Affiliation(s)
- Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin S Kao
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hye-Sook Kwon
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brenda J Velasco
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jessica Poyser
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Angela Chen
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology and the Stanford-UC Berkeley Stem Cell Institute, Stanford, CA 94305, USA
| | - Alan C Le
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Akanksha Chhabra
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cassandra E Burnett
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Devon Cajuste
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Malachia Hoover
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology and the Stanford-UC Berkeley Stem Cell Institute, Stanford, CA 94305, USA
| | - Judith A Shizuru
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology and the Stanford-UC Berkeley Stem Cell Institute, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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19
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Abstract
The liver detoxifies harmful substances, secretes vital proteins, and executes key metabolic activities, thus sustaining life. Consequently, liver failure-which can be caused by chronic alcohol intake, hepatitis, acute poisoning, or other insults-is a severe condition that can culminate in bleeding, jaundice, coma, and eventually death. However, approaches to treat liver failure, as well as studies of liver function and disease, have been stymied in part by the lack of a plentiful supply of human liver cells. To this end, this protocol details the efficient differentiation of human pluripotent stem cells (hPSCs) into hepatocyte-like cells, guided by a developmental roadmap that describes how liver fate is specified across six consecutive differentiation steps. By manipulating developmental signaling pathways to promote liver differentiation and to explicitly suppress the formation of unwanted cell fates, this method efficiently generates populations of human liver bud progenitors and hepatocyte-like cells by days 6 and 18 of PSC differentiation, respectively. This is achieved through the temporally-precise control of developmental signaling pathways, exerted by small molecules and growth factors in a serum-free culture medium. Differentiation in this system occurs in monolayers and yields hepatocyte-like cells that express characteristic hepatocyte enzymes and have the ability to engraft a mouse model of chronic liver failure. The ability to efficiently generate large numbers of human liver cells in vitro has ramifications for treatment of liver failure, for drug screening, and for mechanistic studies of liver disease.
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Affiliation(s)
- Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine; Department of Developmental Biology, Stanford University School of Medicine
| | - Amrita Palaria
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine
| | - Lay Teng Ang
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine;
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20
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Wilkinson AC, Ishida R, Kikuchi M, Sudo K, Morita M, Crisostomo RV, Yamamoto R, Loh KM, Nakamura Y, Watanabe M, Nakauchi H, Yamazaki S. Long-term ex vivo haematopoietic-stem-cell expansion allows nonconditioned transplantation. Nature 2019; 571:117-121. [PMID: 31142833 PMCID: PMC7006049 DOI: 10.1038/s41586-019-1244-x] [Citation(s) in RCA: 230] [Impact Index Per Article: 46.0] [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: 11/30/2018] [Accepted: 04/30/2019] [Indexed: 01/10/2023]
Abstract
Multipotent self-renewing haematopoietic stem cells (HSCs) regenerate the adult blood system after transplantation1, which is a curative therapy for numerous diseases including immunodeficiencies and leukaemias2. Although substantial effort has been applied to identifying HSC maintenance factors through the characterization of the in vivo bone-marrow HSC microenvironment or niche3-5, stable ex vivo HSC expansion has previously been unattainable6,7. Here we describe the development of a defined, albumin-free culture system that supports the long-term ex vivo expansion of functional mouse HSCs. We used a systematic optimization approach, and found that high levels of thrombopoietin synergize with low levels of stem-cell factor and fibronectin to sustain HSC self-renewal. Serum albumin has long been recognized as a major source of biological contaminants in HSC cultures8; we identify polyvinyl alcohol as a functionally superior replacement for serum albumin that is compatible with good manufacturing practice. These conditions afford between 236- and 899-fold expansions of functional HSCs over 1 month, although analysis of clonally derived cultures suggests that there is considerable heterogeneity in the self-renewal capacity of HSCs ex vivo. Using this system, HSC cultures that are derived from only 50 cells robustly engraft in recipient mice without the normal requirement for toxic pre-conditioning (for example, radiation), which may be relevant for HSC transplantation in humans. These findings therefore have important implications for both basic HSC research and clinical haematology.
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Affiliation(s)
- Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Reiko Ishida
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Misako Kikuchi
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Sudo
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Maiko Morita
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ralph Valentine Crisostomo
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryo Yamamoto
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Motoo Watanabe
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamazaki
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. .,Division of Stem Cell Biology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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21
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Ang LT, Tan AKY, Autio MI, Goh SH, Choo SH, Lee KL, Tan J, Pan B, Lee JJH, Lum JJ, Lim CYY, Yeo IKX, Wong CJY, Liu M, Oh JLL, Chia CPL, Loh CH, Chen A, Chen Q, Weissman IL, Loh KM, Lim B. A Roadmap for Human Liver Differentiation from Pluripotent Stem Cells. Cell Rep 2019; 22:2190-2205. [PMID: 29466743 PMCID: PMC5854481 DOI: 10.1016/j.celrep.2018.01.087] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [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: 10/29/2016] [Revised: 12/08/2017] [Accepted: 01/29/2018] [Indexed: 01/02/2023] Open
Abstract
How are closely related lineages, including liver, pancreas, and intestines, diversified from a common endodermal origin? Here, we apply principles learned from developmental biology to rapidly reconstitute liver progenitors from human pluripotent stem cells (hPSCs). Mapping the formation of multiple endodermal lineages revealed how alternate endodermal fates (e.g., pancreas and intestines) are restricted during liver commitment. Human liver fate was encoded by combinations of inductive and repressive extracellular signals at different doses. However, these signaling combinations were temporally re-interpreted: cellular competence to respond to retinoid, WNT, TGF-β, and other signals sharply changed within 24 hr. Consequently, temporally dynamic manipulation of extracellular signals was imperative to suppress the production of unwanted cell fates across six consecutive developmental junctures. This efficiently generated 94.1% ± 7.35% TBX3+HNF4A+ human liver bud progenitors and 81.5% ± 3.2% FAH+ hepatocyte-like cells by days 6 and 18 of hPSC differentiation, respectively; the latter improved short-term survival in the Fah-/-Rag2-/-Il2rg-/- mouse model of liver failure.
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Affiliation(s)
- Lay Teng Ang
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore.
| | - Antson Kiat Yee Tan
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Matias I Autio
- Human Genetics Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Cardiovascular Research Institute, National University of Singapore, Singapore 117599, Singapore
| | - Su Hua Goh
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Siew Hua Choo
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Kian Leong Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jianmin Tan
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Bangfen Pan
- Human Genetics Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; Cardiovascular Research Institute, National University of Singapore, Singapore 117599, Singapore
| | - Jane Jia Hui Lee
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Jen Jen Lum
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Christina Ying Yan Lim
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Isabelle Kai Xin Yeo
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Chloe Jin Yee Wong
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Min Liu
- Humanized Mouse Unit, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Jueween Ling Li Oh
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Cheryl Pei Lynn Chia
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore; School of Engineering, Temasek Polytechnic, Singapore 529757, Singapore
| | - Chet Hong Loh
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Angela Chen
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Qingfeng Chen
- Humanized Mouse Unit, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Department of Microbiology, Yong Yoo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Irving L Weissman
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bing Lim
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore.
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22
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Allen WE, DeNardo LA, Chen MZ, Liu CD, Loh KM, Fenno LE, Ramakrishnan C, Deisseroth K, Luo L. Thirst-associated preoptic neurons encode an aversive motivational drive. Science 2018; 357:1149-1155. [PMID: 28912243 PMCID: PMC5723384 DOI: 10.1126/science.aan6747] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/26/2017] [Indexed: 01/16/2023]
Abstract
Water deprivation produces a drive to seek and consume water. How neural activity creates this motivation remains poorly understood. We used activity-dependent genetic labeling to characterize neurons activated by water deprivation in the hypothalamic median preoptic nucleus (MnPO). Single-cell transcriptional profiling revealed that dehydration-activated MnPO neurons consist of a single excitatory cell type. After optogenetic activation of these neurons, mice drank water and performed an operant lever-pressing task for water reward with rates that scaled with stimulation frequency. This stimulation was aversive, and instrumentally pausing stimulation could reinforce lever-pressing. Activity of these neurons gradually decreased over the course of an operant session. Thus, the activity of dehydration-activated MnPO neurons establishes a scalable, persistent, and aversive internal state that dynamically controls thirst-motivated behavior.
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Affiliation(s)
- William E Allen
- Department of Biology, Stanford University, Stanford, CA 94305, USA.,Neurosciences Program, Stanford University, Stanford, CA 94305, USA
| | - Laura A DeNardo
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Michael Z Chen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Cindy D Liu
- Department of Biology, Stanford University, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lief E Fenno
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA. .,Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- Department of Biology, Stanford University, Stanford, CA 94305, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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23
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Nichane M, Nichane M, Javed A, Sivakamasundari V, Ganesan M, Ang LT, Kraus P, Lufkin T, Loh KM, Lim B. 3D culture of multipotent Sox9+ mouse embryonic lung progenitors: Isolation, Expansion and Cryopreservation. ACTA ACUST UNITED AC 2017. [DOI: 10.1038/protex.2017.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Tan AKY, Loh KM, Ang LT. Evaluating the regenerative potential and functionality of human liver cells in mice. Differentiation 2017; 98:25-34. [PMID: 29078082 DOI: 10.1016/j.diff.2017.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 02/07/2023]
Abstract
Liver diseases afflict millions of patients worldwide. Currently, the only long-term treatment for liver failure is the transplantation of a new liver. However, intravenously transplanting a suspension of human hepatocytes might be a less-invasive approach to partially reconstitute lost liver functions in human patients as evinced by promising outcomes in clinical trials. The purpose of this essay is to emphasize outstanding questions that continue to surround hepatocyte transplantation. While adult primary human hepatocytes are the gold standard for transplantation, hepatocytes are heterogeneous. Whether all hepatocytes engraft equally and what specifically defines an "engraftable" hepatocyte capable of long-term liver reconstitution remains unclear. To this end, mouse models of liver injury enable the evaluation of human hepatocytes and their behavior upon transplantation into a complex injured liver environment. While mouse models may not be fully representative of the injured human liver and human hepatocytes tend to engraft mice less efficiently than mouse hepatocytes, valuable lessons have nonetheless been learned from transplanting human hepatocytes into mouse models. With an eye to the future, it will be crucial to eventually detail the optimal biological source (whether in vivo- or in vitro-derived) and presumptive heterogeneity of human hepatocytes and to understand the mechanisms through which they engraft and regenerate liver tissue in vivo.
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Affiliation(s)
- Antson Kiat Yee Tan
- Stem Cell&Developmental Biology Group, Genome Institute of Singapore, A*STAR, Singapore 138672, Singapore
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology and Regenerative Medicine and the Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lay Teng Ang
- Stem Cell&Developmental Biology Group, Genome Institute of Singapore, A*STAR, Singapore 138672, Singapore.
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25
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Masaki H, Kato-Itoh M, Takahashi Y, Umino A, Sato H, Ito K, Yanagida A, Nishimura T, Yamaguchi T, Hirabayashi M, Era T, Loh KM, Wu SM, Weissman IL, Nakauchi H. Inhibition of Apoptosis Overcomes Stage-Related Compatibility Barriers to Chimera Formation in Mouse Embryos. Cell Stem Cell 2017; 19:587-592. [PMID: 27814480 DOI: 10.1016/j.stem.2016.10.013] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [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: 11/11/2015] [Revised: 09/05/2016] [Accepted: 10/19/2016] [Indexed: 12/19/2022]
Abstract
Cell types more advanced in development than embryonic stem cells, such as EpiSCs, fail to contribute to chimeras when injected into pre-implantation-stage blastocysts, apparently because the injected cells undergo apoptosis. Here we show that transient promotion of cell survival through expression of the anti-apoptotic gene BCL2 enables EpiSCs and Sox17+ endoderm progenitors to integrate into blastocysts and contribute to chimeric embryos. Upon injection into blastocyst, BCL2-expressing EpiSCs contributed to all bodily tissues in chimeric animals while Sox17+ endoderm progenitors specifically contributed in a region-specific fashion to endodermal tissues. In addition, BCL2 expression enabled rat EpiSCs to contribute to mouse embryonic chimeras, thereby forming interspecies chimeras that could survive to adulthood. Our system therefore provides a method to overcome cellular compatibility issues that typically restrict chimera formation. Application of this type of approach could broaden the use of embryonic chimeras, including region-specific chimeras, for basic developmental biology research and regenerative medicine.
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Affiliation(s)
- Hideki Masaki
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Megumi Kato-Itoh
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Yusuke Takahashi
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ayumi Umino
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hideyuki Sato
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Keiichi Ito
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Ayaka Yanagida
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Toshinobu Nishimura
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomoyuki Yamaguchi
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki-shi, Aichi-ken 444-0864, Japan
| | - Takumi Era
- Department of Cell Modulation, Institute of Molecular Embryology and Genetics, Kumamoto University, Chuo-ku, Kumamoto 860-8555, Japan
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine and Ludwig Center for Cancer Stem Cell Biology and Medicine, Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sean M Wu
- Stanford Cardiovascular Institute, Division of Cardiovascular Medicine, Department of Medicine, Institute for Stem Cell Biology and Regenerative Medicine and Child Health Research Institute, Stanford University School of Medicine, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine and Ludwig Center for Cancer Stem Cell Biology and Medicine, Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan; Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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26
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Loh KM, van Amerongen R, Nusse R. Generating Cellular Diversity and Spatial Form: Wnt Signaling and the Evolution of Multicellular Animals. Dev Cell 2017; 38:643-55. [PMID: 27676437 DOI: 10.1016/j.devcel.2016.08.011] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/29/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023]
Abstract
There were multiple prerequisites to the evolution of multicellular animal life, including the generation of multiple cell fates ("cellular diversity") and their patterned spatial arrangement ("spatial form"). Wnt proteins operate as primordial symmetry-breaking signals. By virtue of their short-range nature and their capacity to activate both lineage-specifying and cell-polarizing intracellular signaling cascades, Wnts can polarize cells at their site of contact, orienting the axis of cell division while simultaneously programming daughter cells to adopt diverging fates in a spatially stereotyped way. By coupling cell fate to position, symmetry-breaking Wnt signals were pivotal in constructing the metazoan body by generating cellular diversity and spatial form.
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Affiliation(s)
- Kyle M Loh
- Department of Developmental Biology, Howard Hughes Medical Institute, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Renée van Amerongen
- Section of Molecular Cytology and Van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Roel Nusse
- Department of Developmental Biology, Howard Hughes Medical Institute, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA.
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Loh KM, Chen A, Koh PW, Deng TZ, Sinha R, Tsai JM, Barkal AA, Shen KY, Jain R, Morganti RM, Shyh-Chang N, Fernhoff NB, George BM, Wernig G, Salomon REA, Chen Z, Vogel H, Epstein JA, Kundaje A, Talbot WS, Beachy PA, Ang LT, Weissman IL. Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types. Cell 2017; 166:451-467. [PMID: 27419872 DOI: 10.1016/j.cell.2016.06.011] [Citation(s) in RCA: 279] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/25/2016] [Accepted: 06/01/2016] [Indexed: 01/04/2023]
Abstract
Stem-cell differentiation to desired lineages requires navigating alternating developmental paths that often lead to unwanted cell types. Hence, comprehensive developmental roadmaps are crucial to channel stem-cell differentiation toward desired fates. To this end, here, we map bifurcating lineage choices leading from pluripotency to 12 human mesodermal lineages, including bone, muscle, and heart. We defined the extrinsic signals controlling each binary lineage decision, enabling us to logically block differentiation toward unwanted fates and rapidly steer pluripotent stem cells toward 80%-99% pure human mesodermal lineages at most branchpoints. This strategy enabled the generation of human bone and heart progenitors that could engraft in respective in vivo models. Mapping stepwise chromatin and single-cell gene expression changes in mesoderm development uncovered somite segmentation, a previously unobservable human embryonic event transiently marked by HOPX expression. Collectively, this roadmap enables navigation of mesodermal development to produce transplantable human tissue progenitors and uncover developmental processes. VIDEO ABSTRACT.
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Affiliation(s)
- Kyle M Loh
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Angela Chen
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Pang Wei Koh
- Departments of Genetics and Computer Science, Stanford University School of Medicine, CA 94305, USA
| | - Tianda Z Deng
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Rahul Sinha
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Jonathan M Tsai
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Amira A Barkal
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Kimberle Y Shen
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Rajan Jain
- Department of Cell and Developmental Biology, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel M Morganti
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Ng Shyh-Chang
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Nathaniel B Fernhoff
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Benson M George
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Gerlinde Wernig
- Department of Pathology, Stanford University School of Medicine, CA 94305, USA
| | - Rachel E A Salomon
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Zhenghao Chen
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University School of Medicine, CA 94305, USA
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anshul Kundaje
- Departments of Genetics and Computer Science, Stanford University School of Medicine, CA 94305, USA
| | - William S Talbot
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA
| | - Philip A Beachy
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA; Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, CA 94305, USA
| | - Lay Teng Ang
- Stem Cell & Regenerative Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore.
| | - Irving L Weissman
- Department of Developmental Biology, Institute for Stem Cell Biology & Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, CA 94305, USA.
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Koh PW, Sinha R, Barkal AA, Morganti RM, Chen A, Weissman IL, Ang LT, Kundaje A, Loh KM. An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development. Sci Data 2016; 3:160109. [PMID: 27996962 PMCID: PMC5170597 DOI: 10.1038/sdata.2016.109] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 08/02/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022] Open
Abstract
Mesoderm is the developmental precursor to myriad human tissues including bone, heart, and skeletal muscle. Unravelling the molecular events through which these lineages become diversified from one another is integral to developmental biology and understanding changes in cellular fate. To this end, we developed an in vitro system to differentiate human pluripotent stem cells through primitive streak intermediates into paraxial mesoderm and its derivatives (somites, sclerotome, dermomyotome) and separately, into lateral mesoderm and its derivatives (cardiac mesoderm). Whole-population and single-cell analyses of these purified populations of human mesoderm lineages through RNA-seq, ATAC-seq, and high-throughput surface marker screens illustrated how transcriptional changes co-occur with changes in open chromatin and surface marker landscapes throughout human mesoderm development. This molecular atlas will facilitate study of human mesoderm development (which cannot be interrogated in vivo due to restrictions on human embryo studies) and provides a broad resource for the study of gene regulation in development at the single-cell level, knowledge that might one day be exploited for regenerative medicine.
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Affiliation(s)
- Pang Wei Koh
- Department of Genetics and Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Rahul Sinha
- Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Amira A Barkal
- Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Rachel M Morganti
- Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Angela Chen
- Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Irving L Weissman
- Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lay Teng Ang
- Stem Cell &Regenerative Biology Group, Genome Institute of Singapore, A*STAR, Singapore 138672, Singapore
| | - Anshul Kundaje
- Department of Genetics and Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Kyle M Loh
- Department of Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Ludwig Center for Cancer Stem Cell Biology and Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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Abstract
Pluripotent cells in embryos are situated near the apex of the hierarchy of developmental potential. They are capable of generating all cell types of the mammalian body proper. Therefore, they are the exemplar of stem cells. In vivo, pluripotent cells exist transiently and become expended within a few days of their establishment. Yet, when explanted into artificial culture conditions, they can be indefinitely propagated in vitro as pluripotent stem cell lines. A host of transcription factors and regulatory genes are now known to underpin the pluripotent state. Nonetheless, how pluripotent cells are equipped with their vast multilineage differentiation potential remains elusive. Consensus holds that pluripotency transcription factors prevent differentiation by inhibiting the expression of differentiation genes. However, this does not explain the developmental potential of pluripotent cells. We have presented another emergent perspective, namely, that pluripotency factors function as lineage specifiers that enable pluripotent cells to differentiate into specific lineages, therefore endowing pluripotent cells with their multilineage potential. Here we provide a comprehensive overview of the developmental biology, transcription factors, and extrinsic signaling associated with pluripotent cells, and their accompanying subtypes, in vitro heterogeneity and chromatin states. Although much has been learned since the appreciation of mammalian pluripotency in the 1950s and the derivation of embryonic stem cell lines in 1981, we will specifically emphasize what currently remains unclear. However, the view that pluripotency factors capacitate differentiation, recently corroborated by experimental evidence, might perhaps address the long-standing question of how pluripotent cells are endowed with their multilineage differentiation potential.
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Affiliation(s)
- Kyle M. Loh
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
| | - Bing Lim
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
| | - Lay Teng Ang
- Department of Developmental Biology and the Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California; Genome Institute of Singapore, Stem Cell & Regenerative Biology Group, Agency for Science, Technology & Research, Singapore; and Department of Medicine and the Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Harvard Medical School, Boston, Massachusetts
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Clevers H, Loh KM, Nusse R. Stem cell signaling. An integral program for tissue renewal and regeneration: Wnt signaling and stem cell control. Science 2014; 346:1248012. [PMID: 25278615 DOI: 10.1126/science.1248012] [Citation(s) in RCA: 917] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Stem cells fuel tissue development, renewal, and regeneration, and these activities are controlled by the local stem cell microenvironment, the "niche." Wnt signals emanating from the niche can act as self-renewal factors for stem cells in multiple mammalian tissues. Wnt proteins are lipid-modified, which constrains them to act as short-range cellular signals. The locality of Wnt signaling dictates that stem cells exiting the Wnt signaling domain differentiate, spatially delimiting the niche in certain tissues. In some instances, stem cells may act as or generate their own niche, enabling the self-organization of patterned tissues. In this Review, we discuss the various ways by which Wnt operates in stem cell control and, in doing so, identify an integral program for tissue renewal and regeneration.
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Affiliation(s)
- Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht and CancerGenomics.nl, 3584CT Utrecht, Netherlands
| | - Kyle M Loh
- Department of Developmental Biology, Howard Hughes Medical Institute, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA
| | - Roel Nusse
- Department of Developmental Biology, Howard Hughes Medical Institute, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305, USA.
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Loh KM, Lim B, Teng Ang L. Stem Cell Genomics: Developmental Competence. Genomic Med 2014. [DOI: 10.1093/med/9780199896028.003.0047] [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: 11/12/2022] Open
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32
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Roberts RM, Loh KM, Amita M, Bernardo AS, Adachi K, Alexenko AP, Schust DJ, Schulz LC, Telugu BPVL, Ezashi T, Pedersen RA. Differentiation of trophoblast cells from human embryonic stem cells: to be or not to be? Reproduction 2014; 147:D1-12. [PMID: 24518070 DOI: 10.1530/rep-14-0080] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
It is imperative to unveil the full range of differentiated cell types into which human pluripotent stem cells (hPSCs) can develop. The need is twofold: it will delimit the therapeutic utility of these stem cells and is necessary to place their position accurately in the developmental hierarchy of lineage potential. Accumulated evidence suggested that hPSC could develop in vitro into an extraembryonic lineage (trophoblast (TB)) that is typically inaccessible to pluripotent embryonic cells during embryogenesis. However, whether these differentiated cells are truly authentic TB has been challenged. In this debate, we present a case for and a case against TB differentiation from hPSCs. By analogy to other differentiation systems, our debate is broadly applicable, as it articulates higher and more challenging standards for judging whether a given cell type has been genuinely produced from hPSC differentiation.
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Loh KM, Ang LT, Zhang J, Kumar V, Ang J, Auyeong JQ, Lee KL, Choo SH, Lim CYY, Nichane M, Tan J, Noghabi MS, Azzola L, Ng ES, Durruthy-Durruthy J, Sebastiano V, Poellinger L, Elefanty AG, Stanley EG, Chen Q, Prabhakar S, Weissman IL, Lim B. Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations. Cell Stem Cell 2014; 14:237-52. [PMID: 24412311 DOI: 10.1016/j.stem.2013.12.007] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/25/2013] [Accepted: 12/16/2013] [Indexed: 01/11/2023]
Abstract
Human pluripotent stem cell (hPSC) differentiation typically yields heterogeneous populations. Knowledge of signals controlling embryonic lineage bifurcations could efficiently yield desired cell types through exclusion of alternate fates. Therefore, we revisited signals driving induction and anterior-posterior patterning of definitive endoderm to generate a coherent roadmap for endoderm differentiation. With striking temporal dynamics, BMP and Wnt initially specified anterior primitive streak (progenitor to endoderm), yet, 24 hr later, suppressed endoderm and induced mesoderm. At lineage bifurcations, cross-repressive signals separated mutually exclusive fates; TGF-β and BMP/MAPK respectively induced pancreas versus liver from endoderm by suppressing the alternate lineage. We systematically blockaded alternate fates throughout multiple consecutive bifurcations, thereby efficiently differentiating multiple hPSC lines exclusively into endoderm and its derivatives. Comprehensive transcriptional and chromatin mapping of highly pure endodermal populations revealed that endodermal enhancers existed in a surprising diversity of "pre-enhancer" states before activation, reflecting the establishment of a permissive chromatin landscape as a prelude to differentiation.
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Affiliation(s)
- Kyle M Loh
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore; Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Lay Teng Ang
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore.
| | - Jingyao Zhang
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Vibhor Kumar
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Jasmin Ang
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Jun Qiang Auyeong
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Kian Leong Lee
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Siew Hua Choo
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Christina Y Y Lim
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Massimo Nichane
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Junru Tan
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Monireh Soroush Noghabi
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Lisa Azzola
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - Elizabeth S Ng
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Murdoch Childrens Research Institute, The Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Jens Durruthy-Durruthy
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vittorio Sebastiano
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lorenz Poellinger
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Andrew G Elefanty
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Murdoch Childrens Research Institute, The Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Edouard G Stanley
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia; Murdoch Childrens Research Institute, The Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Qingfeng Chen
- Humanized Mouse Unit, Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Department of Microbiology, Yong Yoo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Shyam Prabhakar
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore
| | - Irving L Weissman
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bing Lim
- Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.
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34
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Affiliation(s)
- Kyle M Loh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, USA
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35
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Heng JCD, Loh KM, Ng HH. Investigating the bona fide differentiation capacity of human pluripotent stem cells. Cell Res 2011; 22:6-8. [PMID: 21876556 DOI: 10.1038/cr.2011.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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36
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Abstract
Understanding the basis of the unrestricted multilineage differentiation potential of pluripotent cells will be of developmental and translational consequence. We propose that pluripotency transcription factors are lineage specifiers that direct commitment to specific fetal lineages. Individual factors bestow the ability to differentiate into particular cell types, and concomitant expression of multiple lineage specifiers within pluripotent cells enables differentiation into every fetal lineage. Moreover, we speculate that, rather than being an intrinsically stable "ground state," pluripotency is an inherently precarious condition in which rival lineage specifiers continually compete to specify differentiation along mutually exclusive lineages.
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Affiliation(s)
- Kyle M Loh
- Genome Institute of Singapore, Stem Cell & Developmental Biology Group, Singapore, Singapore.
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Abstract
Two Matters Arising articles in this issue challenge the conclusions of a previous Cell Stem Cell paper that found extensive transcriptional differences between hESCs and hiPSCs. The original authors provide a response and set in motion a discussion in the field about appropriate methods for microarray data analysis.
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Affiliation(s)
- Kyle M Loh
- Genome Institute of Singapore, Stem Cell & Developmental Biology, Singapore 138672, Singapore
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Loh KM, Soh BS, Tam WL, Lim B. Molecular Principles Underlying Pluripotency and Differentiation of Embryonic Stem Cells. Stem Cells 2010. [DOI: 10.1142/9789814289399_0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Kyle M. Loh
- Genome Institute of Singapore, Stem Cell & Developmental Biology, Singapore 138672, Singapore
| | - Boon Seng Soh
- Genome Institute of Singapore, Stem Cell & Developmental Biology, Singapore 138672, Singapore
| | | | - Bing Lim
- Harvard Medical School, Department of Medicine Beth Israel Deaconess Medical Center, Division of Hematology/Oncology, Boston Massachusetts 02115, USA
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Ichida JK, Blanchard J, Lam K, Son EY, Chung JE, Egli D, Loh KM, Carter AC, Di Giorgio FP, Koszka K, Huangfu D, Akutsu H, Liu DR, Rubin LL, Eggan K. A small-molecule inhibitor of tgf-Beta signaling replaces sox2 in reprogramming by inducing nanog. Cell Stem Cell 2009; 5:491-503. [PMID: 19818703 DOI: 10.1016/j.stem.2009.09.012] [Citation(s) in RCA: 594] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 09/02/2009] [Accepted: 09/23/2009] [Indexed: 02/07/2023]
Abstract
The combined activity of three transcription factors can reprogram adult cells into induced pluripotent stem cells (iPSCs). However, the transgenic methods used for delivering reprogramming factors have raised concerns regarding the future utility of the resulting stem cells. These uncertainties could be overcome if each transgenic factor were replaced with a small molecule that either directly activated its expression from the somatic genome or in some way compensated for its activity. To this end, we have used high-content chemical screening to identify small molecules that can replace Sox2 in reprogramming. We show that one of these molecules functions in reprogramming by inhibiting Tgf-beta signaling in a stable and trapped intermediate cell type that forms during the process. We find that this inhibition promotes the completion of reprogramming through induction of the transcription factor Nanog.
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Affiliation(s)
- Justin K Ichida
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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