1
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Georgieva D, Wang N, Taglialatela A, Jerabek S, Reczek CR, Lim PX, Sung J, Du Q, Horiguchi M, Jasin M, Ciccia A, Baer R, Egli D. BRCA1 and 53BP1 regulate reprogramming efficiency by mediating DNA repair pathway choice at replication-associated double-strand breaks. Cell Rep 2024; 43:114006. [PMID: 38554279 DOI: 10.1016/j.celrep.2024.114006] [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: 02/26/2023] [Revised: 11/26/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
Reprogramming to pluripotency is associated with DNA damage and requires the functions of the BRCA1 tumor suppressor. Here, we leverage separation-of-function mutations in BRCA1/2 as well as the physical and/or genetic interactions between BRCA1 and its associated repair proteins to ascertain the relevance of homology-directed repair (HDR), stalled fork protection (SFP), and replication gap suppression (RGS) in somatic cell reprogramming. Surprisingly, loss of SFP and RGS is inconsequential for the transition to pluripotency. In contrast, cells deficient in HDR, but proficient in SFP and RGS, reprogram with reduced efficiency. Conversely, the restoration of HDR function through inactivation of 53bp1 rescues reprogramming in Brca1-deficient cells, and 53bp1 loss leads to elevated HDR and enhanced reprogramming in mouse and human cells. These results demonstrate that somatic cell reprogramming is especially dependent on repair of replication-associated double-strand breaks (DSBs) by the HDR activity of BRCA1 and BRCA2 and can be improved in the absence of 53BP1.
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Affiliation(s)
- Daniela Georgieva
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Angelo Taglialatela
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Stepan Jerabek
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 160 00 Praha 6, Czech Republic
| | - Colleen R Reczek
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julie Sung
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Qian Du
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michiko Horiguchi
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alberto Ciccia
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Richard Baer
- Department of Pathology & Cell Biology, Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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2
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Cherkaoui I, Du Q, Egli D, Misra S, Rutter GA. Optimized Protocol for Generating Functional Pancreatic Insulin-secreting Cells from Human Pluripotent Stem Cells. J Vis Exp 2024. [PMID: 38372369 DOI: 10.3791/65530] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024] Open
Abstract
Human pluripotent stem cells (hPSCs) can differentiate into any kind of cell, making them an excellent alternative source of human pancreatic β-cells. hPSCs can either be embryonic stem cells (hESCs) derived from the blastocyst or induced pluripotent cells (hiPSCs) generated directly from somatic cells using a reprogramming process. Here a video-based protocol is presented to outline the optimal culture and passage conditions for hPSCs, prior to their differentiation and subsequent generation of insulin-producing pancreatic cells. This methodology follows the six-stage process for β-cell directed differentiation, wherein hPSCs differentiate into definitive endoderm (DE), primitive gut tube, posterior foregut fate, pancreatic progenitors, pancreatic endocrine progenitors, and ultimately pancreatic β-cells. It is noteworthy that this differentiation methodology takes a period of 27 days to generate human pancreatic β-cells. The potential of insulin secretion was evaluated through two experiments, which included immunostaining and glucose-stimulated insulin secretion.
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Affiliation(s)
- Ines Cherkaoui
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Cell Biology and Functional Genomics;
| | - Qian Du
- Departments of Pediatrics, Naomi Berrie Diabetes Center, Obstetrics and Gynecology, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, Columbia University
| | - Dieter Egli
- Departments of Pediatrics, Naomi Berrie Diabetes Center, Obstetrics and Gynecology, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, Columbia University
| | - Shivani Misra
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Cell Biology and Functional Genomics; Department of Diabetes, Imperial College Healthcare NHS Trust
| | - Guy A Rutter
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Cell Biology and Functional Genomics; Faculté de Médicine, Université de Montréal; Lee Kong Chian Imperial Medical School, Nanyang Technological University;
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3
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Zhang Y, Sui L, Du Q, Haataja L, Yin Y, Viola R, Xu S, Nielsson CU, Leibel RL, Barbetti F, Arvan P, Egli D. Permanent neonatal diabetes-causing insulin mutations have dominant negative effects on beta cell identity. Mol Metab 2024; 80:101879. [PMID: 38237895 PMCID: PMC10839447 DOI: 10.1016/j.molmet.2024.101879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
OBJECTIVE Heterozygous coding sequence mutations of the INS gene are a cause of permanent neonatal diabetes (PNDM), requiring insulin therapy similar to T1D. While the negative effects on insulin processing and secretion are known, how dominant insulin mutations result in a continued decline of beta cell function after birth is not well understood. METHODS We explored the causes of beta cell failure in two PNDM patients with two distinct INS mutations using patient-derived iPSCs and mutated hESCs. RESULTS we detected accumulation of misfolded proinsulin and impaired proinsulin processing in vitro, and a dominant-negative effect of these mutations on beta-cell mass and function after transplantation into mice. In addition to anticipated ER stress, we found evidence of beta-cell dedifferentiation, characterized by an increase of cells expressing both Nkx6.1 and ALDH1A3, but negative for insulin and glucagon. CONCLUSIONS These results highlight a novel mechanism, the loss of beta cell identity, contributing to the loss and functional failure of human beta cells with specific insulin gene mutations.
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Affiliation(s)
- Yuwei Zhang
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States
| | - Lina Sui
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States
| | - Qian Du
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States
| | - Leena Haataja
- Metabolism Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI 48105, United States
| | - Yishu Yin
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States
| | - Ryan Viola
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States
| | - Shuangyi Xu
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States
| | - Christian Ulrik Nielsson
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States
| | - Rudolph L Leibel
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States
| | - Fabrizio Barbetti
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome 00133, Italy; Monogenic Diabetes Clinic, Endocrinology and Diabetes Unit, Bambino Gesù Children's Hospital, Rome 00164, Italy
| | - Peter Arvan
- Metabolism Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI 48105, United States
| | - Dieter Egli
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, United States.
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4
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Edwards MM, Wang N, Massey DJ, Bhatele S, Egli D, Koren A. Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells. Cell Rep 2024; 43:113664. [PMID: 38194345 DOI: 10.1016/j.celrep.2023.113664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sakshi Bhatele
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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5
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Xu S, Wang N, Zuccaro MV, Gerhardt J, Baslan T, Koren A, Egli D. DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility. bioRxiv 2023:2023.12.25.573304. [PMID: 38234839 PMCID: PMC10793403 DOI: 10.1101/2023.12.25.573304] [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] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
DNA replication in differentiated cells follows a defined program, but when and how it is established during mammalian development is not known. Here we show using single-cell sequencing, that both bovine and mouse cleavage stage embryos progress through S-phase in a defined pattern. Late replicating regions are associated with the nuclear lamina from the first cell cycle after fertilization, and contain few active origins, and few but long genes. Chromosome breaks, which form spontaneously in bovine embryos at sites concordant with human embryos, preferentially locate to late replicating regions. In mice, late replicating regions show enhanced fragility due to a sparsity of dormant origins that can be activated under conditions of replication stress. This pattern predisposes regions with long neuronal genes to fragility and genetic change prior to segregation of soma and germ line. Our studies show that the formation of early and late replicating regions is among the first layers of epigenetic regulation established on the mammalian genome after fertilization.
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Affiliation(s)
- Shuangyi Xu
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
| | - Ning Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
| | - Michael V Zuccaro
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
- Graduate Program, Department of Cellular Physiology and Biophysics, Columbia University, New York
| | | | - Timour Baslan
- Department of Biomedical Sciences, The University of Pennsylvania, Philadelphia, PA, 19104
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY, 14853, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Columbia University, New York, NY, 10032, USA
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6
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Wang N, Xu S, Egli D. Replication stress in mammalian embryo development, differentiation, and reprogramming. Trends Cell Biol 2023; 33:872-886. [PMID: 37202286 DOI: 10.1016/j.tcb.2023.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/20/2023]
Abstract
Duplicating a genome of 3 billion nucleotides is challenged by a variety of obstacles that can cause replication stress and affect the integrity of the genome. Recent studies show that replication fork slowing and stalling is prevalent in early mammalian development, resulting in genome instability and aneuploidy, and constituting a barrier to development in human reproduction. Genome instability resulting from DNA replication stress is a barrier to the cloning of animals and to the reprogramming of differentiated cells to induced pluripotent stem cells, as well as a barrier to cell transformation. Remarkably, the regions most impacted by replication stress are shared in these different cellular contexts, affecting long genes and flanking intergenic areas. In this review we integrate our knowledge of DNA replication stress in mammalian embryos, in programming, and in reprogramming, and we discuss a potential role for fragile sites in sensing replication stress and restricting cell cycle progression in health and disease.
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Affiliation(s)
- Ning Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shuangyi Xu
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA.
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7
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Zhang Y, Sui L, Du Q, Haataja L, Yin Y, Viola R, Xu S, Nielsson CU, Leibel RL, Barbetti F, Arvan P, Egli D. Permanent Neonatal diabetes-causing Insulin mutations have dominant negative effects on beta cell identity. bioRxiv 2023:2023.09.01.555839. [PMID: 37745320 PMCID: PMC10515756 DOI: 10.1101/2023.09.01.555839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Heterozygous coding sequence mutations of the INS gene are a cause of permanent neonatal diabetes (PNDM) that results from beta cell failure. We explored the causes of beta cell failure in two PNDM patients with two distinct INS mutations. Using b and mutated hESCs, we detected accumulation of misfolded proinsulin and impaired proinsulin processing in vitro, and a dominant-negative effect of these mutations on the in vivo performance of patient-derived SC-beta cells after transplantation into NSG mice. These insulin mutations derange endoplasmic reticulum (ER) homeostasis, and result in the loss of beta-cell mass and function. In addition to anticipated apoptosis, we found evidence of beta-cell dedifferentiation, characterized by an increase of cells expressing both Nkx6.1 and ALDH1A3, but negative for insulin and glucagon. These results highlight both known and novel mechanisms contributing to the loss and functional failure of human beta cells with specific insulin gene mutations.
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Affiliation(s)
- Yuwei Zhang
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
- These authors contributed equally
| | - Lina Sui
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
- These authors contributed equally
| | - Qian Du
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
| | - Leena Haataja
- Metabolism Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI 48105, United States
| | - Yishu Yin
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
| | - Ryan Viola
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
| | - Shuangyi Xu
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
| | - Christian Ulrik Nielsson
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
| | - Rudolph L. Leibel
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
| | - Fabrizio Barbetti
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome 00133, Italy
- Monogenic Diabetes Clinic, Endocrinology and Diabetes Unit, Bambino Gesù Children’s Hospital, Rome 00164, Italy
| | - Peter Arvan
- Metabolism Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI 48105, United States
| | - Dieter Egli
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, United States
- Lead Contact
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8
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Edwards MM, Wang N, Massey DJ, Egli D, Koren A. Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells. bioRxiv 2023:2023.06.12.544654. [PMID: 37398435 PMCID: PMC10312660 DOI: 10.1101/2023.06.12.544654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Induced pluripotent stem cells (iPSC) are a widely used cell system and a foundation for cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which have the potential to affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing - a process linked to both genome regulation and genome stability - is efficiently reprogrammed to the embryonic state. To answer this, we profiled and compared genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicated their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibit delayed replication at heterochromatic regions containing genes downregulated in iPSC with incompletely reprogrammed DNA methylation. DNA replication delays were not the result of gene expression and DNA methylation aberrations and persisted after differentiating cells to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and lead to undesirable phenotypes in iPSCs, establishing it as an important genomic feature to consider when evaluating iPSC lines.
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Affiliation(s)
- Matthew M. Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Dashiell J. Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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9
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Kratka C, Vadapalli PS, Mendola RJ, Zuccaro MV, Garrisi J, Egli D, Treff NR, Marin D. ACCURATE DETECTION AND FREQUENCY OF ABNORMAL PLOIDY IN THE HUMAN BLASTOCYST. Fertil Steril 2022. [DOI: 10.1016/j.fertnstert.2022.09.178] [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: 11/04/2022]
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10
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Robles A, Marin D, Xu J, Treff NR, Egli D. ANTI-CRISPR PROTEIN REGULATES CRISPR Cas9 ACTIVITY IN HUMAN EMBRYOS. Fertil Steril 2022. [DOI: 10.1016/j.fertnstert.2022.08.227] [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: 11/04/2022]
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11
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Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A. Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation. Hum Mol Genet 2022; 31:2899-2917. [PMID: 35394024 PMCID: PMC9433724 DOI: 10.1093/hmg/ddac082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/18/2022] [Accepted: 04/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular proliferation depends on the accurate and timely replication of the genome. Several genetic diseases are caused by mutations in key DNA replication genes; however, it remains unclear whether these genes influence the normal program of DNA replication timing. Similarly, the factors that regulate DNA replication dynamics are poorly understood. To systematically identify trans-acting modulators of replication timing, we profiled replication in 184 cell lines from three cell types, encompassing 60 different gene knockouts or genetic diseases. Through a rigorous approach that considers the background variability of replication timing, we concluded that most samples displayed normal replication timing. However, mutations in two genes showed consistently abnormal replication timing. The first gene was RIF1, a known modulator of replication timing. The second was MCM10, a highly conserved member of the pre-replication complex. Cells from a single patient carrying MCM10 mutations demonstrated replication timing variability comprising 46% of the genome and at different locations than RIF1 knockouts. Replication timing alterations in the mutated MCM10 cells were predominantly comprised of replication delays and initiation site gains and losses. Taken together, this study demonstrates the remarkable robustness of the human replication timing program and reveals MCM10 as a novel candidate modulator of DNA replication timing.
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Affiliation(s)
- Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tiffany Ge
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ana Rita Rebelo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Sean Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Kayla Brooks
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | | | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dongsung Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA
| | - Marcus Smolka
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | | | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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12
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Palmerola KL, Amrane S, De Los Angeles A, Xu S, Wang N, de Pinho J, Zuccaro MV, Taglialatela A, Massey DJ, Turocy J, Robles A, Subbiah A, Prosser B, Lobo R, Ciccia A, Koren A, Baslan T, Egli D. Replication stress impairs chromosome segregation and preimplantation development in human embryos. Cell 2022; 185:2988-3007.e20. [PMID: 35858625 DOI: 10.1016/j.cell.2022.06.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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: 04/04/2021] [Revised: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
Human cleavage-stage embryos frequently acquire chromosomal aneuploidies during mitosis due to unknown mechanisms. Here, we show that S phase at the 1-cell stage shows replication fork stalling, low fork speed, and DNA synthesis extending into G2 phase. DNA damage foci consistent with collapsed replication forks, DSBs, and incomplete replication form in G2 in an ATR- and MRE11-dependent manner, followed by spontaneous chromosome breakage and segmental aneuploidies. Entry into mitosis with incomplete replication results in chromosome breakage, whole and segmental chromosome errors, micronucleation, chromosome fragmentation, and poor embryo quality. Sites of spontaneous chromosome breakage are concordant with sites of DNA synthesis in G2 phase, locating to gene-poor regions with long neural genes, which are transcriptionally silent at this stage of development. Thus, DNA replication stress in mammalian preimplantation embryos predisposes gene-poor regions to fragility, and in particular in the human embryo, to the formation of aneuploidies, impairing developmental potential.
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Affiliation(s)
- Katherine L Palmerola
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Selma Amrane
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alejandro De Los Angeles
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Shuangyi Xu
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA; Masters of Biotechnology Program, Columbia University, New York, NY 10027, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Joao de Pinho
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jenna Turocy
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alex Robles
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Anisa Subbiah
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Bob Prosser
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Rogerio Lobo
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dieter Egli
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA; Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA.
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13
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González BJ, Zhao H, Niu J, Williams DJ, Lee J, Goulbourne CN, Xing Y, Wang Y, Oberholzer J, Blumenkrantz MH, Chen X, LeDuc CA, Chung WK, Colecraft HM, Gromada J, Shen Y, Goland RS, Leibel RL, Egli D. Reduced calcium levels and accumulation of abnormal insulin granules in stem cell models of HNF1A deficiency. Commun Biol 2022; 5:779. [PMID: 35918471 PMCID: PMC9345898 DOI: 10.1038/s42003-022-03696-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 05/20/2021] [Accepted: 07/11/2022] [Indexed: 12/30/2022] Open
Abstract
Mutations in HNF1A cause Maturity Onset Diabetes of the Young (HNF1A-MODY). To understand mechanisms of β-cell dysfunction, we generated stem cell-derived pancreatic endocrine cells with hypomorphic mutations in HNF1A. HNF1A-deficient β-cells display impaired basal and glucose stimulated-insulin secretion, reduced intracellular calcium levels in association with a reduction in CACNA1A expression, and accumulation of abnormal insulin granules in association with SYT13 down-regulation. Knockout of CACNA1A and SYT13 reproduce the relevant phenotypes. In HNF1A deficient β-cells, glibenclamide, a sulfonylurea drug used in the treatment of HNF1A-MODY patients, increases intracellular calcium, and restores insulin secretion. While insulin secretion defects are constitutive in β-cells null for HNF1A, β-cells heterozygous for hypomorphic HNF1A (R200Q) mutations lose the ability to secrete insulin gradually; this phenotype is prevented by correction of the mutation. Our studies illuminate the molecular basis for the efficacy of treatment of HNF1A-MODY with sulfonylureas, and suggest promise for the use of cell therapies.
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Affiliation(s)
- Bryan J González
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Institute of Human Nutrition, Columbia University Medical Center, New York, NY, 10032, USA
| | - Haoquan Zhao
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Jacqueline Niu
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Damian J Williams
- Stem Cell Core Facility, Department of Rehabilitation and Regenerative Medicine, Columbia University, New York, NY, 10032, USA
| | - Jaeyop Lee
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Chris N Goulbourne
- Center for Dementia Research, Nathan S. Kline Institute, Orangeburg, NY, 10962, USA
| | - Yuan Xing
- Department of Surgery, University of Virginia, Charlottesville, VA, 22908, USA
| | - Yong Wang
- Department of Surgery, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jose Oberholzer
- Department of Surgery, University of Virginia, Charlottesville, VA, 22908, USA
| | - Maria H Blumenkrantz
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Xiaojuan Chen
- Columbia Center for Translational Immunology, Department of Surgery, Columbia University Medical Center, New York, NY, 10032, USA
| | - Charles A LeDuc
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Wendy K Chung
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Jesper Gromada
- Regeneron Pharmaceuticals, Tarrytown, NY, 10591, USA.,Vertex Cell and Genetic Therapies, Watertown, MA, 02472, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Robin S Goland
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Rudolph L Leibel
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center & Departments of Pediatrics and Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.
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14
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Edwards MM, Zuccaro MV, Sagi I, Ding Q, Vershkov D, Benvenisty N, Egli D, Koren A. Delayed DNA replication in haploid human embryonic stem cells. Genome Res 2021; 31:2155-2169. [PMID: 34810218 PMCID: PMC8647822 DOI: 10.1101/gr.275953.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Ido Sagi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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15
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Turocy JM, Zuccaro MV, Marin D, Xu J, Treff NR, Egli D. DNA DOUBLE-STRAND BREAKS FREQUENTLY CAUSE CHROMOSOME LOSS IN HUMAN EMBRYOS. Fertil Steril 2021. [DOI: 10.1016/j.fertnstert.2021.07.012] [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: 11/28/2022]
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16
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Affiliation(s)
- Bryan J González
- Naomi Berrie Diabetes Center and Department of Pediatrics, Columbia Stem Cell Initiative, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Remi J Creusot
- Columbia Center for Translational Immunology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Dieter Egli
- Naomi Berrie Diabetes Center and Department of Pediatrics, Columbia Stem Cell Initiative, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.
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17
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Wang L, Liu Y, Stratigopoulos G, Panigrahi S, Sui L, Zhang Y, Leduc CA, Glover HJ, De Rosa MC, Burnett LC, Williams DJ, Shang L, Goland R, Tsang SH, Wardlaw S, Egli D, Zheng D, Doege CA, Leibel RL. Bardet-Biedl syndrome proteins regulate intracellular signaling and neuronal function in patient-specific iPSC-derived neurons. J Clin Invest 2021; 131:146287. [PMID: 33630762 DOI: 10.1172/jci146287] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/23/2021] [Indexed: 12/11/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a rare autosomal recessive disorder caused by mutations in genes encoding components of the primary cilium and is characterized by hyperphagic obesity. To investigate the molecular basis of obesity in human BBS, we developed a cellular model of BBS using induced pluripotent stem cell-derived (iPSC-derived) hypothalamic arcuate-like neurons. BBS mutations BBS1M390R and BBS10C91fsX95 did not affect neuronal differentiation efficiency but caused morphological defects, including impaired neurite outgrowth and longer primary cilia. Single-cell RNA sequencing of BBS1M390R hypothalamic neurons identified several downregulated pathways, including insulin and cAMP signaling and axon guidance. Additional studies demonstrated that BBS1M390R and BBS10C91fsX95 mutations impaired insulin signaling in both human fibroblasts and iPSC-derived neurons. Overexpression of intact BBS10 fully restored insulin signaling by restoring insulin receptor tyrosine phosphorylation in BBS10C91fsX95 neurons. Moreover, mutations in BBS1 and BBS10 impaired leptin-mediated p-STAT3 activation in iPSC-derived hypothalamic neurons. Correction of the BBS mutation by CRISPR rescued leptin signaling. POMC expression and neuropeptide production were decreased in BBS1M390R and BBS10C91fsX95 iPSC-derived hypothalamic neurons. In the aggregate, these data provide insights into the anatomic and functional mechanisms by which components of the BBSome in CNS primary cilia mediate effects on energy homeostasis.
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Affiliation(s)
- Liheng Wang
- Naomi Berrie Diabetes Center and.,Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Yang Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - George Stratigopoulos
- Naomi Berrie Diabetes Center and.,Division of Molecular Genetics, Department of Pediatrics, Columbia University, College of Physicians and Surgeons, New York, New York, USA
| | - Sunil Panigrahi
- Naomi Berrie Diabetes Center and.,Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Lina Sui
- Naomi Berrie Diabetes Center and.,Division of Molecular Genetics, Department of Pediatrics, Columbia University, College of Physicians and Surgeons, New York, New York, USA
| | - Yiying Zhang
- Naomi Berrie Diabetes Center and.,Division of Molecular Genetics, Department of Pediatrics, Columbia University, College of Physicians and Surgeons, New York, New York, USA
| | - Charles A Leduc
- Naomi Berrie Diabetes Center and.,Division of Molecular Genetics, Department of Pediatrics, Columbia University, College of Physicians and Surgeons, New York, New York, USA
| | - Hannah J Glover
- Naomi Berrie Diabetes Center and.,Division of Molecular Genetics, Department of Pediatrics, Columbia University, College of Physicians and Surgeons, New York, New York, USA
| | - Maria Caterina De Rosa
- Naomi Berrie Diabetes Center and.,Division of Molecular Genetics, Department of Pediatrics, Columbia University, College of Physicians and Surgeons, New York, New York, USA
| | - Lisa C Burnett
- Naomi Berrie Diabetes Center and.,Levo Therapeutics, Skokie, Illinois, USA
| | - Damian J Williams
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Linshan Shang
- Naomi Berrie Diabetes Center and.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Stephen H Tsang
- Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, New York, USA.,Columbia Stem Cell Initiative and.,Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Sharon Wardlaw
- Naomi Berrie Diabetes Center and.,Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center and.,Division of Molecular Genetics, Department of Pediatrics, Columbia University, College of Physicians and Surgeons, New York, New York, USA.,New York Stem Cell Foundation Research Institute, New York, New York, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Claudia A Doege
- Naomi Berrie Diabetes Center and.,Columbia Stem Cell Initiative and.,Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Rudolph L Leibel
- Naomi Berrie Diabetes Center and.,Division of Molecular Genetics, Department of Pediatrics, Columbia University, College of Physicians and Surgeons, New York, New York, USA
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18
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Sui L, Xin Y, Du Q, Georgieva D, Diedenhofen G, Haataja L, Su Q, Zuccaro MV, Kim J, Fu J, Xing Y, He Y, Baum D, Goland RS, Wang Y, Oberholzer J, Barbetti F, Arvan P, Kleiner S, Egli D. Reduced replication fork speed promotes pancreatic endocrine differentiation and controls graft size. JCI Insight 2021; 6:141553. [PMID: 33529174 PMCID: PMC8022502 DOI: 10.1172/jci.insight.141553] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 06/22/2020] [Accepted: 01/28/2021] [Indexed: 12/29/2022] Open
Abstract
Limitations in cell proliferation are important for normal function of differentiated tissues and essential for the safety of cell replacement products made from pluripotent stem cells, which have unlimited proliferative potential. To evaluate whether these limitations can be established pharmacologically, we exposed pancreatic progenitors differentiating from human pluripotent stem cells to small molecules that interfere with cell cycle progression either by inducing G1 arrest or by impairing S phase entry or S phase completion and determined growth potential, differentiation, and function of insulin-producing endocrine cells. We found that the combination of G1 arrest with a compromised ability to complete DNA replication promoted the differentiation of pancreatic progenitor cells toward insulin-producing cells and could substitute for endocrine differentiation factors. Reduced replication fork speed during differentiation improved the stability of insulin expression, and the resulting cells protected mice from diabetes without the formation of cystic growths. The proliferative potential of grafts was proportional to the reduction of replication fork speed during pancreatic differentiation. Therefore, a compromised ability to enter and complete S phase is a functionally important property of pancreatic endocrine differentiation, can be achieved by reducing replication fork speed, and is an important determinant of cell-intrinsic limitations of growth.
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Affiliation(s)
- Lina Sui
- Naomi Berrie Diabetes Center, Columbia University, New York, New York, USA.,Department of Pediatrics, Department of Obstetrics and Gynecology, Columbia Stem Cell Initiative, Columbia Irving Medical Center, Columbia University, New York, New York, USA
| | - Yurong Xin
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Qian Du
- Naomi Berrie Diabetes Center, Columbia University, New York, New York, USA.,Department of Pediatrics, Department of Obstetrics and Gynecology, Columbia Stem Cell Initiative, Columbia Irving Medical Center, Columbia University, New York, New York, USA
| | - Daniela Georgieva
- Naomi Berrie Diabetes Center, Columbia University, New York, New York, USA.,Department of Pediatrics, Department of Obstetrics and Gynecology, Columbia Stem Cell Initiative, Columbia Irving Medical Center, Columbia University, New York, New York, USA
| | - Giacomo Diedenhofen
- Naomi Berrie Diabetes Center, Columbia University, New York, New York, USA.,Bambino Gesù Children's Hospital, Rome, Italy
| | - Leena Haataja
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Qi Su
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Michael V Zuccaro
- PhD program in the Department of Physiology and Cellular Biophysics, Columbia Irving Medical Center, Columbia University, New York, New York, USA
| | - Jinrang Kim
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Jiayu Fu
- Naomi Berrie Diabetes Center, Columbia University, New York, New York, USA
| | - Yuan Xing
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Yi He
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Danielle Baum
- Naomi Berrie Diabetes Center, Columbia University, New York, New York, USA
| | - Robin S Goland
- Naomi Berrie Diabetes Center, Columbia University, New York, New York, USA.,Department of Pediatrics, Department of Obstetrics and Gynecology, Columbia Stem Cell Initiative, Columbia Irving Medical Center, Columbia University, New York, New York, USA
| | - Yong Wang
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Jose Oberholzer
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Fabrizio Barbetti
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Peter Arvan
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Sandra Kleiner
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center, Columbia University, New York, New York, USA.,Department of Pediatrics, Department of Obstetrics and Gynecology, Columbia Stem Cell Initiative, Columbia Irving Medical Center, Columbia University, New York, New York, USA
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19
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Turocy J, Adashi EY, Egli D. Heritable human genome editing: Research progress, ethical considerations, and hurdles to clinical practice. Cell 2021; 184:1561-1574. [PMID: 33740453 DOI: 10.1016/j.cell.2021.02.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/29/2021] [Accepted: 02/17/2021] [Indexed: 12/14/2022]
Abstract
Our genome at conception determines much of our health as an adult. Most human diseases have a heritable component and thus may be preventable through heritable genome editing. Preventing disease from the beginning of life before irreversible damage has occurred is an admirable goal, but the path to fruition remains unclear. Here, we review the significant scientific contributions to the field of human heritable genome editing, the unique ethical challenges that cannot be overlooked, and the hurdles that must be overcome prior to translating these technologies into clinical practice.
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Affiliation(s)
- Jenna Turocy
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Eli Y Adashi
- Professor of Medical Science, Brown University, Providence, RI, USA
| | - Dieter Egli
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA; Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
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20
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Skowronski AA, LeDuc CA, Foo KS, Goffer Y, Burnett LC, Egli D, Leibel RL. Physiological consequences of transient hyperleptinemia during discrete developmental periods on body weight in mice. Sci Transl Med 2021; 12:12/524/eaax6629. [PMID: 31894105 DOI: 10.1126/scitranslmed.aax6629] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/29/2019] [Accepted: 12/06/2019] [Indexed: 12/27/2022]
Abstract
Leptin plays a role in central nervous system developmental programs and intercurrent physiological processes related to body fat regulation. The timing and neuromolecular mechanisms for these effects are relevant to the prevention and treatment of obesity. Factors implicated in a body weight "set point" including dietary fat, circulating leptin, and other adipokines tend to covary with adiposity and are difficult to disarticulate experimentally. To dissociate leptin effects from adiposity and diet, we created a transgenic mouse in which leptin expression is regulated by doxycycline exposure. Using this system, we investigated the physiological consequences of developmentally-timed transient hyperleptinemia on subsequent adiposity. We evaluated physiological effects of leptin elevation during adulthood (9 to 29 weeks old), "adolescence" (3 to 8 weeks old), and the immediate postnatal period [postnatal days 0 to 22 (P0 to P22)] on long-term adiposity and susceptibility to gain weight on high-fat diet (HFD) fed ad libitum. We found that inducing chronic hyperleptinemia in adult or "adolescent" mice did not alter body weight when excess leptin was discontinued, and upon later exposure to HFD, weight gain did not differ from controls. However, transient elevation of circulating leptin from P0 to P22 increased weight and fat gain in response to HFD, indicating greater susceptibility to obesity as adults. Thus, transient plasma leptin elevations-mimicking one aspect of transient adiposity-increased later susceptibility to diet-induced obesity, although these effects were restricted to a critical developmental (P0 to P22) time window. These findings may have clinical implications for weight management in infancy.
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Affiliation(s)
- Alicja A Skowronski
- Division of Molecular Genetics, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Charles A LeDuc
- Division of Molecular Genetics, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.,Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kylie S Foo
- Division of Molecular Genetics, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yossef Goffer
- Division of Molecular Genetics, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lisa C Burnett
- Division of Molecular Genetics, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.,Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA.,Department of Obstetrics and Gynecology, and Columbia Stem Cell Initiative, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rudolph L Leibel
- Division of Molecular Genetics, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA. .,Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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21
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Armitage LH, Stimpson SE, Santostefano KE, Sui L, Ogundare S, Newby BN, Castro-Gutierrez R, Huber MK, Taylor JP, Sharma P, Radichev IA, Perry DJ, Fredette NC, Savinov AY, Wallet MA, Terada N, Brusko TM, Russ HA, Chen J, Egli D, Mathews CE. Use of Induced Pluripotent Stem Cells to Build Isogenic Systems and Investigate Type 1 Diabetes. Front Endocrinol (Lausanne) 2021; 12:737276. [PMID: 34858326 PMCID: PMC8630743 DOI: 10.3389/fendo.2021.737276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Type 1 diabetes (T1D) is a disease that arises due to complex immunogenetic mechanisms. Key cell-cell interactions involved in the pathogenesis of T1D are activation of autoreactive T cells by dendritic cells (DC), migration of T cells across endothelial cells (EC) lining capillary walls into the islets of Langerhans, interaction of T cells with macrophages in the islets, and killing of β-cells by autoreactive CD8+ T cells. Overall, pathogenic cell-cell interactions are likely regulated by the individual's collection of genetic T1D-risk variants. To accurately model the role of genetics, it is essential to build systems to interrogate single candidate genes in isolation during the interactions of cells that are essential for disease development. However, obtaining single-donor matched cells relevant to T1D is a challenge. Sourcing these genetic variants from human induced pluripotent stem cells (iPSC) avoids this limitation. Herein, we have differentiated iPSC from one donor into DC, macrophages, EC, and β-cells. Additionally, we also engineered T cell avatars from the same donor to provide an in vitro platform to study genetic influences on these critical cellular interactions. This proof of concept demonstrates the ability to derive an isogenic system from a single donor to study these relevant cell-cell interactions. Our system constitutes an interdisciplinary approach with a controlled environment that provides a proof-of-concept for future studies to determine the role of disease alleles (e.g. IFIH1, PTPN22, SH2B3, TYK2) in regulating cell-cell interactions and cell-specific contributions to the pathogenesis of T1D.
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Affiliation(s)
- Lucas H. Armitage
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Scott E. Stimpson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Katherine E. Santostefano
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
- Century Therapeutics, iPSC Biology, Philadelphia, PA, United States
| | - Lina Sui
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, United States
| | - Similoluwa Ogundare
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Brittney N. Newby
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Roberto Castro-Gutierrez
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Mollie K. Huber
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Jared P. Taylor
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Prerana Sharma
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Ilian A. Radichev
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Daniel J. Perry
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Natalie C. Fredette
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Alexei Y. Savinov
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Mark A. Wallet
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
- Century Therapeutics, Immunology, Philadelphia, PA, United States
| | - Naohiro Terada
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Todd M. Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Holger A. Russ
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Jing Chen
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Dieter Egli
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
- *Correspondence: Clayton E. Mathews,
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22
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Zuccaro MV, Xu J, Mitchell C, Marin D, Zimmerman R, Rana B, Weinstein E, King RT, Palmerola KL, Smith ME, Tsang SH, Goland R, Jasin M, Lobo R, Treff N, Egli D. Allele-Specific Chromosome Removal after Cas9 Cleavage in Human Embryos. Cell 2020; 183:1650-1664.e15. [PMID: 33125898 DOI: 10.1016/j.cell.2020.10.025] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/02/2020] [Accepted: 10/14/2020] [Indexed: 12/24/2022]
Abstract
Correction of disease-causing mutations in human embryos holds the potential to reduce the burden of inherited genetic disorders and improve fertility treatments for couples with disease-causing mutations in lieu of embryo selection. Here, we evaluate repair outcomes of a Cas9-induced double-strand break (DSB) introduced on the paternal chromosome at the EYS locus, which carries a frameshift mutation causing blindness. We show that the most common repair outcome is microhomology-mediated end joining, which occurs during the first cell cycle in the zygote, leading to embryos with non-mosaic restoration of the reading frame. Notably, about half of the breaks remain unrepaired, resulting in an undetectable paternal allele and, after mitosis, loss of one or both chromosomal arms. Correspondingly, Cas9 off-target cleavage results in chromosomal losses and hemizygous indels because of cleavage of both alleles. These results demonstrate the ability to manipulate chromosome content and reveal significant challenges for mutation correction in human embryos.
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Affiliation(s)
- Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Jia Xu
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA
| | - Carl Mitchell
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Diego Marin
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA
| | | | - Bhavini Rana
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA; Department of Molecular Biosciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Everett Weinstein
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Rebeca T King
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Katherine L Palmerola
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Morgan E Smith
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Stephen H Tsang
- Columbia University Stem Cell Initiative, New York, NY 10032, USA; Departments of Ophthalmology, Pathology & Cell Biology, Columbia University. New York, NY, 10032, USA
| | - Robin Goland
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Rogerio Lobo
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Nathan Treff
- Genomic Prediction Inc., North Brunswick, NJ 08902, USA; Department of Molecular Biosciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA.
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23
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Georgieva D, Liu Q, Wang K, Egli D. Detection of base analogs incorporated during DNA replication by nanopore sequencing. Nucleic Acids Res 2020; 48:e88. [PMID: 32710620 PMCID: PMC7470954 DOI: 10.1093/nar/gkaa517] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 01/23/2023] Open
Abstract
DNA synthesis is a fundamental requirement for cell proliferation and DNA repair, but no single method can identify the location, direction and speed of replication forks with high resolution. Mammalian cells have the ability to incorporate thymidine analogs along with the natural A, T, G and C bases during DNA synthesis, which allows for labeling of replicating or repaired DNA. Here, we demonstrate the use of the Oxford Nanopore Technologies MinION to detect 11 different thymidine analogs including CldU, BrdU, IdU as well as EdU alone or coupled to Biotin and other bulky adducts in synthetic DNA templates. We also show that the large adduct Biotin can be distinguished from the smaller analog IdU, which opens the possibility of using analog combinations to identify the location and direction of DNA synthesis. Furthermore, we detect IdU label on single DNA molecules in the genome of mouse pluripotent stem cells and using CRISPR/Cas9-mediated enrichment, determine replication rates using newly synthesized DNA strands in human mitochondrial DNA. We conclude that this novel method, termed Replipore sequencing, has the potential for on target examination of DNA replication in a wide range of biological contexts.
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Affiliation(s)
- Daniela Georgieva
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032, USA.,Naomi Berrie Diabetes Center, Columbia University, New York NY 10032, USA.,Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center, Columbia University, New York NY 10032, USA.,Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA.,Department of Pediatrics and Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
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24
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Paniza T, Deshpande M, Wang N, O’Neil R, Zuccaro MV, Smith ME, Madireddy A, James D, Ecker J, Rosenwaks Z, Egli D, Gerhardt J. Pluripotent stem cells with low differentiation potential contain incompletely reprogrammed DNA replication. J Cell Biol 2020; 219:e201909163. [PMID: 32673399 PMCID: PMC7480103 DOI: 10.1083/jcb.201909163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/26/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Reprogrammed pluripotent stem cells (PSCs) are valuable for research and potentially for cell replacement therapy. However, only a fraction of reprogrammed PSCs are developmentally competent. Genomic stability and accurate DNA synthesis are fundamental for cell development and critical for safety. We analyzed whether defects in DNA replication contribute to genomic instability and the diverse differentiation potentials of reprogrammed PSCs. Using a unique single-molecule approach, we visualized DNA replication in isogenic PSCs generated by different reprogramming approaches, either somatic cell nuclear transfer (NT-hESCs) or with defined factors (iPSCs). In PSCs with lower differentiation potential, DNA replication was incompletely reprogrammed, and genomic instability increased during replicative stress. Reprogramming of DNA replication did not correlate with DNA methylation. Instead, fewer replication origins and a higher frequency of DNA breaks in PSCs with incompletely reprogrammed DNA replication were found. Given the impact of error-free DNA synthesis on the genomic integrity and differentiation proficiency of PSCs, analyzing DNA replication may be a useful quality control tool.
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Affiliation(s)
- Theodore Paniza
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Madhura Deshpande
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Ning Wang
- Department of Pediatrics, Columbia University, New York, NY
| | - Ryan O’Neil
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA
| | - Michael V. Zuccaro
- Department of Pediatrics, Columbia University, New York, NY
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | | | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers University, New Brunswick, NJ
| | - Daylon James
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
| | - Joseph Ecker
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Dieter Egli
- Department of Pediatrics, Columbia University, New York, NY
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
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25
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26
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Gouveia C, Huyser C, Egli D, Pepper MS. Lessons Learned from Somatic Cell Nuclear Transfer. Int J Mol Sci 2020; 21:ijms21072314. [PMID: 32230814 PMCID: PMC7177533 DOI: 10.3390/ijms21072314] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Somatic cell nuclear transfer (SCNT) has been an area of interest in the field of stem cell research and regenerative medicine for the past 20 years. The main biological goal of SCNT is to reverse the differentiated state of a somatic cell, for the purpose of creating blastocysts from which embryonic stem cells (ESCs) can be derived for therapeutic cloning, or for the purpose of reproductive cloning. However, the consensus is that the low efficiency in creating normal viable offspring in animals by SCNT (1–5%) and the high number of abnormalities seen in these cloned animals is due to epigenetic reprogramming failure. In this review we provide an overview of the current literature on SCNT, focusing on protocol development, which includes early SCNT protocol deficiencies and optimizations along with donor cell type and cell cycle synchrony; epigenetic reprogramming in SCNT; current protocol optimizations such as nuclear reprogramming strategies that can be applied to improve epigenetic reprogramming by SCNT; applications of SCNT; the ethical and legal implications of SCNT in humans; and specific lessons learned for establishing an optimized SCNT protocol using a mouse model.
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Affiliation(s)
- Chantel Gouveia
- Institute for Cellular and Molecular Medicine, Department of Immunology and South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria 0002, South Africa;
- Department of Obstetrics and Gynaecology, Reproductive Biology Laboratory, University of Pretoria, Steve Biko Academic Hospital, Pretoria 0002, South Africa;
- Correspondence: ; Tel.: +27-(0)76-546-5119
| | - Carin Huyser
- Department of Obstetrics and Gynaecology, Reproductive Biology Laboratory, University of Pretoria, Steve Biko Academic Hospital, Pretoria 0002, South Africa;
| | - Dieter Egli
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10027, USA;
| | - Michael S. Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology and South African Medical Research Council (SAMRC) Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, Pretoria 0002, South Africa;
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27
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Ackeifi C, Wang P, Karakose E, Manning Fox JE, González BJ, Liu H, Wilson J, Swartz E, Berrouet C, Li Y, Kumar K, MacDonald PE, Sanchez R, Thorens B, DeVita R, Homann D, Egli D, Scott DK, Garcia-Ocaña A, Stewart AF. GLP-1 receptor agonists synergize with DYRK1A inhibitors to potentiate functional human β cell regeneration. Sci Transl Med 2020; 12:eaaw9996. [PMID: 32051230 PMCID: PMC9945936 DOI: 10.1126/scitranslmed.aaw9996] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [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: 02/15/2019] [Revised: 08/07/2019] [Accepted: 01/09/2020] [Indexed: 01/25/2023]
Abstract
Glucagon-like peptide-1 receptor (GLP1R) agonists and dipeptidyl peptidase 4 inhibitors are widely prescribed diabetes drugs due to their ability to stimulate insulin secretion from remaining β cells and to reduce caloric intake. Unfortunately, they fail to increase human β cell proliferation. Small-molecule inhibitors of dual-specificity tyrosine-regulated kinase 1A (DYRK1A) are able to induce adult human β cell proliferation, but rates are modest (~2%), and their specificity to β cells is limited. Here, we provide evidence that combining any member of the GLP1R agonist class with any member of the DYRK1A inhibitor class induces a synergistic increase in human β cell replication (5 to 6%) accompanied by an actual increase in numbers of human β cells. GLP1R agonist-DYRK1A inhibitor synergy required combined inhibition of DYRK1A and an increase in cAMP and did not lead to β cell dedifferentiation. These beneficial effects on proliferation were seen in both normal human β cells and β cells derived from individuals with type 2 diabetes. The ability of the GLP1R agonist-DYRK1A inhibitor combination to enhance human β cell proliferation, human insulin secretion, and blood glucose control extended in vivo to studies of human islets transplanted into euglycemic and streptozotocin-diabetic immunodeficient mice. No adverse events were observed in the mouse studies during a 1-week period. Because of the relative β cell specificity of GLP1R agonists, the combination provides an improved, although not complete, degree of human β cell specificity.
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Affiliation(s)
- Courtney Ackeifi
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peng Wang
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Esra Karakose
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jocelyn E Manning Fox
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Bryan J González
- Naomi Berrie Diabetes Center and Columbia Stem Cell Center, Columbia University, New York, NY 10032, USA
| | - Hongtao Liu
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jessica Wilson
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ethan Swartz
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cecilia Berrouet
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yansui Li
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kunal Kumar
- Department of Pharmacological Sciences, and Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick E MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Roberto Sanchez
- Department of Pharmacological Sciences, and Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernard Thorens
- Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland
| | - Robert DeVita
- Department of Pharmacological Sciences, and Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dirk Homann
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center and Columbia Stem Cell Center, Columbia University, New York, NY 10032, USA
| | - Donald K Scott
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adolfo Garcia-Ocaña
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew F Stewart
- Diabetes, Obesity and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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28
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Romer AI, Singer RA, Sui L, Egli D, Sussel L. Murine Perinatal β-Cell Proliferation and the Differentiation of Human Stem Cell-Derived Insulin-Expressing Cells Require NEUROD1. Diabetes 2019; 68:2259-2271. [PMID: 31519700 PMCID: PMC6868472 DOI: 10.2337/db19-0117] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 09/03/2019] [Indexed: 12/13/2022]
Abstract
Inactivation of the β-cell transcription factor NEUROD1 causes diabetes in mice and humans. In this study, we uncovered novel functions of NEUROD1 during murine islet cell development and during the differentiation of human embryonic stem cells (HESCs) into insulin-producing cells. In mice, we determined that Neurod1 is required for perinatal proliferation of α- and β-cells. Surprisingly, apoptosis only makes a minor contribution to β-cell loss when Neurod1 is deleted. Inactivation of NEUROD1 in HESCs severely impaired their differentiation from pancreatic progenitors into insulin-expressing (HESC-β) cells; however, survival or proliferation was not affected at the time points analyzed. NEUROD1 was also required in HESC-β cells for the full activation of an essential β-cell transcription factor network. These data reveal conserved and distinct functions of NEUROD1 during mouse and human β-cell development and maturation, with important implications about the function of NEUROD1 in diabetes.
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Affiliation(s)
- Anthony I Romer
- Department of Genetics and Development, Columbia University, New York, NY
- Department of Pediatrics, Columbia University, New York, NY
| | - Ruth A Singer
- Department of Genetics and Development, Columbia University, New York, NY
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY
| | - Lina Sui
- Department of Pediatrics, Columbia University, New York, NY
| | - Dieter Egli
- Department of Pediatrics, Columbia University, New York, NY
| | - Lori Sussel
- Department of Genetics and Development, Columbia University, New York, NY
- Department of Pediatrics, University of Colorado Denver School of Medicine, Denver, CO
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29
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Nambiar TS, Billon P, Diedenhofen G, Hayward SB, Taglialatela A, Cai K, Huang JW, Leuzzi G, Cuella-Martin R, Palacios A, Gupta A, Egli D, Ciccia A. Stimulation of CRISPR-mediated homology-directed repair by an engineered RAD18 variant. Nat Commun 2019; 10:3395. [PMID: 31363085 PMCID: PMC6667477 DOI: 10.1038/s41467-019-11105-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/21/2019] [Indexed: 12/24/2022] Open
Abstract
Precise editing of genomic DNA can be achieved upon repair of CRISPR-induced DNA double-stranded breaks (DSBs) by homology-directed repair (HDR). However, the efficiency of this process is limited by DSB repair pathways competing with HDR, such as non-homologous end joining (NHEJ). Here we individually express in human cells 204 open reading frames involved in the DNA damage response (DDR) and determine their impact on CRISPR-mediated HDR. From these studies, we identify RAD18 as a stimulator of CRISPR-mediated HDR. By defining the RAD18 domains required to promote HDR, we derive an enhanced RAD18 variant (e18) that stimulates CRISPR-mediated HDR in multiple human cell types, including embryonic stem cells. Mechanistically, e18 induces HDR by suppressing the localization of the NHEJ-promoting factor 53BP1 to DSBs. Altogether, this study identifies e18 as an enhancer of CRISPR-mediated HDR and highlights the promise of engineering DDR factors to augment the efficiency of precision genome editing.
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Affiliation(s)
- Tarun S Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Pierre Billon
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Giacomo Diedenhofen
- Naomi Berrie Diabetes Center and Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, 00133, Italy
| | - Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Kunheng Cai
- Naomi Berrie Diabetes Center and Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Andrew Palacios
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Anuj Gupta
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center and Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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Kuo T, Damle M, González BJ, Egli D, Lazar MA, Accili D. Induction of α cell-restricted Gc in dedifferentiating β cells contributes to stress-induced β-cell dysfunction. JCI Insight 2019; 5:128351. [PMID: 31120862 DOI: 10.1172/jci.insight.128351] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Diabetic β cell failure is associated with β cell dedifferentiation. To identify effector genes of dedifferentiation, we integrated analyses of histone methylation as a surrogate of gene activation status and RNA expression in β cells sorted from mice with multiparity-induced diabetes. Interestingly, only a narrow subset of genes demonstrated concordant changes to histone methylation and RNA levels in dedifferentiating β cells. Notable among them was the α cell signature gene Gc, encoding a vitamin D-binding protein. While diabetes was associated with Gc induction, Gc-deficient islets did not induce β cell dedifferentiation markers and maintained normal ex vivo insulin secretion in the face of metabolic challenge. Moreover, Gc-deficient mice exhibited a more robust insulin secretory response than normal controls during hyperglycemic clamps. The data are consistent with a functional role of Gc activation in β cell dysfunction, and indicate that multiparity-induced diabetes is associated with altered β cell fate.
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Affiliation(s)
- Taiyi Kuo
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Manashree Damle
- The Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bryan J González
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, New York, USA.,Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Dieter Egli
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, New York, USA.,Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Mitchell A Lazar
- The Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Domenico Accili
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, New York, USA
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31
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Wang P, Karakose E, Liu H, Swartz E, Ackeifi C, Zlatanic V, Wilson J, González BJ, Bender A, Takane KK, Ye L, Harb G, Pagliuca F, Homann D, Egli D, Argmann C, Scott DK, Garcia-Ocaña A, Stewart AF. Combined Inhibition of DYRK1A, SMAD, and Trithorax Pathways Synergizes to Induce Robust Replication in Adult Human Beta Cells. Cell Metab 2019; 29:638-652.e5. [PMID: 30581122 PMCID: PMC6402958 DOI: 10.1016/j.cmet.2018.12.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/03/2018] [Accepted: 11/30/2018] [Indexed: 01/13/2023]
Abstract
Small-molecule inhibitors of dual-specificity tyrosine-regulated kinase 1A (DYRK1A) induce human beta cells to proliferate, generating a labeling index of 1.5%-3%. Here, we demonstrate that combined pharmacologic inhibition of DYRK1A and transforming growth factor beta superfamily (TGFβSF)/SMAD signaling generates remarkable further synergistic increases in human beta cell proliferation (average labeling index, 5%-8%, and as high as 15%-18%), and increases in both mouse and human beta cell numbers. This synergy reflects activation of cyclins and cdks by DYRK1A inhibition, accompanied by simultaneous reductions in key cell-cycle inhibitors (CDKN1C and CDKN1A). The latter results from interference with the basal Trithorax- and SMAD-mediated transactivation of CDKN1C and CDKN1A. Notably, combined DYRK1A and TGFβ inhibition allows preservation of beta cell differentiated function. These beneficial effects extend from normal human beta cells and stem cell-derived human beta cells to those from people with type 2 diabetes, and occur both in vitro and in vivo.
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Affiliation(s)
- Peng Wang
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Esra Karakose
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hongtao Liu
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ethan Swartz
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Courtney Ackeifi
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viktor Zlatanic
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jessica Wilson
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bryan J González
- Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Aaron Bender
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karen K Takane
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lillian Ye
- Semma Therapeutics, Cambridge, MA 02142, USA
| | - George Harb
- Semma Therapeutics, Cambridge, MA 02142, USA
| | | | - Dirk Homann
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Donald K Scott
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adolfo Garcia-Ocaña
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew F Stewart
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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32
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Wang L, De Solis AJ, Goffer Y, Birkenbach KE, Engle SE, Tanis R, Levenson JM, Li X, Rausch R, Purohit M, Lee JY, Tan J, De Rosa MC, Doege CA, Aaron HL, Martins GJ, Brüning JC, Egli D, Costa R, Berbari N, Leibel RL, Stratigopoulos G. Ciliary gene RPGRIP1L is required for hypothalamic arcuate neuron development. JCI Insight 2019; 4:e123337. [PMID: 30728336 PMCID: PMC6413800 DOI: 10.1172/jci.insight.123337] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 01/03/2019] [Indexed: 12/16/2022] Open
Abstract
Intronic polymorphisms in the α-ketoglutarate-dependent dioxygenase gene (FTO) that are highly associated with increased body weight have been implicated in the transcriptional control of a nearby ciliary gene, retinitis pigmentosa GTPase regulator-interacting protein-1 like (RPGRIP1L). Previous studies have shown that congenital Rpgrip1l hypomorphism in murine proopiomelanocortin (Pomc) neurons causes obesity by increasing food intake. Here, we show by congenital and adult-onset Rpgrip1l deletion in Pomc-expressing neurons that the hyperphagia and obesity are likely due to neurodevelopmental effects that are characterized by a reduction in the Pomc/Neuropeptide Y (Npy) neuronal number ratio and marked increases in arcuate hypothalamic-paraventricular hypothalamic (ARH-PVH) axonal projections. Biallelic RPGRIP1L mutations result in fewer cilia-positive human induced pluripotent stem cell-derived (iPSC-derived) neurons and blunted responses to Sonic Hedgehog (SHH). Isogenic human ARH-like embryonic stem cell-derived (ESc-derived) neurons homozygous for the obesity-risk alleles at rs8050136 or rs1421085 have decreased RPGRIP1L expression and have lower numbers of POMC neurons. RPGRIP1L overexpression increases POMC cell number. These findings suggest that apparently functional intronic polymorphisms affect hypothalamic RPGRIP1L expression and impact development of POMC neurons and their derivatives, leading to hyperphagia and increased adiposity.
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Affiliation(s)
- Liheng Wang
- Naomi Berrie Diabetes Center and Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Alain J. De Solis
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Yossef Goffer
- Naomi Berrie Diabetes Center & Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Kathryn E. Birkenbach
- Naomi Berrie Diabetes Center & Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Staci E. Engle
- Department of Biology, Indiana University-Purdue University, Indianapolis, Indiana, USA
| | - Ross Tanis
- University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Jacob M. Levenson
- University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Xueting Li
- Institute of Human Nutrition graduate program, Columbia University, New York, New York, USA
| | - Richard Rausch
- Naomi Berrie Diabetes Center & Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Manika Purohit
- Zuckerman Institute, Columbia University, New York, New York, USA
| | - Jen-Yi Lee
- Cancer Research Laboratory Molecular Imaging Center, University of California, Berkeley, 94720, USA
| | - Jerica Tan
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Maria Caterina De Rosa
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Claudia A. Doege
- Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Holly L. Aaron
- Cancer Research Laboratory Molecular Imaging Center, University of California, Berkeley, 94720, USA
| | | | - Jens C. Brüning
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
- Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Cologne, Germany
- Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- National Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Dieter Egli
- Naomi Berrie Diabetes Center & Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - Rui Costa
- Zuckerman Institute, Columbia University, New York, New York, USA
| | - Nicolas Berbari
- Department of Biology, Indiana University-Purdue University, Indianapolis, Indiana, USA
| | - Rudolph L. Leibel
- Naomi Berrie Diabetes Center & Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
| | - George Stratigopoulos
- Naomi Berrie Diabetes Center & Division of Molecular Genetics, Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York, New York, USA
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Abstract
BACKGROUND Recent advances in single-molecule sequencing techniques, such as Nanopore sequencing, improved read length, increased sequencing throughput, and enabled direct detection of DNA modifications through the analysis of raw signals. These DNA modifications include naturally occurring modifications such as DNA methylations, as well as modifications that are introduced by DNA damage or through synthetic modifications to one of the four standard nucleotides. METHODS To improve the performance of detecting DNA modifications, especially synthetically introduced modifications, we developed a novel computational tool called NanoMod. NanoMod takes raw signal data on a pair of DNA samples with and without modified bases, extracts signal intensities, performs base error correction based on a reference sequence, and then identifies bases with modifications by comparing the distribution of raw signals between two samples, while taking into account of the effects of neighboring bases on modified bases ("neighborhood effects"). RESULTS We evaluated NanoMod on simulation data sets, based on different types of modifications and different magnitudes of neighborhood effects, and found that NanoMod outperformed other methods in identifying known modified bases. Additionally, we demonstrated superior performance of NanoMod on an E. coli data set with 5mC (5-methylcytosine) modifications. CONCLUSIONS In summary, NanoMod is a flexible tool to detect DNA modifications with single-base resolution from raw signals in Nanopore sequencing, and will facilitate large-scale functional genomics experiments that use modified nucleotides.
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Affiliation(s)
- Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Daniela C. Georgieva
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032 USA
| | - Dieter Egli
- Department of Pediatrics, Columbia University, New York, NY 10032 USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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34
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Ma S, Viola R, Sui L, Cherubini V, Barbetti F, Egli D. β Cell Replacement after Gene Editing of a Neonatal Diabetes-Causing Mutation at the Insulin Locus. Stem Cell Reports 2018; 11:1407-1415. [PMID: 30503261 PMCID: PMC6294262 DOI: 10.1016/j.stemcr.2018.11.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 01/29/2023] Open
Abstract
Permanent neonatal diabetes mellitus (PNDM) can be caused by insulin mutations. We generated induced pluripotent stem cells from fibroblasts of a patient with PNDM and undetectable insulin at birth due to a homozygous mutation in the translation start site of the insulin gene. Differentiation of mutant cells resulted in insulin-negative endocrine stem cells expressing MAFA, NKX6.1, and chromogranin A. Correction of the mutation in stem cells and differentiation to pancreatic endocrine cells restored insulin production and insulin secretion to levels comparable to those of wild-type cells. Grafting of corrected cells into mice, followed by ablating mouse β cells using streptozotocin, resulted in normal glucose homeostasis, including at night, and the stem cell-derived grafts adapted insulin secretion to metabolic changes. Our study provides proof of principle for the generation of genetically corrected cells autologous to a patient with non-autoimmune insulin-dependent diabetes. These cases should be readily amenable to autologous cell therapy.
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Affiliation(s)
- Shuangyu Ma
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Ryan Viola
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | - Lina Sui
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA
| | | | | | - Dieter Egli
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY 10032, USA.
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35
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Abstract
Insulin-expressing beta cells are crucial for the maintenance of systemic glucose homeostasis. Elucidation of the molecular and cellular mechanisms of beta cell development, expansion, survival, and function are required for full understanding of the molecular pathogenesis of diabetes. However, access to human beta cells for such studies is limited by virtue of the logistics of acquisition, prior medical status of donor, and imperfect culture systems for maintaining beta cell identity and function after isolation from human pancreas. Here, a technique for generation of beta cells from human pluripotent stem cells (hPSCs) by modification of key signaling pathways during islet development is described. Up to 70% C-peptide-positive beta cells can be obtained from endodermal anlagen after 27 days of differentiation with specific growth factors and small molecules. Although 50% of them are monohormonal C-peptide-positive cells and have molecular and cellular characteristics consistent with human beta cells in the Islets of Langerhans, a sub-population co-expressing other endocrine markers are also generated, indicating the immaturity of these cells. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Lina Sui
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York
| | - Rudolph L Leibel
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York
| | - Dieter Egli
- Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York
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36
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Ogura H, Preston-Hurlburt P, Perdigoto AL, Amodio M, Krishnaswamy S, Clark P, Yu H, Egli D, Fouts A, Steck AK, Herold KC. Identification and Analysis of Islet Antigen-Specific CD8 + T Cells with T Cell Libraries. J Immunol 2018; 201:1662-1670. [PMID: 30082321 PMCID: PMC6449153 DOI: 10.4049/jimmunol.1800267] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/06/2018] [Indexed: 11/19/2022]
Abstract
Type 1 diabetes (T1D) is most likely caused by killing of β cells by autoreactive CD8+ T cells. Methods to isolate and identify these cells are limited by their low frequency in the peripheral blood. We analyzed CD8+ T cells, reactive with diabetes Ags, with T cell libraries and further characterized their phenotype by CyTOF using class I MHC tetramers. In the libraries, the frequency of islet Ag-specific CD45RO+IFN-γ+CD8+ T cells was higher in patients with T1D compared with healthy control subjects. Ag-specific cells from the libraries of patients with T1D were reactive with ZnT8186-194, whereas those from healthy control recognized ZnT8186-194 and other Ags. ZnT8186-194-reactive CD8+ cells expressed an activation phenotype in T1D patients. We found TCR sequences that were used in multiple library wells from patients with T1D, but these sequences were private and not shared between individuals. These sequences could identify the Ag-specific T cells on a repeated draw, ex vivo in the IFN-γ+ CD8+ T cell subset. We conclude that CD8+ T cell libraries can identify Ag-specific T cells in patients with T1D. The T cell clonotypes can be tracked in vivo with identification of the TCR gene sequences.
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Affiliation(s)
- Hideki Ogura
- Department of Immunobiology, Yale University, New Haven, CT 06520
| | | | | | - Matthew Amodio
- Department of Genetics and of Computer Science, Yale University, New Haven, CT 06520
| | - Smita Krishnaswamy
- Department of Genetics and of Computer Science, Yale University, New Haven, CT 06520
| | - Pamela Clark
- Department of Immunobiology, Yale University, New Haven, CT 06520
| | - Hua Yu
- Department of Immunobiology, Yale University, New Haven, CT 06520
| | - Dieter Egli
- Naomi Berrie Diabetes Center, Division of Molecular Genetics, Columbia University, New York, NY 10032
| | - Alexandra Fouts
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO 80045
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO 80045
| | - Kevan C Herold
- Department of Immunobiology, Yale University, New Haven, CT 06520;
- Department of Internal Medicine, Yale University, New Haven, CT 06520
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37
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Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A, Jasin M. Inter-homologue repair in fertilized human eggs? Nature 2018; 560:E5-E7. [PMID: 30089924 DOI: 10.1038/s41586-018-0379-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 04/05/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Dieter Egli
- Department of Obstetrics and Gynecology and Department of Pediatrics, Columbia University, New York, NY, USA.
| | - Michael V Zuccaro
- Graduate Program, Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | | | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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38
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Zakarin Safier L, Gumer A, Kline M, Egli D, Sauer MV. Compensating human subjects providing oocytes for stem cell research: 9-year experience and outcomes. J Assist Reprod Genet 2018; 35:1219-1225. [PMID: 29872942 DOI: 10.1007/s10815-018-1171-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 03/22/2018] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Human oocytes are arguably one of the most important cell types in humans, yet they are one of the least investigated cells. Because oocytes are limited in number, the use of high-quality oocytes is almost entirely in reproduction. Furthermore, regulatory hurdles for research on gametes and regulations on funding related to research on gametes present significant obstacles to research and the advancement of reproductive treatments. Here we report the outcomes of the largest compensated oocyte donation program for research in the USA to date, and probably worldwide. METHODS Women who participated in oocyte donation for research between 2008 and 2017 were contacted in a phone interview and completed a standardized questionnaire. RESULTS Of 114 participants, 98 oocyte donors completed donation, donating 1787 mature MII oocytes and a total of 86 skin biopsies. Complication rate, including minor complications, of oocyte donation was 8/98, or 8.1%, for which two involved follow-up. Fifty-seven donors answered questions about their experience. Participants were incentivized primarily by money and a desire to help others and reported an overall favorable experience. Most, but not all, human subjects recalled that they had donated for research, and approximately half recalled that their oocytes were being used specifically for stem cell research. CONCLUSIONS Compensated oocyte donation provides a reliable path to obtaining high-quality oocytes for research and is reviewed favorably by oocyte donors. The continuation of programs that offer compensation for oocyte donation is invaluable to continued progress and advancements in stem cell research and human embryology, and for the advancement of novel reproductive treatments.
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Affiliation(s)
- L Zakarin Safier
- Center for Women's Reproductive Care, Columbia University Medical Center, New York, NY, USA
| | - A Gumer
- Center for Women's Reproductive Care, Columbia University Medical Center, New York, NY, USA
| | - M Kline
- Center for Women's Reproductive Care, Columbia University Medical Center, New York, NY, USA
| | - D Egli
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA. .,Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.
| | - M V Sauer
- Center for Women's Reproductive Care, Columbia University Medical Center, New York, NY, USA.,Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA.,Robert Wood Johnson Medical School, Rutgers University, Brunswick, NJ, USA
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Millings EJ, De Rosa MC, Fleet S, Watanabe K, Rausch R, Egli D, Li G, Leduc CA, Zhang Y, Fischer SG, Leibel RL. ILDR2 has a negligible role in hepatic steatosis. PLoS One 2018; 13:e0197548. [PMID: 29847571 PMCID: PMC5976177 DOI: 10.1371/journal.pone.0197548] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/03/2018] [Indexed: 11/18/2022] Open
Abstract
We have previously reported that Ildr2 knockdown via adenovirally-delivered shRNA causes hepatic steatosis in mice. In the present study we investigated hepatic biochemical and anatomic phenotypes of Cre-mediated Ildr2 knock-out mice. Liver-specific Ildr2 knock-out mice were generated in C57BL/6J mice segregating for a floxed (exon 1) allele of Ildr2, using congenital and acute (10-13-week-old male mice) Cre expression. In addition, Ildr2 shRNA was administered to Ildr2 knock-out mice to test the effects of Ildr2 shRNA, per se, in the absence of Ildr2 expression. RNA sequencing was performed on livers of these knockdown and knockout mice. Congenital and acute liver-specific and hepatocyte-specific knockout mice did not develop hepatic steatosis. However, administration of Ildr2 shRNA to Ildr2 knock-out mice did cause hepatic steatosis, indicating that the Ildr2 shRNA had apparent "off-target" effects on gene(s) other than Ildr2. RNA sequencing and BLAST sequence alignment revealed Dgka as a candidate gene mediating these "off-target" effects. Ildr2 shRNA is 63% homologous to the Dgka gene, and Dgka expression decreased only in mice displaying hepatic steatosis. Dgka encodes diacylglycerol kinase (DGK) alpha, one of a family of DGKs which convert diacylglycerides to phosphatidic acid for second messenger signaling. Dgka knockdown mice would be expected to accumulate diacylglyceride, contributing to the observed hepatic steatosis. We conclude that ILDR2 plays a negligible role in hepatic steatosis. Rather, hepatic steatosis observed previously in Ildr2 knockdown mice was likely due to shRNA targeting of Dgka and/or other "off-target" genes. We propose that the gene candidates identified in this follow-up study may lead to identification of novel regulators of hepatic lipid metabolism.
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Affiliation(s)
- Elizabeth J Millings
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Maria Caterina De Rosa
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Sarah Fleet
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Kazuhisa Watanabe
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Richard Rausch
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Dieter Egli
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Gen Li
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Charles A Leduc
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Yiying Zhang
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Stuart G Fischer
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
| | - Rudolph L Leibel
- Naomi Berrie Diabetes Center and Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York, United States of America
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Sevilla A, Forero E, Zimmer M, Martinez H, Reggio K, Paull D, Egli D, Noggle S. Derivation and characterization of the NIH registry human stem cell line NYSCF101 under defined feeder-free conditions. Stem Cell Res 2018; 29:197-201. [PMID: 29730569 DOI: 10.1016/j.scr.2018.04.017] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 12/01/2022] Open
Abstract
The human embryonic stem cell line NYSCFe002-A was derived from a day 6 blastocyst in feeder-free and antibiotic free conditions. The blastocyst was voluntarily donated for research as surplus after in vitro fertilization treatment following informed consent. The NYSCFe002-A line expresses all the pluripotency markers and has the potential to differentiate into all three germ layers in vitro. The line presents normal karyotype and is mycoplasma free. This line is registered as NYSCF101 on the NIH Registry.
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Affiliation(s)
- Ana Sevilla
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, United States.
| | - Eliana Forero
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, United States
| | - Matthew Zimmer
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, United States
| | - Hector Martinez
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, United States
| | - Katie Reggio
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, United States
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, United States
| | - Dieter Egli
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, United States
| | - Scott Noggle
- The New York Stem Cell Foundation Research Institute, New York, NY 10019, United States
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Sui L, Danzl N, Campbell SR, Viola R, Williams D, Xing Y, Wang Y, Phillips N, Poffenberger G, Johannesson B, Oberholzer J, Powers AC, Leibel RL, Chen X, Sykes M, Egli D. β-Cell Replacement in Mice Using Human Type 1 Diabetes Nuclear Transfer Embryonic Stem Cells. Diabetes 2018; 67:26-35. [PMID: 28931519 PMCID: PMC5741143 DOI: 10.2337/db17-0120] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 09/14/2017] [Indexed: 12/20/2022]
Abstract
β-Cells derived from stem cells hold great promise for cell replacement therapy for diabetes. Here we examine the ability of nuclear transfer embryonic stem cells (NT-ESs) derived from a patient with type 1 diabetes to differentiate into β-cells and provide a source of autologous islets for cell replacement. NT-ESs differentiate in vitro with an average efficiency of 55% into C-peptide-positive cells, expressing markers of mature β-cells, including MAFA and NKX6.1. Upon transplantation in immunodeficient mice, grafted cells form vascularized islet-like structures containing MAFA/C-peptide-positive cells. These β-cells adapt insulin secretion to ambient metabolite status and show normal insulin processing. Importantly, NT-ES-β-cells maintain normal blood glucose levels after ablation of the mouse endogenous β-cells. Cystic structures, but no teratomas, were observed in NT-ES-β-cell grafts. Isogenic induced pluripotent stem cell lines showed greater variability in β-cell differentiation. Even though different methods of somatic cell reprogramming result in stem cell lines that are molecularly indistinguishable, full differentiation competence is more common in ES cell lines than in induced pluripotent stem cell lines. These results demonstrate the suitability of NT-ES-β-cells for cell replacement for type 1 diabetes and provide proof of principle for therapeutic cloning combined with cell therapy.
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Affiliation(s)
- Lina Sui
- Naomi Berrie Diabetes Center and Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Nichole Danzl
- Columbia Center for Translational Immunology, Department of Medicine, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Sean R Campbell
- Columbia Center for Translational Immunology, Department of Medicine, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Ryan Viola
- Naomi Berrie Diabetes Center and Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Damian Williams
- Columbia Stem Cell Core Facility, Columbia University Medical Center, New York, NY
| | - Yuan Xing
- Department of Surgery/Division of Transplantation, University of Illinois at Chicago, Chicago, IL
| | - Yong Wang
- Department of Surgery/Division of Transplantation, University of Illinois at Chicago, Chicago, IL
| | - Neil Phillips
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Greg Poffenberger
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | | | - Jose Oberholzer
- Department of Surgery/Division of Transplantation, University of Illinois at Chicago, Chicago, IL
| | - Alvin C Powers
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- VA Tennessee Valley Healthcare System, Nashville, TN
| | - Rudolph L Leibel
- Naomi Berrie Diabetes Center and Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Xiaojuan Chen
- Columbia Center for Translational Immunology, Department of Medicine, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
- Department of Surgery, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
- Department of Surgery, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
| | - Dieter Egli
- Naomi Berrie Diabetes Center and Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
- New York Stem Cell Foundation Research Institute, New York, NY
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Sevilla A, Forero E, Zimmer M, Martinez H, Reggio K, Paull D, Egli D, Noggle S. Derivation and characterization of the NYSCFe003-A human embryonic stem cell line. Stem Cell Res 2017; 25:217-220. [PMID: 29161648 DOI: 10.1016/j.scr.2017.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/04/2017] [Accepted: 10/26/2017] [Indexed: 02/02/2023] Open
Abstract
The human embryonic stem cell line NYSCFe003-A was derived from a day 5 to day 6 blastocyst in feeder-free and antibiotic free conditions. The blastocyst was voluntarily donated for research as surplus after in vitro fertilization treatment following informed consent. The NYSCFe003-A line expresses all the pluripotency markers and has the potential to differentiate into all three germ layers in vitro. The line presents normal karyotype and is mycoplasma free.
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Affiliation(s)
- Ana Sevilla
- The New York Stem Cell Foundation Research Institute, NY 10019, New York, United States.
| | - Eliana Forero
- The New York Stem Cell Foundation Research Institute, NY 10019, New York, United States
| | - Matthew Zimmer
- The New York Stem Cell Foundation Research Institute, NY 10019, New York, United States
| | - Hector Martinez
- The New York Stem Cell Foundation Research Institute, NY 10019, New York, United States
| | - Katie Reggio
- The New York Stem Cell Foundation Research Institute, NY 10019, New York, United States
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute, NY 10019, New York, United States
| | - Dieter Egli
- The New York Stem Cell Foundation Research Institute, NY 10019, New York, United States
| | - Scott Noggle
- The New York Stem Cell Foundation Research Institute, NY 10019, New York, United States
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Fischer C, Prosser R, Engelstad K, Lobo R, Sauer M, Egli D. Toward clinical use of mitochondrial replacement therapy. Fertil Steril 2017. [DOI: 10.1016/j.fertnstert.2017.07.468] [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: 11/24/2022]
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Safier L, Zuccaro M, Lobo R, Egli D. Gene editing in haploid human embryonic stem cells using CRISPR/Cas9. Fertil Steril 2017. [DOI: 10.1016/j.fertnstert.2017.07.086] [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: 11/16/2022]
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Georgieva D, Egli D. Tying genetic stability to cell identity. Cell Cycle 2017; 16:1139-1140. [PMID: 28548589 DOI: 10.1080/15384101.2017.1324126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Daniela Georgieva
- a Integrated Program in Cellular, Molecular, and Biomedical Studies , Columbia University , New York , NY , USA
| | - Dieter Egli
- b Department of Pediatrics, Department of Obstetrics and Gynecology , Columbia University , New York , NY , USA.,c Department of Obstetrics and Gynecology , Columbia University , New York , NY , USA
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Wang L, Sui L, Panigrahi SK, Meece K, Xin Y, Kim J, Gromada J, Doege CA, Wardlaw SL, Egli D, Leibel RL. PC1/3 Deficiency Impacts Pro-opiomelanocortin Processing in Human Embryonic Stem Cell-Derived Hypothalamic Neurons. Stem Cell Reports 2017; 8:264-277. [PMID: 28132887 PMCID: PMC5312251 DOI: 10.1016/j.stemcr.2016.12.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/19/2022] Open
Abstract
We recently developed a technique for generating hypothalamic neurons from human pluripotent stem cells. Here, as proof of principle, we examine the use of these cells in modeling of a monogenic form of severe obesity: PCSK1 deficiency. The cognate enzyme, PC1/3, processes many prohormones in neuroendocrine and other tissues. We generated PCSK1 (PC1/3)-deficient human embryonic stem cell (hESC) lines using both short hairpin RNA and CRISPR-Cas9, and investigated pro-opiomelanocortin (POMC) processing using hESC-differentiated hypothalamic neurons. The increased levels of unprocessed POMC and the decreased ratios (relative to POMC) of processed POMC-derived peptides in both PCSK1 knockdown and knockout hESC-derived neurons phenocopied POMC processing reported in PC1/3-null mice and PC1/3-deficient patients. PC1/3 deficiency was associated with increased expression of melanocortin receptors and PRCP (prolylcarboxypeptidase, a catabolic enzyme for α-melanocyte stimulating hormone (αMSH)), and reduced adrenocorticotropic hormone secretion. We conclude that the obesity accompanying PCSK1 deficiency may not be primarily due to αMSH deficiency. Stem cell-derived hypothalamic neurons are used to study human obesity shRNA and CRISPR-Cas9 were used to generate models of PCSK1 deficiency PC1/3 deficiency impaired POMC processing in arcuate-like neurons Adaptive changes occurred in “downstream” POMC processing enzymes
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Affiliation(s)
- Liheng Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Avenue, Room 620A, New York, NY 10032, USA; Department of Medicine and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lina Sui
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Avenue, Room 620A, New York, NY 10032, USA
| | - Sunil K Panigrahi
- Department of Medicine and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Kana Meece
- Department of Medicine and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yurong Xin
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Jinrang Kim
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | - Claudia A Doege
- Department of Pathology and Cell Biology and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Sharon L Wardlaw
- Department of Medicine and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Avenue, Room 620A, New York, NY 10032, USA; New York Stem Cell Foundation Research Institute, 3960 Broadway, New York, NY 10032, USA
| | - Rudolph L Leibel
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, 1150 St. Nicholas Avenue, Room 620A, New York, NY 10032, USA; Department of Medicine and Naomi Berrie Diabetes Center, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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Hua H, Shang L, Martinez H, Freeby M, Gallagher MP, Ludwig T, Deng L, Greenberg E, LeDuc C, Chung WK, Goland R, Leibel RL, Egli D. iPSC-derived β cells model diabetes due to glucokinase deficiency. J Clin Invest 2017; 127:1115. [PMID: 28094769 DOI: 10.1172/jci92775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Affiliation(s)
- Dieter Egli
- Department of Obstetrics and Gynecology, Columbia University, New York, NY.
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Burnett LC, LeDuc CA, Sulsona CR, Paull D, Rausch R, Eddiry S, Carli JFM, Morabito MV, Skowronski AA, Hubner G, Zimmer M, Wang L, Day R, Levy B, Fennoy I, Dubern B, Poitou C, Clement K, Butler MG, Rosenbaum M, Salles JP, Tauber M, Driscoll DJ, Egli D, Leibel RL. Deficiency in prohormone convertase PC1 impairs prohormone processing in Prader-Willi syndrome. J Clin Invest 2016; 127:293-305. [PMID: 27941249 DOI: 10.1172/jci88648] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/20/2016] [Indexed: 12/17/2022] Open
Abstract
Prader-Willi syndrome (PWS) is caused by a loss of paternally expressed genes in an imprinted region of chromosome 15q. Among the canonical PWS phenotypes are hyperphagic obesity, central hypogonadism, and low growth hormone (GH). Rare microdeletions in PWS patients define a 91-kb minimum critical deletion region encompassing 3 genes, including the noncoding RNA gene SNORD116. Here, we found that protein and transcript levels of nescient helix loop helix 2 (NHLH2) and the prohormone convertase PC1 (encoded by PCSK1) were reduced in PWS patient induced pluripotent stem cell-derived (iPSC-derived) neurons. Moreover, Nhlh2 and Pcsk1 expression were reduced in hypothalami of fasted Snord116 paternal knockout (Snord116p-/m+) mice. Hypothalamic Agrp and Npy remained elevated following refeeding in association with relative hyperphagia in Snord116p-/m+ mice. Nhlh2-deficient mice display growth deficiencies as adolescents and hypogonadism, hyperphagia, and obesity as adults. Nhlh2 has also been shown to promote Pcsk1 expression. Humans and mice deficient in PC1 display hyperphagic obesity, hypogonadism, decreased GH, and hypoinsulinemic diabetes due to impaired prohormone processing. Here, we found that Snord116p-/m+ mice displayed in vivo functional defects in prohormone processing of proinsulin, pro-GH-releasing hormone, and proghrelin in association with reductions in islet, hypothalamic, and stomach PC1 content. Our findings suggest that the major neuroendocrine features of PWS are due to PC1 deficiency.
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Grossman L, Chia G, Zuccaro M, Sadowy S, Prosser R, Sauer M, Egli D. Determination of timing and mechanism of diploidization of haploid parthenogenetic and androgenetic human embryos. Fertil Steril 2016. [DOI: 10.1016/j.fertnstert.2016.07.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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