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De Gasperi R, Csernoch L, Dienes B, Gonczi M, Chakrabarty JK, Goeta S, Aslan A, Toro CA, Karasik D, Brown LM, Brotto M, Cardozo CP. Septin 7 interacts with Numb to preserve sarcomere structural organization and muscle contractile function. eLife 2024; 12:RP89424. [PMID: 38695862 PMCID: PMC11065422 DOI: 10.7554/elife.89424] [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] [Indexed: 05/04/2024] Open
Abstract
Here, we investigated the mechanisms by which aging-related reductions of the levels of Numb in skeletal muscle fibers contribute to loss of muscle strength and power, two critical features of sarcopenia. Numb is an adaptor protein best known for its critical roles in development, including asymmetric cell division, cell-type specification, and termination of intracellular signaling. Numb expression is reduced in old humans and mice. We previously showed that, in mouse skeletal muscle fibers, Numb is localized to sarcomeres where it is concentrated near triads; conditional inactivation of Numb and a closely related protein Numb-like (Numbl) in mouse myofibers caused weakness, disorganization of sarcomeres, and smaller mitochondria with impaired function. Here, we found that a single knockout of Numb in myofibers causes reduction in tetanic force comparable to a double Numb, Numbl knockout. We found by proteomics analysis of protein complexes isolated from C2C12 myotubes by immunoprecipitation using antibodies against Numb that Septin 7 is a potential Numb-binding partner. Septin 7 is a member of the family of GTP-binding proteins that organize into filaments, sheets, and rings, and is considered part of the cytoskeleton. Immunofluorescence evaluation revealed a partial overlap of staining for Numb and Septin 7 in myofibers. Conditional, inducible knockouts of Numb led to disorganization of Septin 7 staining in myofibers. These findings indicate that Septin 7 is a Numb-binding partner and suggest that interactions between Numb and Septin 7 are critical for structural organization of the sarcomere and muscle contractile function.
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Affiliation(s)
- Rita De Gasperi
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Spinal Cord Damage Research Center, James J. Peters VA Medical CenterBronxUnited States
| | - Laszlo Csernoch
- Department of Physiology, Faculty of Medicine, University of DebrecenDebrecenHungary
- ELKH-DE Cell Physiology Research Group, University of DebrecenDebrecenHungary
| | - Beatrix Dienes
- Department of Physiology, Faculty of Medicine, University of DebrecenDebrecenHungary
| | - Monika Gonczi
- Department of Physiology, Faculty of Medicine, University of DebrecenDebrecenHungary
| | - Jayanta K Chakrabarty
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Shahar Goeta
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Abdurrahman Aslan
- Spinal Cord Damage Research Center, James J. Peters VA Medical CenterBronxUnited States
- Department of Medicine, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Carlos A Toro
- Spinal Cord Damage Research Center, James J. Peters VA Medical CenterBronxUnited States
- Department of Medicine, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - David Karasik
- Azrieli Faculty of Medicine, Bar Ilan UniversitySafedIsrael
| | - Lewis M Brown
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Marco Brotto
- Bone-Muscle Research Center, College of Nursing & Health Innovation,University of Texas at ArlingtonAustinUnited States
| | - Christopher P Cardozo
- Spinal Cord Damage Research Center, James J. Peters VA Medical CenterBronxUnited States
- Department of Rehabilitation Medicine, Icahn School of Medicine at Mount SinaiNew YorkUnited States
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2
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Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski J, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind BM, Marlin BJ, Gronostajski RM, Fleischmann A, Lomvardas S. Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. eLife 2023; 12:RP87445. [PMID: 38108811 PMCID: PMC10727497 DOI: 10.7554/elife.87445] [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] [Indexed: 12/19/2023] Open
Abstract
Olfactory receptor (OR) choice represents an example of genetically hardwired stochasticity, where every olfactory neuron expresses one out of ~2000 OR alleles in the mouse genome in a probabilistic, yet stereotypic fashion. Here, we propose that topographic restrictions in OR expression are established in neuronal progenitors by two opposing forces: polygenic transcription and genomic silencing, both of which are influenced by dorsoventral gradients of transcription factors NFIA, B, and X. Polygenic transcription of OR genes may define spatially constrained OR repertoires, among which one OR allele is selected for singular expression later in development. Heterochromatin assembly and genomic compartmentalization of OR alleles also vary across the axes of the olfactory epithelium and may preferentially eliminate ectopically expressed ORs with more dorsal expression destinations from this 'privileged' repertoire. Our experiments identify early transcription as a potential 'epigenetic' contributor to future developmental patterning and reveal how two spatially responsive probabilistic processes may act in concert to establish deterministic, precise, and reproducible territories of stochastic gene expression.
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Affiliation(s)
- Elizaveta V Bashkirova
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Nell Klimpert
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Kevin Monahan
- Department of Biochemistry and Molecular Biology, Rutgers UniversityNewarkUnited States
| | - Christine E Campbell
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Jason Osinski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Longzhi Tan
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Ira Schieren
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Ariel Pourmorady
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Beka Stecky
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Gilad Barnea
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Xiaoliang Sunney Xie
- Beijing Innovation Center for Genomics, Peking UniversityBeijingChina
- Biomedical Pioneering Innovation Center, Peking UniversityBeijingChina
| | - Ishmail Abdus-Saboor
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Benjamin M Shykind
- Prevail Therapeutics- a wholly-owned subsidiary of Eli Lilly and CompanyNew YorkUnited States
| | - Bianca J Marlin
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Richard M Gronostajski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Stavros Lomvardas
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
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3
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Pu J, Lin L, Jiang H, Hu Z, Li H, Yan Z, Zhang B, Feng J. Parkin Maintains Robust Pacemaking in Human Induced Pluripotent Stem Cell-Derived A9 Dopaminergic Neurons. Mov Disord 2023. [PMID: 37166002 DOI: 10.1002/mds.29434] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND The degeneration of nigral (A9) dopaminergic (DA) neurons results in cardinal motor symptoms that define Parkinson's disease (PD). Loss-of-function mutations in parkin are linked to a rare form of early-onset PD that is inherited recessively. OBJECTIVE We generated isogenic human A9 DA neurons with or without parkin mutations to establish the causal relationship between parkin mutations and the dysfunction of human A9 DA neurons. METHODS Using TALEN (transcription activator-like effector nuclease)- or CRISPR/Cas9-mediated gene targeting, we produced two isogenic pairs of naivetropic induced pluripotent stem cells (iPSCs) by repairing exon 3 deletions of parkin in iPSCs derived from a PD patient and by introducing the PD-linked A82E mutation into iPSCs from a healthy subject. The four lines of isogenic iPSCs were differentiated to A9 DA neurons, which fired spontaneous pacemaking action potentials (AP) dependent on L-type Ca2+ channels. RESULTS The frequency of the pacemaking APs was significantly reduced by parkin mutations introduced to normal neurons. Consistent with this, isogenic repair of parkin mutations significantly increased the frequency from that observed in patient-derived neurons. CONCLUSIONS The results show that parkin maintains robust pacemaking in human iPSC-derived A9 DA neurons. The function is critical to normal DA transmission required for controlling voluntary locomotor activities. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Jiali Pu
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lin Lin
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Houbo Jiang
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Zhixing Hu
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Hong Li
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
| | - Baorong Zhang
- Department of Neurology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
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Kolesnikova M, Oh JK, Wang J, Lee W, Zernant J, Su PY, Kim AH, Jenny LA, Yang T, Allikmets R, Tsang SH. A pathogenic in-frame deletion-insertion variant in BEST1 phenocopies Stargardt disease. JCI Insight 2022; 7:e162687. [PMID: 36264634 PMCID: PMC9746905 DOI: 10.1172/jci.insight.162687] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/18/2022] [Indexed: 01/12/2023] Open
Abstract
Here, we describe affected members of a 2-generation family with a Stargardt disease-like phenotype caused by a 2-base pair deletion insertion, c.1014_1015delGAinsCT;p.(Trp338_Asn339delinsCysTyr), in BEST1. The variant was identified by whole-exome sequencing, and its pathogenicity was verified through chloride channel recording using WT and transfected mutant HEK293 cells. Clinical examination of both patients revealed similar phenotypes at 2 different disease stages that were attributable to differences in their age at presentation. Hyperautofluorescent flecks along the arcades were observed in the proband, while the affected mother exhibited more advanced retinal pigment epithelium (RPE) loss in the central macula. Full-field electroretinogram testing was unremarkable in the daughter; however, moderate attenuation of generalized cone function was detected in the mother. Results from electrooculogram testing in the daughter were consistent with widespread dysfunction of the RPE characteristic of Best disease. Whole-cell patch-clamp recordings revealed a statistically significant decrease in chloride conductance of the mutant compared with WT cells. This report on a mother and daughter with a BEST1 genotype that phenocopies Stargardt disease broadens the clinical spectrum of BEST1-associated retinopathy.
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Affiliation(s)
- Masha Kolesnikova
- Jonas Children’s Vision Care and Bernard and Shirlee Brown Glaucoma Laboratory, Columbia University, New York, New York, USA
- SUNY Downstate Health Sciences University, New York, New York, USA
| | | | | | - Winston Lee
- Department of Ophthalmology
- Department of Genetics and Development, and
| | | | | | - Angela H. Kim
- Jonas Children’s Vision Care and Bernard and Shirlee Brown Glaucoma Laboratory, Columbia University, New York, New York, USA
- SUNY Downstate Health Sciences University, New York, New York, USA
| | - Laura A. Jenny
- Jonas Children’s Vision Care and Bernard and Shirlee Brown Glaucoma Laboratory, Columbia University, New York, New York, USA
| | | | - Rando Allikmets
- Department of Ophthalmology
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Stephen H. Tsang
- Jonas Children’s Vision Care and Bernard and Shirlee Brown Glaucoma Laboratory, Columbia University, New York, New York, USA
- Department of Ophthalmology
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
- Institute of Human Nutrition, Columbia Stem Cell Initiative, New York, New York, USA
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5
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Li D, Yang J, Malik V, Huang Y, Huang X, Zhou H, Wang J. An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity. Nucleic Acids Res 2022; 50:12462-12479. [PMID: 36416264 PMCID: PMC9757061 DOI: 10.1093/nar/gkac1084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
RNA helicases are involved in multiple steps of RNA metabolism to direct their roles in gene expression, yet their functions in pluripotency control remain largely unexplored. Starting from an RNA interference (RNAi) screen of RNA helicases, we identified that eIF4A3, a DEAD-box (Ddx) helicase component of the exon junction complex (EJC), is essential for the maintenance of embryonic stem cells (ESCs). Mechanistically, we show that eIF4A3 post-transcriptionally controls the pluripotency-related cell cycle regulators and that its depletion causes the loss of pluripotency via cell cycle dysregulation. Specifically, eIF4A3 is required for the efficient nuclear export of Ccnb1 mRNA, which encodes Cyclin B1, a key component of the pluripotency-promoting pathway during the cell cycle progression of ESCs. Our results reveal a previously unappreciated role for eIF4A3 and its associated EJC in maintaining stem cell pluripotency through post-transcriptional control of the cell cycle.
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Affiliation(s)
- Dan Li
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jihong Yang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vikas Malik
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yuting Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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6
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Medina-Cano D, Corrigan EK, Glenn RA, Islam MT, Lin Y, Kim J, Cho H, Vierbuchen T. Rapid and robust directed differentiation of mouse epiblast stem cells into definitive endoderm and forebrain organoids. Development 2022; 149:dev200561. [PMID: 35899604 PMCID: PMC10655922 DOI: 10.1242/dev.200561] [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: 01/26/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022]
Abstract
Directed differentiation of pluripotent stem cells (PSCs) is a powerful model system for deconstructing embryonic development. Although mice are the most advanced mammalian model system for genetic studies of embryonic development, state-of-the-art protocols for directed differentiation of mouse PSCs into defined lineages require additional steps and generates target cell types with lower purity than analogous protocols for human PSCs, limiting their application as models for mechanistic studies of development. Here, we examine the potential of mouse epiblast stem cells cultured in media containing Wnt pathway inhibitors as a starting point for directed differentiation. As a proof of concept, we focused our efforts on two specific cell/tissue types that have proven difficult to generate efficiently and reproducibly from mouse embryonic stem cells: definitive endoderm and neural organoids. We present new protocols for rapid generation of nearly pure definitive endoderm and forebrain-patterned neural organoids that model the development of prethalamic and hippocampal neurons. These differentiation models present new possibilities for combining mouse genetic tools with in vitro differentiation to characterize molecular and cellular mechanisms of embryonic development.
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Affiliation(s)
- Daniel Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Emily K. Corrigan
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Rachel A. Glenn
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Mohammed T. Islam
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Yuan Lin
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Juliet Kim
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Hyunwoo Cho
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
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7
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Schwartz AZA, Tsyba N, Abdu Y, Patel MR, Nance J. Independent regulation of mitochondrial DNA quantity and quality in Caenorhabditis elegans primordial germ cells. eLife 2022; 11:e80396. [PMID: 36200990 PMCID: PMC9536838 DOI: 10.7554/elife.80396] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondria harbor an independent genome, called mitochondrial DNA (mtDNA), which contains essential metabolic genes. Although mtDNA mutations occur at high frequency, they are inherited infrequently, indicating that germline mechanisms limit their accumulation. To determine how germline mtDNA is regulated, we examined the control of mtDNA quantity and quality in C. elegans primordial germ cells (PGCs). We show that PGCs combine strategies to generate a low point in mtDNA number by segregating mitochondria into lobe-like protrusions that are cannibalized by adjacent cells, and by concurrently eliminating mitochondria through autophagy, reducing overall mtDNA content twofold. As PGCs exit quiescence and divide, mtDNAs replicate to maintain a set point of ~200 mtDNAs per germline stem cell. Whereas cannibalism and autophagy eliminate mtDNAs stochastically, we show that the kinase PTEN-induced kinase 1 (PINK1), operating independently of Parkin and autophagy, preferentially reduces the fraction of mutant mtDNAs. Thus, PGCs employ parallel mechanisms to control both the quantity and quality of the founding population of germline mtDNAs.
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Affiliation(s)
- Aaron ZA Schwartz
- Department of Cell Biology, NYU Grossman School of MedicineNew YorkUnited States
- Skirball Institute of Biomolecular Medicine, NYU Grossman School of MedicineNew YorkUnited States
| | - Nikita Tsyba
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
| | - Yusuff Abdu
- Department of Cell Biology, NYU Grossman School of MedicineNew YorkUnited States
- Skirball Institute of Biomolecular Medicine, NYU Grossman School of MedicineNew YorkUnited States
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt UniversityNashvilleUnited States
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
- Diabetes Research and Training Center, Vanderbilt University School of MedicineNashvilleUnited States
| | - Jeremy Nance
- Department of Cell Biology, NYU Grossman School of MedicineNew YorkUnited States
- Skirball Institute of Biomolecular Medicine, NYU Grossman School of MedicineNew YorkUnited States
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8
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Abstract
The cerebellum has a simple cytoarchitecture consisting of a folded cortex with three cell layers that surrounds a nuclear structure housing the output neurons. The excitatory neurons are generated from a unique progenitor zone, the rhombic lip, whereas the inhibitory neurons and astrocytes are generated from the ventricular zone. The growth phase of the cerebellum is driven by lineage-restricted progenitor populations derived from each zone. Research during the past decade has uncovered the importance of cell-to-cell communication between the lineages through largely unknown signaling mechanisms for regulating the scaling of cell numbers and cell plasticity during mouse development and following injury in the neonatal (P0-P14) cerebellum. This Review focuses on how the interplay between cell types is key to morphogenesis, production of robust neural circuits and replenishment of cells after injury, and ends with a discussion of the implications of the greater complexity of the human cerebellar progenitor zones for development and disease.
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Affiliation(s)
- Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - N. Sumru Bayin
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge University, Cambridge CB2 1NQ, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
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9
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Thege FI, Cardle II, Gruber CN, Siemann MJ, Cong S, Wittmann K, Love J, Kirby BJ. Acquired chemoresistance drives spatial heterogeneity, chemoprotection and collective migration in pancreatic tumor spheroids. PLoS One 2022; 17:e0267882. [PMID: 35617275 PMCID: PMC9135276 DOI: 10.1371/journal.pone.0267882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 04/18/2022] [Indexed: 11/18/2022] Open
Abstract
Tumors display rich cellular heterogeneity and typically consist of multiple co-existing clones with distinct genotypic and phenotypic characteristics. The acquisition of resistance to chemotherapy has been shown to contribute to the development of aggressive cancer traits, such as increased migration, invasion and stemness. It has been hypothesized that collective cellular behavior and cooperation of cancer cell populations may directly contribute to disease progression and lack of response to treatment. Here we show that the spontaneous emergence of chemoresistance in a cancer cell population exposed to the selective pressure of a chemotherapeutic agent can result in the emergence of collective cell behavior, including cell-sorting, chemoprotection and collective migration. We derived several gemcitabine resistant subclones from the human pancreatic cancer cell line BxPC3 and determined that the observed chemoresistance was driven of a focal amplification of the chr11p15.4 genomic region, resulting in over-expression of the ribonucleotide reductase (RNR) subunit RRM1. Interestingly, these subclones display a rich cell-sorting behavior when cultured as mixed tumor spheroids. Furthermore, we show that chemoresistant cells are able to exert a chemoprotective effect on non-resistant cells in spheroid co-culture, whereas no protective effect is seen in conventional 2D culture. We also demonstrate that the co-culture of resistant and non-resistant cells leads to collective migration where resistant cells enable migration of otherwise non-migratory cells.
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Affiliation(s)
| | - Ian I. Cardle
- Cornell University, Ithaca, New York, United States of America
| | - Conor N. Gruber
- Cornell University, Ithaca, New York, United States of America
| | - Megan J. Siemann
- MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Sophie Cong
- Cornell University, Ithaca, New York, United States of America
| | | | - Justin Love
- Cornell University, Ithaca, New York, United States of America
| | - Brian J. Kirby
- Cornell University, Ithaca, New York, United States of America
- Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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10
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Li D, Yang J, Huang X, Zhou H, Wang J. eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency. Sci Adv 2022; 8:eabm0478. [PMID: 35353581 PMCID: PMC8967233 DOI: 10.1126/sciadv.abm0478] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Translational control has emerged as a fundamental regulatory layer of proteome complexity that governs cellular identity and functions. As initiation is the rate-limiting step of translation, we carried out an RNA interference screen for key translation initiation factors required to maintain embryonic stem cell (ESC) identity. We identified eukaryotic translation initiation factor 4A2 (eIF4A2) and defined its mechanistic action through ribosomal protein S26-independent and -dependent ribosomes in translation initiation activation of messenger RNAs (mRNAs) encoding pluripotency factors and the histone variant H3.3 with demonstrated roles in maintaining stem cell pluripotency. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent two-cell transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Accordingly, knockdown of eIF4A2 disrupts ESC proteome, causing the loss of ESC identity. Collectively, we establish a translational paradigm of the protein synthesis of pluripotency transcription factors and epigenetic regulators imposed on their established roles in controlling pluripotency.
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Affiliation(s)
- Dan Li
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jihong Yang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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11
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Lee Y, DiMaulo-Milk E, Leslie J, Ding L. Hematopoietic stem cells temporally transition to thrombopoietin dependence in the fetal liver. Sci Adv 2022; 8:eabm7688. [PMID: 35294228 PMCID: PMC8926339 DOI: 10.1126/sciadv.abm7688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Tissue stem cells temporally change intrinsic mechanisms to meet physiological demands. However, little is known whether and how stem cells rely on distinct extrinsic maintenance mechanisms over time. Here, we found that hematopoietic stem cells (HSCs) temporally transition to depend on thrombopoietin (TPO), a key extrinsic factor, from E16.5 onward in the developing liver. Deletion of Tpo reduced mTOR activity, induced differentiation gene expression, and preferentially depleted metabolically active HSCs. Ectopic activation of the JAK2 or MAPK pathway did not rescue HSCs in Tpo-/- mice. Enforced activation of the mTOR pathway by conditionally deleting Tsc1 significantly rescued HSCs and their gene expression in Tpo-/- mice. Lin28b intrinsically promoted mTOR activation in HSCs, and its expression diminished over time. Conditional deletion of Lin28b further reduced mTOR activity and strongly exacerbated HSC depletion in Tpo-/- mice. Therefore, HSCs temporally transition from intrinsic LIN28B-dependent to extrinsic TPO-dependent maintenance in the developing liver.
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12
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Bayin NS, Mizrak D, Stephen DN, Lao Z, Sims PA, Joyner AL. Injury-induced ASCL1 expression orchestrates a transitory cell state required for repair of the neonatal cerebellum. Sci Adv 2021; 7:eabj1598. [PMID: 34878841 PMCID: PMC8654303 DOI: 10.1126/sciadv.abj1598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/20/2021] [Indexed: 05/23/2023]
Abstract
To understand repair processes, it is critical to identify the molecular foundations underlying progenitor diversity and plasticity. Upon injury to the neonatal cerebellum, a normally gliogenic nestin-expressing progenitor (NEP) in the Bergmann glia layer (BgL) undergoes adaptive reprograming to restore granule cell production. However, the cellular states and genes regulating the NEP fate switch are unknown. Using single-cell RNA sequencing and fate mapping, we defined molecular subtypes of NEPs and their lineages under homeostasis and repair. NEPs contain two major subtypes: Hopx+ astrogliogenic and Ascl1+ neurogenic NEPs that are further subdivided based on their location, lineage, and differentiation status. Upon injury, an Ascl1+ transitory cellular state arises from Hopx+ BgL-NEPs. Furthermore, mutational analysis revealed that induction of Ascl1 is required for adaptive reprogramming by orchestrating a glial-to-neural switch in vivo following injury. Thus, we provide molecular and cellular insights into context-dependent progenitor plasticity and repair mechanisms in the brain.
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Affiliation(s)
- N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Dogukan Mizrak
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Daniel N. Stephen
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Zhimin Lao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Peter A. Sims
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biochemistry and Biophysics, Columbia University, New York, NY, USA
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
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13
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Levic DS, Yamaguchi N, Wang S, Knaut H, Bagnat M. Knock-in tagging in zebrafish facilitated by insertion into non-coding regions. Development 2021; 148:dev199994. [PMID: 34495314 PMCID: PMC8513609 DOI: 10.1242/dev.199994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 07/08/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022]
Abstract
Zebrafish provide an excellent model for in vivo cell biology studies because of their amenability to live imaging. Protein visualization in zebrafish has traditionally relied on overexpression of fluorescently tagged proteins from heterologous promoters, making it difficult to recapitulate endogenous expression patterns and protein function. One way to circumvent this problem is to tag the proteins by modifying their endogenous genomic loci. Such an approach is not widely available to zebrafish researchers because of inefficient homologous recombination and the error-prone nature of targeted integration in zebrafish. Here, we report a simple approach for tagging proteins in zebrafish on their N or C termini with fluorescent proteins by inserting PCR-generated donor amplicons into non-coding regions of the corresponding genes. Using this approach, we generated endogenously tagged alleles for several genes that are crucial for epithelial biology and organ development, including the tight junction components ZO-1 and Cldn15la, the trafficking effector Rab11a, the apical polarity protein aPKC and the ECM receptor Integrin β1b. Our approach facilitates the generation of knock-in lines in zebrafish, opening the way for accurate quantitative imaging studies.
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Affiliation(s)
- Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Naoya Yamaguchi
- Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, Department of Cell Biology, New York, NY 10016, USA
| | - Siyao Wang
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine, New York University Grossman School of Medicine, Department of Cell Biology, New York, NY 10016, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
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14
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Gao L, Decker M, Chen H, Ding L. Thrombopoietin from hepatocytes promotes hematopoietic stem cell regeneration after myeloablation. eLife 2021; 10:e69894. [PMID: 34463253 PMCID: PMC8457823 DOI: 10.7554/elife.69894] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
The bone marrow niche plays critical roles in hematopoietic recovery and hematopoietic stem cell (HSC) regeneration after myeloablative stress. However, it is not clear whether systemic factors beyond the local niche are required for these essential processes in vivo. Thrombopoietin (THPO) is a key cytokine promoting hematopoietic rebound after myeloablation and its transcripts are expressed by multiple cellular sources. The upregulation of bone marrow-derived THPO has been proposed to be crucial for hematopoietic recovery and HSC regeneration after stress. Nonetheless, the cellular source of THPO in myeloablative stress has never been investigated genetically. We assessed the functional sources of THPO following two common myeloablative perturbations: 5-fluorouracil (5-FU) administration and irradiation. Using a Thpo translational reporter, we found that the liver but not the bone marrow is the major source of THPO protein after myeloablation. Mice with conditional Thpo deletion from osteoblasts and/or bone marrow stromal cells showed normal recovery of HSCs and hematopoiesis after myeloablation. In contrast, mice with conditional Thpo deletion from hepatocytes showed significant defects in HSC regeneration and hematopoietic rebound after myeloablation. Thus, systemic THPO from the liver is necessary for HSC regeneration and hematopoietic recovery in myeloablative stress conditions.
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Affiliation(s)
- Longfei Gao
- Columbia Stem Cell Initiative, Columbia University Medical CenterNew YorkUnited States
- Department of Rehabilitation and Regenerative Medicine, Columbia University Medical CenterNew YorkUnited States
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, United StatesNew YorkUnited States
| | - Matthew Decker
- Columbia Stem Cell Initiative, Columbia University Medical CenterNew YorkUnited States
- Department of Rehabilitation and Regenerative Medicine, Columbia University Medical CenterNew YorkUnited States
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, United StatesNew YorkUnited States
| | - Haidee Chen
- Columbia Stem Cell Initiative, Columbia University Medical CenterNew YorkUnited States
- Department of Rehabilitation and Regenerative Medicine, Columbia University Medical CenterNew YorkUnited States
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, United StatesNew YorkUnited States
| | - Lei Ding
- Columbia Stem Cell Initiative, Columbia University Medical CenterNew YorkUnited States
- Department of Rehabilitation and Regenerative Medicine, Columbia University Medical CenterNew YorkUnited States
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, United StatesNew YorkUnited States
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15
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Abstract
Independent origins of sociality in bees and ants are associated with independent expansions of particular odorant receptor (OR) gene subfamilies. In ants, one clade within the OR gene family, the 9-exon subfamily, has dramatically expanded. These receptors detect cuticular hydrocarbons (CHCs), key social signaling molecules in insects. It is unclear to what extent 9-exon OR subfamily expansion is associated with the independent evolution of sociality across Hymenoptera, warranting studies of taxa with independently derived social behavior. Here, we describe OR gene family evolution in the northern paper wasp, Polistes fuscatus, and compare it to four additional paper wasp species spanning ∼40 million years of evolutionary divergence. We find 200 putatively functional OR genes in P. fuscatus, matching predictions from neuroanatomy, and more than half of these are in the 9-exon subfamily. Most OR gene expansions are tandemly arrayed at orthologous loci in Polistes genomes, and microsynteny analysis shows species-specific gain and loss of 9-exon ORs within tandem arrays. There is evidence of episodic positive diversifying selection shaping ORs in expanded subfamilies. Values of omega (dN/dS) are higher among 9-exon ORs compared to other OR subfamilies. Within the Polistes OR gene tree, branches in the 9-exon OR clade experience relaxed negative (relaxed purifying) selection relative to other branches in the tree. Patterns of OR evolution within Polistes are consistent with 9-exon OR function in CHC perception by combinatorial coding, with both natural selection and neutral drift contributing to interspecies differences in gene copy number and sequence.
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Affiliation(s)
- Andrew W Legan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Christopher M Jernigan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Sara E Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Matthieu F Fuchs
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
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16
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Yu JR, LeRoy G, Bready D, Frenster JD, Saldaña-Meyer R, Jin Y, Descostes N, Stafford JM, Placantonakis DG, Reinberg D. The H3K36me2 writer-reader dependency in H3K27M-DIPG. Sci Adv 2021; 7:7/29/eabg7444. [PMID: 34261657 PMCID: PMC8279504 DOI: 10.1126/sciadv.abg7444] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/01/2021] [Indexed: 05/12/2023]
Abstract
Histone H3K27M is a driving mutation in diffuse intrinsic pontine glioma (DIPG), a deadly pediatric brain tumor. H3K27M reshapes the epigenome through a global inhibition of PRC2 catalytic activity and displacement of H3K27me2/3, promoting oncogenesis of DIPG. As a consequence, a histone modification H3K36me2, antagonistic to H3K27me2/3, is aberrantly elevated. Here, we investigate the role of H3K36me2 in H3K27M-DIPG by tackling its upstream catalyzing enzymes (writers) and downstream binding factors (readers). We determine that NSD1 and NSD2 are the key writers for H3K36me2. Loss of NSD1/2 in H3K27M-DIPG impedes cellular proliferation and tumorigenesis by disrupting tumor-promoting transcriptional programs. Further, we demonstrate that LEDGF and HDGF2 are the main readers mediating the protumorigenic effects downstream of NSD1/2-H3K36me2. Treatment with a chemically modified peptide mimicking endogenous H3K36me2 dislodges LEDGF/HDGF2 from chromatin and specifically inhibits the proliferation of H3K27M-DIPG. Our results indicate a functional pathway of NSD1/2-H3K36me2-LEDGF/HDGF2 as an acquired dependency in H3K27M-DIPG.
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Affiliation(s)
- Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Gary LeRoy
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Devin Bready
- Department of Neurosurgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Joshua D Frenster
- Department of Neurosurgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Ricardo Saldaña-Meyer
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Ying Jin
- Shared Bioinformatics Core Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
- EMBL Rome, Adriano Buzzati-Traverso Campus, Rome, Italy
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
- Department of Neurological Sciences, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Dimitris G Placantonakis
- Department of Neurosurgery, New York University Grossman School of Medicine, New York, NY, USA
- Kimmel Center for Stem Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, New York University Grossman School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
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17
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Fry AL, Webster AK, Burnett J, Chitrakar R, Baugh LR, Hubbard EJA. DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence. PLoS Genet 2021; 17:e1009650. [PMID: 34288923 PMCID: PMC8294487 DOI: 10.1371/journal.pgen.1009650] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Quiescence, an actively-maintained reversible state of cell cycle arrest, is not well understood. PTEN is one of the most frequently lost tumor suppressors in human cancers and regulates quiescence of stem cells and cancer cells. The sole PTEN ortholog in Caenorhabditis elegans is daf-18. In a C. elegans loss-of-function mutant for daf-18, primordial germ cells (PGCs) divide inappropriately in L1 larvae hatched into starvation conditions, in a TOR-dependent manner. Here, we further investigated the role of daf-18 in maintaining PGC quiescence in L1 starvation. We found that maternal or zygotic daf-18 is sufficient to maintain cell cycle quiescence, that daf-18 acts in the germ line and soma, and that daf-18 affects timing of PGC divisions in fed animals. Importantly, our results also implicate daf-18 in repression of germline zygotic gene activation, though not in germline fate specification. However, TOR is less important to germline zygotic gene expression, suggesting that in the absence of food, daf-18/PTEN prevents inappropriate germline zygotic gene activation and cell division by distinct mechanisms.
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Affiliation(s)
- Amanda L. Fry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Amy K. Webster
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Julia Burnett
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Rojin Chitrakar
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - L. Ryan Baugh
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - E. Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
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18
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Grmai L, Harsh S, Lu S, Korman A, Deb IB, Bach EA. Transcriptomic analysis of feminizing somatic stem cells in the Drosophila testis reveals putative downstream effectors of the transcription factor Chinmo. G3 (Bethesda) 2021; 11:jkab067. [PMID: 33751104 PMCID: PMC8759813 DOI: 10.1093/g3journal/jkab067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/24/2021] [Indexed: 11/12/2022]
Abstract
One of the best examples of sexual dimorphism is the development and function of the gonads, ovaries and testes, which produce sex-specific gametes, oocytes, and spermatids, respectively. The development of these specialized germ cells requires sex-matched somatic support cells. The sexual identity of somatic gonadal cells is specified during development and must be actively maintained during adulthood. We previously showed that the transcription factor Chinmo is required to ensure the male sexual identity of somatic support cells in the Drosophila melanogaster testis. Loss of chinmo from male somatic gonadal cells results in feminization: they transform from squamous to epithelial-like cells that resemble somatic cells in the female gonad but fail to properly ensheath the male germline, causing infertility. To identify potential target genes of Chinmo, we purified somatic cells deficient for chinmo from the adult Drosophila testis and performed next-generation sequencing to compare their transcriptome to that of control somatic cells. Bioinformatics revealed 304 and 1549 differentially upregulated and downregulated genes, respectively, upon loss of chinmo in early somatic cells. Using a combination of methods, we validated several differentially expressed genes. These data sets will be useful resources to the community.
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Affiliation(s)
- Lydia Grmai
- Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY
| | - Sneh Harsh
- Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY
| | - Sean Lu
- Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY
| | - Aryeh Korman
- Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY
| | - Ishan B Deb
- Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY
| | - Erika A Bach
- Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY
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19
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Ding X, Fragoza R, Singh P, Zhang S, Yu H, Schimenti JC. Variants in RABL2A causing male infertility and ciliopathy. Hum Mol Genet 2020; 29:3402-3411. [PMID: 33075816 PMCID: PMC7749704 DOI: 10.1093/hmg/ddaa230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
Approximately 7% of men worldwide suffer from infertility, with sperm abnormalities being the most common defect. Though genetic causes are thought to underlie a substantial fraction of idiopathic cases, the actual molecular bases are usually undetermined. Because the consequences of most genetic variants in populations are unknown, this complicates genetic diagnosis even after genome sequencing of patients. Some patients with ciliopathies, including primary ciliary dyskinesia and Bardet-Biedl syndrome, also suffer from infertility because cilia and sperm flagella share several characteristics. Here, we identified two deleterious alleles of RABL2A, a gene essential for normal function of cilia and flagella. Our in silico predictions and in vitro assays suggest that both alleles destabilize the protein. We constructed and analyzed mice homozygous for these two single-nucleotide polymorphisms, Rabl2L119F (rs80006029) and Rabl2V158F (rs200121688), and found that they exhibit ciliopathy-associated disorders including male infertility, early growth retardation, excessive weight gain in adulthood, heterotaxia, pre-axial polydactyly, neural tube defects and hydrocephalus. Our study provides a paradigm for triaging candidate infertility variants in the population for in vivo functional validation, using computational, in vitro and in vivo approaches.
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Affiliation(s)
- Xinbao Ding
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Robert Fragoza
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Priti Singh
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Shu Zhang
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Haiyuan Yu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - John C Schimenti
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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20
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Abstract
Neuronal replacement therapies rely on the in vitro differentiation of specific cell types from embryonic or induced pluripotent stem cells, or on the direct reprogramming of differentiated adult cells via the expression of transcription factors or signaling molecules. The factors used to induce differentiation or reprogramming are often identified by informed guesses based on differential gene expression or known roles for these factors during development. Moreover, differentiation protocols usually result in partly differentiated cells or the production of a mix of cell types. In this Hypothesis article, we suggest that, to overcome these inefficiencies and improve neuronal differentiation protocols, we need to take into account the developmental history of the desired cell types. Specifically, we present a strategy that uses single-cell sequencing techniques combined with machine learning as a principled method to select a sequence of programming factors that are important not only in adult neurons but also during differentiation.
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Affiliation(s)
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA
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21
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Fu DJ, De Micheli AJ, Bidarimath M, Ellenson LH, Cosgrove BD, Flesken-Nikitin A, Nikitin AY. Cells expressing PAX8 are the main source of homeostatic regeneration of adult mouse endometrial epithelium and give rise to serous endometrial carcinoma. Dis Model Mech 2020; 13:dmm047035. [PMID: 32998907 PMCID: PMC7648606 DOI: 10.1242/dmm.047035] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/15/2020] [Indexed: 01/04/2023] Open
Abstract
Humans and mice have cyclical regeneration of the endometrial epithelium. It is expected that such regeneration is ensured by tissue stem cells, but their location and hierarchy remain debatable. A number of recent studies have suggested the presence of stem cells in the mouse endometrial epithelium. At the same time, it has been reported that this tissue can be regenerated by stem cells of stromal/mesenchymal or bone marrow cell origin. Here, we describe a single-cell transcriptomic atlas of the main cell types of the mouse uterus and epithelial subset transcriptome and evaluate the contribution of epithelial cells expressing the transcription factor PAX8 to the homeostatic regeneration and malignant transformation of adult endometrial epithelium. According to lineage tracing, PAX8+ epithelial cells are responsible for long-term maintenance of both luminal and glandular epithelium. Furthermore, multicolor tracing shows that individual glands and contiguous areas of luminal epithelium are formed by clonal cell expansion. Inactivation of the tumor suppressor genes Trp53 and Rb1 in PAX8+ cells, but not in FOXJ1+ cells, leads to the formation of neoplasms with features of serous endometrial carcinoma, one of the most aggressive types of human endometrial malignancies. Taken together, our results show that the progeny of single PAX8+ cells represents the main source of regeneration of the adult endometrial epithelium. They also provide direct experimental genetic evidence for the key roles of the P53 and RB pathways in the pathogenesis of serous endometrial carcinoma and suggest that PAX8+ cells represent the cell of origin of this neoplasm.
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MESH Headings
- Aging
- Animals
- Cell Proliferation
- Disease Models, Animal
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/pathology
- Endometrium/pathology
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Epithelium/metabolism
- Epithelium/pathology
- Female
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/metabolism
- Gene Expression Profiling
- Homeostasis
- Immunophenotyping
- Integrases/metabolism
- Mice, Transgenic
- Neoplasms, Cystic, Mucinous, and Serous/genetics
- Neoplasms, Cystic, Mucinous, and Serous/pathology
- PAX8 Transcription Factor/genetics
- PAX8 Transcription Factor/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Regeneration
- Uterus/metabolism
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Affiliation(s)
- Dah-Jiun Fu
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Andrea J De Micheli
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
- Cornell Stem Cell Program, Cornell University, Ithaca, NY 14853, USA
| | - Mallikarjun Bidarimath
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Lora H Ellenson
- Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin D Cosgrove
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
- Cornell Stem Cell Program, Cornell University, Ithaca, NY 14853, USA
| | - Andrea Flesken-Nikitin
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Alexander Yu Nikitin
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
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22
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Abstract
Translation control is critical to regulate protein expression. By directly adjusting protein levels, cells can quickly respond to dynamic transitions during stem cell differentiation and embryonic development. Ribosomes are multisubunit cellular assemblies that mediate translation. Previously seen as invariant machines with the same composition of components in all conditions, recent studies indicate that ribosomes are heterogeneous and that different ribosome types can preferentially translate specific subsets of mRNAs. Such heterogeneity and specialized translation functions are very important in stem cells and development, as they allow cells to quickly respond to stimuli through direct changes of protein abundance. In this review, we discuss ribosome heterogeneity that arises from multiple features of rRNAs, including rRNA variants and rRNA modifications, and ribosomal proteins, including their stoichiometry, compositions, paralogues, and posttranslational modifications. We also discuss alterations of ribosome-associated proteins (RAPs), with a particular focus on their consequent specialized translational control in stem cells and development.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY
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23
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Stefani RM, Barbosa S, Tan AR, Setti S, Stoker AM, Ateshian GA, Cadossi R, Vunjak-Novakovic G, Aaron RK, Cook JL, Bulinski JC, Hung CT. Pulsed electromagnetic fields promote repair of focal articular cartilage defects with engineered osteochondral constructs. Biotechnol Bioeng 2020; 117:1584-1596. [PMID: 31985051 PMCID: PMC8845061 DOI: 10.1002/bit.27287] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 09/18/2019] [Revised: 12/14/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022]
Abstract
Articular cartilage injuries are a common source of joint pain and dysfunction. We hypothesized that pulsed electromagnetic fields (PEMFs) would improve growth and healing of tissue-engineered cartilage grafts in a direction-dependent manner. PEMF stimulation of engineered cartilage constructs was first evaluated in vitro using passaged adult canine chondrocytes embedded in an agarose hydrogel scaffold. PEMF coils oriented parallel to the articular surface induced superior repair stiffness compared to both perpendicular PEMF (p = .026) and control (p = .012). This was correlated with increased glycosaminoglycan deposition in both parallel and perpendicular PEMF orientations compared to control (p = .010 and .028, respectively). Following in vitro optimization, the potential clinical translation of PEMF was evaluated in a preliminary in vivo preclinical adult canine model. Engineered osteochondral constructs (∅ 6 mm × 6 mm thick, devitalized bone base) were cultured to maturity and implanted into focal defects created in the stifle (knee) joint. To assess expedited early repair, animals were assessed after a 3-month recovery period, with microfracture repairs serving as an additional clinical control. In vivo, PEMF led to a greater likelihood of normal chondrocyte (odds ratio [OR]: 2.5, p = .051) and proteoglycan (OR: 5.0, p = .013) histological scores in engineered constructs. Interestingly, engineered constructs outperformed microfracture in clinical scoring, regardless of PEMF treatment (p < .05). Overall, the studies provided evidence that PEMF stimulation enhanced engineered cartilage growth and repair, demonstrating a potential low-cost, low-risk, noninvasive treatment modality for expediting early cartilage repair.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Clark T. Hung
- Columbia University, New York, NY
- Clark T. Hung, 351 Engineering Terrace Building, Mail Code 8904, 1210 Amsterdam Avenue, New York, NY 10027, Tel: (212) 854-6542, Fax: (212) 854-8725,
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24
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Willett RT, Bayin NS, Lee AS, Krishnamurthy A, Wojcinski A, Lao Z, Stephen D, Rosello-Diez A, Dauber-Decker KL, Orvis GD, Wu Z, Tessier-Lavigne M, Joyner AL. Cerebellar nuclei excitatory neurons regulate developmental scaling of presynaptic Purkinje cell number and organ growth. eLife 2019; 8:e50617. [PMID: 31742552 PMCID: PMC6890462 DOI: 10.7554/elife.50617] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 07/27/2019] [Accepted: 11/18/2019] [Indexed: 01/17/2023] Open
Abstract
For neural systems to function effectively, the numbers of each cell type must be proportioned properly during development. We found that conditional knockout of the mouse homeobox genes En1 and En2 in the excitatory cerebellar nuclei neurons (eCN) leads to reduced postnatal growth of the cerebellar cortex. A subset of medial and intermediate eCN are lost in the mutants, with an associated cell non-autonomous loss of their presynaptic partner Purkinje cells by birth leading to proportional scaling down of neuron production in the postnatal cerebellar cortex. Genetic killing of embryonic eCN throughout the cerebellum also leads to loss of Purkinje cells and reduced postnatal growth but throughout the cerebellar cortex. Thus, the eCN play a key role in scaling the size of the cerebellum by influencing the survival of their Purkinje cell partners, which in turn regulate production of granule cells and interneurons via the amount of sonic hedgehog secreted.
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Affiliation(s)
- Ryan T Willett
- Developmental Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | - N Sumru Bayin
- Developmental Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | - Andrew S Lee
- Developmental Biology ProgramSloan Kettering InstituteNew YorkUnited States
- Neuroscience ProgramWeill Cornell Graduate School of Medical SciencesNew YorkUnited States
| | - Anjana Krishnamurthy
- Developmental Biology ProgramSloan Kettering InstituteNew YorkUnited States
- Neuroscience ProgramWeill Cornell Graduate School of Medical SciencesNew YorkUnited States
| | | | - Zhimin Lao
- Developmental Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | - Daniel Stephen
- Developmental Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | | | | | - Grant D Orvis
- Developmental Biology ProgramSloan Kettering InstituteNew YorkUnited States
| | - Zhuhao Wu
- The Laboratory of Brain Development and RepairThe Rockefeller UniversityNew YorkUnited States
| | - Marc Tessier-Lavigne
- The Laboratory of Brain Development and RepairThe Rockefeller UniversityNew YorkUnited States
| | - Alexandra L Joyner
- Developmental Biology ProgramSloan Kettering InstituteNew YorkUnited States
- Neuroscience ProgramWeill Cornell Graduate School of Medical SciencesNew YorkUnited States
- Biochemistry, Cell and Molecular Biology ProgramWeill Cornell Graduate School of Medical SciencesNew YorkUnited States
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25
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Singh P, Patel RK, Palmer N, Grenier JK, Paduch D, Kaldis P, Grimson A, Schimenti JC. CDK2 kinase activity is a regulator of male germ cell fate. Development 2019; 146:dev180273. [PMID: 31582414 PMCID: PMC6857589 DOI: 10.1242/dev.180273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/21/2019] [Indexed: 12/27/2022]
Abstract
The ability of men to remain fertile throughout their lives depends upon establishment of a spermatogonial stem cell (SSC) pool from gonocyte progenitors, and thereafter balancing SSC renewal versus terminal differentiation. Here, we report that precise regulation of the cell cycle is crucial for this balance. Whereas cyclin-dependent kinase 2 (Cdk2) is not necessary for mouse viability or gametogenesis stages prior to meiotic prophase I, mice bearing a deregulated allele (Cdk2Y15S ) are severely deficient in spermatogonial differentiation. This allele disrupts an inhibitory phosphorylation site (Tyr15) for the kinase WEE1. Remarkably, Cdk2Y15S/Y15S mice possess abnormal clusters of mitotically active SSC-like cells, but these are eventually removed by apoptosis after failing to differentiate properly. Analyses of lineage markers, germ cell proliferation over time, and single cell RNA-seq data revealed delayed and defective differentiation of gonocytes into SSCs. Biochemical and genetic data demonstrated that Cdk2Y15S is a gain-of-function allele causing elevated kinase activity, which underlies these differentiation defects. Our results demonstrate that precise regulation of CDK2 kinase activity in male germ cell development is crucial for the gonocyte-to-spermatogonia transition and long-term spermatogenic homeostasis.
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Affiliation(s)
- Priti Singh
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - Ravi K Patel
- Cornell University, Department of Molecular Biology and Genetics, Ithaca, NY 14853, USA
| | - Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Singapore 138673
- Department of Biochemistry, National University of Singapore, Singapore 117599, Republic of Singapore
| | - Jennifer K Grenier
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - Darius Paduch
- Cornell University, Weill Cornell Medicine, Department of Urology, New York, NY 10065, USA
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Singapore 138673
- Department of Biochemistry, National University of Singapore, Singapore 117599, Republic of Singapore
| | - Andrew Grimson
- Cornell University, Department of Molecular Biology and Genetics, Ithaca, NY 14853, USA
| | - John C Schimenti
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
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26
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Li KN, Jain P, He CH, Eun FC, Kang S, Tumbar T. Skin vasculature and hair follicle cross-talking associated with stem cell activation and tissue homeostasis. eLife 2019; 8:e45977. [PMID: 31343406 PMCID: PMC6684267 DOI: 10.7554/elife.45977] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/25/2019] [Indexed: 12/21/2022] Open
Abstract
Skin vasculature cross-talking with hair follicle stem cells (HFSCs) is poorly understood. Skin vasculature undergoes dramatic remodeling during adult mouse hair cycle. Specifically, a horizontal plexus under the secondary hair germ (HPuHG) transiently neighbors the HFSC activation zone during the quiescence phase (telogen). Increased density of HPuHG can be induced by reciprocal mutations in the epithelium (Runx1) and endothelium (Alk1) in adult mice, and is accompanied by prolonged HFSC quiescence and by delayed entry and progression into the hair growth phase (anagen). Suggestively, skin vasculature produces BMP4, a well-established HFSC quiescence-inducing factor, thus contributing to a proliferation-inhibitory environment near the HFSC. Conversely, the HFSC activator Runx1 regulates secreted proteins with previously demonstrated roles in vasculature remodeling. We suggest a working model in which coordinated remodeling and molecular cross-talking of the adult epithelial and endothelial skin compartments modulate timing of HFSC activation from quiescence for proper tissue homeostasis of adult skin.
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Affiliation(s)
- Kefei Nina Li
- Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Prachi Jain
- Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Catherine Hua He
- Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Flora Chae Eun
- Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Sangjo Kang
- Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Tudorita Tumbar
- Molecular Biology and GeneticsCornell UniversityIthacaUnited States
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27
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Singh K, Lin J, Zhong Y, Burčul A, Mohan P, Jiang M, Sun L, Yong-Gonzalez V, Viale A, Cross JR, Hendrickson RC, Rätsch G, Ouyang Z, Wendel HG. c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma. J Exp Med 2019; 216:1509-1524. [PMID: 31142587 PMCID: PMC6605752 DOI: 10.1084/jem.20181726] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 09/10/2018] [Revised: 02/22/2019] [Accepted: 04/19/2019] [Indexed: 12/24/2022] Open
Abstract
The oncogenic c-MYC (MYC) transcription factor has broad effects on gene expression and cell behavior. We show that MYC alters the efficiency and quality of mRNA translation into functional proteins. Specifically, MYC drives the translation of most protein components of the electron transport chain in lymphoma cells, and many of these effects are independent from proliferation. Specific interactions of MYC-sensitive RNA-binding proteins (e.g., SRSF1/RBM42) with 5'UTR sequence motifs mediate many of these changes. Moreover, we observe a striking shift in translation initiation site usage. For example, in low-MYC conditions, lymphoma cells initiate translation of the CD19 mRNA from a site in exon 5. This results in the truncation of all extracellular CD19 domains and facilitates escape from CD19-directed CAR-T cell therapy. Together, our findings reveal MYC effects on the translation of key metabolic enzymes and immune receptors in lymphoma cells.
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Affiliation(s)
- Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT
| | - Yi Zhong
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Antonija Burčul
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liping Sun
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vladimir Yong-Gonzalez
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronald C Hendrickson
- Proteomics and Microchemistry, Memorial Sloan- Kettering Cancer Center, New York, NY
| | - Gunnar Rätsch
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology, Zürich, Switzerland
| | - Zhengqing Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Genetics and Genome Sciences and Institute for System Genomics, University of Connecticut Health Center, Farmington, CT
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
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28
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Abstract
The JAK/STAT pathway is a conserved metazoan signaling system that transduces cues from extracellular cytokines into transcriptional changes in the nucleus. JAK/STAT signaling is best known for its roles in immunity. However, recent work has demonstrated that it also regulates critical homeostatic processes in germline and somatic stem cells, as well as regenerative processes in several tissues, including the gonad, intestine and appendages. Here, we provide an overview of JAK/STAT signaling in stem cells and regeneration, focusing on Drosophila and highlighting JAK/STAT pathway functions in proliferation, survival and cell competition that are conserved between Drosophila and vertebrates.
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Affiliation(s)
- Salvador C Herrera
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Erika A Bach
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Helen L. and Martin S. Kimmel Center for Stem Cell Biology, New York University School of Medicine, New York, NY 10016, USA
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29
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Mitchell K, Barreyro L, Todorova TI, Taylor SJ, Antony-Debré I, Narayanagari SR, Carvajal LA, Leite J, Piperdi Z, Pendurti G, Mantzaris I, Paietta E, Verma A, Gritsman K, Steidl U. IL1RAP potentiates multiple oncogenic signaling pathways in AML. J Exp Med 2018; 215:1709-1727. [PMID: 29773641 PMCID: PMC5987926 DOI: 10.1084/jem.20180147] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 04/09/2018] [Indexed: 01/02/2023] Open
Abstract
The surface molecule interleukin-1 receptor accessory protein (IL1RAP) is consistently overexpressed across multiple genetic subtypes of acute myeloid leukemia (AML) and other myeloid malignancies, including at the stem cell level, and is emerging as a novel therapeutic target. However, the cell-intrinsic functions of IL1RAP in AML cells are largely unknown. Here, we show that targeting of IL1RAP via RNA interference, genetic deletion, or antibodies inhibits AML pathogenesis in vitro and in vivo, without perturbing healthy hematopoietic function or viability. Furthermore, we found that the role of IL1RAP is not restricted to the IL-1 receptor pathway, but that IL1RAP physically interacts with and mediates signaling and pro-proliferative effects through FLT3 and c-KIT, two receptor tyrosine kinases with known key roles in AML pathogenesis. Our study provides a new mechanistic basis for the efficacy of IL1RAP targeting in AML and reveals a novel role for this protein in the pathogenesis of the disease.
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Affiliation(s)
- Kelly Mitchell
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Laura Barreyro
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
| | | | - Samuel J Taylor
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Luis A Carvajal
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Joana Leite
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Zubair Piperdi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Gopichand Pendurti
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
| | - Ioannis Mantzaris
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
| | - Elisabeth Paietta
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
- Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY
| | - Amit Verma
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
- Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY
- Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY
| | - Kira Gritsman
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
- Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY
- Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, Bronx, NY
- Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY
- Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY
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30
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Zhou P, Resendez SL, Rodriguez-Romaguera J, Jimenez JC, Neufeld SQ, Giovannucci A, Friedrich J, Pnevmatikakis EA, Stuber GD, Hen R, Kheirbek MA, Sabatini BL, Kass RE, Paninski L. Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data. eLife 2018; 7:e28728. [PMID: 29469809 PMCID: PMC5871355 DOI: 10.7554/elife.28728] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 02/20/2018] [Indexed: 12/12/2022] Open
Abstract
In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to extract single-neuronal activity from microendoscopic data, because of the very large background fluctuations and high spatial overlaps intrinsic to this recording modality. Here, we describe a new constrained matrix factorization approach to accurately separate the background and then demix and denoise the neuronal signals of interest. We compared the proposed method against previous independent components analysis and constrained nonnegative matrix factorization approaches. On both simulated and experimental data recorded from mice, our method substantially improved the quality of extracted cellular signals and detected more well-isolated neural signals, especially in noisy data regimes. These advances can in turn significantly enhance the statistical power of downstream analyses, and ultimately improve scientific conclusions derived from microendoscopic data.
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Affiliation(s)
- Pengcheng Zhou
- Center for the Neural Basis of CognitionCarnegie Mellon UniversityPittsburghUnited States
- Department of StatisticsColumbia UniversityNew YorkUnited States
- Machine Learning DepartmentCarnegie Mellon UniversityPittsburghUnited States
- Grossman Center for the Statistics of MindColumbia UniversityNew YorkUnited States
- Center for Theoretical NeuroscienceColumbia UniversityNew YorkUnited States
| | - Shanna L Resendez
- Department of PsychiatryUniversity of North Carolina at Chapel HillChapel HillUnited States
| | | | - Jessica C Jimenez
- Department of NeuroscienceColumbia UniversityNew YorkUnited States
- Division of Integrative Neuroscience, Department of PsychiatryNew York State Psychiatric InstituteNew YorkUnited States
- Department of Psychiatry & PharmacologyColumbia UniversityNew YorkUnited States
| | - Shay Q Neufeld
- Department of NeurobiologyHarvard Medical School, Howard Hughes Medical InstituteBostonUnited States
| | - Andrea Giovannucci
- Center for Computational BiologyFlatiron Institute, Simons FoundationNew YorkUnited States
| | - Johannes Friedrich
- Center for Computational BiologyFlatiron Institute, Simons FoundationNew YorkUnited States
| | | | - Garret D Stuber
- Department of PsychiatryUniversity of North Carolina at Chapel HillChapel HillUnited States
- Department of Cell Biology and PhysiologyUniversity of North Carolina at Chapel HillChapel HillUnited States
- Neuroscience CenterUniversity of North Carolina at Chapel HillChapel HillUnited States
| | - Rene Hen
- Department of NeuroscienceColumbia UniversityNew YorkUnited States
- Division of Integrative Neuroscience, Department of PsychiatryNew York State Psychiatric InstituteNew YorkUnited States
- Department of Psychiatry & PharmacologyColumbia UniversityNew YorkUnited States
| | - Mazen A Kheirbek
- Weill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoUnited States
- Neuroscience Graduate ProgramUniversity of CaliforniaSan FranciscoUnited States
- Kavli Institute for Fundamental NeuroscienceUniversity of California, San FranciscoSan FranciscoUnited States
- Department of PsychiatryUniversity of California, San FranciscoSan FranciscoUnited States
| | - Bernardo L Sabatini
- Department of NeurobiologyHarvard Medical School, Howard Hughes Medical InstituteBostonUnited States
| | - Robert E Kass
- Center for the Neural Basis of CognitionCarnegie Mellon UniversityPittsburghUnited States
- Machine Learning DepartmentCarnegie Mellon UniversityPittsburghUnited States
- Department of StatisticsCarnegie Mellon UniversityPittsburghUnited States
| | - Liam Paninski
- Department of StatisticsColumbia UniversityNew YorkUnited States
- Grossman Center for the Statistics of MindColumbia UniversityNew YorkUnited States
- Center for Theoretical NeuroscienceColumbia UniversityNew YorkUnited States
- Department of NeuroscienceColumbia UniversityNew YorkUnited States
- Kavli Institute for Brain ScienceColumbia UniversityNew YorkUnited States
- Neurotechnology CenterColumbia UniversityNew YorkUnited States
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31
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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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Barykina NV, Subach OM, Piatkevich KD, Jung EE, Malyshev AY, Smirnov IV, Bogorodskiy AO, Borshchevskiy VI, Varizhuk AM, Pozmogova GE, Boyden ES, Anokhin KV, Enikolopov GN, Subach FV. Green fluorescent genetically encoded calcium indicator based on calmodulin/M13-peptide from fungi. PLoS One 2017; 12:e0183757. [PMID: 28837632 PMCID: PMC5570312 DOI: 10.1371/journal.pone.0183757] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 05/10/2017] [Accepted: 08/10/2017] [Indexed: 11/19/2022] Open
Abstract
Currently available genetically encoded calcium indicators (GECIs) utilize calmodulins (CaMs) or troponin C from metazoa such as mammals, birds, and teleosts, as calcium-binding domains. The amino acid sequences of the metazoan calcium-binding domains are highly conserved, which may limit the range of the GECI key parameters and cause undesired interactions with the intracellular environment in mammalian cells. Here we have used fungi, evolutionary distinct organisms, to derive CaM and its binding partner domains and design new GECI with improved properties. We applied iterative rounds of molecular evolution to develop FGCaMP, a novel green calcium indicator. It includes the circularly permuted version of the enhanced green fluorescent protein (EGFP) sandwiched between the fungal CaM and a fragment of CaM-dependent kinase. FGCaMP is an excitation-ratiometric indicator that has a positive and an inverted fluorescence response to calcium ions when excited at 488 and 405 nm, respectively. Compared with the GCaMP6s indicator in vitro, FGCaMP has a similar brightness at 488 nm excitation, 7-fold higher brightness at 405 nm excitation, and 1.3-fold faster calcium ion dissociation kinetics. Using site-directed mutagenesis, we generated variants of FGCaMP with improved binding affinity to calcium ions and increased the magnitude of FGCaMP fluorescence response to low calcium ion concentrations. Using FGCaMP, we have successfully visualized calcium transients in cultured mammalian cells. In contrast to the limited mobility of GCaMP6s and G-GECO1.2 indicators, FGCaMP exhibits practically 100% molecular mobility at physiological concentrations of calcium ion in mammalian cells, as determined by photobleaching experiments with fluorescence recovery. We have successfully monitored the calcium dynamics during spontaneous activity of neuronal cultures using FGCaMP and utilized whole-cell patch clamp recordings to further characterize its behavior in neurons. Finally, we used FGCaMP in vivo to perform structural and functional imaging of zebrafish using wide-field, confocal, and light-sheet microscopy.
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Affiliation(s)
- Natalia V. Barykina
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- P.K. Anokhin Institute of Normal Physiology of RAMS, Moscow, Russia
| | - Oksana M. Subach
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Kiryl D. Piatkevich
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Erica E. Jung
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Aleksey Y. Malyshev
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia
| | - Ivan V. Smirnov
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia
- Medico-Biological Faculty, N.I. Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | - Anna M. Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
| | - Galina E. Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Edward S. Boyden
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, United States of America
| | - Konstantin V. Anokhin
- P.K. Anokhin Institute of Normal Physiology of RAMS, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Grigori N. Enikolopov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Department of Anesthesiology, Stony Brook University Medical Center, Stony Brook, NY, United States of America
- Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, United States of America
| | - Fedor V. Subach
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
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