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Visvanathan A, Saulnier O, Chen C, Haldipur P, Orisme W, Delaidelli A, Shin S, Millman J, Bryant A, Abeysundara N, Wu X, Hendrikse LD, Patil V, Bashardanesh Z, Golser J, Livingston BG, Nakashima T, Funakoshi Y, Ong W, Rasnitsyn A, Aldinger KA, Richman CM, Van Ommeren R, Lee JJY, Ly M, Vladoiu MC, Kharas K, Balin P, Erickson AW, Fong V, Zhang J, Suárez RA, Wang H, Huang N, Pallota JG, Douglas T, Haapasalo J, Razavi F, Silvestri E, Sirbu O, Worme S, Kameda-Smith MM, Wu X, Daniels C, MichaelRaj AK, Bhaduri A, Schramek D, Suzuki H, Garzia L, Ahmed N, Kleinman CL, Stein LD, Dirks P, Dunham C, Jabado N, Rich JN, Li W, Sorensen PH, Wechsler-Reya RJ, Weiss WA, Millen KJ, Ellison DW, Dimitrov DS, Taylor MD. Early rhombic lip Protogenin +ve stem cells in a human-specific neurovascular niche initiate and maintain group 3 medulloblastoma. Cell 2024:S0092-8674(24)00651-2. [PMID: 38971152 DOI: 10.1016/j.cell.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 03/28/2024] [Accepted: 06/09/2024] [Indexed: 07/08/2024]
Abstract
We identify a population of Protogenin-positive (PRTG+ve) MYChigh NESTINlow stem cells in the four-week-old human embryonic hindbrain that subsequently localizes to the ventricular zone of the rhombic lip (RLVZ). Oncogenic transformation of early Prtg+ve rhombic lip stem cells initiates group 3 medulloblastoma (Gr3-MB)-like tumors. PRTG+ve stem cells grow adjacent to a human-specific interposed vascular plexus in the RLVZ, a phenotype that is recapitulated in Gr3-MB but not in other types of medulloblastoma. Co-culture of Gr3-MB with endothelial cells promotes tumor stem cell growth, with the endothelial cells adopting an immature phenotype. Targeting the PRTGhigh compartment of Gr3-MB in vivo using either the diphtheria toxin system or chimeric antigen receptor T cells constitutes effective therapy. Human Gr3-MBs likely arise from early embryonic RLVZ PRTG+ve stem cells inhabiting a specific perivascular niche. Targeting the PRTGhigh compartment and/or the perivascular niche represents an approach to treat children with Gr3-MB.
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Affiliation(s)
- Abhirami Visvanathan
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Genomics and Development of Childhood Cancers, Institut Curie, PSL University, 75005 Paris, France; INSERM U830, Cancer Heterogeneity Instability and Plasticity, Institut Curie, PSL University, 75005 Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, 75005 Paris, France
| | - Chuan Chen
- Center for Antibody Therapeutics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Wilda Orisme
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Seungmin Shin
- Center for Antibody Therapeutics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jake Millman
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Andrew Bryant
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Namal Abeysundara
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Xujia Wu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Liam D Hendrikse
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Vikas Patil
- MacFeeters-Hamilton Center for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Joseph Golser
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Bryn G Livingston
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Takuma Nakashima
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Yusuke Funakoshi
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Winnie Ong
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Alexandra Rasnitsyn
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Kimberly A Aldinger
- Departments of Pediatrics and Neurology. University of Washington, Seattle, WA, USA
| | - Cory M Richman
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Randy Van Ommeren
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - John J Y Lee
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Michelle Ly
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Maria C Vladoiu
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Kaitlin Kharas
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Polina Balin
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Anders W Erickson
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Vernon Fong
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jiao Zhang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Texas Children's Cancer and Hematology Center, Houston, TX, USA; Department of Pediatrics - Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Raúl A Suárez
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Hao Wang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ning Huang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jonelle G Pallota
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Tajana Douglas
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Joonas Haapasalo
- Department of Neurosurgery, Tampere University Hospital, Tampere, Finland
| | - Ferechte Razavi
- Assistance Publique Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Paris, France
| | - Evelina Silvestri
- Surgical Pathology Unit, San Camillo Forlanini Hospital, Rome, Italy
| | - Olga Sirbu
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Samantha Worme
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Michelle M Kameda-Smith
- Texas Children's Cancer and Hematology Center, Houston, TX, USA; Department of Pediatrics - Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Xiaochong Wu
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Texas Children's Cancer and Hematology Center, Houston, TX, USA; Department of Pediatrics - Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Craig Daniels
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Texas Children's Cancer and Hematology Center, Houston, TX, USA; Department of Pediatrics - Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Antony K MichaelRaj
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Livia Garzia
- Cancer Research Program, McGill University Health Centre Research Institute, Montreal, QC, Canada
| | - Nabil Ahmed
- Centre for Cell and Gene Therapy, Texas Children's Hospital, Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC, Canada; Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Lincoln D Stein
- Adaptive Oncology, Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter Dirks
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Nada Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada; The Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Jeremy N Rich
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Wei Li
- Center for Antibody Therapeutics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - William A Weiss
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Texas Children's Cancer and Hematology Center, Houston, TX, USA; Department of Pediatrics - Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA; Department of Neurosurgery, Texas Children's Hospital, Houston, TX, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Surgery, University of Toronto, Toronto, ON, Canada.
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2
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Kim H, Bedsaul-Fryer JR, Schulze KJ, Sincerbeaux G, Baker S, Rebholz CM, Wu LSF, Gogain J, Cuddeback L, Yager JD, De Luca LM, Siddiqua TJ, West KP. An Early Gestation Plasma Inflammasome in Rural Bangladeshi Women. Biomolecules 2024; 14:736. [PMID: 39062451 PMCID: PMC11274825 DOI: 10.3390/biom14070736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Circulating α1-acid glycoprotein (AGP) and C-reactive protein (CRP) are commonly measured to assess inflammation, but these biomarkers fail to reveal the complex molecular biology of inflammation. We mined the maternal plasma proteome to detect proteins that covary with AGP and CRP. In 435 gravida predominantly in <12-week gestation, we correlated the relative quantification of plasma proteins assessed via a multiplexed aptamer assay (SOMAScan®) with AGP and CRP, quantified by immunoassay. We defined a plasma inflammasome as protein correlates meeting a false discovery rate <0.05. We examined potential pathways using principal component analysis. A total of 147 and 879 of 6431 detected plasma proteins correlated with AGP and CRP, respectively, of which 61 overlapped with both biomarkers. Positive correlates included serum amyloid, complement, interferon-induced, and immunoregulatory proteins. Negative correlates were micronutrient and lipid transporters and pregnancy-related anabolic proteins. The principal components (PCs) of AGP were dominated by negatively correlated anabolic proteins associated with gestational homeostasis, angiogenesis, and neurogenesis. The PCs of CRP were more diverse in function, reflecting cell surface and adhesion, embryogenic, and intracellular and extra-hepatic tissue leakage proteins. The plasma proteome of AGP or CRP reveals wide proteomic variation associated with early gestational inflammation, suggesting mechanisms and pathways that merit future research.
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Affiliation(s)
- Hyunju Kim
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98105, USA
| | - Jacquelyn R. Bedsaul-Fryer
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
- Department of International Health (Human Nutrition), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kerry J. Schulze
- Department of International Health (Human Nutrition), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Gwen Sincerbeaux
- Department of Nutritional Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah Baker
- Department of International Health (Human Nutrition), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Casey M. Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Lee SF Wu
- Department of International Health (Human Nutrition), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | | | - James D. Yager
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Luigi M. De Luca
- Department of International Health (Human Nutrition), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Keith P. West
- Department of International Health (Human Nutrition), Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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3
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Sahota VK, Stone A, Woodling NS, Spiers JG, Steinert JR, Partridge L, Augustin H. Plum modulates Myoglianin and regulates synaptic function in D. melanogaster. Open Biol 2023; 13:230171. [PMID: 37699519 PMCID: PMC10497343 DOI: 10.1098/rsob.230171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Alterations in the neuromuscular system underlie several neuromuscular diseases and play critical roles in the development of sarcopenia, the age-related loss of muscle mass and function. Mammalian Myostatin (MST) and GDF11, members of the TGF-β superfamily of growth factors, are powerful regulators of muscle size in both model organisms and humans. Myoglianin (MYO), the Drosophila homologue of MST and GDF11, is a strong inhibitor of synaptic function and structure at the neuromuscular junction in flies. Here, we identified Plum, a transmembrane cell surface protein, as a modulator of MYO function in the larval neuromuscular system. Reduction of Plum in the larval body-wall muscles abolishes the previously demonstrated positive effect of attenuated MYO signalling on both muscle size and neuromuscular junction structure and function. In addition, downregulation of Plum on its own results in decreased synaptic strength and body weight, classifying Plum as a (novel) regulator of neuromuscular function and body (muscle) size. These findings offer new insights into possible regulatory mechanisms behind ageing- and disease-related neuromuscular dysfunctions in humans and identify potential targets for therapeutic interventions.
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Affiliation(s)
- Virender K. Sahota
- Department of Biological Sciences, Centre for Biomedical Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Aelfwin Stone
- Faculty of Medicine & Health Sciences, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Nathaniel S. Woodling
- Department of Biological Sciences, Centre for Biomedical Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Jereme G. Spiers
- Faculty of Medicine & Health Sciences, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Joern R. Steinert
- Faculty of Medicine & Health Sciences, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Linda Partridge
- Institute of Healthy Ageing, and GEE, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, Cologne 50931, Germany
| | - Hrvoje Augustin
- Department of Biological Sciences, Centre for Biomedical Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- Institute of Healthy Ageing, and GEE, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, Cologne 50931, Germany
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4
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Nickerson KR, Tom I, Cortés E, Abolafia JR, Özkan E, Gonzalez LC, Jaworski A. WFIKKN2 is a bifunctional axon guidance cue that signals through divergent DCC family receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.544950. [PMID: 37398498 PMCID: PMC10312737 DOI: 10.1101/2023.06.15.544950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Axon pathfinding is controlled by attractive and repulsive molecular cues that activate receptors on the axonal growth cone, but the full repertoire of axon guidance molecules remains unknown. The vertebrate DCC receptor family contains the two closely related members DCC and Neogenin with prominent roles in axon guidance and three additional, divergent members - Punc, Nope, and Protogenin - for which functions in neural circuit formation have remained elusive. We identified a secreted Punc/Nope/Protogenin ligand, WFIKKN2, which guides mouse peripheral sensory axons through Nope-mediated repulsion. In contrast, WFIKKN2 attracts motor axons, but not via Nope. These findings identify WFIKKN2 as a bifunctional axon guidance cue that acts through divergent DCC family members, revealing a remarkable diversity of ligand interactions for this receptor family in nervous system wiring. One-Sentence Summary WFIKKN2 is a ligand for the DCC family receptors Punc, Nope, and Prtg that repels sensory axons and attracts motor axons.
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Chen C, Wang Z, Sun Z, Li W, Dimitrov DS. Development of an efficient method for selection of stable cell pools for protein expression and surface display with Expi293F cells. Cell Biochem Funct 2023; 41:355-364. [PMID: 36864545 DOI: 10.1002/cbf.3787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/18/2023] [Indexed: 03/04/2023]
Abstract
Compare with transient expression, stable cell lines generally have higher productivity and better quality for protein expression. However, selection of stable cell line is time-consuming and laborious. Here we describe an optimized selection method to achieve high-efficient stable cell pools with Expi293F suspension cells. This method only takes 2-3 weeks to generate stable cell pools with 2- to 10-fold higher productivity than transient gene expression (TGE). In fed-batch culture with Yeastolate, >1 g/L yield was achieved with our KTN0239-IgG stable cell pool in shaker flasks. This method can be also applied to efficiently display proteins on the cell surface.
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Affiliation(s)
- Chuan Chen
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, USA
| | - Zening Wang
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Zehua Sun
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, USA.,Abound Bio, Pittsburgh, Pennsylvania, USA
| | - Wei Li
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, USA
| | - Dimiter S Dimitrov
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania, USA.,Abound Bio, Pittsburgh, Pennsylvania, USA
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6
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Gonzalez DM, Schrode N, Ebrahim TAM, Broguiere N, Rossi G, Drakhlis L, Zweigerdt R, Lutolf MP, Beaumont KG, Sebra R, Dubois NC. Dissecting mechanisms of chamber-specific cardiac differentiation and its perturbation following retinoic acid exposure. Development 2022; 149:275658. [DOI: 10.1242/dev.200557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The specification of distinct cardiac lineages occurs before chamber formation and acquisition of bona fide atrial or ventricular identity. However, the mechanisms underlying these early specification events remain poorly understood. Here, we performed single cell analysis at the murine cardiac crescent, primitive heart tube and heart tube stages to uncover the transcriptional mechanisms underlying formation of atrial and ventricular cells. We find that progression towards differentiated cardiomyocytes occurs primarily based on heart field progenitor identity, and that progenitors contribute to ventricular or atrial identity through distinct differentiation mechanisms. We identify new candidate markers that define such differentiation processes and examine their expression dynamics using computational lineage trajectory methods. We further show that exposure to exogenous retinoic acid causes defects in ventricular chamber size, dysregulation in FGF signaling and a shunt in differentiation towards orthogonal lineages. Retinoic acid also causes defects in cell-cycle exit resulting in formation of hypomorphic ventricles. Collectively, our data identify, at a single cell level, distinct lineage trajectories during cardiac specification and differentiation, and the precise effects of manipulating cardiac progenitor patterning via retinoic acid signaling.
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Affiliation(s)
- David M. Gonzalez
- Icahn School of Medicine at Mount Sinai 1 Department of Cell, Developmental, and Regenerative Biology , , New York, NY 10029 , USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai 2 , New York, NY 10029 , USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai 3 , New York, NY 10029 , USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai 4 , New York, NY 10029 , USA
| | - Nadine Schrode
- Icahn School of Medicine at Mount Sinai 5 Department of Genetics and Genomic Sciences , , New York, NY 10029 , USA
| | - Tasneem A. M. Ebrahim
- Icahn School of Medicine at Mount Sinai 1 Department of Cell, Developmental, and Regenerative Biology , , New York, NY 10029 , USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai 2 , New York, NY 10029 , USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai 3 , New York, NY 10029 , USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai 4 , New York, NY 10029 , USA
| | - Nicolas Broguiere
- School of Life Sciences, EPFL 6 Laboratory of Stem Cell Bioengineering , , Lausanne CH-1015 , Switzerland
| | - Giuliana Rossi
- School of Life Sciences, EPFL 6 Laboratory of Stem Cell Bioengineering , , Lausanne CH-1015 , Switzerland
| | - Lika Drakhlis
- Roche Institute for Translational Bioengineering 7 , Roche Pharma Research and Early Development , Basel 4052 , Switzerland
| | - Robert Zweigerdt
- Roche Institute for Translational Bioengineering 7 , Roche Pharma Research and Early Development , Basel 4052 , Switzerland
| | - Matthias P. Lutolf
- School of Life Sciences, EPFL 6 Laboratory of Stem Cell Bioengineering , , Lausanne CH-1015 , Switzerland
- Roche Institute for Translational Bioengineering 7 , Roche Pharma Research and Early Development , Basel 4052 , Switzerland
| | - Kristin G. Beaumont
- Icahn School of Medicine at Mount Sinai 5 Department of Genetics and Genomic Sciences , , New York, NY 10029 , USA
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO) 8 , Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG) , , Hannover , Germany
- REBIRTH–Research Center for Translational Regenerative Medicine, Hannover Medical School 8 , Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG) , , Hannover , Germany
| | - Robert Sebra
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai 3 , New York, NY 10029 , USA
- Icahn School of Medicine at Mount Sinai 5 Department of Genetics and Genomic Sciences , , New York, NY 10029 , USA
- Sema4, a Mount Sinai venture 9 , Stamford, CT 06902 , USA
| | - Nicole C. Dubois
- Icahn School of Medicine at Mount Sinai 1 Department of Cell, Developmental, and Regenerative Biology , , New York, NY 10029 , USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai 2 , New York, NY 10029 , USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai 3 , New York, NY 10029 , USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai 4 , New York, NY 10029 , USA
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7
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Mesgarzadeh JS, Buxbaum JN, Wiseman RL. Stress-responsive regulation of extracellular proteostasis. J Cell Biol 2022; 221:213026. [PMID: 35191945 PMCID: PMC8868021 DOI: 10.1083/jcb.202112104] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 12/18/2022] Open
Abstract
Genetic, environmental, and aging-related insults can promote the misfolding and subsequent aggregation of secreted proteins implicated in the pathogenesis of numerous diseases. This has led to considerable interest in understanding the molecular mechanisms responsible for regulating proteostasis in extracellular environments such as the blood and cerebrospinal fluid (CSF). Extracellular proteostasis is largely dictated by biological pathways comprising chaperones, folding enzymes, and degradation factors localized to the ER and extracellular space. These pathways limit the accumulation of nonnative, potentially aggregation-prone proteins in extracellular environments. Many reviews discuss the molecular mechanisms by which these pathways impact the conformational integrity of the secreted proteome. Here, we instead focus on describing the stress-responsive mechanisms responsible for adapting ER and extracellular proteostasis pathways to protect the secreted proteome from pathologic insults that challenge these environments. Further, we highlight new strategies to identify stress-responsive pathways involved in regulating extracellular proteostasis and describe the pathologic and therapeutic implications for these pathways in human disease.
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Affiliation(s)
| | - Joel N Buxbaum
- Department of Molecular Medicine, Scripps Research, La Jolla, CA
| | - R Luke Wiseman
- Department of Molecular Medicine, Scripps Research, La Jolla, CA
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8
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Finding New Ways How to Control BACE1. J Membr Biol 2022; 255:293-318. [PMID: 35305135 DOI: 10.1007/s00232-022-00225-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/24/2022] [Indexed: 01/18/2023]
Abstract
Recently, all applications of BACE1 inhibitors failed as therapeutical targets for Alzheimer´s disease (AD) due to severe side effects. Therefore, alternative ways for treatment development are a hot research topic. The present analysis investigates BACE1 protein-protein interaction networks and attempts to solve the absence of complete knowledge about pathways involving BACE1. A bioinformatics analysis matched the functions of the non-substrate interaction network with Voltage-gated potassium channels, which also appear as top priority protein nodes. Targeting BACE1 interactions with PS1 and GGA-s, blocking of BACE1 access to APP by BRI3 and RTN-s, activation of Wnt signaling and upregulation of β-catenin, and brain delivery of the extracellular domain of p75NTR, are the main alternatives to the use of BACE 1 inhibitors highlighted by the analysis. The pathway enrichment analysis also emphasized substrates and substrate candidates with essential biological functions, which cleavage must remain controlled. They include ephrin receptors, ROBO1, ROBO2, CNTN-s, CASPR-s, CD147, CypB, TTR, APLP1/APLP2, NRXN-s, and PTPR-s. The analysis of the interaction subnetwork of BACE1 functionally related to inflammation identified a connection to three cardiomyopathies, which supports the hypothesis of the common molecular mechanisms with AD. A lot of potential shows the regulation of BACE1 activity through post-translational modifications. The interaction network of BACE1 and its phosphorylation enzyme CSNK1D functionally match the Circadian clock, p53, and Hedgehog signaling pathways. The regulation of BACE1 glycosylation could be achieved through N-acetylglucosamine transferases, α-(1→6)-fucosyltransferase, β-galactoside α-(2→6)-sialyltransferases, galactosyltransferases, and mannosidases suggested by the interaction network analysis of BACE1-MGAT3. The present analysis proposes possibilities for the alternative control of AD pathology.
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9
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Solovieva T, Lu HC, Moverley A, Plachta N, Stern CD. The embryonic node behaves as an instructive stem cell niche for axial elongation. Proc Natl Acad Sci U S A 2022. [PMID: 35101917 DOI: 10.1101/2020.11.10.376913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
In warm-blooded vertebrate embryos (mammals and birds), the axial tissues of the body form from a growth zone at the tail end, Hensen's node, which generates neural, mesodermal, and endodermal structures along the midline. While most cells only pass through this region, the node has been suggested to contain a small population of resident stem cells. However, it is unknown whether the rest of the node constitutes an instructive niche that specifies this self-renewal behavior. Here, we use heterotopic transplantation of groups and single cells and show that cells not destined to enter the node can become resident and self-renew. Long-term resident cells are restricted to the posterior part of the node and single-cell RNA-sequencing reveals that the majority of these resident cells preferentially express G2/M phase cell-cycle-related genes. These results provide strong evidence that the node functions as a niche to maintain self-renewal of axial progenitors.
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Affiliation(s)
- Tatiana Solovieva
- Department of Cell and Developmental Biology, University College London, WC1E 6BT London, United Kingdom
| | - Hui-Chun Lu
- Department of Cell and Developmental Biology, University College London, WC1E 6BT London, United Kingdom
| | - Adam Moverley
- Department of Cell and Developmental Biology, University College London, WC1E 6BT London, United Kingdom
- Institute of Molecular Cell Biology, A*STAR, 138673 Proteos, Singapore
| | - Nicolas Plachta
- Institute of Molecular Cell Biology, A*STAR, 138673 Proteos, Singapore
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, WC1E 6BT London, United Kingdom;
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10
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Tedesco M, Giannese F, Lazarević D, Giansanti V, Rosano D, Monzani S, Catalano I, Grassi E, Zanella ER, Botrugno OA, Morelli L, Panina Bordignon P, Caravagna G, Bertotti A, Martino G, Aldrighetti L, Pasqualato S, Trusolino L, Cittaro D, Tonon G. Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin. Nat Biotechnol 2022; 40:235-244. [PMID: 34635836 DOI: 10.1038/s41587-021-01031-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/22/2021] [Indexed: 02/08/2023]
Abstract
Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. We engineered a hybrid transposase including the chromodomain (CD) of the heterochromatin protein-1α (HP-1α), which is involved in heterochromatin assembly and maintenance through its binding to trimethylation of the lysine 9 on histone 3 (H3K9me3), and developed a single-cell method, single-cell genome and epigenome by transposases sequencing (scGET-seq), that, unlike single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), comprehensively probes both open and closed chromatin and concomitantly records the underlying genomic sequences. We tested scGET-seq in cancer-derived organoids and human-derived xenograft (PDX) models and identified genetic events and plasticity-driven mechanisms contributing to cancer drug resistance. Next, building upon the differential enrichment of closed and open chromatin, we devised a method, Chromatin Velocity, that identifies the trajectories of epigenetic modifications at the single-cell level. Chromatin Velocity uncovered paths of epigenetic reorganization during stem cell reprogramming and identified key transcription factors driving these developmental processes. scGET-seq reveals the dynamics of genomic and epigenetic landscapes underlying any cellular processes.
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Affiliation(s)
- Martina Tedesco
- Università Vita-Salute San Raffaele, Milano, Italy
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | | | - Dejan Lazarević
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Valentina Giansanti
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milano, Italy
| | - Dalia Rosano
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Silvia Monzani
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IEO, IRCCS European Institute of Oncology, Milano, Italy
| | - Irene Catalano
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Elena Grassi
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | | | - Oronza A Botrugno
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Leonardo Morelli
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Paola Panina Bordignon
- Università Vita-Salute San Raffaele, Milano, Italy
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Giulio Caravagna
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Gianvito Martino
- Università Vita-Salute San Raffaele, Milano, Italy
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital, Milano, Italy
| | - Luca Aldrighetti
- Hepatobiliary Surgery Division, IRCCS San Raffaele Hospital, Milano, Italy
| | - Sebastiano Pasqualato
- Biochemistry and Structural Biology Unit, Department of Experimental Oncology, IEO, IRCCS European Institute of Oncology, Milano, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino School of Medicine, Candiolo, Torino, Italy
- Candiolo Cancer Institute FPO- IRCCS, Candiolo, Torino, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy.
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy.
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy.
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11
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Chen S, Xiong J, Chen B, Zhang C, Deng X, He F, Yang L, Chen C, Peng J, Yin F. Autism spectrum disorder and comorbid neurodevelopmental disorders (ASD-NDDs): Clinical and genetic profile of a pediatric cohort. Clin Chim Acta 2022; 524:179-186. [PMID: 34800434 DOI: 10.1016/j.cca.2021.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Autism spectrum disorder (ASD), a neurodevelopmental disorder, is featured by impaired social communication and restricted and repetitive behaviors and interests. ASD and comorbid neurodevelopmental disorders (ASD-NDDs), especially epilepsy and intellectual disability (ID)/global developmental delay (GDD) are frequently presented in genetic disorders. The aim of this study was to explore the clinical and genetic profile of ASD in combination with epilepsy or ID/GDD. METHODS We retrospectively analyzed the clinical characteristics, and genetic spectrum of pediatric patients presenting ASD-NDDs with proven genetic etiology. The pathogenicity of variants was conducted by molecular geneticists and clinicians complied with the guidelines of the American College of Medical Genetics and Genomics (ACMG). RESULTS Among 154 patients with ASD-NDDs, 79 (51.3%) patients gained a genetic diagnosis. Most patients (78/79, 98.7%) had comorbid ID or GDD, and 49 (49/79, 62.0%) had comorbid epilepsy. The clinical characteristics of those 79 patients were varied. 87 genetic variants were found among the 79 pedigrees. Most of the involved genes have roles in gene expression regulation (GER) and neuronal communication (NC). Most genes have been proven to be ASD-related genes, and some of them were not reported to contribute to ASD previously. CONCLUSION We summarized the genetic and clinical profile of 79 ASD-NDDs patients with proven genetic etiology. The genetic spectrum of ASD was expanded, and we highlighted a novel possible ASD candidate gene PRTG.
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Affiliation(s)
- Shimeng Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Baiyu Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ciliu Zhang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Xiaolu Deng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, China; Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China.
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12
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Duffy KA, Bale TL, Epperson CN. Germ Cell Drivers: Transmission of Preconception Stress Across Generations. Front Hum Neurosci 2021; 15:642762. [PMID: 34322003 PMCID: PMC8311293 DOI: 10.3389/fnhum.2021.642762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
Exposure to stress can accelerate maturation and hasten reproduction. Although potentially adaptive, the trade-off is higher risk for morbidity and mortality. In humans, the intergenerational effects of stress have been demonstrated, but the precise mechanisms are unknown. Strikingly, even if parental stress occurs prior to conception, as adults, their offspring show worse mental and physical health. Emerging evidence primarily from preclinical models suggests that epigenetic programming may encode preconception stress exposures in germ cells, potentially impacting the phenotype of the offspring. In this narrative review, we evaluate the strength of the evidence for this mechanism across animals and humans in both males and females. The strongest evidence comes from studies of male mice, in which paternal preconception stress is associated with a host of phenotypic changes in the offspring and stress-induced changes in the small non-coding RNA content in sperm have been implicated. Two recent studies in men provide evidence that some small non-coding RNAs in sperm are responsive to past and current stress, including some of the same ones identified in mice. Although preliminary evidence suggests that findings from mice may map onto men, the next steps will be (1) considering whether stress type, severity, duration, and developmental timing affect germ cell epigenetic markers, (2) determining whether germ cell epigenetic markers contribute to disease risk in the offspring of stress-exposed parents, and (3) overcoming methodological challenges in order to extend this research to females.
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Affiliation(s)
- Korrina A. Duffy
- Colorado Center for Women’s Behavioral Health and Wellness, Department of Psychiatry, University of Colorado School of Medicine, Aurora, CO, United States
| | - Tracy L. Bale
- Center for Epigenetic Research in Child Health and Brain Development, Department of Pharmacology and Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States
| | - C. Neill Epperson
- Colorado Center for Women’s Behavioral Health and Wellness, Department of Psychiatry, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Family Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Center for Women’s Health Research, University of Colorado School of Medicine, Aurora, CO, United States
- Helen and Arthur E. Johnson Depression Center, University of Colorado School of Medicine, Aurora, CO, United States
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13
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Xiang T, Yuan C, Guo X, Wang H, Cai Q, Xiang Y, Luo W, Liu G. The novel ZEB1-upregulated protein PRTG induced by Helicobacter pylori infection promotes gastric carcinogenesis through the cGMP/PKG signaling pathway. Cell Death Dis 2021; 12:150. [PMID: 33542225 PMCID: PMC7862680 DOI: 10.1038/s41419-021-03440-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Helicobacter pylori (H. pylori) is listed as a class I carcinogen in human gastric cancer; however, the underlying mechanisms are poorly understood. In this study, we identified Protogenin (PRTG) was upregulated in both gastric cancer tissues and H. pylori-infected tissues by analyzing dysregulated genes in TCGA and GEO databases. Importantly, upregulated PRTG predicted poor prognosis of gastric cancer patients and integrative analysis revealed that PRTG served as an oncogenic protein in gastric cancer and was required for H. pylori-mediated tumorigenic activities in in vitro cellular and in vivo tumor-bearing mouse models. Mechanistically, H. pylori infection enhanced PRTG expression by promoting transcriptional factor ZEB1 stabilization and recruitment to the PRTG promoter, and which then activated the sub-following cGMP/PKG signaling pathway in bioinformatic and cellular studies. Cellular studies further confirmed that PRTG depended on activating cGMP/PKG axis to promote proliferation, metastasis, and chemoresistance of gastric cancer cells. The PKG inhibitor KT5823 played synergistic anti-tumor effects with cisplatin and paclitaxel to gastric cancer cells in in vitro cellular and in vivo tumor-bearing mouse models. Taken together, our findings suggested that H. pylori infection depends on ZEB1 to induce PRTG upregulation, and which leading to the development and progression of gastric cancer through activating cGMP/PKG signaling pathway. Blocking PRTG/cGMP/PKG axis, therefore, presents a promising novel therapeutic strategy for gastric cancer.
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Affiliation(s)
- Tian Xiang
- Department of Laboratory Medicine, Central Hospital of Enshi Autonomous Prefecture, Enshi Clinical College, Medical School of Hubei Minzu University, 445000, Enshi, Hubei, People's Republic of China
| | - Chunhui Yuan
- Department of Laboratory Medicine, Wuhan Medical and Health Center for Women and Children, Tongji Medical College, Huazhong University of Science and Technology, 430016, Wuhan, People's Republic of China
| | - Xia Guo
- Department of Laboratory Medicine, Wuhan Medical and Health Center for Women and Children, Tongji Medical College, Huazhong University of Science and Technology, 430016, Wuhan, People's Republic of China
| | - Honghao Wang
- Department of Gastrointestinal Surgery, Central Hospital of Enshi Autonomous Prefecture, Enshi Clinical College, Medical School of Hubei Minzu University, 445000, Enshi, Hubei, People's Republic of China
| | - Qinzhen Cai
- Department of Laboratory Medicine, Wuhan Medical and Health Center for Women and Children, Tongji Medical College, Huazhong University of Science and Technology, 430016, Wuhan, People's Republic of China
| | - Yun Xiang
- Department of Laboratory Medicine, Wuhan Medical and Health Center for Women and Children, Tongji Medical College, Huazhong University of Science and Technology, 430016, Wuhan, People's Republic of China
| | - Wei Luo
- Department of Clinical Laboratory, Tianjin Medical University General Hospital, 300052, Tianjin, People's Republic of China.
| | - Gao Liu
- Department of Gastrointestinal Surgery, Central Hospital of Enshi Autonomous Prefecture, Enshi Clinical College, Medical School of Hubei Minzu University, 445000, Enshi, Hubei, People's Republic of China.
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14
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Morgan CP, Shetty AC, Chan JC, Berger DS, Ament SA, Epperson CN, Bale TL. Repeated sampling facilitates within- and between-subject modeling of the human sperm transcriptome to identify dynamic and stress-responsive sncRNAs. Sci Rep 2020; 10:17498. [PMID: 33060642 PMCID: PMC7562703 DOI: 10.1038/s41598-020-73867-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Epidemiological studies from the last century have drawn strong associations between paternal life experiences and offspring health and disease outcomes. Recent studies have demonstrated sperm small non-coding RNA (sncRNA) populations vary in response to diverse paternal insults. However, for studies in retrospective or prospective human cohorts to identify changes in paternal germ cell epigenetics in association with offspring disease risk, a framework must first be built with insight into the expected biological variation inherent in human populations. In other words, how will we know what to look for if we don't first know what is stable and what is dynamic, and what is consistent within and between men over time? From sperm samples from a 'normative' cohort of healthy human subjects collected repeatedly from each subject over 6 months, 17 healthy male participants met inclusion criteria and completed donations and psychological evaluations of perceived stress monthly. sncRNAs (including miRNA, piRNA, and tRNA) isolated from mature sperm from these samples were subjected to Illumina small RNA sequencing, aligned to subtype-specific reference transcriptomes, and quantified. The repeated measures design allowed us to define both within- and between-subject variation in the expression of 254 miRNA, 194 tRNA, and 937 piRNA in sperm over time. We developed screening criteria to identify a subset of potential environmentally responsive 'dynamic' sperm sncRNA. Implementing complex modeling of the relationships between individual dynamic sncRNA and perceived stress states in these data, we identified 5 miRNA (including let-7f-5p and miR-181a-5p) and 4 tRNA that are responsive to the dynamics of prior stress experience and fit our established mouse model. In the current study, we aligned repeated sampling of human sperm sncRNA expression data with concurrent measures of perceived stress as a novel framework that can now be applied across a range of studies focused on diverse environmental factors able to influence germ cell programming and potentially impact offspring development.
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Affiliation(s)
- Christopher P Morgan
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jennifer C Chan
- Department of Biomedical Sciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dara S Berger
- Division of Reproductive Endocrinology and Infertility, Perelman School of Medicine, Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - C Neill Epperson
- Department of Psychiatry, University of Colorado School of Medicine, CU-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Tracy L Bale
- Department of Pharmacology and Center for Epigenetic Research in Child Health and Brain Development, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Departments of Pharmacology and Psychiatry, Center for Epigenetic Research in Child Health and Brain Development, HSF3, Room 9-171, University of Maryland School of Medicine, 670 W. Baltimore St., Baltimore, MD, 21201, USA.
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15
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Fernández V, Martínez-Martínez MÁ, Prieto-Colomina A, Cárdenas A, Soler R, Dori M, Tomasello U, Nomura Y, López-Atalaya JP, Calegari F, Borrell V. Repression of Irs2 by let-7 miRNAs is essential for homeostasis of the telencephalic neuroepithelium. EMBO J 2020; 39:e105479. [PMID: 32985705 PMCID: PMC7604626 DOI: 10.15252/embj.2020105479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 01/01/2023] Open
Abstract
Structural integrity and cellular homeostasis of the embryonic stem cell niche are critical for normal tissue development. In the telencephalic neuroepithelium, this is controlled in part by cell adhesion molecules and regulators of progenitor cell lineage, but the specific orchestration of these processes remains unknown. Here, we studied the role of microRNAs in the embryonic telencephalon as key regulators of gene expression. By using the early recombiner Rx-Cre mouse, we identify novel and critical roles of miRNAs in early brain development, demonstrating they are essential to preserve the cellular homeostasis and structural integrity of the telencephalic neuroepithelium. We show that Rx-Cre;DicerF/F mouse embryos have a severe disruption of the telencephalic apical junction belt, followed by invagination of the ventricular surface and formation of hyperproliferative rosettes. Transcriptome analyses and functional experiments in vivo show that these defects result from upregulation of Irs2 upon loss of let-7 miRNAs in an apoptosis-independent manner. Our results reveal an unprecedented relevance of miRNAs in early forebrain development, with potential mechanistic implications in pediatric brain cancer.
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Affiliation(s)
- Virginia Fernández
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Maria Ángeles Martínez-Martínez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Anna Prieto-Colomina
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Adrián Cárdenas
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Rafael Soler
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Martina Dori
- CRTD-Center for Regenerative Therapies, School of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Ugo Tomasello
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Yuki Nomura
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - José P López-Atalaya
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Federico Calegari
- CRTD-Center for Regenerative Therapies, School of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
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16
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Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics. G3-GENES GENOMES GENETICS 2020; 10:2275-2296. [PMID: 32354705 PMCID: PMC7341126 DOI: 10.1534/g3.120.401290] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ant-infecting Ophiocordyceps fungi are globally distributed, host manipulating, specialist parasites that drive aberrant behaviors in infected ants, at a lethal cost to the host. An apparent increase in activity and wandering behaviors precedes a final summiting and biting behavior onto vegetation, which positions the manipulated ant in a site beneficial for fungal growth and transmission. We investigated the genetic underpinnings of host manipulation by: (i) producing a high-quality hybrid assembly and annotation of the Ophiocordyceps camponoti-floridani genome, (ii) conducting laboratory infections coupled with RNAseq of O. camponoti-floridani and its host, Camponotus floridanus, and (iii) comparing these data to RNAseq data of Ophiocordyceps kimflemingiae and Camponotus castaneus as a powerful method to identify gene expression patterns that suggest shared behavioral manipulation mechanisms across Ophiocordyceps-ant species interactions. We propose differentially expressed genes tied to ant neurobiology, odor response, circadian rhythms, and foraging behavior may result by activity of putative fungal effectors such as enterotoxins, aflatrem, and mechanisms disrupting feeding behaviors in the ant.
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17
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Mégret L, Nair SS, Dancourt J, Aaronson J, Rosinski J, Neri C. Combining feature selection and shape analysis uncovers precise rules for miRNA regulation in Huntington's disease mice. BMC Bioinformatics 2020; 21:75. [PMID: 32093602 PMCID: PMC7041117 DOI: 10.1186/s12859-020-3418-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Background MicroRNA (miRNA) regulation is associated with several diseases, including neurodegenerative diseases. Several approaches can be used for modeling miRNA regulation. However, their precision may be limited for analyzing multidimensional data. Here, we addressed this question by integrating shape analysis and feature selection into miRAMINT, a methodology that we used for analyzing multidimensional RNA-seq and proteomic data from a knock-in mouse model (Hdh mice) of Huntington’s disease (HD), a disease caused by CAG repeat expansion in huntingtin (htt). This dataset covers 6 CAG repeat alleles and 3 age points in the striatum and cortex of Hdh mice. Results Remarkably, compared to previous analyzes of this multidimensional dataset, the miRAMINT approach retained only 31 explanatory striatal miRNA-mRNA pairs that are precisely associated with the shape of CAG repeat dependence over time, among which 5 pairs with a strong change of target expression levels. Several of these pairs were previously associated with neuronal homeostasis or HD pathogenesis, or both. Such miRNA-mRNA pairs were not detected in cortex. Conclusions These data suggest that miRNA regulation has a limited global role in HD while providing accurately-selected miRNA-target pairs to study how the brain may compute molecular responses to HD over time. These data also provide a methodological framework for researchers to explore how shape analysis can enhance multidimensional data analytics in biology and disease.
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Affiliation(s)
- Lucile Mégret
- Sorbonne Université, CNRS UMR8256, INSERM ERL U1164, Brain-C Lab, Paris, France.
| | | | - Julia Dancourt
- Sorbonne Université, CNRS UMR8256, INSERM ERL U1164, Brain-C Lab, Paris, France
| | | | | | - Christian Neri
- Sorbonne Université, CNRS UMR8256, INSERM ERL U1164, Brain-C Lab, Paris, France.
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18
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Wu TS, Cheng YC, Chen PJ, Huang YT, Yu FY, Liu BH. Exposure to aflatoxin B 1 interferes with locomotion and neural development in zebrafish embryos and larvae. CHEMOSPHERE 2019; 217:905-913. [PMID: 30466059 DOI: 10.1016/j.chemosphere.2018.11.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 05/19/2023]
Abstract
Aflatoxin B1 (AFB1) is the major mycotoxin that contaminates aquafeeds and regarded as a causative agent in illnesses and the mortality of aquacultural species. However, the effects of AFB1 on developing fish and associated toxic mechanism are still unknown. This study examines the behavioral changes, neuronal morphology and gene expression in zebrafish embryos and larvae upon exposure to aflatoxin solutions. Treatment of 6 h post fertilization (hpf) embryos with AFB1 at 15-75 ng/mL significantly changed the swimming patterns of seven days post-fertilization (dpf) zebrafish larvae. Larvae in the 15 ng/mL group demonstrated a hypolocomotor activity in free swimming, but hyperlocomotion was observed in the larvae exposed to 30-75 ng/mL AFB1. AFB1 at 75 ng/mL also significantly reduced the startle response of 7 dpf larvae after tapping stimulus. Exposure to AFB1 resulted in an aberrant morphology of trigeminal ganglion and hindbrain neurons in transgenic embryos (HuC:eGFP); this finding was supported by acetylated alpha-tubulin staining in wild-type fish. Additionally, AFB1 altered the levels of neurotoxic markers, including gfap and huC. The transcriptomic profile of AFB1-treated embryos revealed several differentially expressed genes that are related to neuroactivity and neurogenesis. PCR analysis verified that AFB1 significantly down-regulated the expression of ngfa and atp1b1b genes and increased that of prtga gene. The results herein indicate the toxicological impacts of AFB1 on the behaviors and neurodevelopment of fish in the early embryonic stage. Disruption of neural formation and synapse dysfunction may be responsible for the behavioral alteration.
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Affiliation(s)
- Ting-Shuan Wu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Chih Cheng
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Jen Chen
- Department of Agricultural Chemistry, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Ying-Tzu Huang
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Feng-Yih Yu
- Department of Biomedical Sciences, Chung Shan Medical University, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan.
| | - Biing-Hui Liu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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19
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Loveday C, Litchfield K, Levy M, Holroyd A, Broderick P, Kote-Jarai Z, Dunning AM, Muir K, Peto J, Eeles R, Easton DF, Dudakia D, Orr N, Pashayan N, Reid A, Huddart RA, Houlston RS, Turnbull C. Validation of loci at 2q14.2 and 15q21.3 as risk factors for testicular cancer. Oncotarget 2018; 9:12630-12638. [PMID: 29560096 PMCID: PMC5849160 DOI: 10.18632/oncotarget.23117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/15/2017] [Indexed: 01/21/2023] Open
Abstract
Testicular germ cell tumor (TGCT), the most common cancer in men aged 18 to 45 years, has a strong heritable basis. Genome-wide association studies (GWAS) have proposed single nucleotide polymorphisms (SNPs) at a number of loci influencing TGCT risk. To further evaluate the association of recently proposed risk SNPs with TGCT at 2q14.2, 3q26.2, 7q36.3, 10q26.13 and 15q21.3, we analyzed genotype data on 3,206 cases and 7,422 controls. Our analysis provides independent replication of the associations for risk SNPs at 2q14.2 (rs2713206 at P = 3.03 × 10-2; P-meta = 3.92 × 10-8; nearest gene, TFCP2L1) and rs12912292 at 15q21.3 (P = 7.96 × 10-11; P-meta = 1.55 × 10-19; nearest gene PRTG). Case-only analyses did not reveal specific associations with TGCT histology. TFCP2L1 joins the growing list of genes located within TGCT risk loci with biologically plausible roles in developmental transcriptional regulation, further highlighting the importance of this phenomenon in TGCT oncogenesis.
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Affiliation(s)
- Chey Loveday
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Kevin Litchfield
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - Max Levy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Warwick, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Julian Peto
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Darshna Dudakia
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Nick Orr
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
| | - Alison Reid
- Academic Uro-oncology Unit, The Royal Marsden NHS Foundation Trust, Sutton, Surrey, UK
| | - Robert A Huddart
- Academic Radiotherapy Unit, Institute of Cancer Research, Sutton, Surrey, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- William Harvey Research Institute, Queen Mary University, London, UK
- Guys and St Thomas NHS Foundation Trust, London, UK
- National Cancer Registration and Analysis Service, Public Health England, London, UK
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20
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Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat Commun 2018; 9:781. [PMID: 29472610 PMCID: PMC5823944 DOI: 10.1038/s41467-018-03149-4] [Citation(s) in RCA: 364] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/23/2018] [Indexed: 12/29/2022] Open
Abstract
Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.
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Affiliation(s)
- Stephen J Clark
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
| | - Ricard Argelaguet
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | | | - Thomas M Stubbs
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Heather J Lee
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | | | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Scotland, EH8 9AB, UK
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK.
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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21
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Wang Z, McGlynn KA, Rajpert-De Meyts E, Bishop DT, Chung C, Dalgaard MD, Greene MH, Gupta R, Grotmol T, Haugen TB, Karlsson R, Litchfield K, Mitra N, Nielsen K, Pyle LC, Schwartz SM, Thorsson V, Vardhanabhuti S, Wiklund F, Turnbull C, Chanock SJ, Kanetsky PA, Nathanson KL. Meta-analysis of five genome-wide association studies identifies multiple new loci associated with testicular germ cell tumor. Nat Genet 2017; 49:1141-1147. [PMID: 28604732 PMCID: PMC5490654 DOI: 10.1038/ng.3879] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 04/27/2017] [Indexed: 12/24/2022]
Abstract
The international Testicular Cancer Consortium (TECAC) combined five published genome-wide association studies of testicular germ cell tumor (TGCT; 3,558 cases and 13,970 controls) to identify new susceptibility loci. We conducted a fixed-effects meta-analysis, including, to our knowledge, the first analysis of the X chromosome. Eight new loci mapping to 2q14.2, 3q26.2, 4q35.2, 7q36.3, 10q26.13, 15q21.3, 15q22.31, and Xq28 achieved genome-wide significance (P < 5 × 10-8). Most loci harbor biologically plausible candidate genes. We refined previously reported associations at 9p24.3 and 19p12 by identifying one and three additional independent SNPs, respectively. In aggregate, the 39 independent markers identified to date explain 37% of father-to-son familial risk, 8% of which can be attributed to the 12 new signals reported here. Our findings substantially increase the number of known TGCT susceptibility alleles, move the field closer to a comprehensive understanding of the underlying genetic architecture of TGCT, and provide further clues to the etiology of TGCT.
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Affiliation(s)
- Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Katherine A. McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Charles Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Marlene D. Dalgaard
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
- Center of Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mark H. Greene
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Ramneek Gupta
- Center of Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Trine B. Haugen
- Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kevin Litchfield
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Nandita Mitra
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kasper Nielsen
- Center of Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Louise C. Pyle
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Human Genetics and Metabolism, The Children's Hospital of Philadelphia, Philadelphia 19104, PA, USA
| | | | | | - Saran Vardhanabhuti
- Department of Biostatistics, Harvard School of Public Health, Cambridge, Massachusetts, USA
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Genomics England, London, UK
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Peter A. Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Katherine L. Nathanson
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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22
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Plate L, Wiseman RL. Regulating Secretory Proteostasis through the Unfolded Protein Response: From Function to Therapy. Trends Cell Biol 2017. [PMID: 28647092 DOI: 10.1016/j.tcb.2017.05.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Imbalances in secretory proteostasis induced by genetic, environmental, or aging-related insults are pathologically associated with etiologically diverse protein misfolding diseases. To protect the secretory proteome from these insults, organisms evolved stress-responsive signaling pathways that regulate the composition and activity of biologic pathways involved in secretory proteostasis maintenance. The most prominent of these is the endoplasmic reticulum (ER) unfolded protein response (UPR), which functions to regulate ER proteostasis in response to ER stress. While the signaling mechanisms involved in UPR activation are well defined, the impact of UPR activation on secretory proteostasis is only now becoming clear. Here, we highlight recent reports defining how activation of select UPR signaling pathways influences proteostasis within the ER and downstream secretory environments. Furthermore, we describe recent evidence that highlights the therapeutic potential for targeting UPR signaling pathways to correct pathologic disruption in secretory proteostasis associated with diverse types of protein misfolding diseases.
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Affiliation(s)
- Lars Plate
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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23
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Chen HR, Juan HC, Wong YH, Tsai JW, Fann MJ. Cdk12 Regulates Neurogenesis and Late-Arising Neuronal Migration in the Developing Cerebral Cortex. Cereb Cortex 2017; 27:2289-2302. [PMID: 27073218 DOI: 10.1093/cercor/bhw081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA damage response (DDR) pathways are critical for ensuring that replication stress and various types of DNA lesion do not perturb production of neural cells during development. Cdk12 maintains genomic stability by regulating expression of DDR genes. Mutant mice in which Cdk12 is conditionally deleted in neural progenitor cells (NPCs) die after birth and exhibit microcephaly with a thinner cortical plate and an aberrant corpus callosum. We show that NPCs of mutant mice accumulate at G2 and M phase, and have lower expression of DDR genes, more DNA double-strand breaks and increased apoptosis. In addition to there being fewer neurons, there is misalignment of layers IV-II neurons and the presence of abnormal axonal tracts of these neurons, suggesting that Cdk12 is also required for the migration of late-arising cortical neurons. Using in utero electroporation, we demonstrate that the migrating mutant cells remain within the intermediate zone and fail to adopt a bipolar morphology. Overexpression of Cdk5 brings about a partially restoration of the neurons reaching layers IV-II in the mutant mice. Thus, Cdk12 is crucial to the repair of DNA damage during the proliferation of NPCs and is also central to the proper migration of late-arising neurons.
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Affiliation(s)
- Hong-Ru Chen
- Department of Life Sciences and Institute of Genome Sciences.,Brain Research Center
| | - Hsien-Chia Juan
- Department of Life Sciences and Institute of Genome Sciences
| | | | - Jin-Wu Tsai
- Brain Research Center.,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan 11221, Republic of China
| | - Ming-Ji Fann
- Department of Life Sciences and Institute of Genome Sciences.,Brain Research Center
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24
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Neurons Export Extracellular Vesicles Enriched in Cysteine String Protein and Misfolded Protein Cargo. Sci Rep 2017; 7:956. [PMID: 28424476 PMCID: PMC5430488 DOI: 10.1038/s41598-017-01115-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/27/2017] [Indexed: 12/20/2022] Open
Abstract
The fidelity of synaptic transmission depends on the integrity of the protein machinery at the synapse. Unfolded synaptic proteins undergo refolding or degradation in order to maintain synaptic proteostasis and preserve synaptic function, and buildup of unfolded/toxic proteins leads to neuronal dysfunction. Many molecular chaperones contribute to proteostasis, but one in particular, cysteine string protein (CSPα), is critical for proteostasis at the synapse. In this study we report that exported vesicles from neurons contain CSPα. Extracellular vesicles (EV’s) have been implicated in a wide range of functions. However, the functional significance of neural EV’s remains to be established. Here we demonstrate that co-expression of CSPα with the disease-associated proteins, polyglutamine expanded protein 72Q huntingtinex°n1 or superoxide dismutase-1 (SOD-1G93A) leads to the cellular export of both 72Q huntingtinex°n1 and SOD-1G93A via EV’s. In contrast, the inactive CSPαHPD-AAA mutant does not facilitate elimination of misfolded proteins. Furthermore, CSPα-mediated export of 72Q huntingtinex°n1 is reduced by the polyphenol, resveratrol. Our results indicate that by assisting local lysosome/proteasome processes, CSPα-mediated removal of toxic proteins via EVs plays a central role in synaptic proteostasis and CSPα thus represents a potential therapeutic target for neurodegenerative diseases.
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25
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Faden DL, Asthana S, Tihan T, DeRisi J, Kliot M. Whole Exome Sequencing of Growing and Non-Growing Cutaneous Neurofibromas from a Single Patient with Neurofibromatosis Type 1. PLoS One 2017; 12:e0170348. [PMID: 28099461 PMCID: PMC5242532 DOI: 10.1371/journal.pone.0170348] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/03/2017] [Indexed: 11/30/2022] Open
Abstract
The growth behaviors of cutaneous neurofibromas in patients with Neurofibromatosis type 1 are highly variable. The role of the germline NF1 mutation, somatic NF1 mutation and mutations at modifying loci, are poorly understood. We performed whole exome sequencing of three growing and three non-growing neurofibromas from a single individual to assess the role of acquired somatic mutations in neurofibroma growth behavior. 1–11 mutations were identified in each sample, including two deleterious NF1 mutations. No trends were present between the types of somatic mutations identified and growth behavior. Mutations in the HIPPO signaling pathway appeared to be overrepresented.
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Affiliation(s)
- Daniel L. Faden
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| | - Saurabh Asthana
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Tarik Tihan
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
| | - Joseph DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Michel Kliot
- Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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26
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Lee JY, Chen JY, Shaw JL, Chang KT. Maintenance of Stem Cell Niche Integrity by a Novel Activator of Integrin Signaling. PLoS Genet 2016; 12:e1006043. [PMID: 27191715 PMCID: PMC4871447 DOI: 10.1371/journal.pgen.1006043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 04/19/2016] [Indexed: 01/22/2023] Open
Abstract
Stem cells depend critically on the surrounding microenvironment, or niche, for their maintenance and self-renewal. While much is known about how the niche regulates stem cell self-renewal and differentiation, mechanisms for how the niche is maintained over time are not well understood. At the apical tip of the Drosophila testes, germline stem cells (GSCs) and somatic stem cells share a common niche formed by hub cells. Here we demonstrate that a novel protein named Shriveled (Shv) is necessary for the maintenance of hub/niche integrity. Depletion of Shv protein results in age-dependent deterioration of the hub structure and loss of GSCs, whereas upregulation of Shv preserves the niche during aging. We find Shv is a secreted protein that modulates DE-cadherin levels through extracellular activation of integrin signaling. Our work identifies Shv as a novel activator of integrin signaling and suggests a new integration model in which crosstalk between integrin and DE-cadherin in niche cells promote their own preservation by maintaining the niche architecture. Stem cells are vital for development and for regeneration and repair of tissues in an organism. The ability of adult stem cells to maintain their “stemness” depends critically on the localized microenvironment, or niche. While much is known about how the niche regulates stem cell self-renewal and differentiation, mechanisms for how the niche is maintained during aging are not well understood. Using Drosophila testis as a model system, here we demonstrate that a protein we named Shriveled is a secreted protein that activates integrin signaling to preserve niche architecture. We also show that Shriveled-dependent activation of integrin maintains normal E-cadherin levels in the niche cells, providing a mechanism for niche maintenance. Interestingly, upregulation of Shriveled retards the loss of niche and stem cells seen during normal aging. Together, our work identifies Shriveled as a novel molecule required for preservation of the niche structure in the Drosophila testis.
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Affiliation(s)
- Joo Yeun Lee
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Neuroscience Graduate Program, University of Southern California, Los Angeles, California, United States of America
| | - Jessica Y. Chen
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jillian L. Shaw
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Neuroscience Graduate Program, University of Southern California, Los Angeles, California, United States of America
| | - Karen T. Chang
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Neuroscience Graduate Program, University of Southern California, Los Angeles, California, United States of America
- Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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27
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Cho YJ, Kang W, Kim SH, Sa JK, Kim N, Paddison PJ, Kim M, Joo KM, Hwang YI, Nam DH. Involvement of DDX6 gene in radio- and chemoresistance in glioblastoma. Int J Oncol 2016; 48:1053-62. [PMID: 26783102 DOI: 10.3892/ijo.2016.3328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/06/2015] [Indexed: 11/05/2022] Open
Abstract
CCRT (concomitant chemotherapy and radiation therapy) is often used for glioblastoma multiforme (GBM) treatment after surgical therapy, however, patients treated with CCRT undergo poor prognosis due to development of treatment resistant recurrence. Many studies have been performed to overcome these problems and to discover genes influencing treatment resistance. To discover potential genes inducing CCRT resistance in GBM, we used whole genome screening by infecting shRNA pool in patient-derived cell. The cells infected ~8,000 shRNAs were implanted in mouse brain and treated RT/TMZ as in CCRT treated patients. We found DDX6 as the candidate gene for treatment resistance after screening and establishing DDX6 knock down cells for functional validation. Using these cells, we confirmed tumor associated ability of DDX6 in vitro and in vivo. Although proliferation improvement was not found, decreased DDX6 influenced upregulated clonogenic ability and resistant response against radiation treatment in vivo and in vitro. Taken together, we suggest that DDX6 discovered by using whole genome screening was responsible for radio- and chemoresistance in GBM.
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Affiliation(s)
- Yu Jin Cho
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wonyoung Kang
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sung Heon Kim
- Department of Anatomy and Cell Biology, Sungkyunkwan University of Medicine, Suwon, Seoul, Republic of Korea
| | - Jason K Sa
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Nayoung Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Patrick J Paddison
- Department of Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Misuk Kim
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea
| | - Kyeung Min Joo
- Department of Anatomy and Cell Biology, Sungkyunkwan University of Medicine, Suwon, Seoul, Republic of Korea
| | - Young-Il Hwang
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Do-Hyun Nam
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Ai Z, Xiang Z, Li Y, Liu G, Wang H, Zheng Y, Qiu X, Zhao S, Zhu X, Li Y, Ji W, Li T. Conversion of monkey fibroblasts to transplantable telencephalic neuroepithelial stem cells. Biomaterials 2016; 77:53-65. [DOI: 10.1016/j.biomaterials.2015.10.079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 12/11/2022]
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Genereux JC, Qu S, Zhou M, Ryno LM, Wang S, Shoulders MD, Kaufman RJ, Lasmézas CI, Kelly JW, Wiseman RL. Unfolded protein response-induced ERdj3 secretion links ER stress to extracellular proteostasis. EMBO J 2014; 34:4-19. [PMID: 25361606 DOI: 10.15252/embj.201488896] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The Unfolded Protein Response (UPR) indirectly regulates extracellular proteostasis through transcriptional remodeling of endoplasmic reticulum (ER) proteostasis pathways. This remodeling attenuates secretion of misfolded, aggregation-prone proteins during ER stress. Through these activities, the UPR has a critical role in preventing the extracellular protein aggregation associated with numerous human diseases. Here, we demonstrate that UPR activation also directly influences extracellular proteostasis through the upregulation and secretion of the ER HSP40 ERdj3/DNAJB11. Secreted ERdj3 binds misfolded proteins in the extracellular space, substoichiometrically inhibits protein aggregation, and attenuates proteotoxicity of disease-associated toxic prion protein. Moreover, ERdj3 can co-secrete with destabilized, aggregation-prone proteins in a stable complex under conditions where ER chaperoning capacity is overwhelmed, preemptively providing extracellular chaperoning of proteotoxic misfolded proteins that evade ER quality control. This regulated co-secretion of ERdj3 with misfolded clients directly links ER and extracellular proteostasis during conditions of ER stress. ERdj3 is, to our knowledge, the first metazoan chaperone whose secretion into the extracellular space is regulated by the UPR, revealing a new mechanism by which UPR activation regulates extracellular proteostasis.
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Affiliation(s)
- Joseph C Genereux
- Department of Molecular & Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Song Qu
- Department of Molecular & Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Minghai Zhou
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, FL, USA
| | - Lisa M Ryno
- Department of Molecular & Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Shiyu Wang
- Degenerative Disease Research Program, Sanford Burnham Medical Research Institute, La Jolla, CA, USA
| | | | - Randal J Kaufman
- Degenerative Disease Research Program, Sanford Burnham Medical Research Institute, La Jolla, CA, USA
| | - Corinne I Lasmézas
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, FL, USA
| | - Jeffery W Kelly
- Department of Molecular & Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - R Luke Wiseman
- Department of Molecular & Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
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Chen HR, Lin GT, Huang CK, Fann MJ. Cdk12 and Cdk13 regulate axonal elongation through a common signaling pathway that modulates Cdk5 expression. Exp Neurol 2014; 261:10-21. [PMID: 24999027 DOI: 10.1016/j.expneurol.2014.06.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 11/17/2022]
Abstract
Cdk12 and Cdk13 are Cdc2-related proteins that share 92% identity in their kinase domains. Using in situ hybridization and Western blot analysis, we detected the expression of Cdk12 and Cdk13 mRNAs and their proteins in developing mouse embryos, especially during development of the nervous system. We explored the roles of Cdk12 and Cdk13 in neuronal differentiation using the P19 neuronal differentiation model. Upon knockdown of Cdk12 or Cdk13, no effect on differentiated cell numbers was detected, but a substantial decrease of numbers of neurons with long neurites was identified. Similarly, knockdown of Cdk12 or Cdk13 in primarily cultured cortical neurons shortens the averaged axonal length. A microarray analysis was used to examine changes in gene expression after knockdown or overexpression of Cdk12 and we identified Cdk5 as a molecule potentially involved in mediating the effect of Cdk12 and Cdk13. Depletion of Cdk12 or Cdk13 in P19 cells significantly reduces Cdk5 expression at both the mRNA and protein levels. Expression of Cdk5 protein in the developing mouse brain is also reduced in conditional Cdk12-knockout mice in proportion to the residual amount of Cdk12 protein present. This suggests that the reduced axonal outgrowth after knockdown of Cdk12 or Cdk13 might be due to lower Cdk5 expression. Furthermore, overexpression of Cdk5 protein in P19 cells was able to partially rescue the neurite outgrowth defect observed when Cdk12 or Cdk13 is depleted. Together, these findings suggest that Cdk12 and Cdk13 regulate axonal elongation through a common signaling pathway that modulates Cdk5 expression.
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Affiliation(s)
- Hong-Ru Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan, ROC
| | - Guan-Ting Lin
- Institute of Neuroscience, National Yang-Ming University, Taipei 11221, Taiwan, ROC
| | - Chun-Kai Huang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan, ROC
| | - Ming-Ji Fann
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan, ROC; Brain Research Center, National Yang-Ming University, Taipei 11221, Taiwan, ROC.
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31
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Matsunami N, Hensel CH, Baird L, Stevens J, Otterud B, Leppert T, Varvil T, Hadley D, Glessner JT, Pellegrino R, Kim C, Thomas K, Wang F, Otieno FG, Ho K, Christensen GB, Li D, Prekeris R, Lambert CG, Hakonarson H, Leppert MF. Identification of rare DNA sequence variants in high-risk autism families and their prevalence in a large case/control population. Mol Autism 2014; 5:5. [PMID: 24467814 PMCID: PMC4098669 DOI: 10.1186/2040-2392-5-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/24/2013] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genetics clearly plays a major role in the etiology of autism spectrum disorders (ASDs), but studies to date are only beginning to characterize the causal genetic variants responsible. Until recently, studies using multiple extended multi-generation families to identify ASD risk genes had not been undertaken. METHODS We identified haplotypes shared among individuals with ASDs in large multiplex families, followed by targeted DNA capture and sequencing to identify potential causal variants. We also assayed the prevalence of the identified variants in a large ASD case/control population. RESULTS We identified 584 non-conservative missense, nonsense, frameshift and splice site variants that might predispose to autism in our high-risk families. Eleven of these variants were observed to have odds ratios greater than 1.5 in a set of 1,541 unrelated children with autism and 5,785 controls. Three variants, in the RAB11FIP5, ABP1, and JMJD7-PLA2G4B genes, each were observed in a single case and not in any controls. These variants also were not seen in public sequence databases, suggesting that they may be rare causal ASD variants. Twenty-eight additional rare variants were observed only in high-risk ASD families. Collectively, these 39 variants identify 36 genes as ASD risk genes. Segregation of sequence variants and of copy number variants previously detected in these families reveals a complex pattern, with only a RAB11FIP5 variant segregating to all affected individuals in one two-generation pedigree. Some affected individuals were found to have multiple potential risk alleles, including sequence variants and copy number variants (CNVs), suggesting that the high incidence of autism in these families could be best explained by variants at multiple loci. CONCLUSIONS Our study is the first to use haplotype sharing to identify familial ASD risk loci. In total, we identified 39 variants in 36 genes that may confer a genetic risk of developing autism. The observation of 11 of these variants in unrelated ASD cases further supports their role as ASD risk variants.
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Affiliation(s)
- Nori Matsunami
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Lisa Baird
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Jeff Stevens
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Brith Otterud
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Tami Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Tena Varvil
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Dexter Hadley
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Renata Pellegrino
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cecilia Kim
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kelly Thomas
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fengxiang Wang
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Frederick G Otieno
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karen Ho
- Lineagen, Inc, Salt Lake City, UT, USA
| | | | - Dongying Li
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Mark F Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
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MicroRNA-9 regulates survival of chondroblasts and cartilage integrity by targeting protogenin. Cell Commun Signal 2013; 11:66. [PMID: 24007463 PMCID: PMC3848287 DOI: 10.1186/1478-811x-11-66] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 08/23/2013] [Indexed: 12/03/2022] Open
Abstract
Background Studies have shown the roles of miR-9 and its validated target, protogenin (PRTG) in the differentiation of chondroblasts to chondrocyte and in the pathogenesis of osteoarthritis (OA). We hypothesized that miR-9 plays a distinct role in endochondral ossification and OA pathogenesis and the present study was undertaken to identify this role. In the studies, chondroblasts were isolated from limb bud of chick and mouse embryos and articular chondrocytes were isolated from rabbit and human cartilage. Osteoarthritic chondrocytes were isolated from cartilage from patients undergoing total knee replacement. Using these cells, we analyzed the changes in the expression of genes and proteins, tested the expression level of miR-9, and applied a target validation system. We also performed functional study of miR-9 and PRTG. Results With the progression of chondrogenesis, decreased miR-9 level was observed at the time of numerous apoptotic cell deaths. And chondrocytes isolated from normal human articular cartilage expressed miR-9, and this expression was significantly reduced in OA chondrocytes, especially decreased its expression in parallel with the degree of cartilage degradation. Over-expression of PRTG induced the activation of caspase-3 signaling and increased apoptosis. However, the co-treatment with the miR-9 precursor or PRTG-specific siRNA blocked this apoptotic signaling. Conclusion This study shows that PRTG is regulated by miR-9, plays an inhibitory action on survival of chondroblasts and articular chondrocytes during chondrogenesis and OA pathogenesis.
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Towards a 'systems'-level understanding of the nervous system and its disorders. Trends Neurosci 2013; 36:674-84. [PMID: 23988221 DOI: 10.1016/j.tins.2013.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/17/2013] [Accepted: 07/24/2013] [Indexed: 12/26/2022]
Abstract
It is becoming clear that nervous system development and adult functioning are highly coupled with other physiological systems. Accordingly, neurological and psychiatric disorders are increasingly being associated with a range of systemic comorbidities including, most prominently, impairments in immunological and bioenergetic parameters as well as in the gut microbiome. Here, we discuss various aspects of the dynamic crosstalk between these systems that underlies nervous system development, homeostasis, and plasticity. We believe a better definition of this underappreciated systems physiology will yield important insights into how nervous system diseases with systemic comorbidities arise and potentially identify novel diagnostic and therapeutic strategies.
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34
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Plum, an immunoglobulin superfamily protein, regulates axon pruning by facilitating TGF-β signaling. Neuron 2013; 78:456-68. [PMID: 23664613 DOI: 10.1016/j.neuron.2013.03.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2013] [Indexed: 11/22/2022]
Abstract
Axon pruning during development is essential for proper wiring of the mature nervous system, but its regulation remains poorly understood. We have identified an immunoglobulin superfamily (IgSF) transmembrane protein, Plum, that is cell autonomously required for axon pruning of mushroom body (MB) γ neurons and for ectopic synapse refinement at the developing neuromuscular junction in Drosophila. Plum promotes MB γ neuron axon pruning by regulating the expression of Ecdysone Receptor-B1, a key initiator of axon pruning. Genetic analyses indicate that Plum acts to facilitate signaling of Myoglianin, a glial-derived TGF-β, on MB γ neurons upstream of the type-I TGF-β receptor Baboon. Myoglianin, Baboon, and Ecdysone Receptor-B1 are also required for neuromuscular junction ectopic synapse refinement. Our study highlights both IgSF proteins and TGF-β facilitation as key promoters of developmental axon elimination and demonstrates a mechanistic conservation between MB axon pruning during metamorphosis and the refinement of ectopic larval neuromuscular connections.
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Conserved microRNA pathway regulates developmental timing of retinal neurogenesis. Proc Natl Acad Sci U S A 2013; 110:E2362-70. [PMID: 23754433 DOI: 10.1073/pnas.1301837110] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Most regions of the vertebrate central nervous system develop by the sequential addition of different classes of neurons and glia. This phenomenon has been best characterized in laminated structures like the retina and the cerebral cortex, in which the progenitor cells in these structures are thought to change in their competence as development proceeds to generate different types of neurons in a stereotypic sequence that is conserved across vertebrates. We previously reported that conditional deletion of Dicer prevents the change in competence of progenitors to generate later-born cell types, suggesting that specific microRNAs (miRNAs) are required for this developmental transition. In this report, we now show that three miRNAs, let-7, miR-125, and miR-9, are key regulators of the early to late developmental transition in retinal progenitors: (i) members of these three miRNA families increase over the relevant developmental period in normal retinal progenitors; (ii) inhibiting the function of these miRNAs produces changes in retinal development similar to Dicer CKO; (iii) overexpression of members of these three miRNA families in Dicer-CKO retinas can rescue the phenotype, allowing their progression to late progenitors; (iv) overexpression of these miRNAs can accelerate normal retinal development; (v) microarray and computational analyses of Dicer-CKO retinal cells identified two potential targets of the late-progenitor miRNAs: Protogenin (Prtg) and Lin28b; and (vi) overexpression of either Lin28 or Prtg can maintain the early progenitor state. Together, these data demonstrate that a conserved miRNA pathway controls a key step in the progression of temporal identity in retinal progenitors.
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Conserved microRNA pathway regulates developmental timing of retinal neurogenesis. Proc Natl Acad Sci U S A 2013. [PMID: 23754433 DOI: 10.1073/pnas.13018371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Most regions of the vertebrate central nervous system develop by the sequential addition of different classes of neurons and glia. This phenomenon has been best characterized in laminated structures like the retina and the cerebral cortex, in which the progenitor cells in these structures are thought to change in their competence as development proceeds to generate different types of neurons in a stereotypic sequence that is conserved across vertebrates. We previously reported that conditional deletion of Dicer prevents the change in competence of progenitors to generate later-born cell types, suggesting that specific microRNAs (miRNAs) are required for this developmental transition. In this report, we now show that three miRNAs, let-7, miR-125, and miR-9, are key regulators of the early to late developmental transition in retinal progenitors: (i) members of these three miRNA families increase over the relevant developmental period in normal retinal progenitors; (ii) inhibiting the function of these miRNAs produces changes in retinal development similar to Dicer CKO; (iii) overexpression of members of these three miRNA families in Dicer-CKO retinas can rescue the phenotype, allowing their progression to late progenitors; (iv) overexpression of these miRNAs can accelerate normal retinal development; (v) microarray and computational analyses of Dicer-CKO retinal cells identified two potential targets of the late-progenitor miRNAs: Protogenin (Prtg) and Lin28b; and (vi) overexpression of either Lin28 or Prtg can maintain the early progenitor state. Together, these data demonstrate that a conserved miRNA pathway controls a key step in the progression of temporal identity in retinal progenitors.
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Protogenin prevents premature apoptosis of rostral cephalic neural crest cells by activating the α5β1-integrin. Cell Death Dis 2013; 4:e651. [PMID: 23744351 PMCID: PMC3698544 DOI: 10.1038/cddis.2013.177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The bones and connective tissues of the murine jaws and skull are partly derived from cephalic neural crest cells (CNCCs). Here, we report that mice deficient of protogenin (Prtg) protein, an immunoglobulin domain-containing receptor expressed in the developing nervous system, have impairments of the palatine and skull. Data from lineage tracing experiments, expression patterns of neural crest cell (NCC) marker genes and detection of apoptotic cells indicate that the malformation of bones in Prtg-deficient mice is due to increased apoptosis of rostral CNCCs (R-CNCCs). Using a yeast two-hybrid screening, we found that Prtg interacts with Radil, a protein previously shown to affect the migration and survival of NCCs in zebrafish with unknown mechanism. Overexpression of Prtg induces translocation of Radil from cytoplasm to cell membrane in cultured AD293 cells. In addition, overexpression of Prtg and Radil activates α5β1-integrins to high-affinity conformational forms, which is further enhanced by the addition of Prtg ligand ERdj3 into cultured cells. Blockage of Radil by RNA interference abolishes the effect of ERdj3 and Prtg on the α5β1-integrin, suggesting that Radil acts downstream of Prtg. Prtg-deficient R-CNCCs display fewer activated α5β1-integrins in embryos, and these cells show reduced migratory ability in in vitro transwell assay. These results suggest that the inside-out activation of the α5β1-integrin mediated by ERdj3/Prtg/Radil signaling is crucial for proper functions of R-CNCCs, and the deficiency of this pathway causes premature apoptosis of a subset of R-CNCCs and malformation of craniofacial structures.
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Huang ZX, Chen ZS, Ke CH, Zhao J, You WW, Zhang J, Dong WT, Chen J. Pyrosequencing of Haliotis diversicolor transcriptomes: insights into early developmental molluscan gene expression. PLoS One 2012; 7:e51279. [PMID: 23236463 PMCID: PMC3517415 DOI: 10.1371/journal.pone.0051279] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/31/2012] [Indexed: 12/02/2022] Open
Abstract
Background The abalone Haliotis diversicolor is a good model for study of the settlement and metamorphosis, which are widespread marine ecological phenomena. However, information on the global gene backgrounds and gene expression profiles for the early development of abalones is lacking. Methodology/Principal Findings In this study, eight non-normalized and multiplex barcode-labeled transcriptomes were sequenced using a 454 GS system to cover the early developmental stages of the abalone H. diversicolor. The assembly generated 35,415 unigenes, of which 7,566 were assigned GO terms. A global gene expression profile containing 636 scaffolds/contigs was constructed and was proven reliable using qPCR evaluation. It indicated that there may be existing dramatic phase transitions. Bioprocesses were proposed, including the ‘lock system’ in mature eggs, the collagen shells of the trochophore larvae and the development of chambered extracellular matrix (ECM) structures within the earliest postlarvae. Conclusion This study globally details the first 454 sequencing data for larval stages of H. diversicolor. A basic analysis of the larval transcriptomes and cluster of the gene expression profile indicates that each stage possesses a batch of specific genes that are indispensable during embryonic development, especially during the two-cell, trochophore and early postlarval stages. These data will provide a fundamental resource for future physiological works on abalones, revealing the mechanisms of settlement and metamorphosis at the molecular level.
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Affiliation(s)
- Zi-Xia Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Zhi-Sen Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Cai-Huan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jing Zhao
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Wei-Wei You
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jie Zhang
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Wei-Ting Dong
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
| | - Jun Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, People’s Republic of China
- Department of Marine Biology, College of Ocean and Earth Sciences, Xiamen University, Xiamen, People’s Republic of China
- * E-mail:
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Yamakawa T, Yamada K, Sasamura T, Nakazawa N, Kanai M, Suzuki E, Fortini ME, Matsuno K. Deficient Notch signaling associated with neurogenic pecanex is compensated for by the unfolded protein response in Drosophila. Development 2011; 139:558-67. [PMID: 22190636 DOI: 10.1242/dev.073858] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Notch (N) signaling machinery is evolutionarily conserved and regulates a broad spectrum of cell-specification events, through local cell-cell communication. pecanex (pcx) encodes a multi-pass transmembrane protein of unknown function, widely found from Drosophila to humans. The zygotic and maternal loss of pcx in Drosophila causes a neurogenic phenotype (hyperplasia of the embryonic nervous system), suggesting that pcx might be involved in N signaling. Here, we established that Pcx is a component of the N-signaling pathway. Pcx was required upstream of the membrane-tethered and the nuclear forms of activated N, probably in N signal-receiving cells, suggesting that pcx is required prior to or during the activation of N. pcx overexpression revealed that Pcx resides in the endoplasmic reticulum (ER). Disruption of pcx function resulted in enlargement of the ER that was not attributable to the reduced N signaling activity. In addition, hyper-induction of the unfolded protein response (UPR) by the expression of activated Xbp1 or dominant-negative Heat shock protein cognate 3 suppressed the neurogenic phenotype and ER enlargement caused by the absence of pcx. A similar suppression of these phenotypes was induced by overexpression of O-fucosyltransferase 1, an N-specific chaperone. Taking these results together, we speculate that the reduction in N signaling in embryos lacking pcx function might be attributable to defective ER functions, which are compensated for by upregulation of the UPR and possibly by enhancement of N folding. Our results indicate that the ER plays a previously unrecognized role in N signaling and that this ER function depends on pcx activity.
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Affiliation(s)
- Tomoko Yamakawa
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510 Japan
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Watanabe Y, Nakamura H. Nuclear translocation of intracellular domain of Protogenin by proteolytic cleavage. Dev Growth Differ 2011; 54:167-76. [PMID: 22150322 DOI: 10.1111/j.1440-169x.2011.01315.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protogenin (PRTG) is a transmembrane protein of immunoglobulin superfamily, which has multiple roles in embryogenesis as a receptor or an adhesion molecule. In this study, we present sequential proteolytic cleavage of PRTG. The cleavage first occurs at the extracellular domain, then at the interface of the transmembrane and the intracellular domain by γ-secretase, which results in the release of the intracellular domain of PRTG (PRTG-ICD). PRTG-ICD contains putative nuclear localization signal (NLS) at its N-terminal, and translocates to the nucleus in cultured cells and in the neuroepithelial cells of chick embryos. We propose that the PRTG-ICD is cleaved by γ-secretase and translocates to the nucleus, which is potentially implicated in signaling for neural differentiation and in cell adhesion mediated by PRTG.
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Affiliation(s)
- Yuji Watanabe
- Department of Molecular Neurobiology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan.
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Sinkkonen ST, Starlinger V, Galaiya DJ, Laske RD, Myllykangas S, Oshima K, Heller S. Serial analysis of gene expression in the chicken otocyst. J Assoc Res Otolaryngol 2011; 12:697-710. [PMID: 21853378 DOI: 10.1007/s10162-011-0286-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 08/02/2011] [Indexed: 10/17/2022] Open
Abstract
The inner ear arises from multipotent placodal precursors that are gradually committed to the otic fate and further differentiate into all inner ear cell types, with the exception of a few immigrating neural crest-derived cells. The otocyst plays a pivotal role during inner ear development: otic progenitor cells sub-compartmentalize into non-sensory and prosensory domains, giving rise to individual vestibular and auditory organs and their associated ganglia. The genes and pathways underlying this progressive subdivision and differentiation process are not entirely known. The goal of this study was to identify a comprehensive set of genes expressed in the chicken otocyst using the serial analysis of gene expression (SAGE) method. Our analysis revealed several hundred transcriptional regulators, potential signaling proteins, and receptors. We identified a substantial collection of genes that were previously known in the context of inner ear development, but we also found many new candidate genes, such as SOX4, SOX5, SOX7, SOX8, SOX11, and SOX18, which previously were not known to be expressed in the developing inner ear. Despite its limitation of not being all-inclusive, the generated otocyst SAGE library is a practical bioinformatics tool to study otocyst gene expression and to identify candidate genes for developmental studies.
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Affiliation(s)
- Saku T Sinkkonen
- Departments of Otolaryngology-Head & Neck Surgery and Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305-5739, USA
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Protogenin mediates cell adhesion for ingression and re-epithelialization of paraxial mesodermal cells. Dev Biol 2010; 351:13-24. [PMID: 21129372 DOI: 10.1016/j.ydbio.2010.11.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/10/2010] [Accepted: 11/19/2010] [Indexed: 11/22/2022]
Abstract
In the avian embryo, precursor cells of the paraxial mesoderm that reside in the epiblast ingress through the primitive streak and migrate bilaterally in an anterolateral direction. Herein, we report on the roles of Protogenin (PRTG), an immunoglobulin superfamily protein expressed on the surface of the ingressing and migrating cells that give rise to the paraxial mesoderm, in paraxial mesoderm development. An aggregation assay using L-cells showed that PRTG mediates homophilic cell adhesion. Overexpression of PRTG in the presumptive paraxial mesoderm delayed mesodermal cell migration due to augmented adhesiveness. In contrast, siRNA knockdown of PRTG impaired successive ingression of epiblast cells and disorganized the epithelial structure of the somites. These results suggest that PRTG mediates cell adhesion to regulate continuous ingression of cells giving rise to the paraxial mesodermal lineage, as well as tissue integrity.
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Takahashi KF, Kiyoshima T, Kobayashi I, Xie M, Yamaza H, Fujiwara H, Ookuma Y, Nagata K, Wada H, Sakai T, Terada Y, Sakai H. Protogenin, a new member of the immunoglobulin superfamily, is implicated in the development of the mouse lower first molar. BMC DEVELOPMENTAL BIOLOGY 2010; 10:115. [PMID: 21108791 PMCID: PMC3014897 DOI: 10.1186/1471-213x-10-115] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 11/25/2010] [Indexed: 01/21/2023]
Abstract
Background Protogenin (Prtg) has been identified as a gene which is highly expressed in the mouse mandible at embryonic day 10.5 (E10.5) by a cDNA subtraction method between mandibles at E10.5 and E12.0. Prtg is a new member of the deleted in colorectal carcinoma (DCC) family, which is composed of DCC, Neogenin, Punc and Nope. Although these members play an important role in the development of the embryonic central nervous system, recent research has also shed on the non-neuronal organization. However, very little is known regarding the fetal requirement of the non-neuronal organization for Prtg and how this may be associated with the tooth germ development. This study examined the functional implications of Prtg in the developing tooth germ of the mouse lower first molar. Results Ptrg is preferentially expressed in the early stage of organogenesis. Prtg mRNA and protein were widely expressed in the mesenchymal cells in the mandible at E10.5. The oral epithelial cells were also positive for Prtg. The expression intensity of Prtg after E12.0 was markedly reduced in the mesenchymal cells of the mandible, and was restricted to the area where the tooth bud was likely to be formed. Signals were also observed in the epithelial cells of the tooth germ. Weak signals were observed in the inner enamel epithelial cells at E16.0 and E18.0. An inhibition assay using a hemagglutinating virus of Japan-liposome containing Prtg antisense-phosphorothioated-oligodeoxynucleotide (AS-S-ODN) in cultured mandibles at E10.5 showed a significant growth inhibition in the tooth germ. The relationship between Prtg and the odontogenesis-related genes was examined in mouse E10.5 mandible, and we verified that the Bmp-4 expression had significantly been decreased in the mouse E10.5 mandible 24 hr after treatment with Prtg AS-S-ODN. Conclusion These results indicated that the Prtg might be related to the initial morphogenesis of the tooth germ leading to the differentiation of the inner enamel epithelial cells in the mouse lower first molar. A better understanding of the Prtg function might thus play a critical role in revealing a precious mechanism in tooth germ development.
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Affiliation(s)
- Keiko F Takahashi
- Laboratory of Oral Pathology and Medicine, Faculty of Dental Science, Kyushu University, Fukuoka 812-8582, Japan.
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