1
|
Lee U, Zhang Y, Zhu Y, Luo AC, Gong L, Tremmel DM, Kim Y, Villarreal VS, Wang X, Lin RZ, Cui M, Ma M, Yuan K, Wang K, Chen K, Melero-Martin JM. Robust differentiation of human pluripotent stem cells into mural progenitor cells via transient activation of NKX3.1. Nat Commun 2024; 15:8392. [PMID: 39349465 PMCID: PMC11442894 DOI: 10.1038/s41467-024-52678-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 09/13/2024] [Indexed: 10/02/2024] Open
Abstract
Mural cells are central to vascular integrity and function. In this study, we demonstrate the innovative use of the transcription factor NKX3.1 to guide the differentiation of human induced pluripotent stem cells into mural progenitor cells (iMPCs). By transiently activating NKX3.1 in mesodermal intermediates, we developed a method that diverges from traditional growth factor-based differentiation techniques. This approach efficiently generates a robust iMPC population capable of maturing into diverse functional mural cell subtypes, including smooth muscle cells and pericytes. These iMPCs exhibit key mural cell functionalities such as contractility, deposition of extracellular matrix, and the ability to support endothelial cell-mediated vascular network formation in vivo. Our study not only underscores the fate-determining significance of NKX3.1 in mural cell differentiation but also highlights the therapeutic potential of these iMPCs. We envision these insights could pave the way for a broader use of iMPCs in vascular biology and regenerative medicine.
Collapse
Affiliation(s)
- Umji Lee
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Yadong Zhang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yonglin Zhu
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Allen Chilun Luo
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
| | - Liyan Gong
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Daniel M Tremmel
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Yunhye Kim
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | - Xi Wang
- Department of Biological and Environmental Engineering, Cornell University, NY, USA
| | - Ruei-Zeng Lin
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Miao Cui
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA
| | - Minglin Ma
- Department of Biological and Environmental Engineering, Cornell University, NY, USA
| | - Ke Yuan
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Kai Wang
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China.
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Juan M Melero-Martin
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| |
Collapse
|
2
|
Dhaliwal NK, Weng OY, Li Y. Protocol for the efficient and inducible generation of CRISPR-Cas9-edited human cortical neurons from the iCas9-iNgn2 hPSCs. STAR Protoc 2024; 5:103352. [PMID: 39342621 DOI: 10.1016/j.xpro.2024.103352] [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: 06/17/2024] [Revised: 08/09/2024] [Accepted: 09/10/2024] [Indexed: 10/01/2024] Open
Abstract
Generation of CRISPR-Cas9-edited cortical neurons from human pluripotent stem cells (hPSCs) enables the study of gene functions and neural disease mechanisms. Here, we present a protocol for developing iCas9-iNgn2 hPSC, an inducible cell line that allows the simultaneous induction of the neuralizing transcription factor Ngn2 and the Cas9 nuclease to rapidly generate edited human cortical neurons. We describe the steps of the protocol from transducing iCas9-iNgn2 with guide RNA-containing lentivirus to producing edited cortical neurons in about 2 weeks. For complete details on the use and execution of this protocol, please refer to Dhaliwal et al.1.
Collapse
Affiliation(s)
- Navroop K Dhaliwal
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada.
| | - Octavia Yifang Weng
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program in Neurosciences and Mental Health, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Physiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
3
|
Dowrey TW, Cranston SF, Skvir N, Lok Y, Gould B, Petrowitz B, Villar D, Shan J, James M, Dodge M, Belkina AC, Giadone RM, Milman S, Sebastiani P, Perls TT, Andersen SL, Murphy GJ. A longevity-specific bank of induced pluripotent stem cells from centenarians and their offspring. Aging Cell 2024:e14351. [PMID: 39319670 DOI: 10.1111/acel.14351] [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: 04/07/2024] [Revised: 08/02/2024] [Accepted: 09/05/2024] [Indexed: 09/26/2024] Open
Abstract
Centenarians provide a unique lens through which to study longevity, healthy aging, and resiliency. Moreover, models of human aging and resilience to disease that allow for the testing of potential interventions are virtually non-existent. We obtained and characterized over 96 centenarian and offspring peripheral blood samples including those connected to functional independence data highlighting resistance to disability and cognitive impairment. Targeted methylation arrays were used in molecular aging clocks to compare and contrast differences between biological and chronological age in these specialized subjects. Isolated peripheral blood mononuclear cells (PBMCs) from 20 of these subjects were then successfully reprogrammed into high-quality induced pluripotent stem cell (iPSC) lines which were functionally characterized for pluripotency, genomic stability, and the ability to undergo directed differentiation. The result of this work is a one-of-a-kind resource for studies of human longevity and resilience that can fuel the discovery and validation of novel therapeutics for aging-related disease.
Collapse
Affiliation(s)
- Todd W Dowrey
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- Section of Hematology and Medical Oncology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Samuel F Cranston
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- Section of Hematology and Medical Oncology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Nicholas Skvir
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- Section of Hematology and Medical Oncology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Yvonne Lok
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- Section of Hematology and Medical Oncology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Brian Gould
- Section of Geriatrics, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Bradley Petrowitz
- Section of Geriatrics, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Daniel Villar
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jidong Shan
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - Marianne James
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Mark Dodge
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
| | - Anna C Belkina
- Flow Cytometry Core Facility, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Richard M Giadone
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sofiya Milman
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - Paola Sebastiani
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts, USA
| | - Thomas T Perls
- Section of Geriatrics, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Stacy L Andersen
- Section of Geriatrics, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - George J Murphy
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, Massachusetts, USA
- Section of Hematology and Medical Oncology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
4
|
Wan M, Liu Y, Li D, Snyder R, Elkin L, Day C, Rodriguez J, Grunseich C, Mahley R, Watts J, Cheung V. The enhancer RNA, AANCR, regulates APOE expression in astrocytes and microglia. Nucleic Acids Res 2024; 52:10235-10254. [PMID: 39162226 PMCID: PMC11417409 DOI: 10.1093/nar/gkae696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/26/2024] [Accepted: 08/01/2024] [Indexed: 08/21/2024] Open
Abstract
Enhancers, critical regulatory elements within the human genome, are often transcribed into enhancer RNAs. The dysregulation of enhancers leads to diseases collectively termed enhanceropathies. While it is known that enhancers play a role in diseases by regulating gene expression, the specific mechanisms by which individual enhancers cause diseases are not well understood. Studies of individual enhancers are needed to fill this gap. This study delves into the role of APOE-activating noncoding RNA, AANCR, in the central nervous system, elucidating its function as a genetic modifier in Alzheimer's Disease. We employed RNA interference, RNaseH-mediated degradation, and single-molecule RNA fluorescence in situ hybridization to demonstrate that mere transcription of AANCR is insufficient; rather, its transcripts are crucial for promoting APOE expression. Our findings revealed that AANCR is induced by ATM-mediated ERK phosphorylation and subsequent AP-1 transcription factor activation. Once activated, AANCR enhances APOE expression, which in turn imparts an inflammatory phenotype to astrocytes. These findings demonstrate that AANCR is a key enhancer RNA in some cell types within the nervous system, pivotal for regulating APOE expression and influencing inflammatory responses, underscoring its potential as a therapeutic target in neurodegenerative diseases.
Collapse
Affiliation(s)
- Ma Wan
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Yaojuan Liu
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dongjun Li
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan J Snyder
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Lillian B Elkin
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Christopher R Day
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Joseph Rodriguez
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Christopher Grunseich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert W Mahley
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Pathology and Medicine, University of California, San Francisco, CA, USA
| | - Jason A Watts
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Vivian G Cheung
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
5
|
Le NT, Chu N, Joshi G, Higgins NR, Nebie O, Adelakun N, Butts M, Monteiro MJ. Prion protein pathology in Ubiquilin 2 models of ALS. Neurobiol Dis 2024; 201:106674. [PMID: 39299489 DOI: 10.1016/j.nbd.2024.106674] [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: 06/10/2024] [Revised: 09/16/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024] Open
Abstract
Mutations in UBQLN2 cause ALS and frontotemporal dementia (FTD). The pathological signature in UBQLN2 cases is deposition of highly unusual types of inclusions in the brain and spinal cord that stain positive for UBQLN2. However, what role these inclusions play in pathogenesis remains unclear. Here we show cellular prion protein (PrPC) is found in UBQLN2 inclusions in both mouse and human neuronal induced pluripotent (IPSC) models of UBQLN2 mutations, evidenced by the presence of aggregated forms of PrPC with UBQLN2 inclusions. Turnover studies indicated that the P497H UBQLN2 mutation slows PrPC protein degradation and leads to mislocalization of PrPC in the cytoplasm. Immunoprecipitation studies indicated UBQLN2 and PrPC bind together in a complex. The abnormalities in PrPC caused by UBQLN2 mutations may be relevant in disease pathogenesis.
Collapse
Affiliation(s)
- Nhat T Le
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Nam Chu
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Gunjan Joshi
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States of America; Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Nicole R Higgins
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States of America; Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Ouada Nebie
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Niyi Adelakun
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Marie Butts
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, Columbus, OH, United States of America
| | - Mervyn J Monteiro
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, United States of America; Department of Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| |
Collapse
|
6
|
Jensen AMG, Raska J, Fojtik P, Monti G, Lunding M, Bartova S, Pospisilova V, van der Lee SJ, Van Dongen J, Bossaerts L, Van Broeckhoven C, Dols-Icardo O, Lléo A, Bellini S, Ghidoni R, Hulsman M, Petsko GA, Sleegers K, Bohaciakova D, Holstege H, Andersen OM. The SORL1 p.Y1816C variant causes impaired endosomal dimerization and autosomal dominant Alzheimer's disease. Proc Natl Acad Sci U S A 2024; 121:e2408262121. [PMID: 39226352 PMCID: PMC11406263 DOI: 10.1073/pnas.2408262121] [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: 04/30/2024] [Accepted: 07/16/2024] [Indexed: 09/05/2024] Open
Abstract
Truncating genetic variants of SORL1, encoding the endosome recycling receptor SORLA, have been accepted as causal of Alzheimer's disease (AD). However, most genetic variants observed in SORL1 are missense variants, for which it is complicated to determine the pathogenicity level because carriers come from pedigrees too small to be informative for penetrance estimations. Here, we describe three unrelated families in which the SORL1 coding missense variant rs772677709, that leads to a p.Y1816C substitution, segregates with Alzheimer's disease. Further, we investigate the effect of SORLA p.Y1816C on receptor maturation, cellular localization, and trafficking in cell-based assays. Under physiological circumstances, SORLA dimerizes within the endosome, allowing retromer-dependent trafficking from the endosome to the cell surface, where the luminal part is shed into the extracellular space (sSORLA). Our results showed that the p.Y1816C mutant impairs SORLA homodimerization in the endosome, leading to decreased trafficking to the cell surface and less sSORLA shedding. These trafficking defects of the mutant receptor can be rescued by the expression of the SORLA 3Fn-minireceptor. Finally, we find that iPSC-derived neurons with the engineered p.Y1816C mutation have enlarged endosomes, a defining cytopathology of AD. Our studies provide genetic as well as functional evidence that the SORL1 p.Y1816C variant is causal for AD. The partial penetrance of the mutation suggests this mutation should be considered in clinical genetic screening of multiplex early-onset AD families.
Collapse
Affiliation(s)
| | - Jan Raska
- Department of Histology and Embryology, Faculty of Medicine, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne's Faculty Hospital Brno 60200, Brno, Czech Republic
| | - Petr Fojtik
- Department of Biomedicine, Aarhus University, Aarhus C DK8000, Denmark
- Department of Histology and Embryology, Faculty of Medicine, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne's Faculty Hospital Brno 60200, Brno, Czech Republic
| | - Giulia Monti
- Department of Biomedicine, Aarhus University, Aarhus C DK8000, Denmark
| | - Melanie Lunding
- Department of Biomedicine, Aarhus University, Aarhus C DK8000, Denmark
| | - Simona Bartova
- Department of Histology and Embryology, Faculty of Medicine, Brno 62500, Czech Republic
| | - Veronika Pospisilova
- Department of Histology and Embryology, Faculty of Medicine, Brno 62500, Czech Republic
| | - Sven J van der Lee
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam University Medical Center 1081 HV, Amsterdam, The Netherlands
| | - Jasper Van Dongen
- Complex Genetics of Alzheimer's Disease Group, Vlaams Instituut voor Biotechnologie (VIB) Center for Molecular Neurology, VIB 2000, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp 2000, Antwerp, Belgium
| | - Liene Bossaerts
- Department of Biomedical Sciences, University of Antwerp 2000, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, VIB 2000, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Department of Biomedical Sciences, University of Antwerp 2000, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, VIB 2000, Antwerp, Belgium
| | - Oriol Dols-Icardo
- Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona 08041, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas, CIBERNED 28029, Madrid, Spain
| | - Alberto Lléo
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas, CIBERNED 28029, Madrid, Spain
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau-Hospital de Sant Pau, Universitat Autònoma de Barcelona 08025, Barcelona, Spain
| | - Sonia Bellini
- Molecular Markers Laboratory, Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Centro San Giovanni di Dio Fatebenefratelli 25125, Brescia, Italy
| | - Roberta Ghidoni
- Molecular Markers Laboratory, Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Centro San Giovanni di Dio Fatebenefratelli 25125, Brescia, Italy
| | - Marc Hulsman
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam University Medical Center 1081 HV, Amsterdam, The Netherlands
| | - Gregory A Petsko
- Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, Vlaams Instituut voor Biotechnologie (VIB) Center for Molecular Neurology, VIB 2000, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp 2000, Antwerp, Belgium
| | - Dasa Bohaciakova
- Department of Histology and Embryology, Faculty of Medicine, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne's Faculty Hospital Brno 60200, Brno, Czech Republic
| | - Henne Holstege
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam University Medical Center 1081 HV, Amsterdam, The Netherlands
| | - Olav M Andersen
- Department of Biomedicine, Aarhus University, Aarhus C DK8000, Denmark
| |
Collapse
|
7
|
Tomasello DL, Barrasa MI, Mankus D, Alarcon KI, Lytton-Jean AKR, Liu XS, Jaenisch R. Mitochondrial dysfunction and increased reactive oxygen species production in MECP2 mutant astrocytes and their impact on neurons. Sci Rep 2024; 14:20565. [PMID: 39232000 PMCID: PMC11374804 DOI: 10.1038/s41598-024-71040-y] [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: 05/21/2024] [Accepted: 08/23/2024] [Indexed: 09/06/2024] Open
Abstract
Studies on MECP2 function and its implications in Rett Syndrome (RTT) have traditionally centered on neurons. Here, using human embryonic stem cell (hESC) lines, we modeled MECP2 loss-of-function to explore its effects on astrocyte (AST) development and dysfunction in the brain. Ultrastructural analysis of RTT hESC-derived cerebral organoids revealed significantly smaller mitochondria compared to controls (CTRs), particularly pronounced in glia versus neurons. Employing a multiomics approach, we observed increased gene expression and accessibility of a subset of nuclear-encoded mitochondrial genes upon mutation of MECP2 in ASTs compared to neurons. Analysis of hESC-derived ASTs showed reduced mitochondrial respiration and altered key proteins in the tricarboxylic acid cycle and electron transport chain in RTT versus CTRs. Additionally, RTT ASTs exhibited increased cytosolic amino acids under basal conditions, which were depleted upon increased energy demands. Notably, mitochondria isolated from RTT ASTs exhibited increased reactive oxygen species and influenced neuronal activity when transferred to cortical neurons. These findings underscore MECP2 mutation's differential impact on mitochondrial and metabolic pathways in ASTs versus neurons, suggesting that dysfunctional AST mitochondria may contribute to RTT pathophysiology by affecting neuronal health.
Collapse
Affiliation(s)
| | | | - David Mankus
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katia I Alarcon
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Abigail K R Lytton-Jean
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - X Shawn Liu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
8
|
Oakley DH, Chung M, Abrha S, Hyman BT, Frosch MP. β-Amyloid species production and tau phosphorylation in iPSC-neurons with reference to neuropathologically characterized matched donor brains. J Neuropathol Exp Neurol 2024; 83:772-782. [PMID: 38874454 PMCID: PMC11333826 DOI: 10.1093/jnen/nlae053] [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] [Indexed: 06/15/2024] Open
Abstract
A basic assumption underlying induced pluripotent stem cell (iPSC) models of neurodegeneration is that disease-relevant pathologies present in brain tissue are also represented in donor-matched cells differentiated from iPSCs. However, few studies have tested this hypothesis in matched iPSCs and neuropathologically characterized donated brain tissues. To address this, we assessed iPSC-neuron production of β-amyloid (Aβ) Aβ40, Aβ42, and Aβ43 in 24 iPSC lines matched to donor brains with primary neuropathologic diagnoses of sporadic AD (sAD), familial AD (fAD), control, and other neurodegenerative disorders. Our results demonstrate a positive correlation between Aβ43 production by fAD iPSC-neurons and Aβ43 accumulation in matched brain tissues but do not reveal a substantial correlation in soluble Aβ species between control or sAD iPSC-neurons and matched brains. However, we found that the ApoE4 genotype is associated with increased Aβ production by AD iPSC-neurons. Pathologic tau phosphorylation was found to be increased in AD and fAD iPSC-neurons compared to controls and positively correlated with the relative abundance of longer-length Aβ species produced by these cells. Taken together, our results demonstrate that sAD-predisposing genetic factors influence iPSC-neuron phenotypes and that these cells are capturing disease-relevant and patient-specific components of the amyloid cascade.
Collapse
Affiliation(s)
- Derek H Oakley
- Harvard Medical School, Boston, MA, United States
- C.S. Kubik Laboratory for Neuropathology, Boston, MA, United States
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| | - Mirra Chung
- Harvard Medical School, Boston, MA, United States
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Sara Abrha
- Harvard Medical School, Boston, MA, United States
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Bradley T Hyman
- Harvard Medical School, Boston, MA, United States
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, United States
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Matthew P Frosch
- Harvard Medical School, Boston, MA, United States
- C.S. Kubik Laboratory for Neuropathology, Boston, MA, United States
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| |
Collapse
|
9
|
Zlamalova E, Rodger C, Greco F, Cheers SR, Kleniuk J, Nadadhur AG, Kadlecova Z, Reid E. Atlastin-1 regulates endosomal tubulation and lysosomal proteolysis in human cortical neurons. Neurobiol Dis 2024; 199:106556. [PMID: 38851544 PMCID: PMC11300884 DOI: 10.1016/j.nbd.2024.106556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024] Open
Abstract
Mutation of the ATL1 gene is one of the most common causes of hereditary spastic paraplegia (HSP), a group of genetic neurodegenerative conditions characterised by distal axonal degeneration of the corticospinal tract axons. Atlastin-1, the protein encoded by ATL1, is one of three mammalian atlastins, which are homologous dynamin-like GTPases that control endoplasmic reticulum (ER) morphology by fusing tubules to form the three-way junctions that characterise ER networks. However, it is not clear whether atlastin-1 is required for correct ER morphology in human neurons and if so what the functional consequences of lack of atlastin-1 are. Using CRISPR-inhibition we generated human cortical neurons lacking atlastin-1. We demonstrate that ER morphology was altered in these neurons, with a reduced number of three-way junctions. Neurons lacking atlastin-1 had longer endosomal tubules, suggestive of defective tubule fission. This was accompanied by reduced lysosomal proteolytic capacity. As well as demonstrating that atlastin-1 is required for correct ER morphology in human neurons, our results indicate that lack of a classical ER-shaping protein such as atlastin-1 may cause altered endosomal tubulation and lysosomal proteolytic dysfunction. Furthermore, they strengthen the idea that defective lysosome function contributes to the pathogenesis of a broad group of HSPs, including those where the primary localisation of the protein involved is not at the endolysosomal system.
Collapse
Affiliation(s)
- Eliska Zlamalova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Catherine Rodger
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Francesca Greco
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Samuel R Cheers
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Julia Kleniuk
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Aishwarya G Nadadhur
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Zuzana Kadlecova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Evan Reid
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK.
| |
Collapse
|
10
|
Park SJ, Son SM, Barbosa AD, Wrobel L, Stamatakou E, Squitieri F, Balmus G, Rubinsztein DC. Nuclear proteasomes buffer cytoplasmic proteins during autophagy compromise. Nat Cell Biol 2024:10.1038/s41556-024-01488-7. [PMID: 39209961 DOI: 10.1038/s41556-024-01488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/18/2024] [Indexed: 09/04/2024]
Abstract
Autophagy is a conserved pathway where cytoplasmic contents are engulfed by autophagosomes, which then fuse with lysosomes enabling their degradation. Mutations in core autophagy genes cause neurological conditions, and autophagy defects are seen in neurodegenerative diseases such as Parkinson's disease and Huntington's disease. Thus, we have sought to understand the cellular pathway perturbations that autophagy-perturbed cells are vulnerable to by seeking negative genetic interactions such as synthetic lethality in autophagy-null human cells using available data from yeast screens. These revealed that loss of proteasome and nuclear pore complex components cause synergistic viability changes akin to synthetic fitness loss in autophagy-null cells. This can be attributed to the cytoplasm-to-nuclear transport of proteins during autophagy deficiency and subsequent degradation of these erstwhile cytoplasmic proteins by nuclear proteasomes. As both autophagy and cytoplasm-to-nuclear transport are defective in Huntington's disease, such cells are more vulnerable to perturbations of proteostasis due to these synthetic interactions.
Collapse
Affiliation(s)
- So Jung Park
- Department of Medical Genetics, and Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
| | - Sung Min Son
- Department of Medical Genetics, and Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
| | - Antonio Daniel Barbosa
- Department of Medical Genetics, and Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
| | - Lidia Wrobel
- Department of Medical Genetics, and Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
| | - Eleanna Stamatakou
- Department of Medical Genetics, and Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK
| | - Ferdinando Squitieri
- Huntington and Rare Diseases Unit, Fondazione IRCCS Casa Sollievo della Sofferenza Research Hospital, San Giovanni Rotondo, Italy
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, Cluj-Napoca, Romania
| | - David C Rubinsztein
- Department of Medical Genetics, and Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK.
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, UK.
| |
Collapse
|
11
|
Erwin AL, Chang ML, Fernandez MG, Attili D, Russ JE, Sutanto R, Pinarbasi ES, Bekier M, Brant TS, Hahn T, Dykstra M, Thomas D, Li X, Baldridge RD, Tank EMH, Barmada SJ, Mosalaganti S. Molecular Visualization of Neuronal TDP43 Pathology In Situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608477. [PMID: 39229019 PMCID: PMC11370468 DOI: 10.1101/2024.08.19.608477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Nuclear exclusion and cytoplasmic accumulation of the RNA-binding protein TDP43 are characteristic of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Despite this, the origin and ultrastructure of cytosolic TDP43 deposits remain unknown. Accumulating evidence suggests that abnormal RNA homeostasis can drive pathological TDP43 mislocalization, enhancing RNA misprocessing due to loss of nuclear TDP43 and engendering a cycle that ends in cell death. Here, we show that adding small monovalent oligonucleotides successfully recapitulates pathological TDP43 mislocalization and aggregation in iPSC-derived neurons (iNeurons). By employing a multimodal in situ cryo-correlative light and electron microscopy pipeline, we examine how RNA influences the localization and aggregation of TDP43 in near-native conditions. We find that mislocalized TDP43 forms ordered fibrils within lysosomes and autophagosomes in iNeurons as well as in patient tissue, and provide the first high-resolution snapshots of TDP43 aggregates in situ. In so doing, we provide a cellular model for studying initial pathogenic events underlying ALS, FTLD, and related TDP43-proteinopathies.
Collapse
Affiliation(s)
- Amanda L Erwin
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Matthew L Chang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Martin G Fernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, 48109, United States
| | - Durga Attili
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Jennifer E Russ
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Renaldo Sutanto
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Emile S Pinarbasi
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Michael Bekier
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Tyler S Brant
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Terry Hahn
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Megan Dykstra
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, United States
| | - Dafydd Thomas
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Ryan D Baldridge
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, United States
| | - Elizabeth M H Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, United States
- Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| |
Collapse
|
12
|
Wu R, Ye Y, Dong D, Zhang Z, Wang S, Li Y, Wright N, Redding-Ochoa J, Chang K, Xu S, Tu X, Zhu C, Ostrow LW, Roca X, Troncoso JC, Wu B, Sun S. Disruption of nuclear speckle integrity dysregulates RNA splicing in C9ORF72-FTD/ALS. Neuron 2024:S0896-6273(24)00570-1. [PMID: 39181135 DOI: 10.1016/j.neuron.2024.07.025] [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: 11/28/2023] [Revised: 06/15/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024]
Abstract
Expansion of an intronic (GGGGCC)n repeat within the C9ORF72 gene is the most common genetic cause of both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) (C9-FTD/ALS), characterized with aberrant repeat RNA foci and noncanonical translation-produced dipeptide repeat (DPR) protein inclusions. Here, we elucidate that the (GGGGCC)n repeat RNA co-localizes with nuclear speckles and alters their phase separation properties and granule dynamics. Moreover, the essential nuclear speckle scaffold protein SRRM2 is sequestered into the poly-GR cytoplasmic inclusions in the C9-FTD/ALS mouse model and patient postmortem tissues, exacerbating the nuclear speckle dysfunction. Impaired nuclear speckle integrity induces global exon skipping and intron retention in human iPSC-derived neurons and causes neuronal toxicity. Similar alternative splicing changes can be found in C9-FTD/ALS patient postmortem tissues. This work identified novel molecular mechanisms of global RNA splicing defects caused by impaired nuclear speckle function in C9-FTD/ALS and revealed novel potential biomarkers or therapeutic targets.
Collapse
Affiliation(s)
- Rong Wu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yingzhi Ye
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Physiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daoyuan Dong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhe Zhang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaopeng Wang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yini Li
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Noelle Wright
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Javier Redding-Ochoa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaohai Xu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Xueting Tu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chengzhang Zhu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lyle W Ostrow
- Department of Neurology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19122, USA
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shuying Sun
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
13
|
Hao YH, Borenstein-Auerbach N, Grichuk A, Li L, Lafita-Navarro MC, Fang S, Nogueira P, Kim J, Xu L, Shay JW, Conacci-Sorrell M. MYC-Mediated Inhibition of ARNT2 Uncovers a Key Tumor Suppressor in Glioblastoma. RESEARCH SQUARE 2024:rs.3.rs-4810280. [PMID: 39184078 PMCID: PMC11343292 DOI: 10.21203/rs.3.rs-4810280/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Tumor initiation and progression rely on intricate cellular pathways that promote proliferation while suppressing differentiation, yet the importance of pathways inhibiting differentiation in cancer remains incompletely understood. Here, we reveal a novel mechanism centered on the repression of the neuronal-specific transcription factor ARNT2 by the MYC oncogene that governs the balance between proliferation and differentiation. We found that MYC coordinates the transcriptional repression of ARNT2 through the activity of polycomb repressive complex 2 (PRC2). Notably, ARNT2, highly and specifically expressed in the central nervous system, is diminished in glioblastoma, inversely correlating with patient survival. Utilizing in vitro and in vivo models, we demonstrate that ARNT2 knockout (KO) exerts no discernible effect on the in vitro proliferation of glioblastoma cells, but significantly enhances the growth of glioblastoma cells in vivo. Conversely, ARNT2 overexpression severely dampens the growth of fully transformed glioblastoma cells subcutaneously or orthotopically xenografted in mice. Mechanistically, ARNT2 depletion diminishes differentiation and enhances stemness of glioblastoma cells. Our findings provide new insights into the complex mechanisms used by oncogenes to limit differentiation in cancer cells and define ARNT2 as a tumor suppressor in glioblastoma.
Collapse
|
14
|
Anitei M, Bruno F, Valkova C, Dau T, Cirri E, Mestres I, Calegari F, Kaether C. IER3IP1-mutations cause microcephaly by selective inhibition of ER-Golgi transport. Cell Mol Life Sci 2024; 81:334. [PMID: 39115595 PMCID: PMC11335259 DOI: 10.1007/s00018-024-05386-x] [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: 02/05/2024] [Revised: 07/13/2024] [Accepted: 07/27/2024] [Indexed: 08/22/2024]
Abstract
Mutations in the IER3IP1 (Immediate Early Response-3 Interacting Protein 1) gene can give rise to MEDS1 (Microcephaly with Simplified Gyral Pattern, Epilepsy, and Permanent Neonatal Diabetes Syndrome-1), a severe condition leading to early childhood mortality. The small endoplasmic reticulum (ER)-membrane protein IER3IP1 plays a non-essential role in ER-Golgi transport. Here, we employed secretome and cell-surface proteomics to demonstrate that the absence of IER3IP1 results in the mistrafficking of proteins crucial for neuronal development and survival, including FGFR3, UNC5B and SEMA4D. This phenomenon correlates with the distension of ER membranes and increased lysosomal activity. Notably, the trafficking of cargo receptor ERGIC53 and KDEL-receptor 2 are compromised, with the latter leading to the anomalous secretion of ER-localized chaperones. Our investigation extended to in-utero knock-down of Ier3ip1 in mouse embryo brains, revealing a morphological phenotype in newborn neurons. In summary, our findings provide insights into how the loss or mutation of a 10 kDa small ER-membrane protein can cause a fatal syndrome.
Collapse
Affiliation(s)
- Mihaela Anitei
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstr 11, 07745, Jena, Germany
| | - Francesca Bruno
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstr 11, 07745, Jena, Germany
| | - Christina Valkova
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstr 11, 07745, Jena, Germany
| | - Therese Dau
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstr 11, 07745, Jena, Germany
| | - Emilio Cirri
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstr 11, 07745, Jena, Germany
| | - Iván Mestres
- Center for Regenerative Therapies, TU-Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - Federico Calegari
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstr 11, 07745, Jena, Germany
| | - Christoph Kaether
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Beutenbergstr 11, 07745, Jena, Germany.
- Center for Regenerative Therapies, TU-Dresden, Fetscherstraße 105, 01307, Dresden, Germany.
| |
Collapse
|
15
|
Dong D, Zhang Z, Li Y, Latallo MJ, Wang S, Nelson B, Wu R, Krishnan G, Gao FB, Wu B, Sun S. Poly-GR repeats associated with ALS/FTD gene C9ORF72 impair translation elongation and induce a ribotoxic stress response in neurons. Sci Signal 2024; 17:eadl1030. [PMID: 39106320 DOI: 10.1126/scisignal.adl1030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 07/05/2024] [Indexed: 08/09/2024]
Abstract
Hexanucleotide repeat expansion in the C9ORF72 gene is the most frequent inherited cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The expansion results in multiple dipeptide repeat proteins, among which arginine-rich poly-GR proteins are highly toxic to neurons and decrease the rate of protein synthesis. We investigated whether the effect on protein synthesis contributes to neuronal dysfunction and degeneration. We found that the expression of poly-GR proteins inhibited global translation by perturbing translation elongation. In iPSC-differentiated neurons, the translation of transcripts with relatively slow elongation rates was further slowed, and stalled, by poly-GR. Elongation stalling increased ribosome collisions and induced a ribotoxic stress response (RSR) mediated by ZAKα that increased the phosphorylation of the kinase p38 and promoted cell death. Knockdown of ZAKα or pharmacological inhibition of p38 ameliorated poly-GR-induced toxicity and improved the survival of iPSC-derived neurons from patients with C9ORF72-ALS/FTD. Our findings suggest that targeting the RSR may be neuroprotective in patients with ALS/FTD caused by repeat expansion in C9ORF72.
Collapse
Affiliation(s)
- Daoyuan Dong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhe Zhang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yini Li
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Malgorzata J Latallo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaopeng Wang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Blake Nelson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Wu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gopinath Krishnan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Fen-Biao Gao
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shuying Sun
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
16
|
Segura-Roman A, Citron YR, Shin M, Sindoni N, Maya-Romero A, Rapp S, Goul C, Mancias JD, Zoncu R. Autophagosomes coordinate an AKAP11-dependent regulatory checkpoint that shapes neuronal PKA signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606738. [PMID: 39211170 PMCID: PMC11361107 DOI: 10.1101/2024.08.06.606738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Protein Kinase A (PKA) is regulated spatially and temporally via scaffolding of its catalytic (Cα/β) and regulatory (RI/RII) subunits by the A-kinase-anchoring proteins (AKAP). PKA engages in poorly understood interactions with autophagy, a key degradation pathway for neuronal cell homeostasis, partly via its AKAP11 scaffold. Mutations in AKAP11 drive schizophrenia and bipolar disorders (SZ-BP) through unknown mechanisms. Through proteomic-based analysis of immunopurified lysosomes, we identify the Cα-RIα-AKAP11 holocomplex as a prominent autophagy-associated protein kinase complex. AKAP11 scaffolds Cα-RIα to the autophagic machinery via its LC3-interacting region (LIR), enabling both PKA regulation by upstream signals, and its autophagy-dependent degradation. We identify Ser83 on the RIα linker-hinge region as an AKAP11-dependent phospho-residue that modulates RIα-Cα binding and cAMP-induced PKA activation. Decoupling AKAP11-PKA from autophagy alters Ser83 phosphorylation, supporting an autophagy-dependent checkpoint for PKA signaling. Ablating AKAP11 in induced pluripotent stem cell-derived neurons reveals dysregulation of multiple pathways for neuronal homeostasis. Thus, the autophagosome is a novel platform that modulate PKA signaling, providing a possible mechanistic link to SZ/BP pathophysiology.
Collapse
|
17
|
Diarra S, Ghosh S, Cissé L, Coulibaly T, Yalcouyé A, Harmison G, Diallo S, Diallo SH, Coulibaly O, Schindler A, Cissé CAK, Maiga AB, Bamba S, Samassekou O, Khokha MK, Mis EK, Lakhani SA, Donovan FX, Jacobson S, Blackstone C, Guinto CO, Landouré G, Bonifacino JS, Fischbeck KH, Grunseich C. AP2A2 mutation and defective endocytosis in a Malian family with hereditary spastic paraplegia. Neurobiol Dis 2024; 198:106537. [PMID: 38772452 PMCID: PMC11209852 DOI: 10.1016/j.nbd.2024.106537] [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: 01/13/2024] [Revised: 04/17/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024] Open
Abstract
Hereditary spastic paraplegia (HSP) comprises a large group of neurogenetic disorders characterized by progressive lower extremity spasticity. Neurological evaluation and genetic testing were completed in a Malian family with early-onset HSP. Three children with unaffected consanguineous parents presented with symptoms consistent with childhood-onset complicated HSP. Neurological evaluation found lower limb weakness, spasticity, dysarthria, seizures, and intellectual disability. Brain MRI showed corpus callosum thinning with cortical and spinal cord atrophy, and an EEG detected slow background in the index patient. Whole exome sequencing identified a homozygous missense variant in the adaptor protein (AP) complex 2 alpha-2 subunit (AP2A2) gene. Western blot analysis showed reduced levels of AP2A2 in patient-iPSC derived neuronal cells. Endocytosis of transferrin receptor (TfR) was decreased in patient-derived neurons. In addition, we observed increased axon initial segment length in patient-derived neurons. Xenopus tropicalis tadpoles with ap2a2 knockout showed cerebral edema and progressive seizures. Immunoprecipitation of the mutant human AP-2-appendage alpha-C construct showed defective binding to accessory proteins. We report AP2A2 as a novel genetic entity associated with HSP and provide functional data in patient-derived neuron cells and a frog model. These findings expand our understanding of the mechanism of HSP and improve the genetic diagnosis of this condition.
Collapse
Affiliation(s)
- Salimata Diarra
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States; Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Saikat Ghosh
- Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
| | - Lassana Cissé
- Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Thomas Coulibaly
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
| | - Abdoulaye Yalcouyé
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - George Harmison
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | | | | | - Oumar Coulibaly
- Service de Chirurgie Pédiatrique, CHU du Gabriel Touré, Bamako, Mali
| | - Alice Schindler
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - Cheick A K Cissé
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Alassane B Maiga
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Salia Bamba
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Oumar Samassekou
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Mustafa K Khokha
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Emily K Mis
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Saquib A Lakhani
- Yale University, Pediatric Genomics Discovery Program, Department of Pediatrics, New Haven, CT, United States
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, NHGRI, NIH, Bethesda, MD, United States
| | - Steve Jacobson
- Neuroimmunology Division, NINDS, NIH, Bethesda, MD, United States
| | - Craig Blackstone
- Movement Disorders Division, Department of Neurology, Harvard Medicine School, Massachusetts General Hospital, Boston, MA, United States
| | - Cheick O Guinto
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Guida Landouré
- Université des Sciences, des Techniques, et des Technologies de Bamako (USTTB), Bamako, Mali; Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States; Service de Neurologie, CHU du Point "G", Bamako, Mali
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, NICHD, NIH, Bethesda, MD, United States
| | | | | |
Collapse
|
18
|
Snyder A, Ryan VH, Hawrot J, Lawton S, Ramos DM, Qi YA, Johnson KR, Reed X, Johnson NL, Kollasch AW, Duffy MF, VandeVrede L, Cochran JN, Miller BL, Toro C, Bielekova B, Marks DS, Yokoyama JS, Kwan JY, Cookson MR, Ward ME. An ANXA11 P93S variant dysregulates TDP-43 and causes corticobasal syndrome. Alzheimers Dement 2024; 20:5220-5235. [PMID: 38923692 PMCID: PMC11350008 DOI: 10.1002/alz.13915] [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: 02/01/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION Variants of uncertain significance (VUS) surged with affordable genetic testing, posing challenges for determining pathogenicity. We examine the pathogenicity of a novel VUS P93S in Annexin A11 (ANXA11) - an amyotrophic lateral sclerosis/frontotemporal dementia-associated gene - in a corticobasal syndrome kindred. Established ANXA11 mutations cause ANXA11 aggregation, altered lysosomal-RNA granule co-trafficking, and transactive response DNA binding protein of 43 kDa (TDP-43) mis-localization. METHODS We described the clinical presentation and explored the phenotypic diversity of ANXA11 variants. P93S's effect on ANXA11 function and TDP-43 biology was characterized in induced pluripotent stem cell-derived neurons alongside multiomic neuronal and microglial profiling. RESULTS ANXA11 mutations were linked to corticobasal syndrome cases. P93S led to decreased lysosome colocalization, neuritic RNA, and nuclear TDP-43 with cryptic exon expression. Multiomic microglial signatures implicated immune dysregulation and interferon signaling pathways. DISCUSSION This study establishes ANXA11 P93S pathogenicity, broadens the phenotypic spectrum of ANXA11 mutations, underscores neuronal and microglial dysfunction in ANXA11 pathophysiology, and demonstrates the potential of cellular models to determine variant pathogenicity. HIGHLIGHTS ANXA11 P93S is a pathogenic variant. Corticobasal syndrome is part of the ANXA11 phenotypic spectrum. Hybridization chain reaction fluorescence in situ hybridization (HCR FISH) is a new tool for the detection of cryptic exons due to TDP-43-related loss of splicing regulation. Microglial ANXA11 and related immune pathways are important drivers of disease. Cellular models are powerful tools for adjudicating variants of uncertain significance.
Collapse
Affiliation(s)
- Allison Snyder
- Neurogenetics BranchNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMarylandUSA
| | - Veronica H. Ryan
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- National Institute of General Medical SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - James Hawrot
- Neurogenetics BranchNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMarylandUSA
| | - Sydney Lawton
- Neurogenetics BranchNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMarylandUSA
| | - Daniel M. Ramos
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
| | - Y. Andy Qi
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
| | - Kory R. Johnson
- Intramural Bioinformatics CoreNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMarylandUSA
| | - Xylena Reed
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
| | - Nicholas L. Johnson
- Center for Alzheimer's and Related DementiasNational Institutes of HealthBethesdaMarylandUSA
- DataTecnica LLCWashingtonDistrict of ColumbiaUSA
| | - Aaron W. Kollasch
- Department of Systems BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Megan F. Duffy
- Cell Biology and Gene Expression SectionLaboratory of Neurogenetics, National Institute on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Lawren VandeVrede
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | | | - Bruce L. Miller
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Camilo Toro
- Undiagnosed Diseases ProgramNational Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Bibiana Bielekova
- Neuroimmunological Diseases SectionNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Debora S. Marks
- Department of Systems BiologyHarvard Medical SchoolBostonMassachusettsUSA
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Jennifer S. Yokoyama
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Justin Y. Kwan
- National Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMarylandUSA
| | - Mark R. Cookson
- Cell Biology and Gene Expression SectionLaboratory of Neurogenetics, National Institute on AgingNational Institutes of HealthBethesdaMarylandUSA
| | - Michael E. Ward
- Neurogenetics BranchNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMarylandUSA
| |
Collapse
|
19
|
Szebényi K, Vargová I, Petrova V, Turečková J, Gibbons GM, Řehořová M, Abdelgawad M, Sándor A, Marekova D, Kwok JCF, Jendelová P, Fawcett JW, Lakatos A. Inhibition of PHLDA3 expression in human superoxide dismutase 1-mutant amyotrophic lateral sclerosis astrocytes protects against neurotoxicity. Brain Commun 2024; 6:fcae244. [PMID: 39144751 PMCID: PMC11323778 DOI: 10.1093/braincomms/fcae244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 05/06/2024] [Accepted: 07/24/2024] [Indexed: 08/16/2024] Open
Abstract
Pleckstrin homology-like domain family A-member 3 (PHLDA3) has recently been identified as a player in adaptive and maladaptive cellular stress pathways. The outcome of pleckstrin homology-like domain family A-member 3 signalling was shown to vary across different cell types and states. It emerges that its expression and protein level are highly increased in amyotrophic lateral sclerosis (ALS) patient-derived astrocytes. Whether it orchestrates a supportive or detrimental function remains unexplored in the context of neurodegenerative pathologies. To directly address the role of pleckstrin homology-like domain family A-member 3 in healthy and ALS astrocytes, we used overexpression and knockdown strategies. We generated cultures of primary mouse astrocytes and also human astrocytes from control and ALS patient-derived induced pluripotent stem cells harbouring the superoxide dismutase 1 mutation. Then, we assessed astrocyte viability and the impact of their secretome on oxidative stress responses in human stem cell-derived cortical and spinal neuronal cultures. Here, we show that PHLDA3 overexpression or knockdown in control astrocytes does not significantly affect astrocyte viability or reactive oxygen species production. However, PHLDA3 knockdown in ALS astrocytes diminishes reactive oxygen species concentrations in their supernatants, indicating that pleckstrin homology-like domain family A-member 3 can facilitate stress responses in cells with altered homeostasis. In support, supernatants of PHLDA3-silenced ALS and even control spinal astrocytes with a lower pleckstrin homology-like domain family A-member 3 protein content could prevent sodium arsenite-induced stress granule formation in spinal neurons. Our findings provide evidence that reducing pleckstrin homology-like domain family A-member 3 levels may transform astrocytes into a more neurosupportive state relevant to targeting non-cell autonomous ALS pathology.
Collapse
Affiliation(s)
- Kornélia Szebényi
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, CB2 0PY, UK
- Research Centre of Natural Sciences, Institute of Molecular Life Sciences, Budapest, 1117, Hungary
| | - Ingrid Vargová
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 20, Czech Republic
| | - Veselina Petrova
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, CB2 0PY, UK
| | - Jana Turečková
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 20, Czech Republic
| | - George M Gibbons
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, CB2 0PY, UK
| | - Monika Řehořová
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 20, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, 150 06, Czech Republic
| | - Mai Abdelgawad
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, CB2 0PY, UK
| | - Alexandra Sándor
- Research Centre of Natural Sciences, Institute of Molecular Life Sciences, Budapest, 1117, Hungary
- Doctoral School of Molecular Medicine, Semmelweis University, Budapest, 1085, Hungary
| | - Dana Marekova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 20, Czech Republic
| | - Jessica C F Kwok
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 20, Czech Republic
- School of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Pavla Jendelová
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 20, Czech Republic
- Second Faculty of Medicine, Charles University, Prague, 150 06, Czech Republic
| | - James W Fawcett
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, CB2 0PY, UK
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, 142 20, Czech Republic
| | - András Lakatos
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, CB2 0PY, UK
- MRC-WT Cambridge Stem Cell Institute, Biomedical Campus, Cambridge, CB2 0AW, UK
| |
Collapse
|
20
|
Konno T, Parutto P, Crapart CC, Davì V, Bailey DMD, Awadelkareem MA, Hockings C, Brown AI, Xiang KM, Agrawal A, Chambers JE, Vander Werp MJ, Koning KM, Elfari LM, Steen S, Metzakopian E, Westrate LM, Koslover EF, Avezov E. Endoplasmic reticulum morphology regulation by RTN4 modulates neuronal regeneration by curbing luminal transport. Cell Rep 2024; 43:114357. [PMID: 38955182 DOI: 10.1016/j.celrep.2024.114357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/01/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024] Open
Abstract
Cell functions rely on intracellular transport systems distributing bioactive molecules with high spatiotemporal accuracy. The endoplasmic reticulum (ER) tubular network constitutes a system for delivering luminal solutes, including Ca2+, across the cell periphery. How the ER structure enables this nanofluidic transport system is unclear. Here, we show that ER membrane-localized reticulon 4 (RTN4/Nogo) is sufficient to impose neurite outgrowth inhibition in human cortical neurons while acting as an ER morphoregulator. Improving ER transport visualization methodologies combined with optogenetic Ca2+ dynamics imaging and in silico modeling, we observed that ER luminal transport is modulated by ER tubule narrowing and dilation, proportional to the amount of RTN4. Excess RTN4 limited ER luminal transport and Ca2+ release, while RTN4 elimination reversed the effects. The described morphoregulatory effect of RTN4 defines the capacity of the ER for peripheral Ca2+ delivery for physiological releases and thus may constitute a mechanism for controlling the (re)generation of neurites.
Collapse
Affiliation(s)
- Tasuku Konno
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Pierre Parutto
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Cécile C Crapart
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Valentina Davì
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | | | - Mosab Ali Awadelkareem
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK; Department of Neuroscience Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Colin Hockings
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Aidan I Brown
- Department of Physics, University of California, San Diego, 9500 Gilman Dr. #0374, La Jolla, CA 92093-0374, USA; Department of Physics, Toronto Metropolitan University, Toronto, ON M5B 2K3, Canada
| | | | - Anamika Agrawal
- Department of Physics, University of California, San Diego, 9500 Gilman Dr. #0374, La Jolla, CA 92093-0374, USA
| | - Joseph E Chambers
- Cambridge Institute for Medical Research (CIMR), Department of Medicine, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, UK
| | - Molly J Vander Werp
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI 49546, USA
| | - Katherine M Koning
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI 49546, USA
| | - Louis Mounir Elfari
- Wellcome-MRC Cambridge Stem Cell Institute Advanced Imaging Facility, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Sam Steen
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI 49546, USA
| | - Emmanouil Metzakopian
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK
| | - Laura M Westrate
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI 49546, USA
| | - Elena F Koslover
- Department of Physics, University of California, San Diego, 9500 Gilman Dr. #0374, La Jolla, CA 92093-0374, USA.
| | - Edward Avezov
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Cambridge CB2 0AH, UK.
| |
Collapse
|
21
|
Bazarek SF, Krenn MJ, Shah SB, Mandeville RM, Brown JM. Novel Technologies to Address the Lower Motor Neuron Injury and Augment Reconstruction in Spinal Cord Injury. Cells 2024; 13:1231. [PMID: 39056812 PMCID: PMC11274462 DOI: 10.3390/cells13141231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Lower motor neuron (LMN) damage results in denervation of the associated muscle targets and is a significant yet under-appreciated component of spinal cord injury (SCI). Denervated muscle undergoes a progressive degeneration and fibro-fatty infiltration that eventually renders the muscle non-viable unless reinnervated within a limited time window. The distal nerve deprived of axons also undergoes degeneration and fibrosis making it less receptive to axons. In this review, we describe the LMN injury associated with SCI and its clinical consequences. The process of degeneration of the muscle and nerve is broken down into the primary components of the neuromuscular circuit and reviewed, including the nerve and Schwann cells, the neuromuscular junction, and the muscle. Finally, we discuss three promising strategies to reverse denervation atrophy. These include providing surrogate axons from local sources; introducing stem cell-derived spinal motor neurons into the nerve to provide the missing axons; and finally, instituting a training program of high-energy electrical stimulation to directly rehabilitate these muscles. Successful interventions for denervation atrophy would significantly expand reconstructive options for cervical SCI and could be transformative for the predominantly LMN injuries of the conus medullaris and cauda equina.
Collapse
Affiliation(s)
- Stanley F. Bazarek
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (S.F.B.); (M.J.K.); (R.M.M.)
- Department of Neurological Surgery, University Hospitals-Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Matthias J. Krenn
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (S.F.B.); (M.J.K.); (R.M.M.)
- Department of Neurosurgery, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Center for Neuroscience and Neurological Recovery, Methodist Rehabilitation Center, Jackson, MS 39216, USA
- Spinal Cord Injury Medicine and Research Services, VA Medical Center, Jackson, MS 39216, USA
| | - Sameer B. Shah
- Departments of Orthopedic Surgery and Bioengineering, University of California-San Diego, La Jolla, CA 92093, USA;
- Research Division, VA San Diego Medical Center, San Diego, CA 92161, USA
| | - Ross M. Mandeville
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (S.F.B.); (M.J.K.); (R.M.M.)
| | - Justin M. Brown
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; (S.F.B.); (M.J.K.); (R.M.M.)
| |
Collapse
|
22
|
Macarelli V, Harding EC, Gershlick DC, Merkle FT. A Short Sequence Targets Transmembrane Proteins to Primary Cilia. Cells 2024; 13:1156. [PMID: 38995007 PMCID: PMC11240719 DOI: 10.3390/cells13131156] [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: 05/11/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
Primary cilia are finger-like sensory organelles that extend from the bodies of most cell types and have a distinct lipid and protein composition from the plasma membrane. This partitioning is maintained by a diffusion barrier that restricts the entry of non-ciliary proteins, and allows the selective entry of proteins harboring a ciliary targeting sequence (CTS). However, CTSs are not stereotyped and previously reported sequences are insufficient to drive efficient ciliary localisation across diverse cell types. Here, we describe a short peptide sequence that efficiently targets transmembrane proteins to primary cilia in all tested cell types, including human neurons. We generate human-induced pluripotent stem cell (hiPSC) lines stably expressing a transmembrane construct bearing an extracellular HaloTag and intracellular fluorescent protein, which enables the bright, specific labeling of primary cilia in neurons and other cell types to facilitate studies of cilia in health and disease. We demonstrate the utility of this resource by developing an image analysis pipeline for the automated measurement of primary cilia to detect changes in their length associated with altered signaling or disease state.
Collapse
Affiliation(s)
- Viviana Macarelli
- Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Edward C Harding
- Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Florian T Merkle
- Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| |
Collapse
|
23
|
Fuentealba LM, Pizarro H, Marzolo MP. OCRL1 Deficiency Affects the Intracellular Traffic of ApoER2 and Impairs Reelin-Induced Responses. Biomolecules 2024; 14:799. [PMID: 39062513 PMCID: PMC11274606 DOI: 10.3390/biom14070799] [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: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Lowe Syndrome (LS) is a rare X-linked disorder characterized by renal dysfunction, cataracts, and several central nervous system (CNS) anomalies. The mechanisms underlying the neurological dysfunction in LS remain unclear, albeit they share some phenotypic characteristics similar to the deficiency or dysfunction of the Reelin signaling, a relevant pathway with roles in CNS development and neuronal functions. In this study, we investigated the role of OCRL1, an inositol polyphosphate 5-phosphatase encoded by the OCRL gene, mutated in LS, focusing on its impact on endosomal trafficking and receptor recycling in human neuronal cells. Specifically, we tested the effects of OCRL1 deficiency in the trafficking and signaling of ApoER2/LRP8, a receptor for the ligand Reelin. We found that loss of OCRL1 impairs ApoER2 intracellular trafficking, leading to reduced receptor expression and decreased levels at the plasma membrane. Additionally, human neurons deficient in OCRL1 showed impairments in ApoER2/Reelin-induced responses. Our findings highlight the critical role of OCRL1 in regulating ApoER2 endosomal recycling and its impact on the ApoER2/Reelin signaling pathway, providing insights into potential mechanisms underlying the neurological manifestations of LS.
Collapse
Affiliation(s)
| | | | - María-Paz Marzolo
- Laboratorio de Tráfico Intracelular y Señalización, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 7810128, Chile; (L.M.F.); (H.P.)
| |
Collapse
|
24
|
Dykstra MM, Weskamp K, Gómez NB, Waksmacki J, Tank E, Glineburg MR, Snyder A, Pinarbasi E, Bekier M, Li X, Bai J, Shahzad S, Nedumaran J, Wieland C, Stewart C, Willey S, Grotewold N, McBride J, Moran JJ, Suryakumar AV, Lucas M, Tessier P, Ward M, Todd P, Barmada SJ. TDP43 autoregulation gives rise to shortened isoforms that are tightly controlled by both transcriptional and post-translational mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601776. [PMID: 39005384 PMCID: PMC11244999 DOI: 10.1101/2024.07.02.601776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The nuclear RNA-binding protein TDP43 is integrally involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previous studies uncovered N-terminal TDP43 isoforms that are predominantly cytosolic in localization, highly prone to aggregation, and enriched in susceptible spinal motor neurons. In healthy cells, however, these shortened (s)TDP43 isoforms are difficult to detect in comparison to full-length (fl)TDP43, raising questions regarding their origin and selective regulation. Here, we show that sTDP43 is created as a byproduct of TDP43 autoregulation and cleared by nonsense mediated RNA decay (NMD). The sTDP43-encoding transcripts that escape NMD can lead to toxicity but are rapidly degraded post-translationally. Circumventing these regulatory mechanisms by overexpressing sTDP43 results in neurodegeneration in vitro and in vivo via N-terminal oligomerization and impairment of flTDP43 splicing activity, in addition to RNA binding-dependent gain-of-function toxicity. Collectively, these studies highlight endogenous mechanisms that tightly regulate sTDP43 expression and provide insight into the consequences of aberrant sTDP43 accumulation in disease.
Collapse
Affiliation(s)
- Megan M. Dykstra
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
| | - Kaitlin Weskamp
- Chemistry Department, Nebraska Wesleyan University, Lincoln, NE
| | - Nicolás B. Gómez
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Jacob Waksmacki
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Elizabeth Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - M. Rebecca Glineburg
- Biological Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA
| | | | - Emile Pinarbasi
- Department of Neurology, University of Michigan, Ann Arbor, MI
- Neuropathology, Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI
| | - Michael Bekier
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Xingli Li
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Jen Bai
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | | | - Juno Nedumaran
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Clare Wieland
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Corey Stewart
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
| | - Sydney Willey
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
| | - Nikolas Grotewold
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
| | - Jonathon McBride
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI
| | - John J. Moran
- Atlanta Pediatric Research Alliance, Emory University, Atlanta, GA
| | | | - Michael Lucas
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
| | - Peter Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
| | | | - Peter Todd
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
- Veterans Affairs Medical Center, Ann Arbor, MI
| | - Sami J. Barmada
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI
- Graduate Program in Cell and Molecular Biology, University of Michigan, Ann Arbor, MI
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
| |
Collapse
|
25
|
Peterman EL, Ploessl DS, Galloway KE. Accelerating Diverse Cell-Based Therapies Through Scalable Design. Annu Rev Chem Biomol Eng 2024; 15:267-292. [PMID: 38594944 DOI: 10.1146/annurev-chembioeng-100722-121610] [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] [Indexed: 04/11/2024]
Abstract
Augmenting cells with novel, genetically encoded functions will support therapies that expand beyond natural capacity for immune surveillance and tissue regeneration. However, engineering cells at scale with transgenic cargoes remains a challenge in realizing the potential of cell-based therapies. In this review, we introduce a range of applications for engineering primary cells and stem cells for cell-based therapies. We highlight tools and advances that have launched mammalian cell engineering from bioproduction to precision editing of therapeutically relevant cells. Additionally, we examine how transgenesis methods and genetic cargo designs can be tailored for performance. Altogether, we offer a vision for accelerating the translation of innovative cell-based therapies by harnessing diverse cell types, integrating the expanding array of synthetic biology tools, and building cellular tools through advanced genome writing techniques.
Collapse
Affiliation(s)
- Emma L Peterman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Deon S Ploessl
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| |
Collapse
|
26
|
Chung TH, Zhuravskaya A, Makeyev EV. Regulation potential of transcribed simple repeated sequences in developing neurons. Hum Genet 2024; 143:875-895. [PMID: 38153590 PMCID: PMC11294396 DOI: 10.1007/s00439-023-02626-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Simple repeated sequences (SRSs), defined as tandem iterations of microsatellite- to satellite-sized DNA units, occupy a substantial part of the human genome. Some of these elements are known to be transcribed in the context of repeat expansion disorders. Mounting evidence suggests that the transcription of SRSs may also contribute to normal cellular functions. Here, we used genome-wide bioinformatics approaches to systematically examine SRS transcriptional activity in cells undergoing neuronal differentiation. We identified thousands of long noncoding RNAs containing >200-nucleotide-long SRSs (SRS-lncRNAs), with hundreds of these transcripts significantly upregulated in the neural lineage. We show that SRS-lncRNAs often originate from telomere-proximal regions and that they have a strong potential to form multivalent contacts with a wide range of RNA-binding proteins. Our analyses also uncovered a cluster of neurally upregulated SRS-lncRNAs encoded in a centromere-proximal part of chromosome 9, which underwent an evolutionarily recent segmental duplication. Using a newly established in vitro system for rapid neuronal differentiation of induced pluripotent stem cells, we demonstrate that at least some of the bioinformatically predicted SRS-lncRNAs, including those encoded in the segmentally duplicated part of chromosome 9, indeed increase their expression in developing neurons to readily detectable levels. These and other lines of evidence suggest that many SRSs may be expressed in a cell type and developmental stage-specific manner, providing a valuable resource for further studies focused on the functional consequences of SRS-lncRNAs in the normal development of the human brain, as well as in the context of neurodevelopmental disorders.
Collapse
Affiliation(s)
- Tek Hong Chung
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK.
| |
Collapse
|
27
|
Ramadoss GN, Namaganda SJ, Hamilton JR, Sharma R, Chow KG, Macklin BL, Sun M, Liu JC, Fellmann C, Watry HL, Jin J, Perez BS, Sandoval Espinoza CR, Matia MP, Lu SH, Judge LM, Nussenzweig A, Adamson B, Murthy N, Doudna JA, Kampmann M, Conklin BR. Neuronal DNA repair reveals strategies to influence CRISPR editing outcomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600517. [PMID: 38979269 PMCID: PMC11230251 DOI: 10.1101/2024.06.25.600517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Genome editing is poised to revolutionize treatment of genetic diseases, but poor understanding and control of DNA repair outcomes hinders its therapeutic potential. DNA repair is especially understudied in nondividing cells like neurons, which must withstand decades of DNA damage without replicating. This lack of knowledge limits the efficiency and precision of genome editing in clinically relevant cells. To address this, we used induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to examine how postmitotic human neurons repair Cas9-induced DNA damage. We discovered that neurons can take weeks to fully resolve this damage, compared to just days in isogenic iPSCs. Furthermore, Cas9-treated neurons upregulated unexpected DNA repair genes, including factors canonically associated with replication. Manipulating this response with chemical or genetic perturbations allowed us to direct neuronal repair toward desired editing outcomes. By studying DNA repair in postmitotic human cells, we uncovered unforeseen challenges and opportunities for precise therapeutic editing.
Collapse
Affiliation(s)
- Gokul N Ramadoss
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA
| | | | - Jennifer R Hamilton
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Rohit Sharma
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | | | | | - Mengyuan Sun
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Jia-Cheng Liu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Christof Fellmann
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
| | | | - Julianne Jin
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA
| | - Barbara S Perez
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Cindy R Sandoval Espinoza
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
| | | | - Serena H Lu
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Luke M Judge
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Pediatrics, University of California, San Francisco, CA, 94158, USA
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Niren Murthy
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Department of Cellular & Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
- Department of Medicine, University of California, San Francisco, CA, 94158, USA
| |
Collapse
|
28
|
Kolesnikova V, Revishchin A, Fab L, Alekseeva A, Ryabova A, Pronin I, Usachev DY, Kopylov A, Pavlova G. GQIcombi application to subdue glioma via differentiation therapy. Front Oncol 2024; 14:1322795. [PMID: 38988707 PMCID: PMC11233813 DOI: 10.3389/fonc.2024.1322795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Current therapy protocols fail to cure high-grade gliomas and prevent recurrence. Therefore, novel approaches need to be developed. A re-programing of glioma cell fate is an alternative attractive way to stop tumor growth. The two-step protocol applies the antiproliferative GQ bi-(AID-1-T) and small molecule inducers with BDNF to trigger neural differentiation into terminally differentiated cells, and it is very effective on GB cell cultures. This original approach is a successful example of the "differentiation therapy". To demonstrate a versatility of this approach, in this publication we have extended a palette of cell cultures to gliomas of II, III and IV Grades, and proved an applicability of that version of differential therapy for a variety of tumor cells. We have justified a sequential mode of adding of GQIcombi components to the glioma cells. We have shown a significant retardation of tumor growth after a direct injection of GQIcombi into the tumor in rat brain, model 101/8. Thus, the proposed strategy of influencing on cancer cell growth is applicable to be further translated for therapy use.
Collapse
Affiliation(s)
- Varvara Kolesnikova
- Laboratory of Neurogenetics and Genetics Development, Institute of Higher Nervous Activity and Neurophysiology of Russian Academy of Sciences (RAS), Moscow, Russia
| | - Alexander Revishchin
- Laboratory of Neurogenetics and Genetics Development, Institute of Higher Nervous Activity and Neurophysiology of Russian Academy of Sciences (RAS), Moscow, Russia
| | - Lika Fab
- Laboratory of Neurogenetics and Genetics Development, Institute of Higher Nervous Activity and Neurophysiology of Russian Academy of Sciences (RAS), Moscow, Russia
| | - Anna Alekseeva
- Laboratory of Neurogenetics and Genetics Development, Institute of Higher Nervous Activity and Neurophysiology of Russian Academy of Sciences (RAS), Moscow, Russia
- Laboratory of Neuromorphology, Avtsyn Research Institute of Human Morphology of Federal State Budgetary Scientific Institution "Petrovsky National Research Centre of Surgery", Moscow, Russia
| | - Anastasia Ryabova
- Natural Sciences Center of Prokhorov General Physics Institute Russian Academy of Sciences (RAS), Moscow, Russia
| | - Igor Pronin
- Federal State Autonomous Institution «N. N. Burdenko National Medical Research Center of Neurosurgery» of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Dmitry Y Usachev
- Federal State Autonomous Institution «N. N. Burdenko National Medical Research Center of Neurosurgery» of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexey Kopylov
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russia
| | - Galina Pavlova
- Laboratory of Neurogenetics and Genetics Development, Institute of Higher Nervous Activity and Neurophysiology of Russian Academy of Sciences (RAS), Moscow, Russia
- Federal State Autonomous Institution «N. N. Burdenko National Medical Research Center of Neurosurgery» of the Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Genetics, Sechenov First Moscow State Medical University, Moscow, Russia
| |
Collapse
|
29
|
Lemieux MR, Freigassner B, Hanson JL, Thathey Z, Opp MR, Hoeffer CA, Link CD. Multielectrode array characterization of human induced pluripotent stem cell derived neurons in co-culture with primary human astrocytes. PLoS One 2024; 19:e0303901. [PMID: 38917115 PMCID: PMC11198861 DOI: 10.1371/journal.pone.0303901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/02/2024] [Indexed: 06/27/2024] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) derived into neurons offer a powerful in vitro model to study cellular processes. One method to characterize functional network properties of these cells is using multielectrode arrays (MEAs). MEAs can measure the electrophysiological activity of cellular cultures for extended periods of time without disruption. Here we used WTC11 hiPSCs with a doxycycline-inducible neurogenin 2 (NGN2) transgene differentiated into neurons co-cultured with primary human astrocytes. We achieved a synchrony index ∼0.9 in as little as six-weeks with a mean firing rate of ∼13 Hz. Previous reports show that derived 3D brain organoids can take several months to achieve similar strong network burst synchrony. We also used this co-culture to model aspects of blood-brain barrier breakdown by using human serum. Our fully human co-culture achieved strong network burst synchrony in a fraction of the time of previous reports, making it an excellent first pass, high-throughput method for studying network properties and neurodegenerative diseases.
Collapse
Affiliation(s)
- Maddie R. Lemieux
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Bernhard Freigassner
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Jessica L. Hanson
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Zahra Thathey
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Mark R. Opp
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Charles A. Hoeffer
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Christopher D. Link
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States of America
| |
Collapse
|
30
|
Keuss MJ, Harley P, Ryadnov E, Jackson RE, Zanovello M, Wilkins OG, Barattucci S, Mehta PR, Oliveira MG, Parkes JE, Sinha A, Correa-Sánchez AF, Oliver PL, Fisher EM, Schiavo G, Shah M, Burrone J, Fratta P. Loss of TDP-43 induces synaptic dysfunction that is rescued by UNC13A splice-switching ASOs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599684. [PMID: 38979232 PMCID: PMC11230273 DOI: 10.1101/2024.06.20.599684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
TDP-43 loss of function induces multiple splicing changes, including a cryptic exon in the amyotrophic lateral sclerosis and fronto-temporal lobar degeneration risk gene UNC13A, leading to nonsense-mediated decay of UNC13A transcripts and loss of protein. UNC13A is an active zone protein with an integral role in coordinating pre-synaptic function. Here, we show TDP-43 depletion induces a severe reduction in synaptic transmission, leading to an asynchronous pattern of network activity. We demonstrate that these deficits are largely driven by a single cryptic exon in UNC13A. Antisense oligonucleotides targeting the UNC13A cryptic exon robustly rescue UNC13A protein levels and restore normal synaptic function, providing a potential new therapeutic approach for ALS and other TDP-43-related disorders.
Collapse
Affiliation(s)
- Matthew J. Keuss
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Peter Harley
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Eugeni Ryadnov
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Rachel E. Jackson
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | - Matteo Zanovello
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Oscar G. Wilkins
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Simone Barattucci
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Puja R. Mehta
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Marcio G. Oliveira
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | | | - Aparna Sinha
- Nucleic Acid Therapy Accelerator; Harwell, Didcot OX11 0FA, UK
| | | | - Peter L. Oliver
- Nucleic Acid Therapy Accelerator; Harwell, Didcot OX11 0FA, UK
| | - Elizabeth M.C. Fisher
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
| | - Giampietro Schiavo
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- UK Dementia Research Institute at University College London; London, WC1N 3BG, UK
| | - Mala Shah
- Department of Pharmacology, School of Pharmacy, University College London; London, WC1N 4AX, UK
| | - Juan Burrone
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London; London SE1 1UL, UK
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre and Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London; London, WC1N 3BG, UK
- The Francis Crick Institute; London, NW1 1AT, UK
| |
Collapse
|
31
|
Liu Y, Flamier A, Bell GW, Diao AJ, Whitfield TW, Wang HC, Wu Y, Schulte F, Friesen M, Guo R, Mitalipova M, Liu XS, Vos SM, Young RA, Jaenisch R. MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons. Neuron 2024; 112:1943-1958.e10. [PMID: 38697112 DOI: 10.1016/j.neuron.2024.04.007] [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: 11/17/2023] [Revised: 03/08/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type (WT) and mutant MECP2 molecules. MECP2 occupies CpG-rich promoter-proximal regions in over four thousand genes in human neurons, including a plethora of autism risk genes, together with RNA polymerase II (RNA Pol II). MECP2 directly interacts with RNA Pol II, and genes occupied by both proteins showed reduced expression in neurons with MECP2 patient mutations. We conclude that MECP2 acts as a positive cofactor for RNA Pol II gene expression at many neuronal genes that harbor CpG islands in promoter-proximal regions and that RTT is due, in part, to the loss of gene activity of these genes in neurons.
Collapse
Affiliation(s)
- Yi Liu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Anthony Flamier
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Annette Jun Diao
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Troy W Whitfield
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Hao-Che Wang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yizhe Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Max Friesen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ruisi Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Maisam Mitalipova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - X Shawn Liu
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| |
Collapse
|
32
|
McDonald KO, Lyons NMA, Gray LKC, Xu JB, Schoderboeck L, Hughes SM, Basak I. Transcription Factor-Mediated Generation of Dopaminergic Neurons from Human iPSCs-A Comparison of Methods. Cells 2024; 13:1016. [PMID: 38920646 PMCID: PMC11201854 DOI: 10.3390/cells13121016] [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: 02/23/2024] [Revised: 05/23/2024] [Accepted: 06/09/2024] [Indexed: 06/27/2024] Open
Abstract
Dopaminergic neurons are the predominant brain cells affected in Parkinson's disease. With the limited availability of live human brain dopaminergic neurons to study pathological mechanisms of Parkinson's disease, dopaminergic neurons have been generated from human-skin-cell-derived induced pluripotent stem cells. Originally, induced pluripotent stem-cell-derived dopaminergic neurons were generated using small molecules. These neurons took more than two months to mature. However, the transcription-factor-mediated differentiation of induced pluripotent stem cells has revealed quicker and cheaper methods to generate dopaminergic neurons. In this study, we compared and contrasted three protocols to generate induced pluripotent stem-cell-derived dopaminergic neurons using transcription-factor-mediated directed differentiation. We deviated from the established protocols using lentivirus transduction to stably integrate different transcription factors into the AAVS1 safe harbour locus of induced pluripotent stem cells. We used different media compositions to generate more than 90% of neurons in the culture, out of which more than 85% of the neurons were dopaminergic neurons within three weeks. Therefore, from our comparative study, we reveal that a combination of transcription factors along with small molecule treatment may be required to generate a pure population of human dopaminergic neurons.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Indranil Basak
- Department of Biochemistry, Brain Health Research Centre and Genetics Otago, University of Otago, Dunedin 9016, New Zealand
| |
Collapse
|
33
|
Carmen-Orozco RP, Tsao W, Ye Y, Sinha IR, Chang K, Trinh VT, Chung W, Bowden K, Troncoso JC, Blackshaw S, Hayes LR, Sun S, Wong PC, Ling JP. Elevated nuclear TDP-43 induces constitutive exon skipping. Mol Neurodegener 2024; 19:45. [PMID: 38853250 PMCID: PMC11163724 DOI: 10.1186/s13024-024-00732-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 05/20/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Cytoplasmic inclusions and loss of nuclear TDP-43 are key pathological features found in several neurodegenerative disorders, suggesting both gain- and loss-of-function mechanisms of disease. To study gain-of-function, TDP-43 overexpression has been used to generate in vitro and in vivo model systems. METHODS We analyzed RNA-seq datasets from mouse and human neurons overexpressing TDP-43 to explore species specific splicing patterns. We explored the dynamics between TDP-43 levels and exon repression in vitro. Furthermore we analyzed human brain samples and publicly available RNA datasets to explore the relationship between exon repression and disease. RESULTS Our study shows that excessive levels of nuclear TDP-43 protein lead to constitutive exon skipping that is largely species-specific. Furthermore, while aberrant exon skipping is detected in some human brains, it is not correlated with disease, unlike the incorporation of cryptic exons that occurs after loss of TDP-43. CONCLUSIONS Our findings emphasize the need for caution in interpreting TDP-43 overexpression data and stress the importance of controlling for exon skipping when generating models of TDP-43 proteinopathy.
Collapse
Affiliation(s)
- Rogger P Carmen-Orozco
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - William Tsao
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Yingzhi Ye
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Irika R Sinha
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Koping Chang
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Vickie T Trinh
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - William Chung
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Kyra Bowden
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Lindsey R Hayes
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Shuying Sun
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
| |
Collapse
|
34
|
Izadjoo S, Moritz KE, Khayrullina G, Bergman EM, Melvin BM, Stinson MW, Paulson SG, McCormack NM, Anderson KN, Lewis LA, Rotty JD, Burnett BG. Key features of the innate immune response is mediated by the immunoproteasome in microglia. RESEARCH SQUARE 2024:rs.3.rs-4467983. [PMID: 38883799 PMCID: PMC11177974 DOI: 10.21203/rs.3.rs-4467983/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Microglia are the resident immune cells of the central nervous system (CNS). We and others have shown that the inflammatory response of microglia is partially regulated by the immunoproteasome, an inducible form of the proteasome responsible for the generation of major histocompatibility complex (MHC) class I epitopes. While the role of the proteasome in the adaptive immune system is well established, emerging evidence suggests the immunoproteasome may have discrete functions in the innate immune response. Here, we show that inhibiting the immunoproteasome reduces the IFNγ-dependent induction of complement activator C1q, suppresses phagocytosis, and alters the cytokine expression profile in a microglial cell line and microglia derived from human inducible pluripotent stem cells. Moreover, we show that the immunoproteasome regulates the degradation of IκBα, a modulator of NF-κB signaling. Finally, we demonstrate that NADH prevents induction of the immunoproteasome, representing a potential pathway to suppress immunoproteasome-dependent immune responses.
Collapse
|
35
|
Gómez-Deza J, Nebiyou M, Alkaslasi MR, Nadal-Nicolás FM, Somasundaran P, Slavutsky AL, Ward ME, Li W, Watkins TA, Le Pichon CE. DLK-dependent axonal mitochondrial fission drives degeneration following axotomy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.30.526132. [PMID: 36778383 PMCID: PMC9915495 DOI: 10.1101/2023.01.30.526132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Currently there are no effective treatments for an array of neurodegenerative disorders to a large part because cell-based models fail to recapitulate disease. Here we developed a reproducible human iPSC-based model where laser axotomy causes retrograde axon degeneration leading to neuronal cell death. Time-lapse confocal imaging revealed that damage triggers an apoptotic wave of mitochondrial fission proceeding from the site of injury to the soma. We demonstrated that this apoptotic wave is locally initiated in the axon by dual leucine zipper kinase (DLK). We found that mitochondrial fission and resultant cell death are entirely dependent on phosphorylation of dynamin related protein 1 (DRP1) downstream of DLK, revealing a new mechanism by which DLK can drive apoptosis. Importantly, we show that CRISPR mediated Drp1 depletion protected mouse retinal ganglion neurons from degeneration after optic nerve crush. Our results provide a powerful platform for studying degeneration of human neurons, pinpoint key early events in damage related neural death and new focus for therapeutic intervention.
Collapse
Affiliation(s)
- Jorge Gómez-Deza
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Matthew Nebiyou
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Mor R Alkaslasi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | | | | | - Anastasia L Slavutsky
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Wei Li
- National Eye Institute, National Institutes of Health, Bethesda, United States
| | - Trent A Watkins
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
- Department of Neurology, University of California at San Francisco
| | - Claire E Le Pichon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| |
Collapse
|
36
|
Dou D, Aiken J, Holzbaur EL. RAB3 phosphorylation by pathogenic LRRK2 impairs trafficking of synaptic vesicle precursors. J Cell Biol 2024; 223:e202307092. [PMID: 38512027 PMCID: PMC10959120 DOI: 10.1083/jcb.202307092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/01/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Gain-of-function mutations in the LRRK2 gene cause Parkinson's disease (PD), characterized by debilitating motor and non-motor symptoms. Increased phosphorylation of a subset of RAB GTPases by LRRK2 is implicated in PD pathogenesis. We find that increased phosphorylation of RAB3A, a cardinal synaptic vesicle precursor (SVP) protein, disrupts anterograde axonal transport of SVPs in iPSC-derived human neurons (iNeurons) expressing hyperactive LRRK2-p.R1441H. Knockout of the opposing protein phosphatase 1H (PPM1H) in iNeurons phenocopies this effect. In these models, the compartmental distribution of synaptic proteins is altered; synaptophysin and synaptobrevin-2 become sequestered in the neuronal soma with decreased delivery to presynaptic sites along the axon. We find that RAB3A phosphorylation disrupts binding to the motor adaptor MADD, potentially preventing the formation of the RAB3A-MADD-KIF1A/1Bβ complex driving anterograde SVP transport. RAB3A hyperphosphorylation also disrupts interactions with RAB3GAP and RAB-GDI1. Our results reveal a mechanism by which pathogenic hyperactive LRRK2 may contribute to the altered synaptic homeostasis associated with characteristic non-motor and cognitive manifestations of PD.
Collapse
Affiliation(s)
- Dan Dou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayne Aiken
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L.F. Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
37
|
De Pace R, Ghosh S, Ryan VH, Sohn M, Jarnik M, Rezvan Sangsari P, Morgan NY, Dale RK, Ward ME, Bonifacino JS. Messenger RNA transport on lysosomal vesicles maintains axonal mitochondrial homeostasis and prevents axonal degeneration. Nat Neurosci 2024; 27:1087-1102. [PMID: 38600167 PMCID: PMC11156585 DOI: 10.1038/s41593-024-01619-1] [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: 05/16/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
In neurons, RNA granules are transported along the axon for local translation away from the soma. Recent studies indicate that some of this transport involves hitchhiking of RNA granules on lysosome-related vesicles. In the present study, we leveraged the ability to prevent transport of these vesicles into the axon by knockout of the lysosome-kinesin adaptor BLOC-one-related complex (BORC) to identify a subset of axonal mRNAs that depend on lysosome-related vesicles for transport. We found that BORC knockout causes depletion of a large group of axonal mRNAs mainly encoding ribosomal and mitochondrial/oxidative phosphorylation proteins. This depletion results in mitochondrial defects and eventually leads to axonal degeneration in human induced pluripotent stem cell (iPSC)-derived and mouse neurons. Pathway analyses of the depleted mRNAs revealed a mechanistic connection of BORC deficiency with common neurodegenerative disorders. These results demonstrate that mRNA transport on lysosome-related vesicles is critical for the maintenance of axonal homeostasis and that its failure causes axonal degeneration.
Collapse
Affiliation(s)
- Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Saikat Ghosh
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Veronica H Ryan
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mira Sohn
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michal Jarnik
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Paniz Rezvan Sangsari
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Nicole Y Morgan
- Biomedical Engineering and Physical Science Shared Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michael E Ward
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
38
|
Danačíková Š, Straka B, Daněk J, Kořínek V, Otáhal J. In vitro human cell culture models in a bench-to-bedside approach to epilepsy. Epilepsia Open 2024; 9:865-890. [PMID: 38637998 PMCID: PMC11145627 DOI: 10.1002/epi4.12941] [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: 10/23/2023] [Revised: 03/05/2024] [Accepted: 03/31/2024] [Indexed: 04/20/2024] Open
Abstract
Epilepsy is the most common chronic neurological disease, affecting nearly 1%-2% of the world's population. Current pharmacological treatment and regimen adjustments are aimed at controlling seizures; however, they are ineffective in one-third of the patients. Although neuronal hyperexcitability was previously thought to be mainly due to ion channel alterations, current research has revealed other contributing molecular pathways, including processes involved in cellular signaling, energy metabolism, protein synthesis, axon guidance, inflammation, and others. Some forms of drug-resistant epilepsy are caused by genetic defects that constitute potential targets for precision therapy. Although such approaches are increasingly important, they are still in the early stages of development. This review aims to provide a summary of practical aspects of the employment of in vitro human cell culture models in epilepsy diagnosis, treatment, and research. First, we briefly summarize the genetic testing that may result in the detection of candidate pathogenic variants in genes involved in epilepsy pathogenesis. Consequently, we review existing in vitro cell models, including induced pluripotent stem cells and differentiated neuronal cells, providing their specific properties, validity, and employment in research pipelines. We cover two methodological approaches. The first approach involves the utilization of somatic cells directly obtained from individual patients, while the second approach entails the utilization of characterized cell lines. The models are evaluated in terms of their research and clinical benefits, relevance to the in vivo conditions, legal and ethical aspects, time and cost demands, and available published data. Despite the methodological, temporal, and financial demands of the reviewed models they possess high potential to be used as robust systems in routine testing of pathogenicity of detected variants in the near future and provide a solid experimental background for personalized therapy of genetic epilepsies. PLAIN LANGUAGE SUMMARY: Epilepsy affects millions worldwide, but current treatments fail for many patients. Beyond traditional ion channel alterations, various genetic factors contribute to the disorder's complexity. This review explores how in vitro human cell models, either from patients or from cell lines, can aid in understanding epilepsy's genetic roots and developing personalized therapies. While these models require further investigation, they offer hope for improved diagnosis and treatment of genetic forms of epilepsy.
Collapse
Affiliation(s)
- Šárka Danačíková
- Laboratory of Developmental EpileptologyInstitute of Physiology of the Czech Academy of SciencesPragueCzech Republic
- Department of Pathophysiology, Second Faculty of MedicineCharles UniversityPragueCzech Republic
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
- Department of Physiology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Barbora Straka
- Neurogenetics Laboratory of the Department of Paediatric Neurology, Second Faculty of MedicineCharles University and Motol University Hospital, Full Member of the ERN EpiCAREPragueCzech Republic
| | - Jan Daněk
- Laboratory of Developmental EpileptologyInstitute of Physiology of the Czech Academy of SciencesPragueCzech Republic
| | - Vladimír Kořínek
- Laboratory of Cell and Developmental BiologyInstitute of Molecular Genetics of the Czech Academy of SciencesPragueCzech Republic
| | - Jakub Otáhal
- Laboratory of Developmental EpileptologyInstitute of Physiology of the Czech Academy of SciencesPragueCzech Republic
- Department of Pathophysiology, Second Faculty of MedicineCharles UniversityPragueCzech Republic
| |
Collapse
|
39
|
Tan J, Virtue S, Norris DM, Conway OJ, Yang M, Bidault G, Gribben C, Lugtu F, Kamzolas I, Krycer JR, Mills RJ, Liang L, Pereira C, Dale M, Shun-Shion AS, Baird HJ, Horscroft JA, Sowton AP, Ma M, Carobbio S, Petsalaki E, Murray AJ, Gershlick DC, Nathan JA, Hudson JE, Vallier L, Fisher-Wellman KH, Frezza C, Vidal-Puig A, Fazakerley DJ. Limited oxygen in standard cell culture alters metabolism and function of differentiated cells. EMBO J 2024; 43:2127-2165. [PMID: 38580776 PMCID: PMC11148168 DOI: 10.1038/s44318-024-00084-7] [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: 01/12/2024] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 04/07/2024] Open
Abstract
The in vitro oxygen microenvironment profoundly affects the capacity of cell cultures to model physiological and pathophysiological states. Cell culture is often considered to be hyperoxic, but pericellular oxygen levels, which are affected by oxygen diffusivity and consumption, are rarely reported. Here, we provide evidence that several cell types in culture actually experience local hypoxia, with important implications for cell metabolism and function. We focused initially on adipocytes, as adipose tissue hypoxia is frequently observed in obesity and precedes diminished adipocyte function. Under standard conditions, cultured adipocytes are highly glycolytic and exhibit a transcriptional profile indicative of physiological hypoxia. Increasing pericellular oxygen diverted glucose flux toward mitochondria, lowered HIF1α activity, and resulted in widespread transcriptional rewiring. Functionally, adipocytes increased adipokine secretion and sensitivity to insulin and lipolytic stimuli, recapitulating a healthier adipocyte model. The functional benefits of increasing pericellular oxygen were also observed in macrophages, hPSC-derived hepatocytes and cardiac organoids. Our findings demonstrate that oxygen is limiting in many terminally-differentiated cell types, and that considering pericellular oxygen improves the quality, reproducibility and translatability of culture models.
Collapse
Affiliation(s)
- Joycelyn Tan
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sam Virtue
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Dougall M Norris
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Olivia J Conway
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Guillaume Bidault
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Christopher Gribben
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Fatima Lugtu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Ioannis Kamzolas
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - James R Krycer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Lu Liang
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Conceição Pereira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Martin Dale
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amber S Shun-Shion
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Harry Jm Baird
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - James A Horscroft
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Alice P Sowton
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - Marcella Ma
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stefania Carobbio
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Andrew J Murray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
| | - David C Gershlick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Department of Medicine, University of Cambridge, Cambridge, CB2 0AW, UK
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, 4006, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Kelsey H Fisher-Wellman
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, 27834, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC, 27834, USA
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Cologne, 50931, Germany
| | - Antonio Vidal-Puig
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Centro de Investigacion Principe Felipe, Valencia, 46012, Spain.
| | - Daniel J Fazakerley
- Metabolic Research Laboratories, Wellcome-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK.
| |
Collapse
|
40
|
Van Lent J, Prior R, Pérez Siles G, Cutrupi AN, Kennerson ML, Vangansewinkel T, Wolfs E, Mukherjee-Clavin B, Nevin Z, Judge L, Conklin B, Tyynismaa H, Clark AJ, Bennett DL, Van Den Bosch L, Saporta M, Timmerman V. Advances and challenges in modeling inherited peripheral neuropathies using iPSCs. Exp Mol Med 2024; 56:1348-1364. [PMID: 38825644 PMCID: PMC11263568 DOI: 10.1038/s12276-024-01250-x] [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: 11/10/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 06/04/2024] Open
Abstract
Inherited peripheral neuropathies (IPNs) are a group of diseases associated with mutations in various genes with fundamental roles in the development and function of peripheral nerves. Over the past 10 years, significant advances in identifying molecular disease mechanisms underlying axonal and myelin degeneration, acquired from cellular biology studies and transgenic fly and rodent models, have facilitated the development of promising treatment strategies. However, no clinical treatment has emerged to date. This lack of treatment highlights the urgent need for more biologically and clinically relevant models recapitulating IPNs. For both neurodevelopmental and neurodegenerative diseases, patient-specific induced pluripotent stem cells (iPSCs) are a particularly powerful platform for disease modeling and preclinical studies. In this review, we provide an update on different in vitro human cellular IPN models, including traditional two-dimensional monoculture iPSC derivatives, and recent advances in more complex human iPSC-based systems using microfluidic chips, organoids, and assembloids.
Collapse
Grants
- Wellcome Trust
- R01 NS119678 NINDS NIH HHS
- U01 ES032673 NIEHS NIH HHS
- DOC-PRO4 Universiteit Antwerpen (University of Antwerp)
- This work was supported in part by the University of Antwerp (DOC-PRO4 PhD fellowship to J.V.L. and TOP-BOF research grant no. 38694 to V.T.), the Association Française contre les Myopathies (AFM research grant no. 24063 to V.T.), Association Belge contre les Maladies Neuromusculaires (ABMM research grant no. 1 to J.V.L and V.T), the interuniversity research fund (iBOF project to. L.V.D.B, E.W. and V.T.). V.T. is part of the μNEURO Research Centre of Excellence of the University of Antwerp and is an active member of the European Network for Stem Cell Core Facilities (CorEUStem, COST Action CA20140). Work in the M.L.K group was supported by the NHMRC Ideas Grant (APP1186867), CMT Australia Grant awarded to M.L.K and G.P.-S and the Australian Medical Research Future Fund (MRFF) Genomics Health Futures Mission Grant 2007681. B.M.C. is supported by the American Academy of Neurology and the Passano Foundation. L.M.J. and B.R.C. are supported by the Charcot-Marie-Tooth Association, NINDS R01 NS119678, NIEHS U01 ES032673. H.T. is supported by Academy of Finland Centre of Excellence in Stem Cell Metabolism and Sigrid Juselius Foundation. Work in the D.L.B. group is supported by a Wellcome Investigator Grant (223149/Z/21/Z), the MRC (MR/T020113/1), and with funding from the MRC and Versus Arthritis to the PAINSTORM consortium as part of the Advanced Pain Discovery Platform (MR/W002388/1).
- Australian Medical Association (Australian Medical Association Limited)
- Universiteit Hasselt (UHasselt)
- American Academy of Neurology (AAN)
- Gladstone Institutes (J. David Gladstone Institutes)
- Academy of Finland (Suomen Akatemia)
- Academy of Medical Royal Colleges (AoMRC)
- Wellcome Trust (Wellcome)
- Oxford University Hospitals NHS Trust (Oxford University Hospitals National Health Service Trust)
- KU Leuven (Katholieke Universiteit Leuven)
- Vlaams Instituut voor Biotechnologie (Flanders Institute for Biotechnology)
- Miami University | Leonard M. Miller School of Medicine (Miller School of Medicine)
Collapse
Affiliation(s)
- Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, 2610, Antwerp, Belgium
- Institute of Oncology Research (IOR), BIOS+, 6500, Bellinzona, Switzerland
- Università della Svizzera Italiana, 6900, Lugano, Switzerland
| | - Robert Prior
- Universitätsklinikum Bonn (UKB), University of Bonn, Bonn, Germany
| | - Gonzalo Pérez Siles
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Anthony N Cutrupi
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, NSW, Australia
| | - Tim Vangansewinkel
- UHasselt - Hasselt University, BIOMED, Laboratory for Functional Imaging and Research on Stem Cells (FIERCE Lab), Agoralaan, 3590, Diepenbeek, Belgium
- VIB-Center for Brain and Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
| | - Esther Wolfs
- UHasselt - Hasselt University, BIOMED, Laboratory for Functional Imaging and Research on Stem Cells (FIERCE Lab), Agoralaan, 3590, Diepenbeek, Belgium
| | | | | | - Luke Judge
- Gladstone Institutes, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Alex J Clark
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, Oxford University, Oxford, UK
| | - Ludo Van Den Bosch
- VIB-Center for Brain and Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute, KU Leuven-University of Leuven, 3000, Leuven, Belgium
| | - Mario Saporta
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium.
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, 2610, Antwerp, Belgium.
| |
Collapse
|
41
|
Batra S, Vaquer-Alicea JI, Valdez C, Taylor SP, Manon VA, Vega AR, Kashmer OM, Kolay S, Lemoff A, Cairns NJ, White CL, Diamond MI. VCP regulates early tau seed amplification via specific cofactors. RESEARCH SQUARE 2024:rs.3.rs-4307848. [PMID: 38826306 PMCID: PMC11142303 DOI: 10.21203/rs.3.rs-4307848/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Neurodegenerative tauopathies may progress based on seeding by pathological tau assemblies, whereby an aggregate is released from one cell, gains entry to an adjacent or connected cell, and serves as a specific template for its own replication in the cytoplasm. In vitro seeding reactions typically take days, yet seeding into the complex cytoplasmic milieu happens within hours, implicating a machinery with unknown players that controls this process in the acute phase. Methods We used proximity labeling to identify factors that control seed amplification within 5h of seed exposure. We fused split-APEX2 to the C-terminus of tau repeat domain (RD) to reconstitute peroxidase activity 5h after seeded intracellular tau aggregation. Valosin containing protein (VCP/p97) was the top hit. VCP harbors dominant mutations that underlie two neurodegenerative diseases, multisystem proteinopathy and vacuolar tauopathy, but its mechanistic role is unclear. We used immortalized cells and human neurons to study the effects of VCP on tau seeding. We exposed cells to fibrils or brain homogenates in cell culture media and measured effects on uptake and induction of intracellular tau aggregation following various genetic and chemical manipulations of VCP. Results VCP knockdown reduced tau seeding. Chemical inhibitors had opposing effects on aggregation in HEK293T tau biosensor cells and human neurons alike: ML-240 increased seeding efficiency, whereas NMS-873 decreased it. The inhibitors were effective only when administered within 8h of seed exposure, indicating a role for VCP early in seed processing. We screened 30 VCP co-factors in HEK293T biosensor cells by genetic knockout or knockdown. Reduction of ATXN3, NSFL1C, UBE4B, NGLY1, and OTUB1 decreased tau seeding, as did NPLOC4, which also uniquely increased soluble tau levels. By contrast, reduction of FAF2 increased tau seeding. Conclusions Divergent effects on tau seeding of chemical inhibitors and cofactor reduction indicate that VCP regulates this process. This is consistent with a dedicated cytoplasmic processing complex based on VCP that directs seeds acutely towards degradation vs. amplification.
Collapse
Affiliation(s)
- Sushobhna Batra
- UT Southwestern: The University of Texas Southwestern Medical Center
| | | | - Clarissa Valdez
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Skyler P Taylor
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Victor A Manon
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Anthony R Vega
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Omar M Kashmer
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Sourav Kolay
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Andrew Lemoff
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Nigel J Cairns
- University of Exeter Faculty of Health and Life Sciences
| | - Charles L White
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Marc I Diamond
- UT Southwestern: The University of Texas Southwestern Medical Center
| |
Collapse
|
42
|
Canova PN, Charron AJ, Leib DA. Models of Herpes Simplex Virus Latency. Viruses 2024; 16:747. [PMID: 38793628 PMCID: PMC11125678 DOI: 10.3390/v16050747] [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: 04/05/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Our current understanding of HSV latency is based on a variety of clinical observations, and in vivo, ex vivo, and in vitro model systems, each with unique advantages and drawbacks. The criteria for authentically modeling HSV latency include the ability to easily manipulate host genetics and biological pathways, as well as mimicking the immune response and viral pathogenesis in human infections. Although realistically modeling HSV latency is necessary when choosing a model, the cost, time requirement, ethical constraints, and reagent availability are also equally important. Presently, there remains a pressing need for in vivo models that more closely recapitulate human HSV infection. While the current in vivo, ex vivo, and in vitro models used to study HSV latency have limitations, they provide further insights that add to our understanding of latency. In vivo models have shed light on natural infection routes and the interplay between the host immune response and the virus during latency, while in vitro models have been invaluable in elucidating molecular pathways involved in latency. Below, we review the relative advantages and disadvantages of current HSV models and highlight insights gained through each.
Collapse
Affiliation(s)
- Paige N. Canova
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA;
- Guarini School of Graduate and Advanced Studies at Dartmouth, Hanover, NH 03755, USA;
| | - Audra J. Charron
- Guarini School of Graduate and Advanced Studies at Dartmouth, Hanover, NH 03755, USA;
| | - David A. Leib
- Guarini School of Graduate and Advanced Studies at Dartmouth, Hanover, NH 03755, USA;
| |
Collapse
|
43
|
Wrobel L, Hoffmann JL, Li X, Rubinsztein DC. p37 regulates VCP/p97 shuttling and functions in the nucleus and cytosol. SCIENCE ADVANCES 2024; 10:eadl6082. [PMID: 38701207 PMCID: PMC11068011 DOI: 10.1126/sciadv.adl6082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
The AAA+-ATPase valosin-containing protein (VCP; also called p97 or Cdc48), a major protein unfolding machinery with a variety of essential functions, localizes to different subcellular compartments where it has different functions. However, the processes regulating the distribution of VCP between the cytosol and nucleus are not understood. Here, we identified p37 (also called UBXN2B) as a major factor regulating VCP nucleocytoplasmic shuttling. p37-dependent VCP localization was crucial for local cytosolic VCP functions, such as autophagy, and nuclear functions in DNA damage repair. Mutations in VCP causing multisystem proteinopathy enhanced its association with p37, leading to decreased nuclear localization of VCP, which enhanced susceptibility to DNA damage accumulation. Both VCP localization and DNA damage susceptibility in cells with such mutations were normalized by lowering p37 levels. Thus, we uncovered a mechanism by which VCP nucleocytoplasmic distribution is fine-tuned, providing a means for VCP to respond appropriately to local needs.
Collapse
Affiliation(s)
- Lidia Wrobel
- Department of Medical Genetics, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Johanna L. Hoffmann
- Department of Medical Genetics, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Xinyi Li
- Department of Medical Genetics, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - David C. Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| |
Collapse
|
44
|
Nelson AT, Cicardi ME, Markandaiah SS, Han JY, Philp NJ, Welebob E, Haeusler AR, Pasinelli P, Manfredi G, Kawamata H, Trotti D. Glucose hypometabolism prompts RAN translation and exacerbates C9orf72-related ALS/FTD phenotypes. EMBO Rep 2024; 25:2479-2510. [PMID: 38684907 PMCID: PMC11094177 DOI: 10.1038/s44319-024-00140-7] [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: 06/27/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
The most prevalent genetic cause of both amyotrophic lateral sclerosis and frontotemporal dementia is a (GGGGCC)n nucleotide repeat expansion (NRE) occurring in the first intron of the C9orf72 gene (C9). Brain glucose hypometabolism is consistently observed in C9-NRE carriers, even at pre-symptomatic stages, but its role in disease pathogenesis is unknown. Here, we show alterations in glucose metabolic pathways and ATP levels in the brains of asymptomatic C9-BAC mice. We find that, through activation of the GCN2 kinase, glucose hypometabolism drives the production of dipeptide repeat proteins (DPRs), impairs the survival of C9 patient-derived neurons, and triggers motor dysfunction in C9-BAC mice. We also show that one of the arginine-rich DPRs (PR) could directly contribute to glucose metabolism and metabolic stress by inhibiting glucose uptake in neurons. Our findings provide a potential mechanistic link between energy imbalances and C9-ALS/FTD pathogenesis and suggest a feedforward loop model with potential opportunities for therapeutic intervention.
Collapse
Affiliation(s)
- Andrew T Nelson
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Maria Elena Cicardi
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Shashirekha S Markandaiah
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - John Ys Han
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Nancy J Philp
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Emily Welebob
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Aaron R Haeusler
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Piera Pasinelli
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY, 10065, USA
| | - Hibiki Kawamata
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, New York, NY, 10065, USA
| | - Davide Trotti
- Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
| |
Collapse
|
45
|
Cerneckis J, Cai H, Shi Y. Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications. Signal Transduct Target Ther 2024; 9:112. [PMID: 38670977 PMCID: PMC11053163 DOI: 10.1038/s41392-024-01809-0] [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: 07/28/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 04/28/2024] Open
Abstract
The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and holds great promise to advance regenerative medicine. iPSCs have the capacity for an almost unlimited expansion, are amenable to genetic engineering, and can be differentiated into most somatic cell types. iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies. In this review, we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications. We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs. We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency. Subsequently, we discuss various iPSC-based cellular models, from mono-cultures of a single cell type to complex three-dimensional organoids, and how these models can be applied to elucidate the mechanisms of human development and diseases. We use examples of neurological disorders, coronavirus disease 2019 (COVID-19), and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells. We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies. Finally, we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.
Collapse
Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Hongxia Cai
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
| |
Collapse
|
46
|
Sirtori R, J Gregoire M, M Potts E, Collins A, Donatelli L, Fallini C. LINC complex alterations are a key feature of sporadic and familial ALS/FTD. Acta Neuropathol Commun 2024; 12:69. [PMID: 38664831 PMCID: PMC11046770 DOI: 10.1186/s40478-024-01778-z] [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: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder that primarily affects motor neurons, leading to progressive muscle weakness and loss of voluntary muscle control. While the exact cause of ALS is not fully understood, emerging research suggests that dysfunction of the nuclear envelope (NE) may contribute to disease pathogenesis and progression. The NE plays a role in ALS through several mechanisms, including nuclear pore defects, nucleocytoplasmic transport impairment, accumulation of mislocalized proteins, and nuclear morphology abnormalities. The LINC complex is the second biggest multi-protein complex in the NE and consists of the SUN1/2 proteins spanning the inner nuclear membrane and Nesprin proteins embedded in the outer membrane. The LINC complex, by interacting with both the nuclear lamina and the cytoskeleton, transmits mechanical forces to the nucleus regulating its morphology and functional homeostasis. In this study we show extensive alterations to the LINC complex in motor and cortical iPSC-derived neurons and spinal cord organoids carrying the ALS causative mutation in the C9ORF72 gene (C9). Importantly, we show that such alterations are present in vivo in a cohort of sporadic ALS and C9-ALS postmortem spinal cord and motor cortex specimens. We also found that LINC complex disruption strongly correlated with nuclear morphological alterations occurring in ALS neurons, independently of TDP43 mislocalization. Altogether, our data establish morphological and functional alterations to the LINC complex as important events in ALS pathogenic cascade, making this pathway a possible target for both biomarker and therapy development.
Collapse
Affiliation(s)
- Riccardo Sirtori
- Ryan Institute for Neuroscience, University of Rhode Island, 130 Flagg Rd, 02881, Kingston, RI, United States of America
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Rd, 02881, Kingston, RI, United States of America
| | - Michelle J Gregoire
- Ryan Institute for Neuroscience, University of Rhode Island, 130 Flagg Rd, 02881, Kingston, RI, United States of America
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Rd, 02881, Kingston, RI, United States of America
- Interdisciplinary Neuroscience Program, University of Rhode Island, 9 Greenhouse Road, 02881, Kingston, RI, United States of America
| | - Emily M Potts
- Ryan Institute for Neuroscience, University of Rhode Island, 130 Flagg Rd, 02881, Kingston, RI, United States of America
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Rd, 02881, Kingston, RI, United States of America
- Interdisciplinary Neuroscience Program, University of Rhode Island, 9 Greenhouse Road, 02881, Kingston, RI, United States of America
| | - Alicia Collins
- Ryan Institute for Neuroscience, University of Rhode Island, 130 Flagg Rd, 02881, Kingston, RI, United States of America
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Rd, 02881, Kingston, RI, United States of America
- Interdisciplinary Neuroscience Program, University of Rhode Island, 9 Greenhouse Road, 02881, Kingston, RI, United States of America
| | - Liviana Donatelli
- Ryan Institute for Neuroscience, University of Rhode Island, 130 Flagg Rd, 02881, Kingston, RI, United States of America
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Rd, 02881, Kingston, RI, United States of America
- Interdisciplinary Neuroscience Program, University of Rhode Island, 9 Greenhouse Road, 02881, Kingston, RI, United States of America
| | - Claudia Fallini
- Ryan Institute for Neuroscience, University of Rhode Island, 130 Flagg Rd, 02881, Kingston, RI, United States of America.
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Rd, 02881, Kingston, RI, United States of America.
- Interdisciplinary Neuroscience Program, University of Rhode Island, 9 Greenhouse Road, 02881, Kingston, RI, United States of America.
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, United States of America.
| |
Collapse
|
47
|
Mohd Rafiq N, Fujise K, Rosenfeld MS, Xu P, De Camilli P. Parkinsonism Sac domain mutation in Synaptojanin-1 affects ciliary properties in iPSC-derived dopaminergic neurons. Proc Natl Acad Sci U S A 2024; 121:e2318943121. [PMID: 38635628 PMCID: PMC11047088 DOI: 10.1073/pnas.2318943121] [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: 11/06/2023] [Accepted: 03/04/2024] [Indexed: 04/20/2024] Open
Abstract
Synaptojanin-1 (SJ1) is a major neuronal-enriched PI(4, 5)P2 4- and 5-phosphatase implicated in the shedding of endocytic factors during endocytosis. A mutation (R258Q) that impairs selectively its 4-phosphatase activity causes Parkinsonism in humans and neurological defects in mice (SJ1RQKI mice). Studies of these mice showed, besides an abnormal assembly state of endocytic factors at synapses, the presence of dystrophic nerve terminals selectively in a subset of nigro-striatal dopamine (DA)-ergic axons, suggesting a special lability of DA neurons to the impairment of SJ1 function. Here we have further investigated the impact of SJ1 on DA neurons using iPSC-derived SJ1 KO and SJ1RQKI DA neurons and their isogenic controls. In addition to the expected enhanced clustering of endocytic factors in nerve terminals, we observed in both SJ1 mutant neuronal lines increased cilia length. Further analysis of cilia of SJ1RQDA neurons revealed abnormal accumulation of the Ca2+ channel Cav1.3 and of ubiquitin chains, suggesting a defect in the clearing of ubiquitinated proteins at the ciliary base, where a focal concentration of SJ1 was observed. We suggest that SJ1 may contribute to the control of ciliary protein dynamics in DA neurons, with implications on cilia-mediated signaling.
Collapse
Affiliation(s)
- Nisha Mohd Rafiq
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell biology, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Kenshiro Fujise
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell biology, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Martin Shaun Rosenfeld
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell biology, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Peng Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell biology, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell biology, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| |
Collapse
|
48
|
Sachdev A, Gill K, Sckaff M, Birk AM, Aladesuyi Arogundade O, Brown KA, Chouhan RS, Issagholian-Lewin PO, Patel E, Watry HL, Bernardi MT, Keough KC, Tsai YC, Smith AST, Conklin BR, Clelland CD. Reversal of C9orf72 mutation-induced transcriptional dysregulation and pathology in cultured human neurons by allele-specific excision. Proc Natl Acad Sci U S A 2024; 121:e2307814121. [PMID: 38621131 PMCID: PMC11047104 DOI: 10.1073/pnas.2307814121] [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: 05/09/2023] [Accepted: 03/01/2024] [Indexed: 04/17/2024] Open
Abstract
Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived induced pluripotent stem cell (iPSC) line and a non-diseased wild-type (WT) line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 frontotemporal dementia/amyotrophic lateral sclerosis in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes. A coding single nucleotide polymorphism in the patient cell line allowed us to distinguish transcripts from the normal vs. mutant allele. Using digital droplet PCR (ddPCR), we determined that transcription from the mutant allele is upregulated at least 10-fold, and that sense transcription is independently regulated from each allele. Surprisingly, excision of the WT allele increased pathologic dipeptide repeat poly-GP expression from the mutant allele. Importantly, a single allele was sufficient to supply a normal amount of protein, suggesting that the C9orf72 gene is haplo-sufficient in induced motor neurons. Excision of the mutant repeat expansion reverted all pathology (RNA abnormalities, dipeptide repeat production, and TDP-43 pathology) and improved electrophysiological function, whereas silencing sense expression did not eliminate all dipeptide repeat proteins, presumably because of the antisense expression. These data increase our understanding of C9orf72 gene regulation and inform gene therapy approaches, including antisense oligonucleotides (ASOs) and CRISPR gene editing.
Collapse
Affiliation(s)
| | - Kamaljot Gill
- Gladstone Institutes, San Francisco, CA94158
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
| | - Maria Sckaff
- Gladstone Institutes, San Francisco, CA94158
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
| | | | - Olubankole Aladesuyi Arogundade
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Katherine A. Brown
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Runvir S. Chouhan
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Patrick Oliver Issagholian-Lewin
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | - Esha Patel
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| | | | | | | | | | - Alec Simon Tulloch Smith
- Department of Physiology and Biophysics, University of Washington, Seattle, WA98195
- The Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98195
| | - Bruce R. Conklin
- Gladstone Institutes, San Francisco, CA94158
- Department of Medicine, University of California San Francisco, San Francisco, CA94143
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA94143
- Department of Pharmacology, University of California San Francisco, San Francisco, CA94158
| | - Claire Dudley Clelland
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA94158
- Memory & Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA94158
| |
Collapse
|
49
|
Aiken J, Holzbaur ELF. Spastin locally amplifies microtubule dynamics to pattern the axon for presynaptic cargo delivery. Curr Biol 2024; 34:1687-1704.e8. [PMID: 38554708 PMCID: PMC11042977 DOI: 10.1016/j.cub.2024.03.010] [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: 07/31/2023] [Revised: 01/10/2024] [Accepted: 03/08/2024] [Indexed: 04/02/2024]
Abstract
Neurons rely on the long-range trafficking of synaptic components to form and maintain the complex neural networks that encode the human experience. With a single neuron capable of forming thousands of distinct en passant synapses along its axon, spatially precise delivery of the necessary synaptic components is paramount. How these synapses are patterned, as well as how the efficient delivery of synaptic components is regulated, remains largely unknown. Here, we reveal a novel role for the microtubule (MT)-severing enzyme spastin in locally enhancing MT polymerization to influence presynaptic cargo pausing and retention along the axon. In human neurons derived from induced pluripotent stem cells (iPSCs), we identify sites stably enriched for presynaptic components along the axon prior to the robust assembly of mature presynapses apposed by postsynaptic contacts. These sites are capable of cycling synaptic vesicles, are enriched with spastin, and are hotspots for new MT growth and synaptic vesicle precursor (SVP) pausing/retention. The disruption of neuronal spastin level or activity, by CRISPRi-mediated depletion, transient overexpression, or pharmacologic inhibition of enzymatic activity, interrupts the localized enrichment of dynamic MT plus ends and diminishes SVP accumulation. Using an innovative human heterologous synapse model, where microfluidically isolated human axons recognize and form presynaptic connections with neuroligin-expressing non-neuronal cells, we reveal that neurons deficient for spastin do not achieve the same level of presynaptic component accumulation as control neurons. We propose a model where spastin acts locally as an amplifier of MT polymerization to pattern specific regions of the axon for synaptogenesis and guide synaptic cargo delivery.
Collapse
Affiliation(s)
- Jayne Aiken
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
50
|
Casey C, Fullard JF, Sleator RD. Unravelling the genetic basis of Schizophrenia. Gene 2024; 902:148198. [PMID: 38266791 DOI: 10.1016/j.gene.2024.148198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/07/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of some of the key omics methods currently being used in SCZ research, including RNA-seq, the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and high-throughput chromosome conformation capture (3C) approaches (e.g., Hi-C), as well as single-cell/nuclei iterations of these methods. We also discuss how these techniques are being employed to further our understanding of the genetic basis of SCZ, and to identify associated molecular pathways, biomarkers, and candidate drug targets.
Collapse
Affiliation(s)
- Clara Casey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland.
| |
Collapse
|