1
|
Odabasi Y, Yanasik S, Saglam-Metiner P, Kaymaz Y, Yesil-Celiktas O. Comprehensive Transcriptomic Investigation of Rett Syndrome Reveals Increasing Complexity Trends from Induced Pluripotent Stem Cells to Neurons with Implications for Enriched Pathways. ACS OMEGA 2023; 8:44148-44162. [PMID: 38027357 PMCID: PMC10666228 DOI: 10.1021/acsomega.3c06448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Rett syndrome (RTT) is a rare genetic neurodevelopmental disorder that has no cure apart from symptomatic treatments. While intense research efforts are required to fulfill this unmet need, the fundamental challenge is to obtain sufficient patient data. In this study, we used human transcriptomic data of four different sample types from RTT patients including induced pluripotent stem cells, differentiated neural progenitor cells, differentiated neurons, and postmortem brain tissues with an increasing in vivo-like complexity to unveil specific trends in gene expressions across the samples. Based on DEG analysis, we identified F8A3, CNTN6, RPE65, and COL19A1 to have differential expression levels in three sample types and also observed previously reported genes such as MECP2, FOXG1, CACNA1G, SATB2, GABBR2, MEF2C, KCNJ10, and CUX2 in our study. Considering the significantly enriched pathways for each sample type, we observed a consistent increase in numbers from iPSCs to NEUs where MECP2 displayed profound effects. We also validated our GSEA results by using single-cell RNA-seq data. In WGCNA, we elicited a connection among MECP2, TNRC6A, and HOXA5. Our findings highlight the utility of transcriptomic analyses to determine genes that might lead to therapeutic strategies.
Collapse
Affiliation(s)
- Yusuf
Caglar Odabasi
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| | - Sena Yanasik
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| | - Pelin Saglam-Metiner
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| | - Yasin Kaymaz
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| | - Ozlem Yesil-Celiktas
- Department of Bioengineering,
Faculty of Engineering, Ege University, Izmir 35100, Turkey
| |
Collapse
|
2
|
Nair D, Diaz-Rosado A, Varella-Branco E, Ramos I, Black A, Angireddy R, Park J, Murali S, Yoon A, Ciesielski B, O’Brien WT, Passos-Bueno MR, Bhoj E. Heterozygous variants in TBCK cause a mild neurologic syndrome in humans and mice. Am J Med Genet A 2023; 191:2508-2517. [PMID: 37353954 PMCID: PMC10524953 DOI: 10.1002/ajmg.a.63320] [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: 12/23/2022] [Revised: 05/15/2023] [Accepted: 05/26/2023] [Indexed: 06/25/2023]
Abstract
TBCK-related encephalopathy is a rare pediatric neurodegenerative disorder caused by biallelic loss-of-function variants in the TBCK gene. After receiving anecdotal reports of neurologic phenotypes in both human and mouse TBCK heterozygotes, we quantified if TBCK haploinsufficiency causes a phenotype in mice and humans. Using the tbck+/- mouse model, we performed a battery of behavioral assays and mTOR pathway analysis to investigate potential alterations in neurophysiology. We conducted as well a phenome-wide association study (PheWAS) analysis in a large adult biobank to determine the presence of potential phenotypes associated to this variant. The tbck+/- mouse model demonstrates a reduction of exploratory behavior in animals with significant sex and genotype interactions. The concurrent PheWAS analysis of 10,900 unrelated individuals showed that patients with one copy of a TBCK loss-of-function allele had a significantly higher rate of acquired toe and foot deformities, likely indicative of a mild peripheral neuropathy phenotype. This study presents an example of what may be the underappreciated occurrence of mild neurogenic symptoms in heterozygote individuals of recessive neurogenetic syndromes.
Collapse
Affiliation(s)
- Divya Nair
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Abdias Diaz-Rosado
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elisa Varella-Branco
- Centro de Estudos do Genoma Humano e Células-Tronco, Universidade de São Paulo, São Paulo, Brazil
| | - Igor Ramos
- Centro de Estudos do Genoma Humano e Células-Tronco, Universidade de São Paulo, São Paulo, Brazil
| | - Aaron Black
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Rajesh Angireddy
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Joseph Park
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Svathi Murali
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- Department of Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Yoon
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Brianna Ciesielski
- ITMAT, University of Pennsylvania, School of Medicine, Philadelphia, PA, 19104 USA
| | - W. Timothy O’Brien
- ITMAT, University of Pennsylvania, School of Medicine, Philadelphia, PA, 19104 USA
| | | | - Elizabeth Bhoj
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| |
Collapse
|
3
|
Merchant JP, Zhu K, Henrion MYR, Zaidi SSA, Lau B, Moein S, Alamprese ML, Pearse RV, Bennett DA, Ertekin-Taner N, Young-Pearse TL, Chang R. Predictive network analysis identifies JMJD6 and other potential key drivers in Alzheimer's disease. Commun Biol 2023; 6:503. [PMID: 37188718 PMCID: PMC10185548 DOI: 10.1038/s42003-023-04791-5] [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: 12/30/2021] [Accepted: 03/31/2023] [Indexed: 05/17/2023] Open
Abstract
Despite decades of genetic studies on late-onset Alzheimer's disease, the underlying molecular mechanisms remain unclear. To better comprehend its complex etiology, we use an integrative approach to build robust predictive (causal) network models using two large human multi-omics datasets. We delineate bulk-tissue gene expression into single cell-type gene expression and integrate clinical and pathologic traits, single nucleotide variation, and deconvoluted gene expression for the construction of cell type-specific predictive network models. Here, we focus on neuron-specific network models and prioritize 19 predicted key drivers modulating Alzheimer's pathology, which we then validate by knockdown in human induced pluripotent stem cell-derived neurons. We find that neuronal knockdown of 10 of the 19 targets significantly modulates levels of amyloid-beta and/or phosphorylated tau peptides, most notably JMJD6. We also confirm our network structure by RNA sequencing in the neurons following knockdown of each of the 10 targets, which additionally predicts that they are upstream regulators of REST and VGF. Our work thus identifies robust neuronal key drivers of the Alzheimer's-associated network state which may represent therapeutic targets with relevance to both amyloid and tau pathology in Alzheimer's disease.
Collapse
Affiliation(s)
- Julie P Merchant
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kuixi Zhu
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Marc Y R Henrion
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, Pembroke Place, L3 5QA, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi
| | - Syed S A Zaidi
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Branden Lau
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
- Arizona Research Labs, Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Sara Moein
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Melissa L Alamprese
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Boston, MA, USA.
| | - Rui Chang
- The Center for Innovation in Brain Sciences, University of Arizona, Tucson, AZ, USA.
- Department of Neurology, University of Arizona, Tucson, AZ, USA.
- INTelico Therapeutics LLC, Tucson, AZ, USA.
- PATH Biotech LLC, Tucson, AZ, USA.
| |
Collapse
|
4
|
Chong ZS, Khong ZJ, Tay SH, Ng SY. Metabolic contributions to neuronal deficits caused by genomic disruption of schizophrenia risk gene SETD1A. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2022; 8:115. [PMID: 36581615 PMCID: PMC9800576 DOI: 10.1038/s41537-022-00326-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
Regulation of neuronal metabolism during early brain development is crucial for directing synaptic plasticity and proper circuit formation. Alterations in neuronal glycolysis or mitochondrial function are associated with several neuropsychiatric disorders, including schizophrenia. Recently, loss-of-function mutations in SETD1A, a histone methyltransferase, have been linked to increased schizophrenia risk and global developmental delay. Here, we show that heterozygous disruption of SETD1A in human induced pluripotent stem cell (hiPSC)-derived neurons results in reduced neurite outgrowth and spontaneous activity, two phenotypes commonly associated with schizophrenia, as well as alterations in metabolic capacity. Furthermore, supplementing culture media with metabolic intermediates ameliorated changes in neurite outgrowth and spontaneous activity, suggesting that metabolic dysfunction contributes to neuronal phenotypes caused by SETD1A haploinsufficiency. These findings highlight a previously unknown connection between SETD1A function, metabolic regulation, and neuron development, and identifies alternative avenues for therapeutic development.
Collapse
Affiliation(s)
- Zheng-Shan Chong
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore
| | - Zi Jian Khong
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, Singapore, Singapore
| | - Shermaine Huiping Tay
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore
| | - Shi-Yan Ng
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431National University of Singapore, Yong Loo Lin School of Medicine (Department of Physiology, Singapore, Singapore ,grid.276809.20000 0004 0636 696XNational Neuroscience Institute, Singapore, Singapore
| |
Collapse
|
5
|
van der Linden RJ, Gerritsen JS, Liao M, Widomska J, Pearse RV, White FM, Franke B, Young-Pearse TL, Poelmans G. RNA-binding protein ELAVL4/HuD ameliorates Alzheimer's disease-related molecular changes in human iPSC-derived neurons. Prog Neurobiol 2022; 217:102316. [PMID: 35843356 PMCID: PMC9912016 DOI: 10.1016/j.pneurobio.2022.102316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/18/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022]
Abstract
The RNA binding protein ELAVL4/HuD regulates the translation and splicing of multiple Alzheimer's disease (AD) candidate genes. We generated ELAVL4 knockout (KO) human induced pluripotent stem cell-derived neurons to study the effect that ELAVL4 has on AD-related cellular phenotypes. ELAVL4 KO significantly increased the levels of specific APP isoforms and intracellular phosphorylated tau, molecular changes that are related to the pathological hallmarks of AD. Overexpression of ELAVL4 in wild-type neurons and rescue experiments in ELAVL4 KO cells showed opposite effects and also led to a reduction of the extracellular amyloid-beta (Aβ)42/40 ratio. All these observations were made in familial AD (fAD) and fAD-corrected neurons. To gain insight into the molecular cascades involved in neuronal ELAVL4 signaling, we conducted pathway and upstream regulator analyses of transcriptomic and proteomic data from the generated neurons. These analyses revealed that ELAVL4 affects multiple biological pathways linked to AD, including those involved in synaptic function, as well as gene expression downstream of APP and tau signaling. The analyses also suggest that ELAVL4 expression is regulated by insulin receptor-FOXO1 signaling in neurons. Taken together, ELAVL4 expression ameliorates AD-related molecular changes in neurons and affects multiple synaptic pathways, making it a promising target for novel drug development.
Collapse
Affiliation(s)
- Robert J van der Linden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacqueline S Gerritsen
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Meichen Liao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joanna Widomska
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Forest M White
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Barbara Franke
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands; Department of Psychiatry, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
| |
Collapse
|
6
|
Fernandez MA, Bah F, Ma L, Lee Y, Schmidt M, Welch E, Morrow EM, Young-Pearse TL. Loss of endosomal exchanger NHE6 leads to pathological changes in tau in human neurons. Stem Cell Reports 2022; 17:2111-2126. [PMID: 36055242 PMCID: PMC9481919 DOI: 10.1016/j.stemcr.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 12/09/2022] Open
Abstract
Disruption of endolysosomal and autophagy-lysosomal systems is increasingly implicated in neurodegeneration. Sodium-proton exchanger 6 (NHE6) contributes to the maintenance of proper endosomal pH, and loss-of function mutations in the X-linked NHE6 lead to Christianson syndrome (CS) in males. Neurodegenerative features of CS are increasingly recognized, with postmortem and clinical data implicating a role for tau. We generated cortical neurons from NHE6 knockout (KO) and isogenic wild-type control human induced pluripotent stem cells. We report elevated phosphorylated and sarkosyl-insoluble tau in NHE6 KO neurons. We demonstrate that NHE6 KO leads to lysosomal and autophagy dysfunction involving reduced lysosomal number and protease activity, diminished autophagic flux, and p62 accumulation. Finally, we show that treatment with trehalose or rapamycin, two enhancers of autophagy-lysosomal function, each partially rescue this tau phenotype. We provide insight into the neurodegenerative processes underlying NHE6 loss of function and into the broader role of the endosome-lysosome-autophagy network in neurodegeneration.
Collapse
Affiliation(s)
- Marty A Fernandez
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Fatmata Bah
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Li Ma
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA; Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - YouJin Lee
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA; Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Michael Schmidt
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA; Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Elizabeth Welch
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA; Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA; Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA.
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
7
|
Modelling the Human Blood-Brain Barrier in Huntington Disease. Int J Mol Sci 2022; 23:ijms23147813. [PMID: 35887162 PMCID: PMC9321930 DOI: 10.3390/ijms23147813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/05/2023] Open
Abstract
While blood–brain barrier (BBB) dysfunction has been described in neurological disorders, including Huntington’s disease (HD), it is not known if endothelial cells themselves are functionally compromised when promoting BBB dysfunction. Furthermore, the underlying mechanisms of BBB dysfunction remain elusive given the limitations with mouse models and post mortem tissue to identify primary deficits. We established models of BBB and undertook a transcriptome and functional analysis of human induced pluripotent stem cell (iPSC)-derived brain-like microvascular endothelial cells (iBMEC) from HD patients or unaffected controls. We demonstrated that HD-iBMECs have abnormalities in barrier properties, as well as in specific BBB functions such as receptor-mediated transcytosis.
Collapse
|
8
|
Wu CI, Vinton EA, Pearse RV, Heo K, Aylward AJ, Hsieh YC, Bi Y, Adeleye S, Fancher S, Duong DM, Seyfried NT, Schwarz TL, Young-Pearse TL. APP and DYRK1A regulate axonal and synaptic vesicle protein networks and mediate Alzheimer's pathology in trisomy 21 neurons. Mol Psychiatry 2022; 27:1970-1989. [PMID: 35194165 PMCID: PMC9133025 DOI: 10.1038/s41380-022-01454-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 01/18/2022] [Indexed: 11/09/2022]
Abstract
Trisomy 21 (T21) causes Down syndrome and an early-onset form of Alzheimer's disease (AD). Here, we used human induced pluripotent stem cells (hiPSCs) along with CRISPR-Cas9 gene editing to investigate the contribution of chromosome 21 candidate genes to AD-relevant neuronal phenotypes. We utilized a direct neuronal differentiation protocol to bypass neurodevelopmental cell fate phenotypes caused by T21 followed by unbiased proteomics and western blotting to define the proteins dysregulated in T21 postmitotic neurons. We show that normalization of copy number of APP and DYRK1A each rescue elevated tau phosphorylation in T21 neurons, while reductions of RCAN1 and SYNJ1 do not. To determine the T21 alterations relevant to early-onset AD, we identified common pathways altered in familial Alzheimer's disease neurons and determined which of these were rescued by normalization of APP and DYRK1A copy number in T21 neurons. These studies identified disruptions in T21 neurons in both the axonal cytoskeletal network and presynaptic proteins that play critical roles in axonal transport and synaptic vesicle cycling. These alterations in the proteomic profiles have functional consequences: fAD and T21 neurons exhibit dysregulated axonal trafficking and T21 neurons display enhanced synaptic vesicle release. Taken together, our findings provide insights into the initial molecular alterations within neurons that ultimately lead to synaptic loss and axonal degeneration in Down syndrome and early-onset AD.
Collapse
Affiliation(s)
- Chun-I Wu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Vinton
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Keunjung Heo
- Harvard Medical School, Boston, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Aimee J Aylward
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Yi-Chen Hsieh
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yan Bi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Sopefoluwa Adeleye
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Seeley Fancher
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Duc M Duong
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory School of Medicine, Atlanta, GA, USA
| | - Thomas L Schwarz
- Harvard Medical School, Boston, MA, USA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
9
|
Luo SS, Zou KX, Zhu H, Cheng Y, Yan YS, Sheng JZ, Huang HF, Ding GL. Integrated Multi-Omics Analysis Reveals the Effect of Maternal Gestational Diabetes on Fetal Mouse Hippocampi. Front Cell Dev Biol 2022; 10:748862. [PMID: 35237591 PMCID: PMC8883435 DOI: 10.3389/fcell.2022.748862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/19/2022] [Indexed: 11/25/2022] Open
Abstract
Growing evidence suggests that adverse intrauterine environments could affect the long-term health of offspring. Recent evidence indicates that gestational diabetes mellitus (GDM) is associated with neurocognitive changes in offspring. However, the mechanism remains unclear. Using a GDM mouse model, we collected hippocampi, the structure critical to cognitive processes, for electron microscopy, methylome and transcriptome analyses. Reduced representation bisulfite sequencing (RRBS) and RNA-seq in the GDM fetal hippocampi showed altered methylated modification and differentially expressed genes enriched in common pathways involved in neural synapse organization and signal transmission. We further collected fetal mice brains for metabolome analysis and found that in GDM fetal brains, the metabolites displayed significant changes, in addition to directly inducing cognitive dysfunction, some of which are important to methylation status such as betaine, fumaric acid, L-methionine, succinic acid, 5-methyltetrahydrofolic acid, and S-adenosylmethionine (SAM). These results suggest that GDM affects metabolites in fetal mice brains and further affects hippocampal DNA methylation and gene regulation involved in cognition, which is a potential mechanism for the adverse neurocognitive effects of GDM in offspring.
Collapse
Affiliation(s)
- Si-Si Luo
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Ke-Xin Zou
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Hong Zhu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi Cheng
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi-Shang Yan
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Jian-Zhong Sheng
- The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - He-Feng Huang
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.,The Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Guo-Lian Ding
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| |
Collapse
|
10
|
Lagomarsino VN, Pearse RV, Liu L, Hsieh YC, Fernandez MA, Vinton EA, Paull D, Felsky D, Tasaki S, Gaiteri C, Vardarajan B, Lee H, Muratore CR, Benoit CR, Chou V, Fancher SB, He A, Merchant JP, Duong DM, Martinez H, Zhou M, Bah F, Vicent MA, Stricker JMS, Xu J, Dammer EB, Levey AI, Chibnik LB, Menon V, Seyfried NT, De Jager PL, Noggle S, Selkoe DJ, Bennett DA, Young-Pearse TL. Stem cell-derived neurons reflect features of protein networks, neuropathology, and cognitive outcome of their aged human donors. Neuron 2021; 109:3402-3420.e9. [PMID: 34473944 DOI: 10.1016/j.neuron.2021.08.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 11/26/2022]
Abstract
We have generated a controlled and manipulable resource that captures genetic risk for Alzheimer's disease: iPSC lines from 53 individuals coupled with RNA and proteomic profiling of both iPSC-derived neurons and brain tissue of the same individuals. Data collected for each person include genome sequencing, longitudinal cognitive scores, and quantitative neuropathology. The utility of this resource is exemplified here by analyses of neurons derived from these lines, revealing significant associations between specific Aβ and tau species and the levels of plaque and tangle deposition in the brain and, more importantly, with the trajectory of cognitive decline. Proteins and networks are identified that are associated with AD phenotypes in iPSC neurons, and relevant associations are validated in brain. The data presented establish this iPSC collection as a resource for investigating person-specific processes in the brain that can aid in identifying and validating molecular pathways underlying AD.
Collapse
Affiliation(s)
- Valentina N Lagomarsino
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Richard V Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lei Liu
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yi-Chen Hsieh
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Marty A Fernandez
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Vinton
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel Paull
- New York Stem Cell Foundation Research Institute, New York, NY, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada; Department of Psychiatry and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Badri Vardarajan
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Hyo Lee
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Christina R Muratore
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Courtney R Benoit
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Vicky Chou
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Seeley B Fancher
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Amy He
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Julie P Merchant
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Duc M Duong
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, USA
| | - Hector Martinez
- New York Stem Cell Foundation Research Institute, New York, NY, USA
| | - Monica Zhou
- New York Stem Cell Foundation Research Institute, New York, NY, USA
| | - Fatmata Bah
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria A Vicent
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan M S Stricker
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jishu Xu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, Emory School of Medicine, Atlanta, GA, USA
| | - Lori B Chibnik
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory School of Medicine, Atlanta, GA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for the Study of Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Scott Noggle
- New York Stem Cell Foundation Research Institute, New York, NY, USA
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
11
|
NeuriteNet: A convolutional neural network for assessing morphological parameters of neurite growth. J Neurosci Methods 2021; 363:109349. [PMID: 34480956 DOI: 10.1016/j.jneumeth.2021.109349] [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: 05/27/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND During development or regeneration, neurons extend processes (i.e., neurites) via mechanisms that can be readily analyzed in culture. However, defining the impact of a drug or genetic manipulation on such mechanisms can be challenging due to the complex arborization and heterogeneous patterns of neurite growth in vitro. New Method: NeuriteNet is a Convolutional Neural Network (CNN) sorting model that uses a novel adaptation of the XRAI saliency map overlay, which is a region-based attribution method. NeuriteNet compares neuronal populations based on differences in neurite growth patterns, sorts them into respective groups, and overlays a saliency map indicating which areas differentiated the image for the sorting procedure. RESULTS In this study, we demonstrate that NeuriteNet effectively sorts images corresponding to dissociated neurons into control and treatment groups according to known morphological differences. Furthermore, the saliency map overlay highlights the distinguishing features of the neuron when sorting the images into treatment groups. NeuriteNet also identifies novel morphological differences in neurons cultured from control and genetically modified mouse strains. Comparison with Existing Methods: Unlike other neurite analysis platforms, NeuriteNet does not require manual manipulations, such as segmentation of neurites prior to analysis, and is more accurate than experienced researchers for categorizing neurons according to their pattern of neurite growth. CONCLUSIONS NeuriteNet can be used to effectively screen for morphological differences in a heterogeneous group of neurons and to provide feedback on the key features distinguishing those groups via the saliency map overlay.
Collapse
|
12
|
Lead (Pb) and neurodevelopment: A review on exposure and biomarkers of effect (BDNF, HDL) and susceptibility. Int J Hyg Environ Health 2021; 238:113855. [PMID: 34655857 DOI: 10.1016/j.ijheh.2021.113855] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
Lead (Pb) is a ubiquitous environmental pollutant and a potent toxic compound. Humans are exposed to Pb through inhalation, ingestion, and skin contact via food, water, tobacco smoke, air, dust, and soil. Pb accumulates in bones, brain, liver and kidney. Fetal exposure occurs via transplacental transmission. The most critical health effects are developmental neurotoxicity in infants and cardiovascular effects and nephrotoxicity in adults. Pb exposure has been steadily decreasing over the past decades, but there are few recent exposure data from the general European population; moreover, no safe Pb limit has been set. Sensitive biomarkers of exposure, effect and susceptibility, that reliably and timely indicate Pb-associated toxicity are required to assess human exposure-health relationships in a situation of low to moderate exposure. Therefore, a systematic literature review based on PubMed entries published before July 2019 that addressed Pb exposure and biomarkers of effect and susceptibility, neurodevelopmental toxicity, epigenetic modifications, and transcriptomics was conducted. Finally included were 58 original papers on Pb exposure and 17 studies on biomarkers. The biomarkers that are linked to Pb exposure and neurodevelopment were grouped into effect biomarkers (serum brain-derived neurotrophic factor (BDNF) and serum/saliva cortisol), susceptibility markers (epigenetic markers and gene sequence variants) and other biomarkers (serum high-density lipoprotein (HDL), maternal iron (Fe) and calcium (Ca) status). Serum BDNF and plasma HDL are potential candidates to be further validated as effect markers for routine use in HBM studies of Pb, complemented by markers of Fe and Ca status to also address nutritional interactions related to neurodevelopmental disorders. For several markers, a causal relationship with Pb-induced neurodevelopmental toxicity is likely. Results on BDNF are discussed in relation to Adverse Outcome Pathway (AOP) 13 ("Chronic binding of antagonist to N-methyl-D-aspartate receptors (NMDARs) during brain development induces impairment of learning and memory abilities") of the AOP-Wiki. Further studies are needed to validate sensitive, reliable, and timely effect biomarkers, especially for low to moderate Pb exposure scenarios.
Collapse
|
13
|
Florentinus-Mefailoski A, Bowden P, Scheltens P, Killestein J, Teunissen C, Marshall JG. The plasma peptides of Alzheimer's disease. Clin Proteomics 2021; 18:17. [PMID: 34182925 PMCID: PMC8240224 DOI: 10.1186/s12014-021-09320-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background A practical strategy to discover proteins specific to Alzheimer’s dementia (AD) may be to compare the plasma peptides and proteins from patients with dementia to normal controls and patients with neurological conditions like multiple sclerosis or other diseases. The aim was a proof of principle for a method to discover proteins and/or peptides of plasma that show greater observation frequency and/or precursor intensity in AD. The endogenous tryptic peptides of Alzheimer’s were compared to normals, multiple sclerosis, ovarian cancer, breast cancer, female normal, sepsis, ICU Control, heart attack, along with their institution-matched controls, and normal samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from blinded, individual AD and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins identified using the X!TANDEM algorithm. Observation frequency of the identified proteins was counted using SEQUEST algorithm. The proteins with apparently increased observation frequency in AD versus AD Control were revealed graphically and subsequently tested by Chi Square analysis. The proteins specific to AD plasma by Chi Square with FDR correction were analyzed by the STRING algorithm. The average protein or peptide log10 precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as complement C2, C7, and C1QBP among others showed increased observation frequency by Chi Square and/or precursor intensity in AD. Cellular gene symbols with large Chi Square values (χ2 ≥ 25, p ≤ 0.001) from tryptic peptides included KIF12, DISC1, OR8B12, ZC3H12A, TNF, TBC1D8B, GALNT3, EME2, CD1B, BAG1, CPSF2, MMP15, DNAJC2, PHACTR4, OR8B3, GCK, EXOSC7, HMGA1 and NT5C3A among others. Similarly, increased frequency of tryptic phosphopeptides were observed from MOK, SMIM19, NXNL1, SLC24A2, Nbla10317, AHRR, C10orf90, MAEA, SRSF8, TBATA, TNIK, UBE2G1, PDE4C, PCGF2, KIR3DP1, TJP2, CPNE8, and NGF amongst others. STRING analysis showed an increase in cytoplasmic proteins and proteins associated with alternate splicing, exocytosis of luminal proteins, and proteins involved in the regulation of the cell cycle, mitochondrial functions or metabolism and apoptosis. Increases in mean precursor intensity of peptides from common plasma proteins such as DISC1, EXOSC5, UBE2G1, SMIM19, NXNL1, PANO, EIF4G1, KIR3DP1, MED25, MGRN1, OR8B3, MGC24039, POLR1A, SYTL4, RNF111, IREB2, ANKMY2, SGKL, SLC25A5, CHMP3 among others were associated with AD. Tryptic peptides from the highly conserved C-terminus of DISC1 within the sequence MPGGGPQGAPAAAGGGGVSHRAGSRDCLPPAACFR and ARQCGLDSR showed a higher frequency and highest intensity in AD compared to all other disease and controls. Conclusion Proteins apparently expressed in the brain that were directly related to Alzheimer’s including Nerve Growth Factor (NFG), Sphingomyelin Phosphodiesterase, Disrupted in Schizophrenia 1 (DISC1), the cell death regulator retinitis pigmentosa (NXNl1) that governs the loss of nerve cells in the retina and the cell death regulator ZC3H12A showed much higher observation frequency in AD plasma vs the matched control. There was a striking agreement between the proteins known to be mutated or dis-regulated in the brains of AD patients with the proteins observed in the plasma of AD patients from endogenous peptides including NBN, BAG1, NOX1, PDCD5, SGK3, UBE2G1, SMPD3 neuronal proteins associated with synapse function such as KSYTL4, VTI1B and brain specific proteins such as TBATA. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09320-2.
Collapse
Affiliation(s)
- Angelique Florentinus-Mefailoski
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Peter Bowden
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada
| | - Philip Scheltens
- Alzheimer Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- MS Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- Neurochemistry Lab and Biobank, Dept of Clinical Chemistry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - John G Marshall
- Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON, Canada. .,International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (Formerly CRP Sante Luxembourg), Strassen, Luxembourg.
| |
Collapse
|
14
|
Reiner BC, Doyle GA, Weller AE, Levinson RN, Rao AM, Davila Perea E, Namoglu E, Pigeon A, Arauco-Shapiro G, Weickert CS, Turecki G, Crist RC, Berrettini WH. Inherited L1 Retrotransposon Insertions Associated With Risk for Schizophrenia and Bipolar Disorder. SCHIZOPHRENIA BULLETIN OPEN 2021; 2:sgab031. [PMID: 34901866 PMCID: PMC8650070 DOI: 10.1093/schizbullopen/sgab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Studies of the genetic heritability of schizophrenia and bipolar disorder examining single nucleotide polymorphisms (SNPs) and copy number variations have failed to explain a large portion of the genetic liability, resulting in substantial missing heritability. Long interspersed element 1 (L1) retrotransposons are a type of inherited polymorphic variant that may be associated with risk for schizophrenia and bipolar disorder. We performed REBELseq, a genome wide assay for L1 sequences, on DNA from male and female persons with schizophrenia and controls (n = 63 each) to identify inherited L1 insertions and validated priority insertions. L1 insertions of interest were genotyped in DNA from a replication cohort of persons with schizophrenia, bipolar disorder, and controls (n = 2268 each) to examine differences in carrier frequencies. We identified an inherited L1 insertion in ARHGAP24 and a quadallelic SNP (rs74169643) inside an L1 insertion in SNTG2 that are associated with risk for developing schizophrenia and bipolar disorder (all odds ratios ~1.2). Pathway analysis identified 15 gene ontologies that were differentially affected by L1 burden, including multiple ontologies related to glutamatergic signaling and immune function, which have been previously associated with schizophrenia. These findings provide further evidence supporting the role of inherited repetitive genetic elements in the heritability of psychiatric disorders.
Collapse
Affiliation(s)
- Benjamin C Reiner
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Glenn A Doyle
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew E Weller
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel N Levinson
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditya M Rao
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emilie Davila Perea
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Esin Namoglu
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alicia Pigeon
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabriella Arauco-Shapiro
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cyndi Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia & School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Richard C Crist
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wade H Berrettini
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
15
|
Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation. Neuron 2020; 107:891-908.e8. [PMID: 32681824 DOI: 10.1016/j.neuron.2020.06.021] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/07/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
The mechanisms by which mutant huntingtin (mHTT) leads to neuronal cell death in Huntington's disease (HD) are not fully understood. To gain new molecular insights, we used single nuclear RNA sequencing (snRNA-seq) and translating ribosome affinity purification (TRAP) to conduct transcriptomic analyses of caudate/putamen (striatal) cell type-specific gene expression changes in human HD and mouse models of HD. In striatal spiny projection neurons, the most vulnerable cell type in HD, we observe a release of mitochondrial RNA (mtRNA) (a potent mitochondrial-derived innate immunogen) and a concomitant upregulation of innate immune signaling in spiny projection neurons. Further, we observe that the released mtRNAs can directly bind to the innate immune sensor protein kinase R (PKR). We highlight the importance of studying cell type-specific gene expression dysregulation in HD pathogenesis and reveal that the activation of innate immune signaling in the most vulnerable HD neurons provides a novel framework to understand the basis of mHTT toxicity and raises new therapeutic opportunities.
Collapse
|
16
|
Sanyal A, Novis HS, Gasser E, Lin S, LaVoie MJ. LRRK2 Kinase Inhibition Rescues Deficits in Lysosome Function Due to Heterozygous GBA1 Expression in Human iPSC-Derived Neurons. Front Neurosci 2020; 14:442. [PMID: 32499675 PMCID: PMC7243441 DOI: 10.3389/fnins.2020.00442] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022] Open
Abstract
A growing number of genes associated with Parkinson’s disease are implicated in the regulation of lysosome function, including LRRK2, whose missense mutations are perhaps the most common monogenic cause of this neurodegenerative disease. These mutations are collectively thought to introduce a pathologic increase in LRRK2 kinase activity, which is currently a major target for therapeutic intervention. Heterozygous carriers of many missense mutations in the GBA1 gene have dramatically increased risk of Parkinson’s disease. A critical question has recently emerged regarding the potential interplay between the proteins encoded by these two disease-linked genes. Our group has recently demonstrated that knockin mutation of a Parkinson’s-linked GBA1 variant induces severe lysosomal and cytokine abnormalities in murine astrocytes and that these deficits were normalized via inhibition of wild-type LRRK2 kinase activity in these cells. Another group independently found that LRRK2 inhibition increases glucocerebrosidase activity in wild-type human iPSC-derived neurons, as well as those whose activity is disrupted by GBA1 or LRRK2 mutation. Fundamental questions remain in terms of the lysosomal abnormalities and the effects of LRRK2 kinase inhibition in human neurons deficient in glucocerebrosidase activity. Here, we further elucidate the physiological crosstalk between LRRK2 signaling and glucocerebrosidase activity in human iPSC-derived neurons. Our studies show that the allelic loss of GBA1 manifests broad defects in lysosomal morphology and function. Furthermore, our data show an increase in both the accumulation and secretion of oligomeric α-synuclein protein in these GBA1-heterozygous-null neurons, compared to isogenic controls. Consistent with recent findings in murine astrocytes, we observed that multiple indices of lysosomal dysfunction in GBA1-deficient human neurons were normalized by LRRK2 kinase inhibition, while some defects were preserved. Our findings demonstrate a selective but functional intersection between glucocerebrosidase dysfunction and LRRK2 signaling in the cell and may have implications in the pathogenesis and treatment of Parkinson’s disease.
Collapse
Affiliation(s)
- Anwesha Sanyal
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Hailey S Novis
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Emile Gasser
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Steven Lin
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Matthew J LaVoie
- Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
17
|
Sullivan SE, Liao M, Smith RV, White C, Lagomarsino VN, Xu J, Taga M, Bennett DA, De Jager PL, Young-Pearse TL. Candidate-based screening via gene modulation in human neurons and astrocytes implicates FERMT2 in Aβ and TAU proteostasis. Hum Mol Genet 2020; 28:718-735. [PMID: 30371777 DOI: 10.1093/hmg/ddy376] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 11/13/2022] Open
Abstract
Large-scale 'omic' studies investigating the pathophysiological processes that lead to Alzheimer's disease (AD) dementia have identified an increasing number of susceptibility genes, many of which are poorly characterized and have not previously been implicated in AD. Here, we evaluated the utility of human induced pluripotent stem cell-derived neurons and astrocytes as tools to systematically test AD-relevant cellular phenotypes following perturbation of candidate genes identified by genome-wide studies. Lentiviral-mediated delivery of shRNAs was used to modulate expression of 66 genes in astrocytes and 52 genes in induced neurons. Five genes (CNN2, GBA, GSTP1, MINT2 and FERMT2) in neurons and nine genes (CNN2, ITGB1, MINT2, SORL1, VLDLR, NPC1, NPC2, PSAP and SCARB2) in astrocytes significantly altered extracellular amyloid-β (Aβ) levels. Knockdown of AP3M2, CNN2, GSTP1, NPC1, NPC2, PSAP and SORL1 reduced interleukin-6 levels in astrocytes. Only knockdown of FERMT2 led to a reduction in the proportion of TAU that is phosphorylated. Further, CRISPR-Cas9 targeting of FERMT2 in both familial AD (fAD) and fAD-corrected human neurons validated the findings of reduced extracellular Aβ. Interestingly, FERMT2 reduction had no effect on the Aβ42:40 ratio in corrected neurons and a reduction of phospho-tau, but resulted in an elevation in Aβ42:40 ratio and no reduction in phospho-tau in fAD neurons. Taken together, this study has prioritized 15 genes as being involved in contributing to Aβ accumulation, phosphorylation of tau and/or cytokine secretion, and, as illustrated with FERMT2, it sets the stage for further cell-type-specific dissection of the role of these genes in AD.
Collapse
Affiliation(s)
- Sarah E Sullivan
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meichen Liao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert V Smith
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Charles White
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Valentina N Lagomarsino
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jishu Xu
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Mariko Taga
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA.,Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| |
Collapse
|
18
|
Sanderson JB, De S, Jiang H, Rovere M, Jin M, Zaccagnini L, Hays Watson A, De Boni L, Lagomarsino VN, Young-Pearse TL, Liu X, Pochapsky TC, Hyman BT, Dickson DW, Klenerman D, Selkoe DJ, Bartels T. Analysis of α-synuclein species enriched from cerebral cortex of humans with sporadic dementia with Lewy bodies. Brain Commun 2020; 2:fcaa010. [PMID: 32280944 PMCID: PMC7130446 DOI: 10.1093/braincomms/fcaa010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/23/2019] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
Since researchers identified α-synuclein as the principal component of Lewy bodies and Lewy neurites, studies have suggested that it plays a causative role in the pathogenesis of dementia with Lewy bodies and other ‘synucleinopathies’. While α-synuclein dyshomeostasis likely contributes to the neurodegeneration associated with the synucleinopathies, few direct biochemical analyses of α-synuclein from diseased human brain tissue currently exist. In this study, we analysed sequential protein extracts from a substantial number of patients with neuropathological diagnoses of dementia with Lewy bodies and corresponding controls, detecting a shift of cytosolic and membrane-bound physiological α-synuclein to highly aggregated forms. We then fractionated aqueous extracts (cytosol) from cerebral cortex using non-denaturing methods to search for soluble, disease-associated high molecular weight species potentially associated with toxicity. We applied these fractions and corresponding insoluble fractions containing Lewy-type aggregates to several reporter assays to determine their bioactivity and cytotoxicity. Ultimately, high molecular weight cytosolic fractions enhances phospholipid membrane permeability, while insoluble, Lewy-associated fractions induced morphological changes in the neurites of human stem cell-derived neurons. While the concentrations of soluble, high molecular weight α-synuclein were only slightly elevated in brains of dementia with Lewy bodies patients compared to healthy, age-matched controls, these observations suggest that a small subset of soluble α-synuclein aggregates in the brain may drive early pathogenic effects, while Lewy body-associated α-synuclein can drive neurotoxicity.
Collapse
Affiliation(s)
- John B Sanderson
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Suman De
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.,UK Dementia Research Institute, Department of Chemistry, University of Cambridge, Cambridge CB2 0AH, UK
| | - Haiyang Jiang
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matteo Rovere
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ming Jin
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ludovica Zaccagnini
- UK Dementia Research Institute, Department of Neurology, University College London, London WC1E 6BT, UK
| | - Aurelia Hays Watson
- UK Dementia Research Institute, Department of Neurology, University College London, London WC1E 6BT, UK
| | - Laura De Boni
- UK Dementia Research Institute, Department of Neurology, University College London, London WC1E 6BT, UK
| | - Valentina N Lagomarsino
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tracy L Young-Pearse
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xinyue Liu
- Department of Chemistry, Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02453, USA
| | - Thomas C Pochapsky
- Department of Chemistry, Rosenstiel Institute for Basic Biomedical Research, Brandeis University, Waltham, MA 02453, USA
| | - Bradley T Hyman
- Massachusetts General Hospital, Harvard Medical School, Department of Neurology, Massachusetts Institute for Neurodegenerative Disease, Boston, MA 02129, USA
| | - Dennis W Dickson
- Neuropathology Laboratory, Department of Neuroscience, Mayo Clinic Jacksonville, Jacksonville, FL 32224, USA
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.,UK Dementia Research Institute, Department of Chemistry, University of Cambridge, Cambridge CB2 0AH, UK
| | - Dennis J Selkoe
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tim Bartels
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,UK Dementia Research Institute, Department of Neurology, University College London, London WC1E 6BT, UK
| |
Collapse
|
19
|
Hoffmann A, Ziller M, Spengler D. Focus on Causality in ESC/iPSC-Based Modeling of Psychiatric Disorders. Cells 2020; 9:E366. [PMID: 32033412 PMCID: PMC7072492 DOI: 10.3390/cells9020366] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified an increasing number of genetic variants that significantly associate with psychiatric disorders. Despite this wealth of information, our knowledge of which variants causally contribute to disease, how they interact, and even more so of the functions they regulate, is still poor. The availability of embryonic stem cells (ESCs) and the advent of patient-specific induced pluripotent stem cells (iPSCs) has opened new opportunities to investigate genetic risk variants in living disease-relevant cells. Here, we analyze how this progress has contributed to the analysis of causal relationships between genetic risk variants and neuronal phenotypes, especially in schizophrenia (SCZ) and bipolar disorder (BD). Studies on rare, highly penetrant risk variants have originally led the field, until more recently when the development of (epi-) genetic editing techniques spurred studies on cause-effect relationships between common low risk variants and their associated neuronal phenotypes. This reorientation not only offers new insights, but also raises issues on interpretability. Concluding, we consider potential caveats and upcoming developments in the field of ESC/iPSC-based modeling of causality in psychiatric disorders.
Collapse
Affiliation(s)
| | | | - Dietmar Spengler
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, 80804 Munich, Germany; (A.H.); (M.Z.)
| |
Collapse
|