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Dhaliwal NK, Weng OY, Dong X, Bhattacharya A, Ahmed M, Nishimura H, Choi WWY, Aggarwal A, Luikart BW, Shu Q, Li X, Wilson MD, Moffat J, Wang LY, Muffat J, Li Y. Synergistic hyperactivation of both mTORC1 and mTORC2 underlies the neural abnormalities of PTEN-deficient human neurons and cortical organoids. Cell Rep 2024; 43:114173. [PMID: 38700984 DOI: 10.1016/j.celrep.2024.114173] [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: 09/22/2023] [Revised: 03/20/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
Mutations in the phosphatase and tensin homolog (PTEN) gene are associated with severe neurodevelopmental disorders. Loss of PTEN leads to hyperactivation of the mechanistic target of rapamycin (mTOR), which functions in two distinct protein complexes, mTORC1 and mTORC2. The downstream signaling mechanisms that contribute to PTEN mutant phenotypes are not well delineated. Here, we show that pluripotent stem cell-derived PTEN mutant human neurons, neural precursors, and cortical organoids recapitulate disease-relevant phenotypes, including hypertrophy, electrical hyperactivity, enhanced proliferation, and structural overgrowth. PTEN loss leads to simultaneous hyperactivation of mTORC1 and mTORC2. We dissect the contribution of mTORC1 and mTORC2 by generating double mutants of PTEN and RPTOR or RICTOR, respectively. Our results reveal that the synergistic hyperactivation of both mTORC1 and mTORC2 is essential for the PTEN mutant human neural phenotypes. Together, our findings provide insights into the molecular mechanisms that underlie PTEN-related neural disorders and highlight novel therapeutic targets.
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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
| | - Xiaoxue Dong
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China; The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Afrin Bhattacharya
- 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
| | - Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Haruka Nishimura
- 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
| | - Wendy W Y Choi
- 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; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Aditi Aggarwal
- 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
| | - Bryan W Luikart
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Qiang Shu
- The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Xuekun Li
- The Children's Hospital, National Clinical Research Center for Child Health, School of Medicine, Zhejiang University, Hangzhou 310052, China; The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Michael D Wilson
- 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; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Lu-Yang Wang
- 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
| | - Julien Muffat
- Program in Neurosciences and Mental Health, 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
| | - 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.
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2
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Noguchi J, Watanabe S, Oga T, Isoda R, Nakagaki K, Sakai K, Sumida K, Hoshino K, Saito K, Miyawaki I, Sugano E, Tomita H, Mizukami H, Watakabe A, Yamamori T, Ichinohe N. Altered projection-specific synaptic remodeling and its modification by oxytocin in an idiopathic autism marmoset model. Commun Biol 2024; 7:642. [PMID: 38802535 PMCID: PMC11130163 DOI: 10.1038/s42003-024-06345-9] [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: 10/22/2023] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Alterations in the experience-dependent and autonomous elaboration of neural circuits are assumed to underlie autism spectrum disorder (ASD), though it is unclear what synaptic traits are responsible. Here, utilizing a valproic acid-induced ASD marmoset model, which shares common molecular features with idiopathic ASD, we investigate changes in the structural dynamics of tuft dendrites of upper-layer pyramidal neurons and adjacent axons in the dorsomedial prefrontal cortex through two-photon microscopy. In model marmosets, dendritic spine turnover is upregulated, and spines are generated in clusters and survived more often than in control marmosets. Presynaptic boutons in local axons, but not in commissural long-range axons, demonstrate hyperdynamic turnover in model marmosets, suggesting alterations in projection-specific plasticity. Intriguingly, nasal oxytocin administration attenuates clustered spine emergence in model marmosets. Enhanced clustered spine generation, possibly unique to certain presynaptic partners, may be associated with ASD and be a potential therapeutic target.
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Affiliation(s)
- Jun Noguchi
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.
| | - Satoshi Watanabe
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Tomofumi Oga
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Risa Isoda
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Keiko Nakagaki
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Kazuhisa Sakai
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Kayo Sumida
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., Osaka, Japan
| | - Kohei Hoshino
- Preclinical Research Laboratories, Sumitomo Pharma Co., Ltd., Osaka, Japan
| | - Koichi Saito
- Environmental Health Science Laboratory, Sumitomo Chemical Co., Ltd., Osaka, Japan
| | - Izuru Miyawaki
- Preclinical Research Laboratories, Sumitomo Pharma Co., Ltd., Osaka, Japan
| | - Eriko Sugano
- Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, Morioka, Japan
| | - Hiroshi Tomita
- Laboratory of Visual Neuroscience, Graduate Course in Biological Sciences, Iwate University, Morioka, Japan
| | - Hiroaki Mizukami
- Division of Genetic Therapeutics, Jichi Medical University, Shimotsuke, Japan
| | - Akiya Watakabe
- Laboratory for Molecular Analysis of Higher Brain Function, Center for Brain Science, RIKEN, Wako, Japan
| | - Tetsuo Yamamori
- Laboratory for Molecular Analysis of Higher Brain Function, Center for Brain Science, RIKEN, Wako, Japan
- Laboratory for Haptic Perception and Cognitive Physiology, Center for Brain Science, RIKEN, Wako, Japan
- Department of Marmoset Biology and Medicine, CIEM, Kawasaki, Japan
| | - Noritaka Ichinohe
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.
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3
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Eng C, Kim A, Yehia L. Genomic diversity in functionally relevant genes modifies neurodevelopmental versus neoplastic risks in individuals with germline PTEN variants. RESEARCH SQUARE 2023:rs.3.rs-3734368. [PMID: 38168271 PMCID: PMC10760312 DOI: 10.21203/rs.3.rs-3734368/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Individuals with germline PTEN variants (PHTS) have increased risks of the seemingly disparate phenotypes of cancer and neurodevelopmental disorders (NDD), including autism spectrum disorder (ASD). Etiology of the phenotypic variability remains elusive. Here, we hypothesized that decreased genomic diversity, manifested by increased homozygosity, may be one etiology. Comprehensive analyses of 376 PHTS patients of European ancestry revealed significant enrichment of homozygous common variants in genes involved in inflammatory processes in the PHTS-NDD group and in genes involved in differentiation and chromatin structure regulation in the PHTS-ASD group. Pathway analysis revealed pathways germane to NDD/ASD, including neuroinflammation and synaptogenesis. Collapsing analysis of the homozygous variants identified suggestive modifier NDD/ASD genes. In contrast, we found enrichment of homozygous ultra-rare variants in genes modulating cell death in the PHTS-cancer group. Finally, homozygosity burden as a predictor of ASD versus cancer outcomes in our validated prediction model for NDD/ASD performed favorably.
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Hitomi M, Venegas J, Kang SC, Eng C. Differential cell cycle checkpoint evasion by PTEN germline mutations associated with dichotomous phenotypes of cancer versus autism spectrum disorder. Oncogene 2023; 42:3698-3707. [PMID: 37907589 DOI: 10.1038/s41388-023-02867-4] [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: 03/29/2023] [Revised: 09/29/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023]
Abstract
Individuals with a PTEN germline mutation receive the molecular diagnosis of PTEN hamartoma tumor syndrome (PHTS). PHTS displays a complex spectrum of clinical phenotypes including harmartomas, predisposition to cancers, and autism spectrum disorder (ASD). Clear-cut genotype-phenotype correlations are yet to be established due to insufficient information on the PTEN function being impacted by mutations. To fill this knowledge gap, we compared functional impacts of two selected missense PTEN mutant alleles, G132D and M134R, each respectively being associated with distinct clinical phenotype, ASD or thyroid cancer without ASD using gene-edited human induced pluripotent stem cells (hiPSCs). In homozygous hiPSCs, PTEN expression was severely reduced by M134R mutation due to shortened protein half-life. G132D suppressed PTEN expression to a lesser extent than Μ134R mutation without altering protein half-life. When challenged with γ-irradiation, G132D heterozygous cells exited radiation-induced G2 arrest earlier than wildtype and M134R heterozygous hiPSCs despite the similar DNA damage levels as the latter two. Immunoblotting analyses suggested that γ-irradiation induced apoptosis in G132D heterozygous cells to lesser degrees than in the hiPSCs of other genotypes. These data suggest that ASD-associated G132D allele promotes genome instability by premature cell cycle reentry with incomplete DNA repair.
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Affiliation(s)
- Masahiro Hitomi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, The Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Juan Venegas
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Shin Chung Kang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, The Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA.
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Genetics and Genome Science, Case Western Reserve University School of Medicine, Cleveland, OH, 44116, USA.
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44116, USA.
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5
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Liu D, MacFarland SP, Yehia L, Duvall MM, Mamula P, Kurowski JA, Greene CS, Radhakrishnan K, Eng C. A Bi-Institutional Study of Gastrointestinal and Hepatic Manifestations in Children With PTEN Hamartoma Tumor Syndrome. GASTRO HEP ADVANCES 2023; 3:250-259. [PMID: 39129943 PMCID: PMC11307957 DOI: 10.1016/j.gastha.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/16/2023] [Indexed: 08/13/2024]
Abstract
Background and Aims PTEN hamartoma tumor syndrome (PHTS) confers a high risk of specific cancers and is the most common genetic cause of autism spectrum disorder (ASD). Gastrointestinal (GI) phenotypes in PHTS are poorly characterized in children. Thus, we aimed to characterize the GI and hepatic manifestations in children with PHTS and to investigate genotype-phenotype associations. Methods We performed a retrospective chart review of prospectively accrued children with PHTS at 2 tertiary-care centers. Wilcoxon rank-sum, Chi-squared, and Fisher's exact tests and Firth's logistic regression were utilized to explore associations between variables. Results This series included 80 children with disease-causing PTEN variants. Common GI manifestations included constipation in 41 (51%), feeding issues in 31 (39%), and polyps in 22 (28%) children. The polyps were of mixed histologic types. Eosinophilic gastrointestinal disorders were observed in 5 (6%) children. Crohn's disease, celiac disease, and protein-losing enteropathy were observed once each. Eosinophilic gastrointestinal disorders were observed exclusively in patients without ASD (P = .052). Nonsense PTEN variants were enriched in those with polyps (P = .029). Missense PTEN variants (OR 2.9, P = .034) and upper GI polyps (OR 4.4, P = .018) were associated with increased odds of constipation. Conclusion Constipation and feeding issues are common in children with PHTS. Polyps are more prevalent in children with PHTS than previously described and associated with nonsense PTEN variants. Children without ASD represent a distinct patient subset with a predisposition to eosinophilic gastrointestinal disorders and possibly upper GI polyps. Endoscopic evaluation should continue to be performed in symptomatic children with PHTS, with consideration of closer follow-up in those without ASD.
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Affiliation(s)
- Darren Liu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Suzanne P. MacFarland
- Division of Oncology, Children’s Hospital of Philadelphia, The University of Pennsylvania, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Melani M. Duvall
- Division of Oncology, Children’s Hospital of Philadelphia, The University of Pennsylvania, Philadelphia, Pennsylvania
| | - Petar Mamula
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jacob A. Kurowski
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic, Cleveland, Ohio
| | - Colleen S. Greene
- Division of Oncology, Children’s Hospital of Philadelphia, The University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kadakkal Radhakrishnan
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Cleveland Clinic, Cleveland, Ohio
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
- Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
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Yim YY, Nestler EJ. Cell-Type-Specific Neuroproteomics of Synapses. Biomolecules 2023; 13:998. [PMID: 37371578 PMCID: PMC10296650 DOI: 10.3390/biom13060998] [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: 05/11/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
In the last two decades, our knowledge of synaptic proteomes and their relationship to normal brain function and neuropsychiatric disorders has been expanding rapidly through the use of more powerful neuroproteomic approaches. However, mass spectrometry (MS)-based neuroproteomic studies of synapses still require cell-type, spatial, and temporal proteome information. With the advancement of sample preparation and MS techniques, we have just begun to identify and understand proteomes within a given cell type, subcellular compartment, and cell-type-specific synapse. Here, we review the progress and limitations of MS-based neuroproteomics of synapses in the mammalian CNS and highlight the recent applications of these approaches in studying neuropsychiatric disorders such as major depressive disorder and substance use disorders. Combining neuroproteomic findings with other omics studies can generate an in-depth, comprehensive map of synaptic proteomes and possibly identify new therapeutic targets and biomarkers for several central nervous system disorders.
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Affiliation(s)
- Yun Young Yim
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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7
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Cheung SKK, Kwok J, Or PMY, Wong CW, Feng B, Choy KW, Chang RCC, Burbach JPH, Cheng ASL, Chan AM. Neuropathological signatures revealed by transcriptomic and proteomic analysis in Pten-deficient mouse models. Sci Rep 2023; 13:6763. [PMID: 37185447 PMCID: PMC10130134 DOI: 10.1038/s41598-023-33869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 04/20/2023] [Indexed: 05/17/2023] Open
Abstract
PTEN hamartoma tumour syndrome is characterised by mutations in the human PTEN gene. We performed transcriptomic and proteomic analyses of neural tissues and primary cultures from heterozygous and homozygous Pten-knockout mice. The somatosensory cortex of heterozygous Pten-knockout mice was enriched in immune response and oligodendrocyte development Gene Ontology (GO) terms. Parallel proteomic analysis revealed differentially expressed proteins (DEPs) related to dendritic spine development, keratinisation and hamartoma signatures. However, primary astrocytes (ASTs) from heterozygous Pten-knockout mice were enriched in the extracellular matrix GO term, while primary cortical neurons (PCNs) were enriched in immediate-early genes. In ASTs from homozygous Pten-knockout mice, cilium-related activity was enriched, while PCNs exhibited downregulation of forebrain neuron generation and differentiation, implying an altered excitatory/inhibitory balance. By integrating DEPs with pre-filtered differentially expressed genes, we identified the enrichment of traits of intelligence, cognitive function and schizophrenia, while DEPs in ASTs were significantly associated with intelligence and depression.
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Affiliation(s)
- Stanley K K Cheung
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Jacinda Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Canada
| | - Penelope M Y Or
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Chi Wai Wong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Bo Feng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Raymond C C Chang
- Laboratory of Neurodegenerative Diseases, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, SAR, China
| | - J Peter H Burbach
- Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alfred S L Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Andrew M Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, SAR, China.
- Brain and Mind Institute, The Chinese University of Hong Kong, 4/F, Hui Yeung Shing Building, Hong Kong, SAR, China.
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8
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Arenella M, Mota NR, Teunissen MWA, Brunner HG, Bralten J. Autism spectrum disorder and brain volume link through a set of mTOR-related genes. J Child Psychol Psychiatry 2023. [PMID: 36922714 DOI: 10.1111/jcpp.13783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Larger than average head and brain sizes are often observed in individuals with autism spectrum disorders (ASDs). ASD and brain volume are both highly heritable, with multiple genetic variants contributing. However, it is unclear whether ASD and brain volume share any genetic mechanisms. Genes from the mammalian target of rapamycin (mTOR) pathway influence brain volume, and variants are found in rare genetic syndromes that include ASD features. Here we investigated whether variants in mTOR-related genes are also associated with ASD and if they constitute a genetic link between large brains and ASD. METHODS We extended our analyses between large heads (macrocephaly) and rare de novo mTOR-related variants in an intellectual disability cohort (N = 2,258). Subsequently using Fisher's exact tests we investigated the co-occurrence of mTOR-related de novo variants and ASD in the de-novo-db database (N = 23,098). We next selected common genetic variants within a set of 96 mTOR-related genes in genome-wide genetic association data of ASD (N = 46,350) to test gene-set association using MAGMA. Lastly, we tested genetic correlation between genome-wide genetic association data of ASD (N = 46,350) and intracranial volume (N = 25,974) globally using linkage disequilibrium score regression as well as mTOR specific by restricting the genetic correlation to the mTOR-related genes using GNOVA. RESULTS Our results show that both macrocephaly and ASD occur above chance level in individuals carrying rare de novo variants in mTOR-related genes. We found a significant mTOR gene-set association with ASD (p = .0029) and an mTOR-stratified positive genetic correlation between ASD and intracranial volume (p = .027), despite the absence of a significant genome-wide correlation (p = .81). CONCLUSIONS This work indicates that both rare and common variants in mTOR-related genes are associated with brain volume and ASD and genetically correlate them in the expected direction. We demonstrate that genes involved in mTOR signalling are potential mediators of the relationship between having a large brain and having ASD.
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Affiliation(s)
- Martina Arenella
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Department of Forensic and Neurodevelopmental Science, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Nina R Mota
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Mariel W A Teunissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Department of Neurology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands.,GROW School of Development and Oncology, MHENS School of Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Janita Bralten
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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9
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Postsynaptic autism spectrum disorder genes and synaptic dysfunction. Neurobiol Dis 2021; 162:105564. [PMID: 34838666 DOI: 10.1016/j.nbd.2021.105564] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 12/20/2022] Open
Abstract
This review provides an overview of the synaptic dysfunction of neuronal circuits and the ensuing behavioral alterations caused by mutations in autism spectrum disorder (ASD)-linked genes directly or indirectly affecting the postsynaptic neuronal compartment. There are plenty of ASD risk genes, that may be broadly grouped into those involved in gene expression regulation (epigenetic regulation and transcription) and genes regulating synaptic activity (neural communication and neurotransmission). Notably, the effects mediated by ASD-associated genes can vary extensively depending on the developmental time and/or subcellular site of expression. Therefore, in order to gain a better understanding of the mechanisms of disruptions in postsynaptic function, an effort to better model ASD in experimental animals is required to improve standardization and increase reproducibility within and among studies. Such an effort holds promise to provide deeper insight into the development of these disorders and to improve the translational value of preclinical studies.
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10
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Sarn N, Thacker S, Lee H, Eng C. Germline nuclear-predominant Pten murine model exhibits impaired social and perseverative behavior, microglial activation, and increased oxytocinergic activity. Mol Autism 2021; 12:41. [PMID: 34088332 PMCID: PMC8176582 DOI: 10.1186/s13229-021-00448-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/17/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) has a strong genetic etiology. Germline mutation in the tumor suppressor gene PTEN is one of the best described monogenic risk cases for ASD. Animal modeling of cell-specific Pten loss or mutation has provided insight into how disruptions to the function of PTEN affect neurodevelopment, neurobiology, and social behavior. As such, there is a growing need to understand more about how various aspects of PTEN activity and cell-compartment-specific functions, contribute to certain neurological or behavior phenotypes. METHODS To understand more about the relationship between Pten localization and downstream effects on neurophenotypes, we generated the nuclear-predominant PtenY68H/+ mouse, which is identical to the genotype of some PTEN-ASD individuals. We subjected the PtenY68H/+ mouse to morphological and behavioral phenotyping, including the three-chamber sociability, open field, rotarod, and marble burying tests. We subsequently performed in vivo and in vitro cellular phenotyping and concluded the work with a transcriptomic survey of the PtenY68H/+ cortex, which profiled gene expression. RESULTS We observe a significant increase in P-Akt downstream of canonical Pten signaling, macrocephaly, decreased sociability, decreased preference for novel social stimuli, increased repetitive behavior, and increased thigmotaxis in PtenY68H/+ six-week-old (P40) mice. In addition, we found significant microglial activation with increased expression of complement and neuroinflammatory proteins in vivo and in vitro accompanied by enhanced phagocytosis. These observations were subsequently validated with RNA-seq and qRT-PCR, which revealed overexpression of many genes involved in neuroinflammation and neuronal function, including oxytocin. Oxytocin transcript was fivefold overexpressed (P = 0.0018), and oxytocin protein was strongly overexpressed in the PtenY68H/+ hypothalamus. CONCLUSIONS The nuclear-predominant PtenY68H/+ model has clarified that Pten dysfunction links to microglial pathology and this associates with increased Akt signaling. We also demonstrate that Pten dysfunction associates with changes in the oxytocin system, an important connection between a prominent ASD risk gene and a potent neuroendocrine regulator of social behavior. These cellular and molecular pathologies may related to the observed changes in social behavior. Ultimately, the findings from this work may reveal important biomarkers and/or novel therapeutic modalities that could be explored in individuals with germline mutations in PTEN with ASD.
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Affiliation(s)
- Nick Sarn
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Stetson Thacker
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195 USA
| | - Hyunpil Lee
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195 USA
- Germline High Risk Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
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11
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Transcriptome-(phospho)proteome characterization of brain of a germline model of cytoplasmic-predominant Pten expression with autism-like phenotypes. NPJ Genom Med 2021; 6:42. [PMID: 34078911 PMCID: PMC8173008 DOI: 10.1038/s41525-021-00201-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/13/2021] [Indexed: 11/08/2022] Open
Abstract
PTEN has a strong Mendelian association with autism spectrum disorder (ASD), representing a special case in autism's complex genetic architecture. Animal modeling for constitutional Pten mutation creates an opportunity to study how disruption of Pten affects neurobiology and glean potential insight into ASD pathogenesis. Subsequently, we comprehensively characterized the neural (phospho)proteome of Ptenm3m4/m3m4 mice, which exhibits cytoplasmic-predominant Pten expression, by applying mass spectrometry technology to their brains at two-weeks- (P14) and six-weeks-of-age (P40). The differentially expressed/phosphorylated proteins were subjected to gene enrichment, pathway, and network analyses to assess the affected biology. We identified numerous differentially expressed/phosphorylated proteins, finding greater dysregulation at P40 consistent with prior transcriptomic data. The affected pathways were largely related to PTEN function or neurological processes, while scant direct overlap was found across datasets. Network analysis pointed to ASD risk genes like Pten and Psd-95 as major regulatory hubs, suggesting they likely contribute to initiation or maintenance of cellular and perhaps organismal phenotypes related to ASD.
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12
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Weiss FD, Calderon L, Wang YF, Georgieva R, Guo Y, Cvetesic N, Kaur M, Dharmalingam G, Krantz ID, Lenhard B, Fisher AG, Merkenschlager M. Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin. Nat Commun 2021; 12:2919. [PMID: 34006846 PMCID: PMC8131595 DOI: 10.1038/s41467-021-23141-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a human developmental disorder caused by mutations that compromise the function of cohesin, a major regulator of 3D genome organization. Cognitive impairment is a universal and as yet unexplained feature of CdLS. We characterize the transcriptional profile of cortical neurons from CdLS patients and find deregulation of hundreds of genes enriched for neuronal functions related to synaptic transmission, signalling processes, learning and behaviour. Inducible proteolytic cleavage of cohesin disrupts 3D genome organization and transcriptional control in post-mitotic cortical mouse neurons, demonstrating that cohesin is continuously required for neuronal gene expression. The genes affected by acute depletion of cohesin belong to similar gene ontology classes and show significant numerical overlap with genes deregulated in CdLS. Interestingly, reconstitution of cohesin function largely rescues altered gene expression, including the expression of genes deregulated in CdLS.
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Affiliation(s)
- Felix D Weiss
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Lesly Calderon
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Radina Georgieva
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ya Guo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nevena Cvetesic
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Maninder Kaur
- Division of Human Genetics, The Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ian D Krantz
- Division of Human Genetics, The Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Boris Lenhard
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Amanda G Fisher
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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13
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Hardan AY, Jo B, Frazier TW, Klaas P, Busch RM, Dies KA, Filip-Dhima R, Snow AV, Eng C, Hanna R, Zhang B, Sahin M. A randomized double-blind controlled trial of everolimus in individuals with PTEN mutations: Study design and statistical considerations. Contemp Clin Trials Commun 2021; 21:100733. [PMID: 33644493 PMCID: PMC7887633 DOI: 10.1016/j.conctc.2021.100733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/03/2021] [Accepted: 01/16/2021] [Indexed: 11/24/2022] Open
Abstract
This randomized, double-blind controlled trial of everolimus in individuals with germline phosphatase and tensin homolog mutations (PTEN) was designed to evaluate the safety of everolimus compared with placebo and to evaluate the efficacy of everolimus on neurocognition and behavior compared to placebo as measured by standardized neurocognitive and motor measures as well as behavioral questionnaires. The safety profile of everolimus is characterized by manageable adverse events that are generally reversible and non-cumulative. The primary safety endpoint of this study was drop-out rate due to side effects, comparing everolimus versus placebo. We also sought to determine the frequency of adverse events by type and severity. The main efficacy endpoint was a neurocognitive composite computed in two ways: 1) an average for working memory, processing speed, and fine motor subtests; and 2) the same average as above except weighted 2/3, and an additional average based on all other available neurocognitive testing measures assessing the additional domains of nonverbal ability, visuomotor skills, verbal learning, and receptive and expressive language, weighted 1/3. Secondary efficacy endpoints examined the effect of everolimus on overall global clinical improvement, autism symptoms, behavioral problems, and adaptive abilities as measured by validated, standardized instruments. We predicted that the rate of adverse events would be no more than 10% higher in the everolimus group compared to placebo, and overall severity of side effects would be minimal. We also expected that individuals receiving everolimus would show more improvement, relative to those taking placebo, on the composite neurocognitive index.
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Affiliation(s)
- Antonio Y Hardan
- Department of Psychiatry and Behavioral Science, Stanford University, Stanford, CA, USA
| | - Booil Jo
- Department of Psychiatry and Behavioral Science, Stanford University, Stanford, CA, USA
| | - Thomas W Frazier
- Autism Speaks, New York, NY, USA.,Department of Psychology, John Carroll University, Cleveland Heights, Ohio, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Patricia Klaas
- Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Robyn M Busch
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA
| | - Kira A Dies
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,F.M. Kirby Neurobiology Center, Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rajna Filip-Dhima
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,F.M. Kirby Neurobiology Center, Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anne V Snow
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA.,Department of Pediatric Hematology Oncology and Bone Marrow Transplantation, Cleveland Clinic Children's Hospital, Cleveland, OH, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Germline High Risk Cancer Focus Group, Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rabi Hanna
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA.,Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,F.M. Kirby Neurobiology Center, Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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14
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Bae M, Roh JD, Kim Y, Kim SS, Han HM, Yang E, Kang H, Lee S, Kim JY, Kang R, Jung H, Yoo T, Kim H, Kim D, Oh H, Han S, Kim D, Han J, Bae YC, Kim H, Ahn S, Chan AM, Lee D, Kim JW, Kim E. SLC6A20 transporter: a novel regulator of brain glycine homeostasis and NMDAR function. EMBO Mol Med 2021; 13:e12632. [PMID: 33428810 PMCID: PMC7863395 DOI: 10.15252/emmm.202012632] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 10/22/2020] [Accepted: 11/19/2020] [Indexed: 12/25/2022] Open
Abstract
Glycine transporters (GlyT1 and GlyT2) that regulate levels of brain glycine, an inhibitory neurotransmitter with co-agonist activity for NMDA receptors (NMDARs), have been considered to be important targets for the treatment of brain disorders with suppressed NMDAR function such as schizophrenia. However, it remains unclear whether other amino acid transporters expressed in the brain can also regulate brain glycine levels and NMDAR function. Here, we report that SLC6A20A, an amino acid transporter known to transport proline based on in vitro data but is understudied in the brain, regulates proline and glycine levels and NMDAR function in the mouse brain. SLC6A20A transcript and protein levels were abnormally increased in mice carrying a mutant PTEN protein lacking the C terminus through enhanced β-catenin binding to the Slc6a20a gene. These mice displayed reduced extracellular levels of brain proline and glycine and decreased NMDAR currents. Elevating glycine levels back to normal ranges by antisense oligonucleotide-induced SLC6A20 knockdown, or the competitive GlyT1 antagonist sarcosine, normalized NMDAR currents and repetitive climbing behavior observed in these mice. Conversely, mice lacking SLC6A20A displayed increased extracellular glycine levels and NMDAR currents. Lastly, both mouse and human SLC6A20 proteins mediated proline and glycine transports, and SLC6A20 proteins could be detected in human neurons. These results suggest that SLC6A20 regulates proline and glycine homeostasis in the brain and that SLC6A20 inhibition has therapeutic potential for brain disorders involving NMDAR hypofunction.
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Affiliation(s)
- Mihyun Bae
- Center for Synaptic Brain DysfunctionsInstitute for Basic Science (IBS)DaejeonKorea
| | - Junyeop Daniel Roh
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
| | - Youjoung Kim
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
| | - Seong Soon Kim
- Therapeutics and Biotechnology DivisionKorea Research Institute of Chemical Technology (KRICT)DaejeonKorea
| | - Hye Min Han
- Department of Anatomy and NeurobiologySchool of DentistryKyungpook National UniversityDaeguKorea
| | - Esther Yang
- Department of Anatomy and Division of Brain Korea 21Biomedical ScienceCollege of MedicineKorea UniversitySeoulKorea
| | - Hyojin Kang
- Division of National SupercomputingKISTIDaejeonKorea
| | - Suho Lee
- Center for Synaptic Brain DysfunctionsInstitute for Basic Science (IBS)DaejeonKorea
| | - Jin Yong Kim
- Department of Anatomy and Division of Brain Korea 21Biomedical ScienceCollege of MedicineKorea UniversitySeoulKorea
| | - Ryeonghwa Kang
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
| | - Hwajin Jung
- Center for Synaptic Brain DysfunctionsInstitute for Basic Science (IBS)DaejeonKorea
| | - Taesun Yoo
- Center for Synaptic Brain DysfunctionsInstitute for Basic Science (IBS)DaejeonKorea
| | - Hyosang Kim
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
| | - Doyoun Kim
- Center for Synaptic Brain DysfunctionsInstitute for Basic Science (IBS)DaejeonKorea
| | - Heejeong Oh
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
| | - Sungwook Han
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
| | - Dayeon Kim
- Graduate School of Medical Science and EngineeringKAISTDaejeonKorea
| | - Jinju Han
- Graduate School of Medical Science and EngineeringKAISTDaejeonKorea
| | - Yong Chul Bae
- Department of Anatomy and NeurobiologySchool of DentistryKyungpook National UniversityDaeguKorea
| | - Hyun Kim
- Department of Anatomy and Division of Brain Korea 21Biomedical ScienceCollege of MedicineKorea UniversitySeoulKorea
| | - Sunjoo Ahn
- Therapeutics and Biotechnology DivisionKorea Research Institute of Chemical Technology (KRICT)DaejeonKorea
| | - Andrew M Chan
- School of Biomedical SciencesThe Chinese University of Hong KongHong KongHong Kong SARChina
| | - Daeyoup Lee
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
| | - Jin Woo Kim
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
| | - Eunjoon Kim
- Center for Synaptic Brain DysfunctionsInstitute for Basic Science (IBS)DaejeonKorea
- Department of Biological SciencesKorea Advanced Institute for Science and Technology (KAIST)DaejeonKorea
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15
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Frazier TW, Jaini R, Busch RM, Wolf M, Sadler T, Klaas P, Hardan AY, Martinez-Agosto JA, Sahin M, Eng C. Cross-level analysis of molecular and neurobehavioral function in a prospective series of patients with germline heterozygous PTEN mutations with and without autism. Mol Autism 2021; 12:5. [PMID: 33509259 PMCID: PMC7841880 DOI: 10.1186/s13229-020-00406-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/15/2020] [Indexed: 01/13/2023] Open
Abstract
Background PTEN is a well-established risk gene for autism spectrum disorder (ASD). Yet, little is known about how PTEN mutations and associated molecular processes influence neurobehavioral function in mutation carriers with (PTEN-ASD) and without ASD (PTEN no-ASD). The primary aim of the present study was to examine group differences in peripheral blood-derived PTEN pathway protein levels between PTEN-ASD, PTEN no-ASD, and idiopathic macrocephalic ASD patients (macro-ASD). Secondarily, associations between protein levels and neurobehavioral functions were examined in the full cohort.
Methods Patients were recruited at four tertiary medical centers. Peripheral blood-derived protein levels from canonical PTEN pathways (PI3K/AKT and MAPK/ERK) were analyzed using Western blot analyses blinded to genotype and ASD status. Neurobehavioral measures included standardized assessments of global cognitive ability and multiple neurobehavioral domains. Analysis of variance models examined group differences in demographic, neurobehavioral, and protein measures. Bivariate correlations, structural models, and statistical learning procedures estimated associations between molecular and neurobehavioral variables. To complement patient data, Western blots for downstream proteins were generated to evaluate canonical PTEN pathways in the PTEN-m3m4 mouse model.
Results Participants included 61 patients (25 PTEN-ASD, 16 PTEN no-ASD, and 20 macro-ASD). Decreased PTEN and S6 were observed in both PTEN mutation groups. Reductions in MnSOD and increases in P-S6 were observed in ASD groups. Elevated neural P-AKT/AKT and P-S6/S6 from PTEN murine models parallel our patient observations. Patient PTEN and AKT levels were independently associated with global cognitive ability, and p27 expression was associated with frontal sub-cortical functions. As a group, molecular measures added significant predictive value to several neurobehavioral domains over and above PTEN mutation status. Limitations Sample sizes were small, precluding within-group analyses. Protein and neurobehavioral data were limited to a single evaluation. A small number of patients were excluded with invalid protein data, and cognitively impaired patients had missing data on some assessments. Conclusions Several canonical PTEN pathway molecules appear to influence the presence of ASD and modify neurobehavioral function in PTEN mutation patients. Protein assays of the PTEN pathway may be useful for predicting neurobehavioral outcomes in PTEN patients. Future longitudinal analyses are needed to replicate these findings and evaluate within-group relationships between protein and neurobehavioral measures. Trial registration ClinicalTrials.gov Identifier NCT02461446
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Affiliation(s)
- Thomas W Frazier
- Department of Psychology, John Carroll University, University Heights, OH, 44118, USA. .,Autism Speaks, Cleveland, OH, USA. .,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
| | - Ritika Jaini
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Robyn M Busch
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Neurology and Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Matthew Wolf
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Tammy Sadler
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Patricia Klaas
- Department of Neurology and Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Antonio Y Hardan
- Department of Child Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Mustafa Sahin
- Translational Neurosciences Center, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA. .,Center for Personalized Genetic Healthcare, Cleveland Clinic Community Care and Population Health, Cleveland, OH, 44195, USA. .,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA. .,Cleveland Clinic Genomic Medicine Institute, 9500 Euclid Avenue, NE-50, Cleveland, OH, 44195, USA.
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16
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Sarn N, Jaini R, Thacker S, Lee H, Dutta R, Eng C. Cytoplasmic-predominant Pten increases microglial activation and synaptic pruning in a murine model with autism-like phenotype. Mol Psychiatry 2021; 26:1458-1471. [PMID: 32055008 PMCID: PMC8159731 DOI: 10.1038/s41380-020-0681-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 01/04/2020] [Accepted: 02/03/2020] [Indexed: 01/04/2023]
Abstract
Germline mutations in PTEN account for ~10% of cases of autism spectrum disorder (ASD) with coincident macrocephaly. To explore the importance of nuclear PTEN in the development of ASD and macrocephaly, we previously generated a mouse model with predominantly cytoplasmic localization of Pten (Ptenm3m4/m3m4).Cytoplasmic predominant Pten localization results in a phenotype of extreme macrocephaly and autistic-like traits. Transcriptomic analysis of the Ptenm3m4/m3m4 cortex found upregulated gene pathways related to myeloid cell activation, myeloid cell migration, and phagocytosis. These transcriptomic findings were used to direct in vitro assays on Pten wild-type and Ptenm3m4/m3m4 microglia. We found increased Iba1 and C1q expression with enhanced phagocytic capacity in Ptenm3m4/m3m4 microglia, indicating microglial activation. Moreover, through a series of neuron-microglia co-culture experiments, we found Ptenm3m4/m3m4 microglia are more efficient at synaptic pruning compared with wild-type controls. In addition, we found evidence for neuron-microglia cross-talk, where Ptenm3m4/m3m4 neurons elicit enhanced pruning from innately activated microglia. Subsequent in vivo studies validated our in vitro findings. We observed a concurrent decline in the expression of Pten and synaptic markers in the Ptenm3m4/m3m4 cortex. At ~3 weeks of age, with a 50% drop in Pten expression compared with wild-type levels, we observed enhanced activation of microglia in the Ptenm3m4/m3m4 brain. Collectively, our data provide evidence that dysregulated Pten in microglia has an etiological role in microglial activation, phagocytosis, and synaptic pruning, creating avenues for future studies on the importance of PTEN in maintaining microglia homeostasis.
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Affiliation(s)
- Nicholas Sarn
- grid.239578.20000 0001 0675 4725Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH USA ,Department of Genetics and Genome Sciences, Cleveland, OH USA
| | - Ritika Jaini
- grid.239578.20000 0001 0675 4725Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH USA ,grid.67105.350000 0001 2164 3847Germline High Risk Cancer Focus Group, Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH USA ,grid.254293.b0000 0004 0435 0569Cleveland Clinic Lerner College of Medicine, Cleveland, OH 44195 USA
| | - Stetson Thacker
- grid.239578.20000 0001 0675 4725Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH USA ,grid.254293.b0000 0004 0435 0569Cleveland Clinic Lerner College of Medicine, Cleveland, OH 44195 USA
| | - Hyunpil Lee
- grid.239578.20000 0001 0675 4725Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH USA
| | - Ranjan Dutta
- grid.254293.b0000 0004 0435 0569Cleveland Clinic Lerner College of Medicine, Cleveland, OH 44195 USA ,grid.239578.20000 0001 0675 4725Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA. .,Department of Genetics and Genome Sciences, Cleveland, OH, USA. .,Germline High Risk Cancer Focus Group, Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA. .,Cleveland Clinic Lerner College of Medicine, Cleveland, OH, 44195, USA.
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17
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Christian DL, Wu DY, Martin JR, Moore JR, Liu YR, Clemens AW, Nettles SA, Kirkland NM, Papouin T, Hill CA, Wozniak DF, Dougherty JD, Gabel HW. DNMT3A Haploinsufficiency Results in Behavioral Deficits and Global Epigenomic Dysregulation Shared across Neurodevelopmental Disorders. Cell Rep 2020; 33:108416. [PMID: 33238114 PMCID: PMC7716597 DOI: 10.1016/j.celrep.2020.108416] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 09/17/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Mutations in DNA methyltransferase 3A (DNMT3A) have been detected in autism and related disorders, but how these mutations disrupt nervous system function is unknown. Here, we define the effects of DNMT3A mutations associated with neurodevelopmental disease. We show that diverse mutations affect different aspects of protein activity but lead to shared deficiencies in neuronal DNA methylation. Heterozygous DNMT3A knockout mice mimicking DNMT3A disruption in disease display growth and behavioral alterations consistent with human phenotypes. Strikingly, in these mice, we detect global disruption of neuron-enriched non-CG DNA methylation, a binding site for the Rett syndrome protein MeCP2. Loss of this methylation leads to enhancer and gene dysregulation that overlaps with models of Rett syndrome and autism. These findings define the effects of DNMT3A haploinsufficiency in the brain and uncover disruption of the non-CG methylation pathway as a convergence point across neurodevelopmental disorders.
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Affiliation(s)
- Diana L Christian
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - J Russell Moore
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Yiran R Liu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Nicole M Kirkland
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - David F Wozniak
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110-1093, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110-1093, USA.
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18
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Alternative splicing landscape of the neural transcriptome in a cytoplasmic-predominant Pten expression murine model of autism-like Behavior. Transl Psychiatry 2020; 10:380. [PMID: 33159038 PMCID: PMC7648763 DOI: 10.1038/s41398-020-01068-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 01/01/2023] Open
Abstract
Alternative splicing (AS) is a posttranscriptional mechanism regulating gene expression that complex organisms utilize to expand proteome diversity from a comparatively limited set of genes. Recent research has increasingly associated AS with increased functional complexity in the central nervous systems in higher order mammals. This work has heavily implicated aberrant AS in several neurocognitive and neurodevelopmental disorders, including autism. Due to the strong genetic association between germline PTEN mutations and autism spectrum disorder (ASD), we hypothesized that germline PTEN mutations would alter AS patterns, contributing to the pathophysiology of ASD. In a murine model of constitutional mislocalization of Pten, recapitulating an autism-like phenotype, we found significant changes in AS patterns across the neural transcriptome by analyzing RNA-sequencing data with the program rMATS. A few hundred significant alternative splicing events (ASEs) that differentiate each m3m4 genotype were identified. These ASEs occur in genes enriched in PTEN signaling, inositol metabolism, and several other pathways relevant to the pathophysiology of ASD. In addition, we identified expression changes in several splicing factors known to be enriched in the nervous system. For instance, the master regulator of microexons, Srrm4, has decreased expression, and consequently, we found decreased inclusion of microexons in the Ptenm3m4/m3m4 cortex (~10% decrease). We also demonstrated that the m3m4 mutation disrupts the interaction between Pten and U2af2, a member of the spliceosome. In sum, our observations point to germline Pten disruption changing the landscape of alternative splicing in the brain, and these changes may be relevant to the pathogenesis and/or maintenance of PTEN-ASD phenotypes.
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19
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An N, Bassil K, Al Jowf GI, Steinbusch HWM, Rothermel M, de Nijs L, Rutten BPF. Dual-specificity phosphatases in mental and neurological disorders. Prog Neurobiol 2020; 198:101906. [PMID: 32905807 DOI: 10.1016/j.pneurobio.2020.101906] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 01/01/2023]
Abstract
The dual-specificity phosphatase (DUSP) family includes a heterogeneous group of protein phosphatases that dephosphorylate both phospho-tyrosine and phospho-serine/phospho-threonine residues within a single substrate. These protein phosphatases have many substrates and modulate diverse neural functions, such as neurogenesis, differentiation, and apoptosis. DUSP genes have furthermore been associated with mental disorders such as depression and neurological disorders such as Alzheimer's disease. Herein, we review the current literature on the DUSP family of genes concerning mental and neurological disorders. This review i) outlines the structure and general functions of DUSP genes, and ii) overviews the literature on DUSP genes concerning mental and neurological disorders, including model systems, while furthermore providing perspectives for future research.
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Affiliation(s)
- Ning An
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; European Graduate School of Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Katherine Bassil
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; European Graduate School of Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Ghazi I Al Jowf
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; College of Applied Medical Sciences, Department of Public Health, King Faisal University, Al-Ahsa, Saudi Arabia; European Graduate School of Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Harry W M Steinbusch
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; European Graduate School of Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Markus Rothermel
- European Graduate School of Neuroscience, Maastricht University, Maastricht, the Netherlands; Department of Chemosensation - AG Neuromodulation, RWTH Aachen University, Aachen, Germany
| | - Laurence de Nijs
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; European Graduate School of Neuroscience, Maastricht University, Maastricht, the Netherlands
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands; European Graduate School of Neuroscience, Maastricht University, Maastricht, the Netherlands.
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20
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An Integrated Deep-Mutational-Scanning Approach Provides Clinical Insights on PTEN Genotype-Phenotype Relationships. Am J Hum Genet 2020; 106:818-829. [PMID: 32442409 DOI: 10.1016/j.ajhg.2020.04.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/21/2020] [Indexed: 01/03/2023] Open
Abstract
Germline variation in PTEN results in variable clinical presentations, including benign and malignant neoplasia and neurodevelopmental disorders. Despite decades of research, it remains unclear how the PTEN genotype is related to clinical outcomes. In this study, we combined two recent deep mutational scanning (DMS) datasets probing the effects of single amino acid variation on enzyme activity and steady-state cellular abundance with a large, well-curated clinical cohort of PTEN-variant carriers. We sought to connect variant-specific molecular phenotypes to the clinical outcomes of individuals with PTEN variants. We found that DMS data partially explain quantitative clinical traits, including head circumference and Cleveland Clinic (CC) score, which is a semiquantitative surrogate of disease burden. We built logistic regression models that use DMS and CADD scores to separate clinical PTEN variation from gnomAD control-only variation with high accuracy. By using a survival-like analysis, we identified molecular phenotype groups with differential risk of early cancer onset as well as lifetime risk of cancer. Finally, we identified classes of DMS-defined variants with significantly different risk levels for classical hamartoma-related features (odds ratio [OR] range of 4.1-102.9). In stark contrast, the risk for developing autism or developmental delay does not significantly change across variant classes (OR range of 5.4-12.4). Together, these findings highlight the potential impact of combining DMS datasets with rich clinical data and provide new insights that might guide personalized clinical decisions for PTEN-variant carriers.
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21
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Kang SC, Jaini R, Hitomi M, Lee H, Sarn N, Thacker S, Eng C. Decreased nuclear Pten in neural stem cells contributes to deficits in neuronal maturation. Mol Autism 2020; 11:43. [PMID: 32487265 PMCID: PMC7268763 DOI: 10.1186/s13229-020-00337-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND PTEN, a syndromic autism spectrum disorder (ASD) risk gene, is mutated in approximately 10% of macrocephalic ASD cases. Despite the described genetic association between PTEN and ASD and ensuing studies, we continue to have a limited understanding of how PTEN disruption drives ASD pathogenesis and maintenance. METHODS We derived neural stem cells (NSCs) from the dentate gyrus (DG) of Ptenm3m4 mice, a model that recapitulates PTEN-ASD phenotypes. We subsequently characterized the expression of stemness factors, proliferation, and differentiation of neurons and glia in Ptenm3m4 NSCs using immunofluorescent and immunoblotting approaches. We also measured Creb phosphorylation by Western blot analysis and expression of Creb-regulated genes with qRT-PCR. RESULTS The m3m4 mutation decreases Pten localization to the nucleus and its global expression over time. Ptenm3m4 NSCs exhibit persistent stemness characteristics associated with increased proliferation and a resistance to neuronal maturation during differentiation. Given the increased proliferation of Ptenm3m4 NSCs, a significant increase in the population of immature neurons relative to mature neurons occurs, an approximately tenfold decrease in the ratio between the homozygous mutant and wildtype. There is an opposite pattern of differentiation in some Ptenm3m4 glia, specifically an increase in astrocytes. These aberrant differentiation patterns associate with changes in Creb activation in Ptenm3m4/m3m4 NSCs. We specifically observed loss of Creb phosphorylation at S133 in Ptenm3m4/m3m4 NSCs and a subsequent decrease in expression of Creb-regulated genes important to neuronal function (i.e., Bdnf). Interestingly, Bdnf treatment is able to partially rescue the stunted neuronal maturation phenotype in Ptenm3m4/m3m4 NSCs. CONCLUSIONS Constitutional disruption of Pten nuclear localization with subsequent global decrease in Pten expression generates abnormal patterns of differentiation, a stunting of neuronal maturation. The propensity of Pten disruption to restrain neurons to a more progenitor-like state may be an important feature contributing to PTEN-ASD pathogenesis.
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Affiliation(s)
- Shin Chung Kang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Ritika Jaini
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Masahiro Hitomi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Hyunpil Lee
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Nick Sarn
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Stetson Thacker
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA. .,Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Avenue, Cleveland, OH, 44195, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA. .,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA. .,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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22
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Abstract
Germline pathogenic phosphatase and tensin homolog (PTEN) mutations cause PTEN hamartoma tumor syndrome (PHTS), characterized by various benign and malignant tumors of the thyroid, breast, endometrium, and other organs. Patients with PHTS may present with other clinical features such as macrocephaly, intestinal polyposis, cognitive changes, and pathognomonic skin changes. Clinically, deregulation of PTEN function is implicated in other human diseases in addition to many types of human cancer. PTEN is an important phosphatase that counteracts one of the most critical cancer pathways: the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathways. Although PTEN can dephosphorylate lipids and proteins, it also has functions independent of phosphatase activity in normal and pathological states. It is positively and negatively regulated at the transcriptional level as well as posttranslationally by phosphorylation, ubiquitylation, oxidation, and acetylation. Although most of its tumor-suppressor activity is likely to be caused by lipid dephosphorylation at the plasma membrane, PTEN also resides in the cytoplasm and nucleus, and its subcellular distribution is under strict control. In this review, we highlight our current knowledge of PTEN function and recent discoveries in understanding PTEN function regulation and how this can be exploited therapeutically for cancer treatment.
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Affiliation(s)
- Joanne Ngeow
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 639798.,Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore 169610.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.,Germline High Risk Cancer Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
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23
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Abbas A, Padmanabhan R, Romigh T, Eng C. PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy. Hum Mol Genet 2020; 28:2826-2834. [PMID: 31127935 PMCID: PMC6735678 DOI: 10.1093/hmg/ddz112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/27/2019] [Accepted: 05/20/2019] [Indexed: 12/13/2022] Open
Abstract
Control of gene expression is one of the most complex yet continuous physiological processes impacting cellular homeostasis. RNA polymerase II (Pol II) transcription is tightly regulated at promoter-proximal regions by intricate dynamic processes including Pol II pausing, release into elongation and premature termination. Pol II pausing is a phenomenon where Pol II complex pauses within 30–60 nucleotides after initiating the transcription. Negative elongation factor (NELF) and DRB sensitivity inducing factor (DSIF) contribute in the establishment of Pol II pausing, and positive transcription elongation factor b releases (P-TEFb) paused complex after phosphorylating DSIF that leads to dissociation of NELF. Pol II pausing is observed in most expressed genes across the metazoan. The precise role of Pol II pausing is not well understood; however, it’s required for integration of signals for gene regulation. In the present study, we investigated the role of phosphatase and tensin homolog (PTEN) in genome-wide transcriptional regulation using PTEN overexpression and PTEN knock-down models. Here we identify that PTEN alters the expression of hundreds of genes, and its restoration establishes genome-wide Pol II promoter-proximal pausing in PTEN null cells. Furthermore, PTEN re-distributes Pol II occupancy across the genome and possibly impacts Pol II pause duration, release and elongation rate in order to enable precise gene regulation at the genome-wide scale. Our observations demonstrate an imperative role of PTEN in global transcriptional regulation that will provide a new direction to understand PTEN-associated pathologies and its management.
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Affiliation(s)
- Ata Abbas
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Roshan Padmanabhan
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Todd Romigh
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Germline High Risk Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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24
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Lauria A, Peirone S, Giudice MD, Priante F, Rajan P, Caselle M, Oliviero S, Cereda M. Identification of altered biological processes in heterogeneous RNA-sequencing data by discretization of expression profiles. Nucleic Acids Res 2020; 48:1730-1747. [PMID: 31889184 PMCID: PMC7038995 DOI: 10.1093/nar/gkz1208] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/31/2022] Open
Abstract
Heterogeneity is a fundamental feature of complex phenotypes. So far, genomic screenings have profiled thousands of samples providing insights into the transcriptome of the cell. However, disentangling the heterogeneity of these transcriptomic Big Data to identify defective biological processes remains challenging. Here we present GSECA, a method exploiting the bimodal behavior of RNA-sequencing gene expression profiles to identify altered gene sets in heterogeneous patient cohorts. Using simulated and experimental RNA-sequencing data sets, we show that GSECA provides higher performances than other available algorithms in detecting truly altered biological processes in large cohorts. Applied to 5941 samples from 14 different cancer types, GSECA correctly identified the alteration of the PI3K/AKT signaling pathway driven by the somatic loss of PTEN and verified the emerging role of PTEN in modulating immune-related processes. In particular, we showed that, in prostate cancer, PTEN loss appears to establish an immunosuppressive tumor microenvironment through the activation of STAT3, and low PTEN expression levels have a detrimental impact on patient disease-free survival. GSECA is available at https://github.com/matteocereda/GSECA.
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Affiliation(s)
- Andrea Lauria
- Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Serena Peirone
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Department of Physics and INFN, Università degli Studi di Torino, via P.Giuria 1, 10125 Turin, Italy
| | - Marco Del Giudice
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Francesca Priante
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Prabhakar Rajan
- Centre for Cell and Molecular Biology, Barts Cancer Institute, Cancer Research UK Barts Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London, NW1 2DB, UK
| | - Michele Caselle
- Department of Physics and INFN, Università degli Studi di Torino, via P.Giuria 1, 10125 Turin, Italy
| | - Salvatore Oliviero
- Department of Life Science and System Biology, Università degli Studi di Torino, via Accademia Albertina 13, 10123 Turin, Italy
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Matteo Cereda
- IIGM - Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str. Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
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25
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A myelin-related transcriptomic profile is shared by Pitt-Hopkins syndrome models and human autism spectrum disorder. Nat Neurosci 2020; 23:375-385. [PMID: 32015540 PMCID: PMC7065955 DOI: 10.1038/s41593-019-0578-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/16/2019] [Indexed: 12/19/2022]
Abstract
Autism spectrum disorder (ASD) is genetically heterogeneous with convergent symptomatology, suggesting common dysregulated pathways. We analyzed brain transcriptional changes in five mouse models of Pitt-Hopkins Syndrome (PTHS), a syndromic form of ASD caused by mutations in TCF4 (transcription factor 4, not TCF7L2 / T-Cell Factor 4). Analyses of differentially expressed genes (DEGs) highlighted oligodendrocyte (OL) dysregulation, which we confirmed in two additional mouse models of syndromic ASD (Ptenm3m4/m3m4 and Mecp2tm1.1Bird). The PTHS mouse models showed cell-autonomous reductions in OL numbers and myelination, functionally confirming OL transcriptional signatures. Next, we integrated PTHS mouse model DEGs with human idiopathic ASD postmortem brain RNA-seq data, and found significant enrichment of overlapping DEGs and common myelination-associated pathways. Importantly, DEGs from syndromic ASD mouse models, and reduced deconvoluted OL numbers, distinguished human idiopathic ASD cases from controls across three postmortem brain datasets. These results implicate disruptions in OL biology as a cellular mechanism in ASD pathology.
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26
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Chen CJ, Sgritta M, Mays J, Zhou H, Lucero R, Park J, Wang IC, Park JH, Kaipparettu BA, Stoica L, Jafar-Nejad P, Rigo F, Chin J, Noebels JL, Costa-Mattioli M. Therapeutic inhibition of mTORC2 rescues the behavioral and neurophysiological abnormalities associated with Pten-deficiency. Nat Med 2019; 25:1684-1690. [PMID: 31636454 PMCID: PMC7082835 DOI: 10.1038/s41591-019-0608-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/10/2019] [Indexed: 01/05/2023]
Abstract
Dysregulation of the mammalian target of rapamycin (mTOR) signaling, which is mediated by two structurally and functionally distinct complexes, mTORC1 and mTORC2, has been implicated in several neurological disorders1-3. Individuals carrying loss-of-function mutations in the phosphatase and tensin homolog (PTEN) gene, a negative regulator of mTOR signaling, are prone to developing macrocephaly, autism spectrum disorder (ASD), seizures and intellectual disability2,4,5. It is generally believed that the neurological symptoms associated with loss of PTEN and other mTORopathies (for example, mutations in the tuberous sclerosis genes TSC1 or TSC2) are due to hyperactivation of mTORC1-mediated protein synthesis1,2,4,6,7. Using molecular genetics, we unexpectedly found that genetic deletion of mTORC2 (but not mTORC1) activity prolonged lifespan, suppressed seizures, rescued ASD-like behaviors and long-term memory, and normalized metabolic changes in the brain of mice lacking Pten. In a more therapeutically oriented approach, we found that administration of an antisense oligonucleotide (ASO) targeting mTORC2's defining component Rictor specifically inhibits mTORC2 activity and reverses the behavioral and neurophysiological abnormalities in adolescent Pten-deficient mice. Collectively, our findings indicate that mTORC2 is the major driver underlying the neuropathophysiology associated with Pten-deficiency, and its therapeutic reduction could represent a promising and broadly effective translational therapy for neurological disorders where mTOR signaling is dysregulated.
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Affiliation(s)
- Chien-Ju Chen
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Martina Sgritta
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Jacqunae Mays
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongyi Zhou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Rocco Lucero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Jin Park
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - I-Ching Wang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benny Abraham Kaipparettu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Loredana Stoica
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Jeannie Chin
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey L Noebels
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Mauro Costa-Mattioli
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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27
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Busch RM, Srivastava S, Hogue O, Frazier TW, Klaas P, Hardan A, Martinez-Agosto JA, Sahin M, Eng C. Neurobehavioral phenotype of autism spectrum disorder associated with germline heterozygous mutations in PTEN. Transl Psychiatry 2019; 9:253. [PMID: 31594918 PMCID: PMC6783427 DOI: 10.1038/s41398-019-0588-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/04/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
Germline mutations in PTEN, the gene that encodes phosphatase and tensin homolog, have been identified in up to 20% of children with autism spectrum disorder (ASD) and macrocephaly and are associated with marked abnormalities in the white matter of the brain. This study sought to characterize the neurobehavioral phenotype of PTEN-ASD. Comprehensive neurobehavioral evaluations were conducted in 36 participants (ages 3-21 years) with PTEN-ASD and compared to two groups of controls: non-syndromic ASD with macrocephaly (Macro-ASD, n = 25) and those with PTEN mutations without ASD (PTEN-no ASD, n = 23). Linear regression analysis or Kruskal-Wallis tests were used to examine group differences on neurobehavioral measures (cognitive, behavioral, sensory, and adaptive functioning) and, for select measures, one-sample t-tests were used to compare group performance to healthy control norms. These analyses revealed a distinct neuropsychological profile associated with mutations in PTEN suggesting primary disruption of frontal lobe systems (i.e., attention, impulsivity, reaction time, processing speed, and motor coordination). Cognitive deficits in PTEN-ASD are more severe than those in PTEN-no ASD and extend to other areas of neurobehavioral function, specifically, adaptive behavior and sensory deficits. While core ASD symptoms are similar in PTEN-ASD and Macro-ASD, PTEN-ASD had lower clinical ratings of autism severity and showed more sensory abnormalities suggestive of less sensory responsiveness. Together, these results suggest that PTEN-ASD has a distinct neurobehavioral phenotype compared to idiopathic ASD that is likely to warrant special consideration for overall assessment and treatment.
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Affiliation(s)
- Robyn M. Busch
- 0000 0001 0675 4725grid.239578.2Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH USA ,0000 0001 0675 4725grid.239578.2Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA ,0000 0004 0378 8438grid.2515.3Harvard Medical School and Boston Children’s Hospital, Boston, MA USA
| | - Olivia Hogue
- 0000 0001 0675 4725grid.239578.2Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH USA
| | - Thomas W. Frazier
- 0000 0001 0675 4725grid.239578.2Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH USA ,0000 0004 4663 7867grid.427598.5Autism Speaks, Cleveland, OH USA ,0000 0001 0675 4725grid.239578.2Pediatrics Institute, Cleveland Clinic, Cleveland, OH USA
| | - Patricia Klaas
- 0000 0001 0675 4725grid.239578.2Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH USA
| | - Antonio Hardan
- 0000000087342732grid.240952.8Psychiatry and Behavioral Sciences, Stanford University Medical Center, Stanford, CA USA
| | - Julian A. Martinez-Agosto
- 0000 0000 9632 6718grid.19006.3eDepartment of Human Genetics, University of California Los Angeles, Los Angeles, CA USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA ,0000 0004 0378 8438grid.2515.3Harvard Medical School and Boston Children’s Hospital, Boston, MA USA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA. .,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA. .,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
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Frazier TW. Autism Spectrum Disorder Associated with Germline Heterozygous PTEN Mutations. Cold Spring Harb Perspect Med 2019; 9:a037002. [PMID: 31307976 PMCID: PMC6771360 DOI: 10.1101/cshperspect.a037002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This review examines our current understanding of autism spectrum disorder (ASD), its prevalence, impact, behavioral treatment, and outcomes. Building on this knowledge, ASD associated with PTEN mutations is introduced and recent human studies of neurobehavioral and neuroimaging findings in patients with PTEN mutations with and without ASD are reviewed. In doing so, we present evidence supporting a model of PTEN loss leading to neurobehavioral deficits, including ASD and intellectual disability. Next, we describe the neurobehavioral spectrum observed across PTEN mutation cases, adding specificity where possible, based on data from recent studies of child and adult PTEN patients. Finally, we end with a discussion of potential clinical recommendations for improving interventions and supports for people with PTEN-ASD and future research avenues for understanding and treating the functional and cognitive deficits in PTEN-ASD.
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29
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Abbas A, Romigh T, Eng C. PTEN interacts with RNA polymerase II to dephosphorylate polymerase II C-terminal domain. Oncotarget 2019; 10:4951-4959. [PMID: 31452836 PMCID: PMC6697640 DOI: 10.18632/oncotarget.27128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/17/2019] [Indexed: 11/25/2022] Open
Abstract
Gene transcription is a highly complex and strictly regulated process. RNA polymerase II (Pol II) C-terminal domain (CTD) undergoes massive cycles of phosphorylation and dephosphorylation during the process of gene transcription. These post-translational modifications of CTD provide an interactive platform for various factors required for transcription initiation, elongation, termination, and co-transcriptional RNA processing. Pol II CTD kinases and phosphatases are key regulators and any deviation may cause genome-wide transcriptional dysregulation leading to various pathological conditions including cancer. PTEN, a well known tumor suppressor, is one of the most commonly somatically altered in diverse malignancies. When mutated in the germline, PTEN causes cancer predisposition. Numerous studies have demonstrated that PTEN regulates the expression of hundreds of genes, however, no mechanism is known so far. PTEN is a dual specificity phosphatase, using both lipid and protein as substrates. In the present study, we demonstrate that PTEN interacts with the RNA Pol II and that PTEN expression is inversely correlated with global phosphorylation of Pol II CTD. Furthermore, PTEN dephosphorylates Pol II CTD in vitro with a significant specificity for Ser5p. Interestingly, ChIP-seq data analysis revealed that PTEN globally binds to promoter proximal regions, and PTEN loss increases genome-wide Pol II Ser5p occupancy, suggest that PTEN is a Pol II CTD phosphatase. Our observations demonstrate an unexplored function of PTEN with the potential of global transcriptional regulation, adding a new dimension to somatic carcinogenesis and germline cancer predisposition.
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Affiliation(s)
- Ata Abbas
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, 44195 OH, USA.,Present address: Division of Hematology Oncology, Department of Medicine, Case Western Reserve University, Cleveland, 44106 OH, USA
| | - Todd Romigh
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, 44195 OH, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, 44195 OH, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, 44195 OH, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, 44116 OH, USA.,Germline High Risk Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, 44116 OH, USA
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30
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Forés-Martos J, Catalá-López F, Sánchez-Valle J, Ibáñez K, Tejero H, Palma-Gudiel H, Climent J, Pancaldi V, Fañanás L, Arango C, Parellada M, Baudot A, Vogt D, Rubenstein JL, Valencia A, Tabarés-Seisdedos R. Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer. Mol Autism 2019; 10:17. [PMID: 31007884 PMCID: PMC6454734 DOI: 10.1186/s13229-019-0262-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/19/2019] [Indexed: 12/27/2022] Open
Abstract
Background Epidemiological and clinical evidence points to cancer as a comorbidity in people with autism spectrum disorders (ASD). A significant overlap of genes and biological processes between both diseases has also been reported. Methods Here, for the first time, we compared the gene expression profiles of ASD frontal cortex tissues and 22 cancer types obtained by differential expression meta-analysis and report gene, pathway, and drug set-based overlaps between them. Results Four cancer types (brain, thyroid, kidney, and pancreatic cancers) presented a significant overlap in gene expression deregulations in the same direction as ASD whereas two cancer types (lung and prostate cancers) showed differential expression profiles significantly deregulated in the opposite direction from ASD. Functional enrichment and LINCS L1000 based drug set enrichment analyses revealed the implication of several biological processes and pathways that were affected jointly in both diseases, including impairments of the immune system, and impairments in oxidative phosphorylation and ATP synthesis among others. Our data also suggest that brain and kidney cancer have patterns of transcriptomic dysregulation in the PI3K/AKT/MTOR axis that are similar to those found in ASD. Conclusions Comparisons of ASD and cancer differential gene expression meta-analysis results suggest that brain, kidney, thyroid, and pancreatic cancers are candidates for direct comorbid associations with ASD. On the other hand, lung and prostate cancers are candidates for inverse comorbid associations with ASD. Joint perturbations in a set of specific biological processes underlie these associations which include several pathways previously implicated in both cancer and ASD encompassing immune system alterations, impairments of energy metabolism, cell cycle, and signaling through PI3K and G protein-coupled receptors among others. These findings could help to explain epidemiological observations pointing towards direct and inverse comorbid associations between ASD and specific cancer types and depict a complex scenario regarding the molecular patterns of association between ASD and cancer. Electronic supplementary material The online version of this article (10.1186/s13229-019-0262-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaume Forés-Martos
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain
| | - Ferrán Catalá-López
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,2Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Blasco-Ibañez 15, 46010 Valencia, Spain.,3INCLIVA Health Research Institute, Valencia, Spain.,4Department of Health Planning and Economics, National School of Public Health/IMIENS, Institute of Health Carlos III, Madrid, Spain
| | | | | | - Héctor Tejero
- 7Structural Biology Program, Spanish National Cancer Research Program (CNIO), Madrid, Spain
| | - Helena Palma-Gudiel
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,8Anthropology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biomedicine Institute (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Joan Climent
- 3INCLIVA Health Research Institute, Valencia, Spain.,9Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Ramon y Cajal s/n 46115 Alfara del Patriarca, Valencia, Spain
| | - Vera Pancaldi
- 5Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Lourdes Fañanás
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,8Anthropology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biomedicine Institute (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Celso Arango
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Mara Parellada
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Anaïs Baudot
- 11Aix-Marseille Univ, Inserm, MMG, Marseille Medical Genetics, Marseille, France
| | - Daniel Vogt
- 12Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824 USA
| | - John L Rubenstein
- 13Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158 USA.,14Department of Psychiatry, University of California, San Francisco, CA 94158 USA
| | - Alfonso Valencia
- 5Barcelona Supercomputing Center (BSC), Barcelona, Spain.,15Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Rafael Tabarés-Seisdedos
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,2Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Blasco-Ibañez 15, 46010 Valencia, Spain.,3INCLIVA Health Research Institute, Valencia, Spain
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31
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Yehia L, Jindal S, Komar AA, Eng C. Non-canonical role of cancer-associated mutant SEC23B in the ribosome biogenesis pathway. Hum Mol Genet 2019; 27:3154-3164. [PMID: 29893852 PMCID: PMC6121187 DOI: 10.1093/hmg/ddy226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/04/2018] [Indexed: 02/07/2023] Open
Abstract
SEC23B is a component of coat protein complex II (COPII) vesicles that transport secretory proteins from the endoplasmic reticulum (ER) to the Golgi apparatus. Loss-of-function SEC23B mutations cause a rare form of anemia, resulting from decreased SEC23B levels. We recently identified germline heterozygous SEC23B variants as potentially cancer-predisposing. Mutant SEC23B associated with ER stress-mediated tumorigenesis, without decreased SEC23B expression. However, our understanding of the processes behind these observations remain limited. Here, we show mutant SEC23B exists within nucleoli, in addition to classical distribution at the ER/Golgi. This occurs independent of other COPII proteins and does not compromise secretory function. Mutant cells have increased ribosomal protein and translation-related gene expression, and enhanced translational capacity, in the presence of ER stress. We show that mutant SEC23B binds to UBF transcription factor, with increased UBF transcription factor binding at the ribosomal DNA promoter. Our data indicate SEC23B has potential non-canonical COPII-independent function, particularly within the ribosome biogenesis pathway, and that may contribute to the pathogenesis of cancer-predisposition.
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Affiliation(s)
- Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Supriya Jindal
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
| | - Anton A Komar
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA.,Germline High Risk Cancer Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Germline High Risk Cancer Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.,Taussig Cancer Institute, Cleveland Clinic, OH, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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32
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Matsuda S, Ikeda Y, Murakami M, Nakagawa Y, Tsuji A, Kitagishi Y. Roles of PI3K/AKT/GSK3 Pathway Involved in Psychiatric Illnesses. Diseases 2019; 7:diseases7010022. [PMID: 30781836 PMCID: PMC6473240 DOI: 10.3390/diseases7010022] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/31/2022] Open
Abstract
Psychiatric illnesses may be qualified to the cellular impairments of the function for survival or death in neurons, which may consequently appear as abnormalities in the neuroplasticity. The molecular mechanism has not been well understood, however, it seems that PI3K, AKT, GSK3, and their downstream molecules have crucial roles in the pathogenesis. Through transducing cell surviving signal, the PI3K/AKT/GSK3 pathway may organize an intracellular central network for the action of the synaptic neuroplasticity. In addition, the pathways may also regulate cell proliferation, cell migration, and apoptosis. Several lines of evidence have supported a role for this signaling network underlying the development and treatment for psychiatric illnesses. Indeed, the discovery of molecular biochemical phenotypes would represent a breakthrough in the research for effective treatment. In this review, we summarize advances on the involvement of the PI3K/AKT/GSK3 pathways in cell signaling of neuronal cells. This study may provide novel insights on the mechanism of mental disorder involved in psychiatric illnesses and would open future opportunity for contributions suggesting new targets for diagnostic and/or therapeutic procedures.
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Affiliation(s)
- Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Yuka Ikeda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Mutsumi Murakami
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Yukie Nakagawa
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Ai Tsuji
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
| | - Yasuko Kitagishi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan.
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Lee H, Thacker S, Sarn N, Dutta R, Eng C. Constitutional mislocalization of Pten drives precocious maturation in oligodendrocytes and aberrant myelination in model of autism spectrum disorder. Transl Psychiatry 2019; 9:13. [PMID: 30664625 PMCID: PMC6341090 DOI: 10.1038/s41398-018-0364-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 12/18/2022] Open
Abstract
There is a strong genetic association between germline PTEN mutation and autism spectrum disorder (ASD), making Pten-mutant models exemplary for the study of ASD pathophysiology. We developed the Ptenm3m4 mouse, where Pten is largely restricted from the nucleus, which recapitulates patient-like, autism-related phenotypes: behavioral changes, macrocephaly, and white matter abnormalities. This study aimed to investigate the contribution of oligodendrocyte (OL) lineage differentiation and functional changes in myelination to the white matter phenotype. OL lineage differentiation and myelination in Ptenm3m4 mice was studied using immunohistochemical and electron microscopic analyses. We also used primary oligodendrocyte progenitor cells (OPCs) to determine the effect of the Ptenm3m4 mutation on OPC proliferation, migration and maturation. Finally, we assessed the myelinating competency of mutant OLs via co-culture with wildtype dorsal root ganglia (DRG) neurons. The in vivo analyses of Ptenm3m4/m3m4 murine brains showed deficits in proteolipid protein (Plp) trafficking in myelinating OLs. Despite the increased expression of myelin proteins in the brain, myelin deposition was observed to be abnormal, often occurring adjacent to, rather than around axons. Mutant primary OPCs showed enhanced proliferation and migration. Furthermore, mutant OPCs matured precociously, exhibiting aberrant myelination in vitro. Mutant OPCs, when co-cultured with wildtype DRG neurons, showed an inability to properly ensheath axons. Our findings provide evidence that the Ptenm3m4 mutation disrupts the differentiation and myelination programs of developing OLs. OL dysfunction in the Ptenm3m4 model explains the leukodystrophy phenotype, a feature commonly associated with autism, and highlights the growing importance of glial dysfunction in autism pathogenesis.
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Affiliation(s)
- Hyunpil Lee
- 0000 0001 0675 4725grid.239578.2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, USA
| | - Stetson Thacker
- 0000 0001 0675 4725grid.239578.2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, USA ,0000 0004 0435 0569grid.254293.bCleveland Clinic Lerner College of Medicine, Cleveland, OH 44195 USA
| | - Nicholas Sarn
- 0000 0001 0675 4725grid.239578.2Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, USA ,0000 0001 2164 3847grid.67105.35Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, USA
| | - Ranjan Dutta
- 0000 0004 0435 0569grid.254293.bCleveland Clinic Lerner College of Medicine, Cleveland, OH 44195 USA ,0000 0001 0675 4725grid.239578.2Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, USA. .,Cleveland Clinic Lerner College of Medicine, Cleveland, OH, 44195, USA. .,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, USA. .,Germline High Risk Cancer Focus Group, Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, USA.
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34
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Yehia L, Ngeow J, Eng C. PTEN-opathies: from biological insights to evidence-based precision medicine. J Clin Invest 2019; 129:452-464. [PMID: 30614812 DOI: 10.1172/jci121277] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The tumor suppressor phosphatase and tensin homolog (PTEN) classically counteracts the PI3K/AKT/mTOR signaling cascade. Germline pathogenic PTEN mutations cause PTEN hamartoma tumor syndrome (PHTS), featuring various benign and malignant tumors, as well as neurodevelopmental disorders such as autism spectrum disorder. Germline and somatic mosaic mutations in genes encoding components of the PI3K/AKT/mTOR pathway downstream of PTEN predispose to syndromes with partially overlapping clinical features, termed the "PTEN-opathies." Experimental models of PTEN pathway disruption uncover the molecular and cellular processes influencing clinical phenotypic manifestations. Such insights not only teach us about biological mechanisms in states of health and disease, but also enable more accurate gene-informed cancer risk assessment, medical management, and targeted therapeutics. Hence, the PTEN-opathies serve as a prototype for bedside to bench, and back to the bedside, practice of evidence-based precision medicine.
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Affiliation(s)
- Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Joanne Ngeow
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.,Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore.,Oncology Academic Program, Duke-NUS Graduate Medical School, Singapore
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
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35
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Jyonouchi H, Geng L, Rose S, Bennuri SC, Frye RE. Variations in Mitochondrial Respiration Differ in IL-1ß/IL-10 Ratio Based Subgroups in Autism Spectrum Disorders. Front Psychiatry 2019; 10:71. [PMID: 30842746 PMCID: PMC6391925 DOI: 10.3389/fpsyt.2019.00071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 01/30/2019] [Indexed: 12/31/2022] Open
Abstract
Autism spectrum disorder (ASD)7 is associated with multiple physiological abnormalities, including immune dysregulation, and mitochondrial dysfunction. However, an association between these two commonly reported abnormalities in ASD has not been studied in depth. This study assessed the association between previously identified alterations in cytokine profiles by ASD peripheral blood monocytes (PBMo) and mitochondrial dysfunction. In 112 ASD and 38 non-ASD subjects, cytokine production was assessed by culturing purified PBMo overnight with stimuli of innate immunity. Parameters of mitochondrial respiration including proton-leak respiration (PLR), ATP-linked respiration (ALR), maximal respiratory capacity (MRC), and reserve capacity (RC) were measured in peripheral blood mononuclear cells (PBMCs). The ASD samples were analyzed by subgrouping them into high, normal, and low IL-1ß/IL-10 ratio groups, which was previously shown to be associated with changes in behaviors and PBMo miRNA expression. MRC, RC, and RC/PLR, a marker of electron transport chain (ETC) efficiency, were higher in ASD PBMCs than controls. The expected positive associations between PLR and ALR were found in control non-ASD PBMCs, but not in ASD PBMCs. Higher MRC, RC, RC/PLR in ASD PBMCs were secondary to higher levels of these parameters in the high and normal IL-1ß/IL-10 ratio ASD subgroups than controls. Associations between mitochondrial parameters and monocyte cytokine profiles differed markedly across the IL-1ß/IL-10 ratio based ASD subgroups, rendering such associations less evident when ASD samples as a whole were compared to non-ASD controls. Our results indicate for the first time, an association between PBMC mitochondrial function and PBMo cytokine profiles in ASD subjects. This relationship differs across the IL-1ß/IL-10 ratio based ASD subgroups. Changes in mitochondrial function are likely due to adaptive changes or mitochondrial dysfunction, resulting from chronic oxidative stress. These results may indicate alteration in molecular pathways affecting both the immune system and mitochondrial function in some ASD subjects.
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Affiliation(s)
- Harumi Jyonouchi
- Department of Pediatrics, Saint Peter's University Hospital, New Brunswick, NJ, United States.,Robert Wood Johnson Medical School-Rutgers, New Brunswick, NJ, United States
| | - Lee Geng
- Department of Pediatrics, Saint Peter's University Hospital, New Brunswick, NJ, United States
| | - Shannon Rose
- Arkansas Children's Research Institute, Little Rock, AR, United States.,Department of Pediatrics, University of Arkansas of Medical Sciences, Little Rock, AR, United States
| | - Sirish C Bennuri
- Arkansas Children's Research Institute, Little Rock, AR, United States.,Department of Pediatrics, University of Arkansas of Medical Sciences, Little Rock, AR, United States
| | - Richard E Frye
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, United States.,Barrow Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ, United States
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36
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Jehi L, Yehia L, Peterson C, Niazi F, Busch R, Prayson R, Ying Z, Bingaman W, Najm I, Eng C. Preliminary report: Late seizure recurrence years after epilepsy surgery may be associated with alterations in brain tissue transcriptome. Epilepsia Open 2018; 3:299-304. [PMID: 29881812 PMCID: PMC5983127 DOI: 10.1002/epi4.12119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2018] [Indexed: 11/22/2022] Open
Abstract
We recently proposed that the maturation of a new epileptic focus (epileptogenesis) may explain late seizure recurrences, starting months to years after resective epilepsy surgery. We explore here the hypothesis that inherent transcriptomic changes may distinguish such “late relapsers.” An in‐depth clinical review of 2 patients with recurrent seizures starting years after surgery is contrasted to 4 controls who remained seizure‐free postoperatively. This clinical analysis is combined with RNA sequencing from the resected brain tissue, followed by unsupervised hierarchical clustering, independent pathway analysis, and multidimensional scaling analysis. Late‐recurrence patients clustered apart from seizure‐free patients, with late recurrence patients clustering together in the central space, whereas the seizure‐free patients clustered together in the periphery. We utilized RNA‐seq to identify differentially expressed genes between late‐recurrence and seizure‐free samples. We found 29 annotated genes with statistically significant differential expression (q < 0.05). The top canonical pathways identified as distinctly separating the late‐recurrence patients from the seizure‐free patients included the intrinsic prothrombin activation pathway (p = 1.55E‐06), the complement system (p = 4.57E‐05), and the atherosclerosis signaling pathway (p = 4.57E‐05). Our observations suggest that late recurrences after epilepsy surgery may be influenced partly by differences in gene expression in neuroinflammatory and brain healing/remodeling pathways. Such a hypothesis needs to be validated in the future.
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Affiliation(s)
- Lara Jehi
- Epilepsy Center Neurological Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - Lamis Yehia
- Genomic Medicine Institute Lerner Research Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - Charissa Peterson
- Genomic Medicine Institute Lerner Research Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - Farshad Niazi
- Genomic Medicine Institute Lerner Research Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - Robyn Busch
- Epilepsy Center Neurological Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - Richard Prayson
- Department of Pathology Tomsich Pathology and Laboratory Medicine Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - Zhong Ying
- Epilepsy Center Neurological Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - William Bingaman
- Epilepsy Center Neurological Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - Imad Najm
- Epilepsy Center Neurological Institute Cleveland Clinic Cleveland Ohio U.S.A
| | - Charis Eng
- Genomic Medicine Institute Lerner Research Institute Cleveland Clinic Cleveland Ohio U.S.A.,Taussig Cancer Institute Cleveland Clinic Cleveland Ohio U.S.A.,Stanley Shalom Zielony Institute of Nursing Excellence Cleveland Clinic Cleveland Ohio U.S.A.,Department of Genetics and Genome Sciences Case Western Reserve University School of Medicine Cleveland Ohio U.S.A.,Case Comprehensive Cancer Center Case Western Reserve University School of Medicine Cleveland Ohio U.S.A
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37
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Jyonouchi H, Geng L, Streck DL, Dermody JJ, Toruner GA. MicroRNA expression changes in association with changes in interleukin-1ß/interleukin10 ratios produced by monocytes in autism spectrum disorders: their association with neuropsychiatric symptoms and comorbid conditions (observational study). J Neuroinflammation 2017; 14:229. [PMID: 29178897 PMCID: PMC5702092 DOI: 10.1186/s12974-017-1003-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) play a major role in regulating immune responses at post-transcriptional levels. Previously, we have reported fluctuating interlukine-1ß (IL-1ß)/IL-10 ratios produced by peripheral blood monocytes (PBMo) in some patients with autism spectrum disorders (ASD). This study examined whether changes in miRNA expression by PBMo are associated with changes in IL-1ß/IL-10 ratios and how such changes are associated with ASD clinical features. METHODS miRNA expression by purified PBMo from ASD subjects (N = 69) and non-ASD controls (N = 27) were determined by high-throughput sequencing. Cytokine production by PBMo in responses to stimuli of innate immunity, and behavioral symptoms [assessed by aberrant behavioral checklist (ABC)] were also evaluated at the same time of sample obtainment. RESULTS As a whole, there was no difference in miRNA expression between ASD and control non-ASD PBMo. However, when ASD cells were subdivided into 3 groups with high, normal, or low IL-1ß/IL-10 ratios as defined in the "Results" section, in comparison with the data obtained from non-ASD controls, we observed marked changes in miRNA expression. Namely, over 3-fold changes in expression of miR-181a, miR-93, miR-223, miR-342, and miR-1248 were observed in ASD PBMo with high or low IL-1ß/IL-10 ratios, but not in ASD PBMo with normal ratios. These miRNAs that had altered in expression are those closely associated with the regulation of key signaling pathways. With changes in IL-1ß/IL-10 ratios, we also observed changes in the production of cytokines (IL-6, TNF-α, and TGF-ß) other than IL-1ß/IL-10 by ASD PBMo. The association between behavioral symptoms and cytokine levels was different when ASD cells exhibit high/low IL-1ß/IL-10 ratios vs. when ASD cells exhibited normal ratios. Non-IgE-mediated food allergy was also observed at higher frequency in ASD subjects with high/low IL-1ß/IL-10 ratios than with normal ratios. CONCLUSIONS Changes in cytokine profiles and miRNA expression by PBMo appear to be associated with changes in ASD behavioral symptoms. miRNAs that are altered in expression in ASD PBMo with high/low IL-1ß/IL-10 ratios are those associated with inflammatory responses. Changes in IL-1ß/IL-10 ratios along with changes in miRNA expression may serve as biomarkers for immune-mediated inflammation in ASD.
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Affiliation(s)
- Harumi Jyonouchi
- Department of Pediatrics, Saint Peter's University Hospital (SPUH), Rutgers-Robert Wood Johnson Medical School, 254 Easton Ave., New Brunswick, NJ, 08901, USA.
| | - Lee Geng
- Department of Pediatrics, Saint Peter's University Hospital (SPUH), Rutgers-Robert Wood Johnson Medical School, 254 Easton Ave., New Brunswick, NJ, 08901, USA
| | - Deanna L Streck
- Institute of Genomic Medicine, Rutgers-New Jersey Medical School (NJMS), Newark, NJ, USA
| | - James J Dermody
- Institute of Genomic Medicine, Rutgers-New Jersey Medical School (NJMS), Newark, NJ, USA
| | - Gokce A Toruner
- Clinical cytogenetics/Department of Hematopathology, MD Anderson Cancer Center, Houston, TX, USA
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38
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Targeted sequencing and functional analysis reveal brain-size-related genes and their networks in autism spectrum disorders. Mol Psychiatry 2017; 22:1282-1290. [PMID: 28831199 DOI: 10.1038/mp.2017.140] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 03/31/2017] [Accepted: 05/19/2017] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorder (ASD) represents a set of complex neurodevelopmental disorders with large degrees of heritability and heterogeneity. We sequenced 136 microcephaly or macrocephaly (Mic-Mac)-related genes and 158 possible ASD-risk genes in 536 Chinese ASD probands and detected 22 damaging de novo mutations (DNMs) in 20 genes, including CHD8 and SCN2A, with recurrent events. Nine of the 20 genes were previously reported to harbor DNMs in ASD patients from other populations, while 11 of them were first identified in present study. We combined genetic variations of the 294 sequenced genes from publicly available whole-exome or whole-genome sequencing studies (4167 probands plus 1786 controls) with our Chinese population (536 cases plus 1457 controls) to optimize the power of candidate-gene prioritization. As a result, we prioritized 67 ASD-candidate genes that exhibited significantly higher probabilities of haploinsufficiency and genic intolerance, and significantly interacted and co-expressed with each another, as well as other known ASD-risk genes. Probands with DNMs or rare inherited mutations in the 67 candidate genes exhibited significantly lower intelligence quotients, supporting their strong functional impact. In addition, we prioritized 39 ASD-related Mic-Mac-risk genes, and showed their interaction and co-expression in a functional network that converged on chromatin remodeling, synapse transmission and cell cycle progression. Genes within the three functional subnetworks exhibited distinct and recognizable spatiotemporal-expression patterns in human brains and laminar-expression profiles in the developing neocortex, highlighting their important roles in brain development. Our results indicate some of Mic-Mac-risk genes are involved in ASD.
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39
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Oswald F, Klöble P, Ruland A, Rosenkranz D, Hinz B, Butter F, Ramljak S, Zechner U, Herlyn H. The FOXP2-Driven Network in Developmental Disorders and Neurodegeneration. Front Cell Neurosci 2017; 11:212. [PMID: 28798667 PMCID: PMC5526973 DOI: 10.3389/fncel.2017.00212] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/04/2017] [Indexed: 12/24/2022] Open
Abstract
The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (SH-SY5Y) stably overexpressing FOXP2 cDNA of either humans or the common chimpanzee, Rhesus monkey, and marmoset, respectively. RNA-seq led to identification of 27 genes with differential regulation under the control of human FOXP2, which were previously reported to have FOXP2-driven and/or songbird song-related expression regulation. RT-qPCR and Western blotting indicated differential regulation of additional 13 new target genes in response to overexpression of human FOXP2. These genes may be directly regulated by FOXP2 considering numerous matches of established FOXP2-binding motifs as well as publicly available FOXP2-ChIP-seq reads within their putative promoters. Ontology analysis of the new and reproduced targets, along with their interactors in a network, revealed an enrichment of terms relating to cellular signaling and communication, metabolism and catabolism, cellular migration and differentiation, and expression regulation. Notably, terms including the words "neuron" or "axonogenesis" were also enriched. Complementary literature screening uncovered many connections to human developmental (autism spectrum disease, schizophrenia, Down syndrome, agenesis of corpus callosum, trismus-pseudocamptodactyly, ankyloglossia, facial dysmorphology) and neurodegenerative diseases and disorders (Alzheimer's, Parkinson's, and Huntington's diseases, Lewy body dementia, amyotrophic lateral sclerosis). Links to deafness and dyslexia were detected, too. Such relations existed for single proteins (e.g., DCDC2, NURR1, PHOX2B, MYH8, and MYH13) and groups of proteins which conjointly function in mRNA processing, ribosomal recruitment, cell-cell adhesion (e.g., CDH4), cytoskeleton organization, neuro-inflammation, and processing of amyloid precursor protein. Conspicuously, many links pointed to an involvement of the FOXP2-driven network in JAK/STAT signaling and the regulation of the ezrin-radixin-moesin complex. Altogether, the applied phylogenetic perspective substantiated FOXP2's importance for nervous system development, maintenance, and functioning. However, the study also disclosed new regulatory pathways that might prove to be useful for understanding the molecular background of the aforementioned developmental disorders and neurodegenerative diseases.
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Affiliation(s)
- Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center UlmUlm, Germany
| | - Patricia Klöble
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center UlmUlm, Germany
| | - André Ruland
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center UlmUlm, Germany
| | - David Rosenkranz
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-University MainzMainz, Germany
| | - Bastian Hinz
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-University MainzMainz, Germany
- Institute of Human Genetics, University Medical Center MainzMainz, Germany
| | - Falk Butter
- Institute of Molecular BiologyMainz, Germany
| | | | - Ulrich Zechner
- Institute of Human Genetics, University Medical Center MainzMainz, Germany
- Dr. Senckenbergisches Zentrum für HumangenetikFrankfurt, Germany
| | - Holger Herlyn
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-University MainzMainz, Germany
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40
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Chen HJ, Romigh T, Sesock K, Eng C. Characterization of cryptic splicing in germline PTEN intronic variants in Cowden syndrome. Hum Mutat 2017; 38:1372-1377. [PMID: 28677221 PMCID: PMC5599331 DOI: 10.1002/humu.23288] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 05/31/2017] [Accepted: 06/29/2017] [Indexed: 02/01/2023]
Abstract
Germline mutations in the tumor‐suppressor gene PTEN predispose to subsets of Cowden syndrome (CS), Bannayan–Riley–Ruvalcaba syndrome, and autism. Evidence‐based classification of PTEN variants as either deleterious or benign is urgently needed for accurate molecular diagnosis and gene‐informed genetic counseling. We studied 34 different germline PTEN intronic variants from 61 CS patients, characterized their PTEN mRNA processing, and analyzed PTEN expression and downstream readouts of P‐AKT and P‐ERK1/2. While we found that many mutations near splice junctions result in exon skipping, we also identified the presence of cryptic splicing that resulted in premature termination or a shift in isoform usage. PTEN protein expression is significantly lower in the group with splicing changes while P‐AKT, but not P‐ERK1/2, is significantly increased. Our observations of these PTEN intronic variants should contribute to the determination of pathogenicity of PTEN intronic variants and aid in genetic counseling.
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Affiliation(s)
- Hannah Jinlian Chen
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio.,Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Todd Romigh
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio.,Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Kaitlin Sesock
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio.,Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio.,Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
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41
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Bozzi Y, Provenzano G, Casarosa S. Neurobiological bases of autism-epilepsy comorbidity: a focus on excitation/inhibition imbalance. Eur J Neurosci 2017; 47:534-548. [PMID: 28452083 DOI: 10.1111/ejn.13595] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/18/2017] [Accepted: 04/21/2017] [Indexed: 12/13/2022]
Abstract
Autism spectrum disorders (ASD) and epilepsy are common neurological diseases of childhood, with an estimated incidence of approximately 0.5-1% of the worldwide population. Several genetic, neuroimaging and neuropathological studies clearly showed that both ASD and epilepsy have developmental origins and a substantial degree of heritability. Most importantly, ASD and epilepsy frequently coexist in the same individual, suggesting a common neurodevelopmental basis for these disorders. Genome-wide association studies recently allowed for the identification of a substantial number of genes involved in ASD and epilepsy, some of which are mutated in syndromes presenting both ASD and epilepsy clinical features. At the cellular level, both preclinical and clinical studies indicate that the different genetic causes of ASD and epilepsy may converge to perturb the excitation/inhibition (E/I) balance, due to the dysfunction of excitatory and inhibitory circuits in various brain regions. Metabolic and immune dysfunctions, as well as environmental causes also contribute to ASD pathogenesis. Thus, an E/I imbalance resulting from neurodevelopmental deficits of multiple origins might represent a common pathogenic mechanism for both diseases. Here, we will review the most significant studies supporting these hypotheses. A deeper understanding of the molecular and cellular determinants of autism-epilepsy comorbidity will pave the way to the development of novel therapeutic strategies.
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Affiliation(s)
- Yuri Bozzi
- Neurodevelopmental Disorders Research Group, Centre for Mind/Brain Sciences, University of Trento, via Sommarive 9, 38123, Povo, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
| | - Giovanni Provenzano
- Laboratory of Molecular Neuropathology, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Simona Casarosa
- CNR Neuroscience Institute, Pisa, Italy.,Laboratory of Neural Development and Regeneration, Centre for Integrative Biology, University of Trento, Trento, Italy
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42
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Reim D, Distler U, Halbedl S, Verpelli C, Sala C, Bockmann J, Tenzer S, Boeckers TM, Schmeisser MJ. Proteomic Analysis of Post-synaptic Density Fractions from Shank3 Mutant Mice Reveals Brain Region Specific Changes Relevant to Autism Spectrum Disorder. Front Mol Neurosci 2017; 10:26. [PMID: 28261056 PMCID: PMC5306440 DOI: 10.3389/fnmol.2017.00026] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/23/2017] [Indexed: 12/03/2022] Open
Abstract
Disruption of the human SHANK3 gene can cause several neuropsychiatric disease entities including Phelan-McDermid syndrome, autism spectrum disorder (ASD), and intellectual disability. Although, a wide array of neurobiological studies strongly supports a major role for SHANK3 in organizing the post-synaptic protein scaffold, the molecular processes at synapses of individuals harboring SHANK3 mutations are still far from being understood. In this study, we biochemically isolated the post-synaptic density (PSD) fraction from striatum and hippocampus of adult Shank3Δ11-/- mutant mice and performed ion-mobility enhanced data-independent label-free LC-MS/MS to obtain the corresponding PSD proteomes (Data are available via ProteomeXchange with identifier PXD005192). This unbiased approach to identify molecular disturbances at Shank3 mutant PSDs revealed hitherto unknown brain region specific alterations including a striatal decrease of several molecules encoded by ASD susceptibility genes such as the serine/threonine kinase Cdkl5 and the potassium channel KCa1.1. Being the first comprehensive analysis of brain region specific PSD proteomes from a Shank3 mutant line, our study provides crucial information on molecular alterations that could foster translational treatment studies for SHANK3 mutation-associated synaptopathies and possibly also ASD in general.
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Affiliation(s)
- Dominik Reim
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany
- International Graduate School in Molecular Medicine, Ulm UniversityUlm, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University MainzMainz, Germany
- Focus Program Translational Neurosciences, University Medical Center of the Johannes-Gutenberg University MainzMainz, Germany
| | - Sonja Halbedl
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany
- International Graduate School in Molecular Medicine, Ulm UniversityUlm, Germany
| | - Chiara Verpelli
- CNR Neuroscience InstituteMilan, Italy
- BIOMETRA, University of MilanMilan, Italy
| | - Carlo Sala
- CNR Neuroscience InstituteMilan, Italy
- BIOMETRA, University of MilanMilan, Italy
| | - Juergen Bockmann
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center of the Johannes-Gutenberg University MainzMainz, Germany
| | | | - Michael J. Schmeisser
- Institute for Anatomy and Cell Biology, Ulm UniversityUlm, Germany
- Division of Neuroanatomy, Institute of Anatomy, Otto-von-Guericke UniversityMagdeburg, Germany
- Leibniz Institute for NeurobiologyMagdeburg, Germany
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43
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Knafo S, Esteban JA. PTEN: Local and Global Modulation of Neuronal Function in Health and Disease. Trends Neurosci 2017; 40:83-91. [PMID: 28081942 DOI: 10.1016/j.tins.2016.11.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 11/27/2022]
Abstract
Phosphatase and tensin homolog deleted on chromosome ten (PTEN) was recently revealed to be a synaptic player during plasticity events in addition to its well-established role as a general controlling factor in cell proliferation and neuronal growth during development. Alterations of these direct actions of PTEN at synapses may lead to synaptic dysfunction with behavioral and cognitive consequences. A recent paradigmatic example of this situation, Alzheimer's disease (AD), is associated with excessive recruitment of PTEN into synapses leading to pathological synaptic depression. By contrast, some forms of autism are characterized by failure to weaken synaptic connections, which may be related to insufficient PTEN signaling. Understanding the modulation of synaptic function by PTEN in these pathologies may contribute to the development of new therapies.
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Affiliation(s)
- Shira Knafo
- Biophysics Institute, CSIC-UPV/EHU, Campus Universidad del País Vasco, Barrio Sarriena s/n, 48940 Leioa, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Basque Country, Spain.
| | - José A Esteban
- Department of Molecular Neurobiology, Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas (CSIC)/Universidad Autónoma de Madrid, 28049 Madrid, Spain.
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44
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Lin YC, Frei JA, Kilander MBC, Shen W, Blatt GJ. A Subset of Autism-Associated Genes Regulate the Structural Stability of Neurons. Front Cell Neurosci 2016; 10:263. [PMID: 27909399 PMCID: PMC5112273 DOI: 10.3389/fncel.2016.00263] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 12/15/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a range of neurological conditions that affect individuals’ ability to communicate and interact with others. People with ASD often exhibit marked qualitative difficulties in social interaction, communication, and behavior. Alterations in neurite arborization and dendritic spine morphology, including size, shape, and number, are hallmarks of almost all neurological conditions, including ASD. As experimental evidence emerges in recent years, it becomes clear that although there is broad heterogeneity of identified autism risk genes, many of them converge into similar cellular pathways, including those regulating neurite outgrowth, synapse formation and spine stability, and synaptic plasticity. These mechanisms together regulate the structural stability of neurons and are vulnerable targets in ASD. In this review, we discuss the current understanding of those autism risk genes that affect the structural connectivity of neurons. We sub-categorize them into (1) cytoskeletal regulators, e.g., motors and small RhoGTPase regulators; (2) adhesion molecules, e.g., cadherins, NCAM, and neurexin superfamily; (3) cell surface receptors, e.g., glutamatergic receptors and receptor tyrosine kinases; (4) signaling molecules, e.g., protein kinases and phosphatases; and (5) synaptic proteins, e.g., vesicle and scaffolding proteins. Although the roles of some of these genes in maintaining neuronal structural stability are well studied, how mutations contribute to the autism phenotype is still largely unknown. Investigating whether and how the neuronal structure and function are affected when these genes are mutated will provide insights toward developing effective interventions aimed at improving the lives of people with autism and their families.
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Affiliation(s)
- Yu-Chih Lin
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Jeannine A Frei
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Michaela B C Kilander
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Wenjuan Shen
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Gene J Blatt
- Laboratory of Autism Neurocircuitry, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
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45
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Provenzano G, Corradi Z, Monsorno K, Fedrizzi T, Ricceri L, Scattoni ML, Bozzi Y. Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2 (-/-) Hippocampus. Front Neurosci 2016; 10:396. [PMID: 27610074 PMCID: PMC4996997 DOI: 10.3389/fnins.2016.00396] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/12/2016] [Indexed: 02/01/2023] Open
Abstract
Autism spectrum disorders (ASD) are characterized by a high degree of genetic heterogeneity. Genomic studies identified common pathological processes underlying the heterogeneous clinical manifestations of ASD, and transcriptome analyses revealed that gene networks involved in synapse development, neuronal activity, and immune function are deregulated in ASD. Mouse models provide unique tools to investigate the neurobiological basis of ASD; however, a comprehensive approach to identify transcriptional abnormalities in different ASD models has never been performed. Here we used two well-recognized ASD mouse models, BTBR T+Itpr3tf/J (BTBR) and Engrailed-2 knockout (En2−/−), to identify conserved ASD-related molecular signatures. En2−/− mice bear a mutation within the EN2 transcription factor homeobox, while BTBR is an inbred strain with unknown genetic defects. Hippocampal RNA samples from BTBR, En2−/− and respective control (C57Bl/6J and En2+/+) adult mice were assessed for differential gene expression using microarrays. A total of 153 genes were similarly deregulated in the BTBR and En2−/− hippocampus. Mouse phenotype and gene ontology enrichment analyses were performed on BTBR and En2−/− hippocampal differentially expressed genes (DEGs). Pathways represented in both BTBR and En2−/− hippocampal DEGs included abnormal behavioral response and chemokine/MAP kinase signaling. Genes involved in abnormal function of the immune system and abnormal synaptic transmission/seizures were significantly represented among BTBR and En2−/− DEGs, respectively. Interestingly, both BTBR and En2−/− hippocampal DEGs showed a significant enrichment of ASD and schizophrenia (SCZ)-associated genes. Specific gene sets were enriched in the two models: microglial genes were significantly enriched among BTBR DEGs, whereas GABAergic/glutamatergic postsynaptic genes, FMRP-interacting genes and epilepsy-related genes were significantly enriched among En2−/− DEGs. Weighted correlation network analysis (WGCNA) performed on BTBR and En2−/− hippocampal transcriptomes together identified six modules significantly enriched in ASD-related genes. Each of these modules showed a specific enrichment profile in neuronal and glial genes, as well as in genes associated to ASD comorbidities such as epilepsy and SCZ. Our data reveal significant transcriptional similarities and differences between the BTBR and En2−/− hippocampus, indicating that transcriptome analysis of ASD mouse models may contribute to identify novel molecular targets for pharmacological studies.
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Affiliation(s)
- Giovanni Provenzano
- Laboratory of Molecular Neuropathology, Centre for Integrative Biology, University of Trento Trento, Italy
| | - Zelia Corradi
- Laboratory of Molecular Neuropathology, Centre for Integrative Biology, University of Trento Trento, Italy
| | - Katia Monsorno
- Laboratory of Molecular Neuropathology, Centre for Integrative Biology, University of Trento Trento, Italy
| | - Tarcisio Fedrizzi
- Bioinformatics Core Facility, Centre for Integrative Biology, University of Trento Trento, Italy
| | - Laura Ricceri
- Neurotoxicology and Neuroendocrinology Section, Department of Cell Biology and Neuroscience, Istituto Superiore di Sanità Rome, Italy
| | - Maria L Scattoni
- Neurotoxicology and Neuroendocrinology Section, Department of Cell Biology and Neuroscience, Istituto Superiore di Sanità Rome, Italy
| | - Yuri Bozzi
- Laboratory of Molecular Neuropathology, Centre for Integrative Biology, University of TrentoTrento, Italy; National Research Council Neuroscience InstitutePisa, Italy
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