1
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Devine EA, Imami AS, Eby H, Sahay S, Hamoud AR, Golchin H, Ryan W, Shedroff EA, Arvay T, Joyce AW, Asah SM, Walss-Bass C, O'Donovan S, McCullumsmith RE. Neuronal alterations in AKT isotype expression in schizophrenia. Mol Psychiatry 2024:10.1038/s41380-024-02770-8. [PMID: 39424930 DOI: 10.1038/s41380-024-02770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 09/05/2024] [Accepted: 09/25/2024] [Indexed: 10/21/2024]
Abstract
Schizophrenia is characterized by substantial alterations in brain function, and previous studies suggest insulin signaling pathways, particularly involving AKT, are implicated in the pathophysiology of the disorder. This study demonstrates elevated mRNA expression of AKT1-3 in neurons from schizophrenia subjects, contrary to unchanged or diminished total AKT protein expression reported in previous postmortem studies, suggesting a potential decoupling of transcript and protein levels. Sex-specific differential AKT activity was observed, indicating divergent roles in males and females with schizophrenia. Alongside AKT, upregulation of PDPK1, a critical component of the insulin signaling pathway, and several protein phosphatases known to regulate AKT were detected. Moreover, enhanced expression of the transcription factor FOXO1, a regulator of glucose metabolism, hints at possible compensatory mechanisms related to insulin signaling dysregulation. Findings were largely independent of antipsychotic medication use, suggesting inherent alterations in schizophrenia. These results highlight the significance of AKT and related signaling pathways in schizophrenia, proposing that these changes might represent a compensatory response to a primary defect of canonical insulin signaling pathways. This research underscores the need for a detailed understanding of these signaling pathways for the development of effective therapeutic strategies.
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Affiliation(s)
- Emily A Devine
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA.
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Ali S Imami
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Hunter Eby
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Smita Sahay
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Abdul-Rizaq Hamoud
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Hasti Golchin
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - William Ryan
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Elizabeth A Shedroff
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Taylen Arvay
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Alex W Joyce
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Sophie M Asah
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Consuelo Walss-Bass
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sinead O'Donovan
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Robert E McCullumsmith
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
- Department of Psychiatry, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
- Neurosciences Institute, ProMedica, Toledo, OH, USA
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2
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Auvergne A, Traut N, Henches L, Troubat L, Frouin A, Boetto C, Kazem S, Julienne H, Toro R, Aschard H. Multitrait analysis to decipher the intertwined genetic architecture of neuroanatomical phenotypes and psychiatric disorders. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2024:S2451-9022(24)00266-0. [PMID: 39260564 DOI: 10.1016/j.bpsc.2024.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/28/2024] [Accepted: 08/12/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND There is increasing evidence of shared genetic factors between psychiatric disorders and brain magnetic resonance imaging (MRI) phenotypes. However, deciphering the joint genetic architecture of these outcomes has proven challenging, and new approaches are needed to infer potential genetic structure underlying those phenotypes. Multivariate analyses is arising as a meaningful approach to reveal links between MRI phenotypes and psychiatric disorders missed by univariate approaches. METHODS We first conducted univariate and multivariate genome-wide association studies (GWAS) for nine MRI-derived brain volume phenotypes in 20K UK Biobank participants. We next performed various complementary enrichment analyses to assess whether and how univariate and multitrait approaches can distinguish disorder-associated and non-disorder-associated variants from six psychiatric disorders: bipolarity, attention-deficit/hyperactivity disorder (ADHD), autism, schizophrenia, obsessive-compulsive disorder, and major depressive disorder. Finally, we conducted a clustering analysis of top associated variants based on their MRI multitrait association using an optimized k-medoids approach. RESULTS Univariate MRI GWAS displayed only negligible genetic correlation with psychiatric disorders, while multitrait GWAS identified multiple new associations and showed significant enrichment for variants related to both ADHD and schizophrenia. Clustering analyses further detected two clusters displaying not only enrichment for association with ADHD and schizophrenia, but also consistent direction of effects. Functional annotation analyses of those clusters pointed to multiple potential mechanisms, suggesting in particular a role of neurotrophins pathways on both MRI and schizophrenia. CONCLUSIONS Our results show that multitrait association signature can be used to infer genetically-driven latent MRI variables associated with psychiatric disorders, opening paths for future biomarker development.
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Affiliation(s)
- Antoine Auvergne
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France.
| | - Nicolas Traut
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
| | - Léo Henches
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
| | - Lucie Troubat
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
| | - Arthur Frouin
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
| | - Christophe Boetto
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
| | - Sayeh Kazem
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
| | - Hanna Julienne
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
| | - Roberto Toro
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France
| | - Hugues Aschard
- Institut Pasteur, Université Paris Cité, Department of Computational Biology, F-75015 Paris, France; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA.
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3
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Sahay S, Pulvender P, Rami Reddy MVSR, McCullumsmith RE, O’Donovan SM. Metabolic Insights into Neuropsychiatric Illnesses and Ketogenic Therapies: A Transcriptomic View. Int J Mol Sci 2024; 25:8266. [PMID: 39125835 PMCID: PMC11312282 DOI: 10.3390/ijms25158266] [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: 05/31/2024] [Revised: 07/21/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
The disruption of brain energy metabolism, leading to alterations in synaptic signaling, neural circuitry, and neuroplasticity, has been implicated in severe mental illnesses such as schizophrenia, bipolar disorder, and major depressive disorder. The therapeutic potential of ketogenic interventions in these disorders suggests a link between metabolic disturbances and disease pathology; however, the precise mechanisms underlying these metabolic disturbances, and the therapeutic effects of metabolic ketogenic therapy, remain poorly understood. In this study, we conducted an in silico analysis of transcriptomic data to investigate perturbations in metabolic pathways in the brain across severe mental illnesses via gene expression profiling. We also examined dysregulation of the same pathways in rodent or cell culture models of ketosis, comparing these expression profiles to those observed in the disease states. Our analysis revealed significant perturbations across all metabolic pathways, with the greatest perturbations in glycolysis, the tricarboxylic acid (TCA) cycle, and the electron transport chain (ETC) across all three disorders. Additionally, we observed some discordant gene expression patterns between disease states and ketogenic intervention studies, suggesting a potential role for ketone bodies in modulating pathogenic metabolic changes. Our findings highlight the importance of understanding metabolic dysregulation in severe mental illnesses and the potential therapeutic benefits of ketogenic interventions in restoring metabolic homeostasis. This study provides insights into the complex relationship between metabolism and neuropsychiatric disorders and lays the foundation for further experimental investigations aimed at appreciating the implications of the present transcriptomic findings as well as developing targeted therapeutic strategies.
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Affiliation(s)
- Smita Sahay
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Priyanka Pulvender
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | | | - Robert E. McCullumsmith
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
- Department of Psychiatry, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
- Neuroscience Institute, ProMedica, Toledo, OH 43614, USA
| | - Sinead M. O’Donovan
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
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4
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Salama A, Hamed Salama A, Hasanein Asfour M. Tannic acid coated nanosuspension for oral delivery of chrysin intended for anti-schizophrenic effect in mice. Int J Pharm 2024; 656:124085. [PMID: 38580073 DOI: 10.1016/j.ijpharm.2024.124085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/17/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Chrysin is a flavonoid drug with numerous therapeutic activities. It suffers from low intestinal absorption owing to its hydrophobicity. Therefore, the aim of this study is to exploit the efficient technique of nanosuspension (NSP) to formulate chrysin-NSP coated with tannic acid (TA) to improve the solubility and anti-schizophrenic activity of chrysin. A 23 full factorial design was constructed where the independent factors were type of polymer, surfactant concentration (0.5 or 1 %) and the aqueous phase volume (5 or 15 mL), while the dependent responses were the particle size (PS) of the obtained formulation as well as the % chrysin dissolved after 2 h (Q2h). The optimum formulation (NSP-4) composed of 1 % PEG 400 and 1 % Cremophor RH40 in 15 mL aqueous phase. It achieved a PS and Q2h values of 108.00 nm and 38.77 %, respectively. NSP-4 was then coated with TA (TA-coated NSP-4) for further enhancement of chrysin solubility. TA-coated NSP-4 revealed PS and zeta potential values of 150 ± 14 nm and -32.54 ± 2.45 mV, respectively. After 6 h, chrysin dissolved % were 53.97 and 80.22 for uncoated NSP-4 and TA-coated NSP-4, respectively, compared with only 9.47 for free chrysin. The developed formulations and free chrysin were assessed regarding their effect on schizophrenia induced in mice by cuprizone (CPZ). Treatment with the developed formulations and free chrysin ameliorated demyelination and behavioral deficit induced by CPZ via elevating MBP and PI3K/PKC activities as well as reducing GFAP expression levels. The developed formulations and free chrysin inhibited Galactin-3 and TGF-β expressions and stimulated GST antioxidant enzyme. Furthermore, they maintained the balances in glutamatergic and dopaminergic neurotransmission via modulation on neuregulin-1 and alleviated nuclear pyknosis and degeneration in the neurons. The order of activity was: TA-coated NSP-4 > NSP-4 > free chrysin.
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Affiliation(s)
- Abeer Salama
- Pharmacology Department, National Research Centre, El- Buhouth St., Dokki, Cairo 12622, Egypt
| | - Alaa Hamed Salama
- Pharmaceutical Technology Department, National Research Centre, El-Buhouth St., Dokki, Cairo 12622, Egypt; Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ahram Canadian University, 6(th) of October City, Cairo, Egypt
| | - Marwa Hasanein Asfour
- Pharmaceutical Technology Department, National Research Centre, El-Buhouth St., Dokki, Cairo 12622, Egypt.
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5
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Devine EA, Imami AS, Eby H, Hamoud AR, Golchin H, Ryan W, Sahay S, Shedroff EA, Arvay T, Joyce AW, Asah SM, Walss-Bass C, O'Donovan S, McCullumsmith RE. Neuronal alterations in AKT isotype expression in schizophrenia. RESEARCH SQUARE 2024:rs.3.rs-3940448. [PMID: 38559131 PMCID: PMC10980160 DOI: 10.21203/rs.3.rs-3940448/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Schizophrenia is characterized by substantial alterations in brain function, and previous studies suggest insulin signaling pathways, particularly involving AKT, are implicated in the pathophysiology of the disorder. This study demonstrates elevated mRNA expression of AKT1-3 in neurons from schizophrenia subjects, contrary to unchanged or diminished total AKT protein expression reported in previous postmortem studies, suggesting a potential decoupling of transcript and protein levels. Sex-specific differential AKT activity was observed, indicating divergent roles in males and females with schizophrenia. Alongside AKT, upregulation of PDPK1, a critical component of the insulin signaling pathway, and several protein phosphatases known to regulate AKT were detected. Moreover, enhanced expression of the transcription factor FOXO1, a regulator of glucose metabolism, hints at possible compensatory mechanisms related to insulin signaling dysregulation. Findings were largely independent of antipsychotic medication use, suggesting inherent alterations in schizophrenia. These results highlight the significance of AKT and related signaling pathways in schizophrenia, proposing that these changes might represent a compensatory response to a primary defect of conical insulin signaling pathways. This research underscores the need for a detailed understanding of these signaling pathways for the development of effective therapeutic strategies.
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Affiliation(s)
- Emily A Devine
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ali S Imami
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Hunter Eby
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Abdul-Rizaq Hamoud
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Hasti Golchin
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - William Ryan
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Smita Sahay
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Elizabeth A Shedroff
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Taylen Arvay
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Alex W Joyce
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Sophie M Asah
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Consuelo Walss-Bass
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Sinead O'Donovan
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Robert E McCullumsmith
- Department of Neuroscience, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
- Neurosciences Institute, ProMedica, Toledo, OH, USA
- Department of Psychiatry, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
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6
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Nguyen JH, Curtis MA, Imami AS, Ryan WG, Alganem K, Neifer KL, Saferin N, Nawor CN, Kistler BP, Miller GW, Shukla R, McCullumsmith RE, Burkett JP. Developmental pyrethroid exposure disrupts molecular pathways for MAP kinase and circadian rhythms in mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.28.555113. [PMID: 37745438 PMCID: PMC10515776 DOI: 10.1101/2023.08.28.555113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Neurodevelopmental disorders (NDDs) are a category of pervasive disorders of the developing nervous system with few or no recognized biomarkers. A significant portion of the risk for NDDs, including attention deficit hyperactivity disorder (ADHD), is contributed by the environment, and exposure to pyrethroid pesticides during pregnancy has been identified as a potential risk factor for NDD in the unborn child. We recently showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice causes male-biased changes to ADHD- and NDD-relevant behaviors as well as the striatal dopamine system. Here, we used an integrated multiomics approach to determine the broadest possible set of biological changes in the mouse brain caused by developmental pyrethroid exposure (DPE). Using a litter-based, split-sample design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood, euthanized them, and pulverized and divided whole brain samples for split-sample transcriptomics, kinomics and multiomics integration. Transcriptome analysis revealed alterations to multiple canonical clock genes, and kinome analysis revealed changes in the activity of multiple kinases involved in synaptic plasticity, including the mitogen-activated protein (MAP) kinase ERK. Multiomics integration revealed a dysregulated protein-protein interaction network containing primary clusters for MAP kinase cascades, regulation of apoptosis, and synaptic function. These results demonstrate that DPE causes a multi-modal biophenotype in the brain relevant to ADHD and identifies new potential mechanisms of action. NEW & NOTEWORTHY Here, we provide the first evidence that low-dose developmental exposure to the pyrethroid pesticide, deltamethrin, results in molecular disruptions in the adult mouse brain in pathways regulating circadian rhythms and neuronal growth (MAP kinase). This same exposure causes a neurodevelopmental disorder (NDD) relevant behavioral changes in adult mice, making these findings relevant to the prevention of NDDs.
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7
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Sahay S, Henkel ND, Vargas CFA, McCullumsmith RE, O’Donovan SM. Activity of Protein Kinase A in the Frontal Cortex in Schizophrenia. Brain Sci 2023; 14:13. [PMID: 38248228 PMCID: PMC10813263 DOI: 10.3390/brainsci14010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/21/2023] [Accepted: 12/02/2023] [Indexed: 01/23/2024] Open
Abstract
Schizophrenia is a serious cognitive disorder characterized by disruptions in neurotransmission, a process requiring the coordination of multiple kinase-mediated signaling events. Evidence suggests that the observed deficits in schizophrenia may be due to imbalances in kinase activity that propagate through an intracellular signaling network. Specifically, 3'-5'-cyclic adenosine monophosphate (cAMP)-associated signaling pathways are coupled to the activation of neurotransmitter receptors and modulate cellular functions through the activation of protein kinase A (PKA), an enzyme whose function is altered in the frontal cortex in schizophrenia. In this study, we measured the activity of PKA in human postmortem anterior cingulate cortex (ACC) and dorsolateral prefrontal cortex (DLPFC) tissue from schizophrenia and age- and sex-matched control subjects. No significant differences in PKA activity were observed in male and female individuals in either brain region; however, correlation analyses indicated that PKA activity in the ACC may be influenced by tissue pH in all subjects and by age and tissue pH in females. Our data provide novel insights into the function of PKA in the ACC and DLPFC in schizophrenia.
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Affiliation(s)
- Smita Sahay
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (S.S.); (N.D.H.); (C.F.-A.V.); (R.E.M.)
| | - Nicholas Daniel Henkel
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (S.S.); (N.D.H.); (C.F.-A.V.); (R.E.M.)
| | - Christina Flora-Anabelle Vargas
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (S.S.); (N.D.H.); (C.F.-A.V.); (R.E.M.)
| | - Robert Erne McCullumsmith
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (S.S.); (N.D.H.); (C.F.-A.V.); (R.E.M.)
- Neuroscience Institute, Promedica, Toledo, OH 43606, USA
| | - Sinead Marie O’Donovan
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (S.S.); (N.D.H.); (C.F.-A.V.); (R.E.M.)
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8
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Mukhopadhyay A, Deshpande SN, Bhatia T, Thelma BK. Significance of an altered lncRNA landscape in schizophrenia and cognition: clues from a case-control association study. Eur Arch Psychiatry Clin Neurosci 2023; 273:1677-1691. [PMID: 37009928 DOI: 10.1007/s00406-023-01596-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/20/2023] [Indexed: 04/04/2023]
Abstract
Genetic etiology of schizophrenia is poorly understood despite large genome-wide association data. Long non-coding RNAs (lncRNAs) with a probable regulatory role are emerging as important players in neuro-psychiatric disorders including schizophrenia. Prioritising important lncRNAs and analyses of their holistic interaction with their target genes may provide insights into disease biology/etiology. Of the 3843 lncRNA SNPs reported in schizophrenia GWASs extracted using lincSNP 2.0, we prioritised n = 247 based on association strength, minor allele frequency and regulatory potential and mapped them to lncRNAs. lncRNAs were then prioritised based on their expression in brain using lncRBase, epigenetic role using 3D SNP and functional relevance to schizophrenia etiology. 18 SNPs were finally tested for association with schizophrenia (n = 930) and its endophenotypes-tardive dyskinesia (n = 176) and cognition (n = 565) using a case-control approach. Associated SNPs were characterised by ChIP seq, eQTL, and transcription factor binding site (TFBS) data using FeatSNP. Of the eight SNPs significantly associated, rs2072806 in lncRNA hsaLB_IO39983 with regulatory effect on BTN3A2 was associated with schizophrenia (p = 0.006); rs2710323 in hsaLB_IO_2331 with role in dysregulation of ITIH1 with tardive dyskinesia (p < 0.05); and four SNPs with significant cognition score reduction (p < 0.05) in cases. Two of these with two additional variants in eQTL were observed among controls (p < 0.05), acting likely as enhancer SNPs and/or altering TFBS of eQTL mapped downstream genes. This study highlights important lncRNAs in schizophrenia and provides a proof of concept of novel interactions of lncRNAs with protein-coding genes to elicit alterations in immune/inflammatory pathways of schizophrenia.
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Affiliation(s)
- Anirban Mukhopadhyay
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Smita N Deshpande
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Triptish Bhatia
- Department of Psychiatry, Postgraduate Institute of Medical Education and Research-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India.
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9
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Meyer JM, Correll CU. Increased Metabolic Potential, Efficacy, and Safety of Emerging Treatments in Schizophrenia. CNS Drugs 2023; 37:545-570. [PMID: 37470979 PMCID: PMC10374807 DOI: 10.1007/s40263-023-01022-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/21/2023] [Indexed: 07/21/2023]
Abstract
Patients with schizophrenia experience a broad range of detrimental health outcomes resulting from illness severity, heterogeneity of disease, lifestyle behaviors, and adverse effects of antipsychotics. Because of these various factors, patients with schizophrenia have a much higher risk of cardiometabolic abnormalities than people without psychiatric illness. Although exposure to many antipsychotics increases cardiometabolic risk factors, mortality is higher in patients who are not treated versus those who are treated with antipsychotics. This indicates both direct and indirect benefits of adequately treated illness, as well as the need for beneficial medications that result in fewer cardiometabolic risk factors and comorbidities. The aim of the current narrative review was to outline the association between cardiometabolic dysfunction and schizophrenia, as well as discuss the confluence of factors that increase cardiometabolic risk in this patient population. An increased understanding of the pathophysiology of schizophrenia has guided discovery of novel treatments that do not directly target dopamine and that not only do not add, but may potentially minimize relevant cardiometabolic burden for these patients. Key discoveries that have advanced the understanding of the neural circuitry and pathophysiology of schizophrenia now provide possible pathways toward the development of new and effective treatments that may mitigate the risk of metabolic dysfunction in these patients. Novel targets and preclinical and clinical data on emerging treatments, such as glycine transport inhibitors, nicotinic and muscarinic receptor agonists, and trace amine-associated receptor-1 agonists, offer promise toward relevant therapeutic advancements. Numerous areas of investigation currently exist with the potential to considerably progress our knowledge and treatment of schizophrenia.
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Affiliation(s)
- Jonathan M Meyer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
| | - Christoph U Correll
- Department of Psychiatry, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Department of Psychiatry and Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Child and Adolescent Psychiatry, Charité Universitätsmedizin, Berlin, Germany
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10
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Zhang X, Wolfinger A, Wu X, Alnafisah R, Imami A, Hamoud AR, Lundh A, Parpura V, McCullumsmith RE, Shukla R, O’Donovan SM. Gene Enrichment Analysis of Astrocyte Subtypes in Psychiatric Disorders and Psychotropic Medication Datasets. Cells 2022; 11:3315. [PMID: 36291180 PMCID: PMC9600295 DOI: 10.3390/cells11203315] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/26/2022] Open
Abstract
Astrocytes have many important functions in the brain, but their roles in psychiatric disorders and their responses to psychotropic medications are still being elucidated. Here, we used gene enrichment analysis to assess the relationships between different astrocyte subtypes, psychiatric diseases, and psychotropic medications (antipsychotics, antidepressants and mood stabilizers). We also carried out qPCR analyses and "look-up" studies to assess the chronic effects of these drugs on astrocyte marker gene expression. Our bioinformatic analysis identified gene enrichment of different astrocyte subtypes in psychiatric disorders. The highest level of enrichment was found in schizophrenia, supporting a role for astrocytes in this disorder. We also found differential enrichment of astrocyte subtypes associated with specific biological processes, highlighting the complex responses of astrocytes under pathological conditions. Enrichment of protein phosphorylation in astrocytes and disease was confirmed by biochemical analysis. Analysis of LINCS chemical perturbagen gene signatures also found that kinase inhibitors were highly discordant with astrocyte-SCZ associated gene signatures. However, we found that common gene enrichment of different psychotropic medications and astrocyte subtypes was limited. These results were confirmed by "look-up" studies and qPCR analysis, which also reported little effect of psychotropic medications on common astrocyte marker gene expression, suggesting that astrocytes are not a primary target of these medications. Conversely, antipsychotic medication does affect astrocyte gene marker expression in postmortem schizophrenia brain tissue, supporting specific astrocyte responses in different pathological conditions. Overall, this study provides a unique view of astrocyte subtypes and the effect of medications on astrocytes in disease, which will contribute to our understanding of their role in psychiatric disorders and offers insights into targeting astrocytes therapeutically.
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Affiliation(s)
- Xiaolu Zhang
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
| | - Alyssa Wolfinger
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
| | - Xiaojun Wu
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
| | - Rawan Alnafisah
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
| | - Ali Imami
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
| | - Abdul-rizaq Hamoud
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
| | - Anna Lundh
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
| | - Vladimir Parpura
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert E. McCullumsmith
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
- Promedica Neurosciences Institute, Toledo, OH 43606, USA
| | - Rammohan Shukla
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA
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11
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Prefrontal Cortex Response to Prenatal Insult and Postnatal Opioid Exposure. Genes (Basel) 2022; 13:genes13081371. [PMID: 36011282 PMCID: PMC9407090 DOI: 10.3390/genes13081371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/11/2022] Open
Abstract
The influence of proinflammatory challenges, such as maternal immune activation (MIA) or postnatal exposure to drugs of abuse, on brain molecular pathways has been reported. On the other hand, the simultaneous effects of MIA and drugs of abuse have been less studied and sometimes offered inconsistent results. The effects of morphine exposure on a pig model of viral-elicited MIA were characterized in the prefrontal cortex of males and females using RNA-sequencing and gene network analysis. Interacting and main effects of morphine, MIA, and sex were detected in approximately 2000 genes (false discovery rate-adjusted p-value < 0.05). Among the enriched molecular categories (false discovery rate-adjusted p-value < 0.05 and −1.5 > normalized enrichment score > 1.5) were the cell adhesion molecule pathways associated with inflammation and neuronal development and the long-term depression pathway associated with synaptic strength. Gene networks that integrate gene connectivity and expression profiles displayed the impact of morphine-by-MIA interaction effects on the pathways. The cell adhesion molecules and long-term depression networks presented an antagonistic effect between morphine and MIA. The differential expression between the double-challenged group and the baseline saline-treated Controls was less extreme than the individual challenges. The previous findings advance the knowledge about the effects of prenatal MIA and postnatal morphine exposure on the prefrontal cortex pathways.
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12
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Disruption of Alternative Splicing in the Amygdala of Pigs Exposed to Maternal Immune Activation. IMMUNO 2021. [DOI: 10.3390/immuno1040035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The inflammatory response of gestating females to infection or stress can disrupt gene expression in the offspring’s amygdala, resulting in lasting neurodevelopmental, physiological, and behavioral disorders. The effects of maternal immune activation (MIA) can be impacted by the offspring’s sex and exposure to additional stressors later in life. The objectives of this study were to investigate the disruption of alternative splicing patterns associated with MIA in the offspring’s amygdala and characterize this disruption in the context of the second stress of weaning and sex. Differential alternative splicing was tested on the RNA-seq profiles of a pig model of viral-induced MIA. Compared to controls, MIA was associated with the differential alternative splicing (FDR-adjusted p-value < 0.1) of 292 and 240 genes in weaned females and males, respectively, whereas 132 and 176 genes were differentially spliced in control nursed female and male, respectively. The majority of the differentially spliced (FDR-adjusted p-value < 0.001) genes (e.g., SHANK1, ZNF672, KCNA6) and many associated enriched pathways (e.g., Fc gamma R-mediated phagocytosis, non-alcoholic fatty liver disease, and cGMP-PKG signaling) have been reported in MIA-related disorders including autism and schizophrenia in humans. Differential alternative splicing associated with MIA was detected in the gene MAG across all sex-stress groups except for unstressed males and SLC2A11 across all groups except unstressed females. Precise understanding of the effect of MIA across second stressors and sexes necessitates the consideration of splicing isoform profiles.
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13
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Chadha R, Alganem K, Mccullumsmith RE, Meador-Woodruff JH. mTOR kinase activity disrupts a phosphorylation signaling network in schizophrenia brain. Mol Psychiatry 2021; 26:6868-6879. [PMID: 33990769 DOI: 10.1038/s41380-021-01135-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 04/06/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022]
Abstract
The AKT-mTOR signaling transduction pathway plays an important role in neurodevelopment and synaptic plasticity. mTOR is a serine/threonine kinase that modulates signals from multiple neurotransmitters and phosphorylates specific proteins to regulate protein synthesis and cytoskeletal organization. There is substantial evidence demonstrating abnormalities in AKT expression and activity in different schizophrenia (SZ) models. However, direct evidence for dysregulated mTOR kinase activity and its consequences on downstream effector proteins in SZ pathophysiology is lacking. Recently, we reported reduced phosphorylation of mTOR at an activating site and abnormal mTOR complex formation in the SZ dorsolateral prefrontal cortex (DLPFC). Here, we expand on our hypothesis of disrupted mTOR signaling in the SZ brain and studied the expression and activity of downstream effector proteins of mTOR complexes and the kinase activity profiles of SZ subjects. We found that S6RP phosphorylation, downstream of mTOR complex I, is reduced, whereas PKCα phosphorylation, downstream of mTOR complex II, is increased in SZ DLPFC. In rats chronically treated with haloperidol, we showed that S6RP phosphorylation is increased in the rat frontal cortex, suggesting a potential novel mechanism of action for antipsychotics. We also demonstrated key differences in kinase signaling networks between SZ and comparison subjects for both males and females using kinome peptide arrays. We further investigated the role of mTOR kinase activity by inhibiting it with rapamycin in postmortem tissue and compared the impact of mTOR inhibition in SZ and comparison subjects using kinome arrays. We found that SZ subjects are globally more sensitive to rapamycin treatment and AMP-activated protein kinase (AMPK) contributes to this differential kinase activity. Together, our findings provide new insights into the role of mTOR as a master regulator of kinase activity in SZ and suggest potential targets for therapeutic intervention.
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Affiliation(s)
- Radhika Chadha
- Department of Neurobiology, University of Utah, Salt Lake City, UT, USA.
| | - Khaled Alganem
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, USA
| | - Robert E Mccullumsmith
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, USA
- Neurosciences Institute, ProMedica, Toledo, OH, USA
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
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14
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Su RC, Breidenbach JD, Alganem K, Khalaf FK, French BW, Dube P, Malhotra D, McCullumsmith R, Presloid JB, Wooten RM, Kennedy DJ, Haller ST. Microcystin-LR (MC-LR) Triggers Inflammatory Responses in Macrophages. Int J Mol Sci 2021; 22:9939. [PMID: 34576099 PMCID: PMC8472269 DOI: 10.3390/ijms22189939] [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: 05/25/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 12/16/2022] Open
Abstract
We were the first to previously report that microcystin-LR (MC-LR) has limited effects within the colons of healthy mice but has toxic effects within colons of mice with pre-existing inflammatory bowel disease. In the current investigation, we aimed to elucidate the mechanism by which MC-LR exacerbates colitis and to identify effective therapeutic targets. Through our current investigation, we report that there is a significantly greater recruitment of macrophages into colonic tissue with pre-existing colitis in the presence of MC-LR than in the absence of MC-LR. This is seen quantitatively through IHC staining and the enumeration of F4/80-positive macrophages and through gene expression analysis for Cd68, Cd11b, and Cd163. Exposure of isolated macrophages to MC-LR was found to directly upregulate macrophage activation markers Tnf and Il1b. Through a high-throughput, unbiased kinase activity profiling strategy, MC-LR-induced phosphorylation events were compared with potential inhibitors, and doramapimod was found to effectively prevent MC-LR-induced inflammatory responses in macrophages.
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Affiliation(s)
- Robin C. Su
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (R.C.S.); (J.D.B.); (F.K.K.); (B.W.F.); (P.D.); (D.M.)
| | - Joshua D. Breidenbach
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (R.C.S.); (J.D.B.); (F.K.K.); (B.W.F.); (P.D.); (D.M.)
| | - Khaled Alganem
- Department of Neuroscience, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (K.A.); (R.M.)
| | - Fatimah K. Khalaf
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (R.C.S.); (J.D.B.); (F.K.K.); (B.W.F.); (P.D.); (D.M.)
| | - Benjamin W. French
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (R.C.S.); (J.D.B.); (F.K.K.); (B.W.F.); (P.D.); (D.M.)
| | - Prabhatchandra Dube
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (R.C.S.); (J.D.B.); (F.K.K.); (B.W.F.); (P.D.); (D.M.)
| | - Deepak Malhotra
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (R.C.S.); (J.D.B.); (F.K.K.); (B.W.F.); (P.D.); (D.M.)
| | - Robert McCullumsmith
- Department of Neuroscience, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (K.A.); (R.M.)
- Neurosciences Center, Promedica, Toledo, OH 43614, USA
| | - John B. Presloid
- Department of Medical Microbiology and Immunology, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (J.B.P.); (R.M.W.)
| | - R. Mark Wooten
- Department of Medical Microbiology and Immunology, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (J.B.P.); (R.M.W.)
| | - David J. Kennedy
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (R.C.S.); (J.D.B.); (F.K.K.); (B.W.F.); (P.D.); (D.M.)
| | - Steven T. Haller
- Department of Medicine, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (R.C.S.); (J.D.B.); (F.K.K.); (B.W.F.); (P.D.); (D.M.)
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15
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Grubisha MJ, Sweet RA, MacDonald ML. Investigating Post-translational Modifications in Neuropsychiatric Disease: The Next Frontier in Human Post-mortem Brain Research. Front Mol Neurosci 2021; 14:689495. [PMID: 34335181 PMCID: PMC8322442 DOI: 10.3389/fnmol.2021.689495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Gene expression and translation have been extensively studied in human post-mortem brain tissue from subjects with psychiatric disease. Post-translational modifications (PTMs) have received less attention despite their implication by unbiased genetic studies and importance in regulating neuronal and circuit function. Here we review the rationale for studying PTMs in psychiatric disease, recent findings in human post-mortem tissue, the required controls for these types of studies, and highlight the emerging mass spectrometry approaches transforming this research direction.
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Affiliation(s)
- Melanie J. Grubisha
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robert A. Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Matthew L. MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, United States
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16
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Bentea E, Villers A, Moore C, Funk AJ, O’Donovan SM, Verbruggen L, Lara O, Janssen P, De Pauw L, Declerck NB, DePasquale EAK, Churchill MJ, Sato H, Hermans E, Arckens L, Meshul CK, Ris L, McCullumsmith RE, Massie A. Corticostriatal dysfunction and social interaction deficits in mice lacking the cystine/glutamate antiporter. Mol Psychiatry 2021; 26:4754-4769. [PMID: 32366950 PMCID: PMC7609546 DOI: 10.1038/s41380-020-0751-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/07/2020] [Accepted: 04/21/2020] [Indexed: 12/11/2022]
Abstract
The astrocytic cystine/glutamate antiporter system xc- represents an important source of extracellular glutamate in the central nervous system, with potential impact on excitatory neurotransmission. Yet, its function and importance in brain physiology remain incompletely understood. Employing slice electrophysiology and mice with a genetic deletion of the specific subunit of system xc-, xCT (xCT-/- mice), we uncovered decreased neurotransmission at corticostriatal synapses. This effect was partly mitigated by replenishing extracellular glutamate levels, indicating a defect linked with decreased extracellular glutamate availability. We observed no changes in the morphology of striatal medium spiny neurons, the density of dendritic spines, or the density or ultrastructure of corticostriatal synapses, indicating that the observed functional defects are not due to morphological or structural abnormalities. By combining electron microscopy with glutamate immunogold labeling, we identified decreased intracellular glutamate density in presynaptic terminals, presynaptic mitochondria, and in dendritic spines of xCT-/- mice. A proteomic and kinomic screen of the striatum of xCT-/- mice revealed decreased expression of presynaptic proteins and abnormal kinase network signaling, that may contribute to the observed changes in postsynaptic responses. Finally, these corticostriatal deregulations resulted in a behavioral phenotype suggestive of autism spectrum disorder in the xCT-/- mice; in tests sensitive to corticostriatal functioning we recorded increased repetitive digging behavior and decreased sociability. To conclude, our findings show that system xc- plays a previously unrecognized role in regulating corticostriatal neurotransmission and influences social preference and repetitive behavior.
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Affiliation(s)
- Eduard Bentea
- grid.8767.e0000 0001 2290 8069Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Agnès Villers
- grid.8364.90000 0001 2184 581XDepartment of Neurosciences, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Cynthia Moore
- grid.410404.50000 0001 0165 2383Research Services, Neurocytology Laboratory, Veterans Affairs Medical Center, Portland, OR USA
| | - Adam J. Funk
- grid.267337.40000 0001 2184 944XDepartment of Neurosciences, University of Toledo College of Medicine, Toledo, OH USA
| | - Sinead M. O’Donovan
- grid.267337.40000 0001 2184 944XDepartment of Neurosciences, University of Toledo College of Medicine, Toledo, OH USA
| | - Lise Verbruggen
- grid.8767.e0000 0001 2290 8069Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Olaya Lara
- grid.8767.e0000 0001 2290 8069Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Pauline Janssen
- grid.8767.e0000 0001 2290 8069Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Laura De Pauw
- grid.8767.e0000 0001 2290 8069Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Noemi B. Declerck
- grid.8767.e0000 0001 2290 8069Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Erica A. K. DePasquale
- grid.239573.90000 0000 9025 8099Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH USA
| | - Madeline J. Churchill
- grid.410404.50000 0001 0165 2383Research Services, Neurocytology Laboratory, Veterans Affairs Medical Center, Portland, OR USA
| | - Hideyo Sato
- grid.260975.f0000 0001 0671 5144Department of Medical Technology, Faculty of Medicine, Laboratory of Biochemistry and Molecular Biology, Niigata University, Niigata, Japan
| | - Emmanuel Hermans
- grid.7942.80000 0001 2294 713XInstitute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium
| | - Lutgarde Arckens
- grid.5596.f0000 0001 0668 7884Laboratory of Neuroplasticity and Neuroproteomics, and Leuven Brain Institute (LBI), KU Leuven—University of Leuven, Leuven, Belgium
| | - Charles K. Meshul
- grid.410404.50000 0001 0165 2383Research Services, Neurocytology Laboratory, Veterans Affairs Medical Center, Portland, OR USA ,grid.5288.70000 0000 9758 5690Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR USA
| | - Laurence Ris
- grid.8364.90000 0001 2184 581XDepartment of Neurosciences, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Robert E. McCullumsmith
- grid.267337.40000 0001 2184 944XDepartment of Neurosciences, University of Toledo College of Medicine, Toledo, OH USA
| | - Ann Massie
- Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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17
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Creeden JF, Alganem K, Imami AS, Brunicardi FC, Liu SH, Shukla R, Tomar T, Naji F, McCullumsmith RE. Kinome Array Profiling of Patient-Derived Pancreatic Ductal Adenocarcinoma Identifies Differentially Active Protein Tyrosine Kinases. Int J Mol Sci 2020; 21:ijms21228679. [PMID: 33213062 PMCID: PMC7698519 DOI: 10.3390/ijms21228679] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer remains one of the most difficult malignancies to treat. Minimal improvements in patient outcomes and persistently abysmal patient survival rates underscore the great need for new treatment strategies. Currently, there is intense interest in therapeutic strategies that target tyrosine protein kinases. Here, we employed kinome arrays and bioinformatic pipelines capable of identifying differentially active protein tyrosine kinases in different patient-derived pancreatic ductal adenocarcinoma (PDAC) cell lines and wild-type pancreatic tissue to investigate the unique kinomic networks of PDAC samples and posit novel target kinases for pancreatic cancer therapy. Consistent with previously described reports, the resultant peptide-based kinome array profiles identified increased protein tyrosine kinase activity in pancreatic cancer for the following kinases: epidermal growth factor receptor (EGFR), fms related receptor tyrosine kinase 4/vascular endothelial growth factor receptor 3 (FLT4/VEGFR-3), insulin receptor (INSR), ephrin receptor A2 (EPHA2), platelet derived growth factor receptor alpha (PDGFRA), SRC proto-oncogene kinase (SRC), and tyrosine kinase non receptor 2 (TNK2). Furthermore, this study identified increased activity for protein tyrosine kinases with limited prior evidence of differential activity in pancreatic cancer. These protein tyrosine kinases include B lymphoid kinase (BLK), Fyn-related kinase (FRK), Lck/Yes-related novel kinase (LYN), FYN proto-oncogene kinase (FYN), lymphocyte cell-specific kinase (LCK), tec protein kinase (TEC), hemopoietic cell kinase (HCK), ABL proto-oncogene 2 kinase (ABL2), discoidin domain receptor 1 kinase (DDR1), and ephrin receptor A8 kinase (EPHA8). Together, these results support the utility of peptide array kinomic analyses in the generation of potential candidate kinases for future pancreatic cancer therapeutic development.
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Affiliation(s)
- Justin F. Creeden
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
- Correspondence: ; Tel.: +1-419-383-6474
| | - Khaled Alganem
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - Ali S. Imami
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - F. Charles Brunicardi
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Shi-He Liu
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Rammohan Shukla
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - Tushar Tomar
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Faris Naji
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Robert E. McCullumsmith
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
- Neurosciences Institute, ProMedica, Toledo, OH 43606, USA
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18
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Chadha R, Meador-Woodruff JH. Downregulated AKT-mTOR signaling pathway proteins in dorsolateral prefrontal cortex in Schizophrenia. Neuropsychopharmacology 2020; 45:1059-1067. [PMID: 31952070 PMCID: PMC7162985 DOI: 10.1038/s41386-020-0614-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 11/09/2022]
Abstract
Abnormal neurotransmission is central to schizophrenia (SZ). Alterations across multiple neurotransmitter systems in SZ suggest that this illness may be associated with dysregulation of core intracellular processes such as signaling pathways that underlie the regulation and integration of these systems. The AKT-mTOR signaling cascade has been implicated in SZ by gene association, postmortem brain and animal studies. AKT and mTOR are serine/threonine kinases which play important roles in cell growth, proliferation, survival, and differentiation. Both AKT and mTOR require phosphorylation at specific sites for their complete activation. mTOR forms two functionally distinct multiprotein complexes, mTOR Complex 1 (mTORC1) and Complex 2 (mTORC2). mTORC1 mediates ribosome biogenesis, protein translation, and autophagy, whereas mTORC2 contributes to actin dynamics. Altered protein synthesis and actin dynamics can lead to an abnormal neuronal morphology resulting in deficits in learning and memory. Currently, there is a lack of direct evidence to support the hypothesis of disrupted mTOR signaling in SZ, and we have addressed this by characterizing this signaling pathway in SZ brain. We found a reduction in AKT and mTOR protein expression and/or phosphorylation state in dorsolateral prefrontal cortex (DLPFC) from 22 pairs of SZ and matched comparison subjects. We also found reduced protein expression of GβL, a subunit protein common to both mTOR complexes. We further investigated mTOR complex-specific subunit composition and phosphorylation state, and found abnormal mTOR expression in both complexes in SZ DLPFC. These findings provide evidence that proteins associated with the AKT-mTOR signaling cascade are downregulated in SZ DLPFC.
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Affiliation(s)
- Radhika Chadha
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, 1719 6th Avenue South, Birmingham, AL, 35294-0021, USA.
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, 1719 6th Avenue South, Birmingham, AL, 35294-0021, USA
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19
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Wang HY, MacDonald ML, Borgmann-Winter KE, Banerjee A, Sleiman P, Tom A, Khan A, Lee KC, Roussos P, Siegel SJ, Hemby SE, Bilker WB, Gur RE, Hahn CG. mGluR5 hypofunction is integral to glutamatergic dysregulation in schizophrenia. Mol Psychiatry 2020; 25:750-760. [PMID: 30214040 PMCID: PMC7500805 DOI: 10.1038/s41380-018-0234-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/18/2018] [Accepted: 07/09/2018] [Indexed: 11/19/2022]
Abstract
Multiple lines of evidence point to glutamatergic signaling in the postsynaptic density (PSD) as a pathophysiologic mechanism in schizophrenia. Integral to PSD glutamatergic signaling is reciprocal interplay between GluN and mGluR5 signaling. We examined agonist-induced mGluR5 signaling in the postmortem dorsolateral prefrontal cortex (DLPFC) derived from 17 patients and age-matched and sex-matched controls. The patient group showed a striking reduction in mGluR5 signaling, manifested by decreases in Gq/11 coupling and association with PI3K and Homer compared to controls (p < 0.01 for all). This was accompanied by increases in serine and tyrosine phosphorylation of mGluR5, which can decrease mGluR5 activity via desensitization (p < 0.01). In addition, we find altered protein-protein interaction (PPI) of mGluR5 with RGS4, norbin, Preso 1 and tamalin, which can also attenuate mGluR5 activity. We previously reported molecular underpinnings of GluN hypofunction (decreased GluN2 phosphorylation) and here we show those of reduced mGluR5 signaling in schizophrenia. We find that reduced GluN2 phosphorylation can be precipitated by attenuated mGluR5 activity and that increased mGluR5 phosphorylation can result from decreased GluN function, suggesting a reciprocal interplay between the two pathways in schizophrenia. Interestingly, the patient group showed decreased mGluR5-GluN association (p < 0.01), a mechanistic basis for the reciprocal facilitation. In sum, we present the first direct evidence for mGluR5 hypoactivity, propose a reciprocal interplay between GluN and mGluR5 pathways as integral to glutamatergic dysregulation and suggest protein-protein interactions in mGluR5-GluN complexes as potential targets for intervention in schizophrenia.
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Affiliation(s)
- Hoau-Yan Wang
- Department of Physiology, Pharmacology and Neuroscience, City University of New York School of Medicine, New York, NY 10031,Department of Biology and Neuroscience, Graduate School of the City University of New York, NY 10016
| | - Mathew L. MacDonald
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104-3403
| | - Karin E. Borgmann-Winter
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104-3403,Department of Child and Adolescent Psychiatry and Behavioral Sciences, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Anamika Banerjee
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104-3403
| | - Patrick Sleiman
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, and Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104
| | - Andrew Tom
- Department of Physiology, Pharmacology and Neuroscience, City University of New York School of Medicine, New York, NY 10031
| | - Amber Khan
- Department of Physiology, Pharmacology and Neuroscience, City University of New York School of Medicine, New York, NY 10031,Department of Biology and Neuroscience, Graduate School of the City University of New York, NY 10016
| | - Kuo-Chieh Lee
- Department of Physiology, Pharmacology and Neuroscience, City University of New York School of Medicine, New York, NY 10031
| | - Panos Roussos
- Department of Psychiatry, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Steven J. Siegel
- Department of Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, CA, 90007
| | - Scott E Hemby
- Department of Basic Pharmaceutical Sciences, High Point University, High Point, NC, 27106
| | - Warren B. Bilker
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104-3403
| | - Chang-Gyu Hahn
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, 19104-3403, USA.
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20
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Lyashenko E, Niepel M, Dixit PD, Lim SK, Sorger PK, Vitkup D. Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks. eLife 2020; 9:50342. [PMID: 31961323 PMCID: PMC7046471 DOI: 10.7554/elife.50342] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Detecting relative rather than absolute changes in extracellular signals enables cells to make decisions in constantly fluctuating environments. It is currently not well understood how mammalian signaling networks store the memories of past stimuli and subsequently use them to compute relative signals, that is perform fold change detection. Using the growth factor-activated PI3K-Akt signaling pathway, we develop here computational and analytical models, and experimentally validate a novel non-transcriptional mechanism of relative sensing in mammalian cells. This mechanism relies on a new form of cellular memory, where cells effectively encode past stimulation levels in the abundance of cognate receptors on the cell surface. The surface receptor abundance is regulated by background signal-dependent receptor endocytosis and down-regulation. We show the robustness and specificity of relative sensing for two physiologically important ligands, epidermal growth factor (EGF) and hepatocyte growth factor (HGF), and across wide ranges of background stimuli. Our results suggest that similar mechanisms of cell memory and fold change detection may be important in diverse signaling cascades and multiple biological contexts.
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Affiliation(s)
- Eugenia Lyashenko
- Department of Systems Biology, Columbia University, New York, United States
| | - Mario Niepel
- HMS LINCS Center Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Purushottam D Dixit
- Department of Systems Biology, Columbia University, New York, United States.,Department of Physics, University of Florida, Gainesville, United States
| | - Sang Kyun Lim
- HMS LINCS Center Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Peter K Sorger
- Department of Systems Biology, Columbia University, New York, United States.,HMS LINCS Center Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Dennis Vitkup
- Department of Systems Biology, Columbia University, New York, United States.,Center for Computational Biology and Bioinformatics, Columbia University, New York, United States.,Department of Biomedical Informatics, Columbia University, New York, United States
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21
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MacDonald ML, Garver M, Newman J, Sun Z, Kannarkat J, Salisbury R, Glausier J, Ding Y, Lewis DA, Yates N, Sweet RA. Synaptic Proteome Alterations in the Primary Auditory Cortex of Individuals With Schizophrenia. JAMA Psychiatry 2020; 77:86-95. [PMID: 31642882 PMCID: PMC6813579 DOI: 10.1001/jamapsychiatry.2019.2974] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/10/2019] [Indexed: 12/28/2022]
Abstract
Importance Findings from unbiased genetic studies have consistently implicated synaptic protein networks in schizophrenia, but the molecular pathologic features within these networks and their contribution to the synaptic and circuit deficits thought to underlie disease symptoms remain unknown. Objective To determine whether protein levels are altered within synapses from the primary auditory cortex (A1) of individuals with schizophrenia and, if so, whether these differences are restricted to the synapse or occur throughout the gray matter. Design, Setting, and Participants This paired case-control study included tissue samples from individuals with schizophrenia obtained from the Allegheny County Office of the Medical Examiner. An independent panel of health care professionals made consensus DSM-IV diagnoses. Each tissue sample from an individual with schizophrenia was matched by sex, age, and postmortem interval with 1 sample from an unaffected control individual. Targeted mass spectrometry was used to measure protein levels in A1 gray matter homogenate and synaptosome preparations. All experimenters were blinded to diagnosis. Mass spectrometry data were collected from September 26 through November 4, 2016, and analyzed from November 3, 2016, to July 15, 2019. Main Outcomes and Measures Primary measures were homogenate and synaptosome protein levels and their coregulation network features. Hypotheses generated before data collection were (1) that levels of canonical postsynaptic proteins in A1 synaptosome preparations would differ between individuals with schizophrenia and controls and (2) that these differences would not be explained by changes in total A1 homogenate protein levels. Results Synaptosome and homogenate protein levels were investigated in 48 individuals with a schizophrenia diagnosis and 48 controls (mean age in both groups, 48 years [range, 17-83 years]); each group included 35 males (73%) and 13 females (27%). Robust alterations (statistical cutoff set at an adjusted Limma P < .05) were observed in synaptosome levels of canonical mitochondrial and postsynaptic proteins that were highly coregulated and not readily explained by postmortem interval, antipsychotic drug treatment, synaptosome yield, or underlying alterations in homogenate protein levels. Conclusions and Relevance These findings suggest a robust and highly coordinated rearrangement of the synaptic proteome. In line with unbiased genetic findings, alterations in synaptic levels of postsynaptic proteins were identified, providing a road map to identify the specific cells and circuits that are impaired in individuals with schizophrenia A1.
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Affiliation(s)
- Matthew L. MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Megan Garver
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jason Newman
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Zhe Sun
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Joseph Kannarkat
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ryan Salisbury
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jill Glausier
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David A. Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Nathan Yates
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert A. Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
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22
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Kushima I, Aleksic B, Nakatochi M, Shimamura T, Okada T, Uno Y, Morikawa M, Ishizuka K, Shiino T, Kimura H, Arioka Y, Yoshimi A, Takasaki Y, Yu Y, Nakamura Y, Yamamoto M, Iidaka T, Iritani S, Inada T, Ogawa N, Shishido E, Torii Y, Kawano N, Omura Y, Yoshikawa T, Uchiyama T, Yamamoto T, Ikeda M, Hashimoto R, Yamamori H, Yasuda Y, Someya T, Watanabe Y, Egawa J, Nunokawa A, Itokawa M, Arai M, Miyashita M, Kobori A, Suzuki M, Takahashi T, Usami M, Kodaira M, Watanabe K, Sasaki T, Kuwabara H, Tochigi M, Nishimura F, Yamasue H, Eriguchi Y, Benner S, Kojima M, Yassin W, Munesue T, Yokoyama S, Kimura R, Funabiki Y, Kosaka H, Ishitobi M, Ohmori T, Numata S, Yoshikawa T, Toyota T, Yamakawa K, Suzuki T, Inoue Y, Nakaoka K, Goto YI, Inagaki M, Hashimoto N, Kusumi I, Son S, Murai T, Ikegame T, Okada N, Kasai K, Kunimoto S, Mori D, Iwata N, Ozaki N. Comparative Analyses of Copy-Number Variation in Autism Spectrum Disorder and Schizophrenia Reveal Etiological Overlap and Biological Insights. Cell Rep 2019; 24:2838-2856. [PMID: 30208311 DOI: 10.1016/j.celrep.2018.08.022] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/24/2018] [Accepted: 08/08/2018] [Indexed: 01/06/2023] Open
Abstract
Compelling evidence in Caucasian populations suggests a role for copy-number variations (CNVs) in autism spectrum disorder (ASD) and schizophrenia (SCZ). We analyzed 1,108 ASD cases, 2,458 SCZ cases, and 2,095 controls in a Japanese population and confirmed an increased burden of rare exonic CNVs in both disorders. Clinically significant (or pathogenic) CNVs, including those at 29 loci common to both disorders, were found in about 8% of ASD and SCZ cases, which was significantly higher than in controls. Phenotypic analysis revealed an association between clinically significant CNVs and intellectual disability. Gene set analysis showed significant overlap of biological pathways in both disorders including oxidative stress response, lipid metabolism/modification, and genomic integrity. Finally, based on bioinformatics analysis, we identified multiple disease-relevant genes in eight well-known ASD/SCZ-associated CNV loci (e.g., 22q11.2, 3q29). Our findings suggest an etiological overlap of ASD and SCZ and provide biological insights into these disorders.
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Affiliation(s)
- Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masahiro Nakatochi
- Division of Data Science, Data Coordinating Center, Department of Advanced Medicine, Nagoya University Hospital, Nagoya, Aichi 466-8560, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Takashi Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yota Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Laboratory for Psychiatric and Molecular Neuroscience, McLean Hospital, Belmont, MA 02478, USA
| | - Mako Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kanako Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tomoko Shiino
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8553, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yuko Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan; Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Aichi 466-8560, Japan
| | - Akira Yoshimi
- Division of Clinical Sciences and Neuropsychopharmacology, Faculty and Graduate School of Pharmacy, Meijo University, Nagoya, Aichi 468-8503, Japan
| | - Yuto Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yanjie Yu
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yukako Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Maeri Yamamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tetsuya Iidaka
- Department of Physical and Occupational Therapy, Nagoya University Graduate School of Medicine, Nagoya, Aichi 461-8673, Japan
| | - Shuji Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Toshiya Inada
- Department of Psychiatry and Psychobiology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Nanayo Ogawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Emiko Shishido
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Youta Torii
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Center for Postgraduate Clinical Training and Career Development, Nagoya University Hospital, Nagoya, Aichi 466-8560, Japan
| | - Naoko Kawano
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yutaka Omura
- Aichi Psychiatric Medical Center, Nagoya, Aichi 464-0031, Japan
| | - Toru Yoshikawa
- Department of Child Psychiatry, Aichi Prefectural Colony Central Hospital, Kasugai, Aichi 480-0392, Japan
| | - Tokio Uchiyama
- Department of Clinical Psychology, Taisho University, Tokyo 170-8470, Japan
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Ryota Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita, Osaka 565-0871, Japan; Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8553, Japan
| | - Hidenaga Yamamori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yuka Yasuda
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Ayako Nunokawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan
| | - Masanari Itokawa
- Center for Medical Cooperation, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Makoto Arai
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Mitsuhiro Miyashita
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Akiko Kobori
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Michio Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama 930-0194, Japan
| | - Tsutomu Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama 930-0194, Japan
| | - Masahide Usami
- Department of Child and Adolescent Psychiatry, Kohnodai Hospital, National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan
| | - Masaki Kodaira
- Department of Child and Adolescent Psychiatry, Kohnodai Hospital, National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan
| | - Kyota Watanabe
- Department of Child and Adolescent Psychiatry, Kohnodai Hospital, National Center for Global Health and Medicine, Ichikawa, Chiba 272-8516, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hitoshi Kuwabara
- Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Mamoru Tochigi
- Department of Neuropsychiatry, Teikyo University School of Medicine, Tokyo 173-8605, Japan
| | - Fumichika Nishimura
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hidenori Yamasue
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Yosuke Eriguchi
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Seico Benner
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Masaki Kojima
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Walid Yassin
- Department of Child Neuropsychiatry, School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Toshio Munesue
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Shigeru Yokoyama
- Research Center for Child Mental Development, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yasuko Funabiki
- Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hirotaka Kosaka
- Research Center for Child Mental Development University of Fukui, Eiheiji, Fukui 910-1193, Japan; Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui 910-1193, Japan
| | - Makoto Ishitobi
- Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui 910-1193, Japan; Department of Child and Adolescent Mental Health, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Kazuhiro Yamakawa
- Laboratory for Neurogenetics, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Toshimitsu Suzuki
- Laboratory for Neurogenetics, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Yushi Inoue
- National Epilepsy Center, Shizuoka Institute of Epilepsy and Neurological Disorder, Shizuoka 420-8688, Japan
| | - Kentaro Nakaoka
- Aichi Psychiatric Medical Center, Nagoya, Aichi 464-0031, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Masumi Inagaki
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8553, Japan
| | - Naoki Hashimoto
- Department of Psychiatry, Hokkaido University Graduate School of Medicine, Hokkaido, Sapporo 060-8638, Japan
| | - Ichiro Kusumi
- Department of Psychiatry, Hokkaido University Graduate School of Medicine, Hokkaido, Sapporo 060-8638, Japan
| | - Shuraku Son
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Tempei Ikegame
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Naohiro Okada
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; The International Research Center for Neurointelligence (WPI-IRCN) at The University of Tokyo Institutes for Advanced Study (UTIAS), Tokyo 113-0033, Japan
| | - Shohko Kunimoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan; Brain and Mind Research Center, Nagoya University, Nagoya, Aichi 466-8550, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan.
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23
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Schrode N, Ho SM, Yamamuro K, Dobbyn A, Huckins L, Matos MR, Cheng E, Deans PJM, Flaherty E, Barretto N, Topol A, Alganem K, Abadali S, Gregory J, Hoelzli E, Phatnani H, Singh V, Girish D, Aronow B, Mccullumsmith R, Hoffman GE, Stahl EA, Morishita H, Sklar P, Brennand KJ. Synergistic effects of common schizophrenia risk variants. Nat Genet 2019; 51:1475-1485. [PMID: 31548722 PMCID: PMC6778520 DOI: 10.1038/s41588-019-0497-5] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/13/2019] [Indexed: 12/19/2022]
Abstract
The mechanisms by which common risk variants of small effect interact to contribute to complex genetic disorders are unclear. Here, we apply a genetic approach, using isogenic human induced pluripotent stem cells, to evaluate the effects of schizophrenia (SZ)-associated common variants predicted to function as SZ expression quantitative trait loci (eQTLs). By integrating CRISPR-mediated gene editing, activation and repression technologies to study one putative SZ eQTL (FURIN rs4702) and four top-ranked SZ eQTL genes (FURIN, SNAP91, TSNARE1 and CLCN3), our platform resolves pre- and postsynaptic neuronal deficits, recapitulates genotype-dependent gene expression differences and identifies convergence downstream of SZ eQTL gene perturbations. Our observations highlight the cell-type-specific effects of common variants and demonstrate a synergistic effect between SZ eQTL genes that converges on synaptic function. We propose that the links between rare and common variants implicated in psychiatric disease risk constitute a potentially generalizable phenomenon occurring more widely in complex genetic disorders.
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Affiliation(s)
- Nadine Schrode
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seok-Man Ho
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kazuhiko Yamamuro
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Dobbyn
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Huckins
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marliette R Matos
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P J Michael Deans
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erin Flaherty
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie Barretto
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aaron Topol
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Khaled Alganem
- Department of Neurosciences, Institute in the College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Sonya Abadali
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Gregory
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Emily Hoelzli
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Vineeta Singh
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Deeptha Girish
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce Aronow
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert Mccullumsmith
- Department of Neurosciences, Institute in the College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hirofumi Morishita
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pamela Sklar
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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24
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Bentea E, Depasquale EA, O’Donovan SM, Sullivan CR, Simmons M, Meador-Woodruff JH, Zhou Y, Xu C, Bai B, Peng J, Song H, Ming GL, Meller J, Wen Z, McCullumsmith RE. Kinase network dysregulation in a human induced pluripotent stem cell model of DISC1 schizophrenia. Mol Omics 2019; 15:173-188. [PMID: 31106784 PMCID: PMC6563817 DOI: 10.1039/c8mo00173a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein kinases orchestrate signal transduction pathways involved in central nervous system functions ranging from neurodevelopment to synaptic transmission and plasticity. Abnormalities in kinase-mediated signaling are involved in the pathophysiology of neurological disorders, including neuropsychiatric disorders. Here, we expand on the hypothesis that kinase networks are dysregulated in schizophrenia. We investigated changes in serine/threonine kinase activity in cortical excitatory neurons differentiated from induced pluripotent stem cells (iPSCs) from a schizophrenia patient presenting with a 4 bp mutation in the disrupted in schizophrenia 1 (DISC1) gene and a corresponding control. Using kinome peptide arrays, we demonstrate large scale abnormalities in DISC1 cells, including a global depression of serine/threonine kinase activity, and changes in activity of kinases, including AMP-activated protein kinase (AMPK), extracellular signal-regulated kinases (ERK), and thousand-and-one amino acid (TAO) kinases. Using isogenic cell lines in which the DISC1 mutation is either introduced in the control cell line, or rescued in the schizophrenia cell line, we ascribe most of these changes to a direct effect of the presence of the DISC1 mutation. Investigating the gene expression signatures downstream of the DISC1 kinase network, and mapping them on perturbagen signatures obtained from the Library of Integrated Network-based Cellular Signatures (LINCS) database, allowed us to propose novel drug targets able to reverse the DISC1 kinase dysregulation gene expression signature. Altogether, our findings provide new insight into abnormalities of kinase networks in schizophrenia and suggest possible targets for disease intervention.
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Affiliation(s)
- Eduard Bentea
- Center for Neurosciences (C4N), Department of Pharmaceutical Biotechnology and Molecular Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Erica A.K. Depasquale
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sinead M. O’Donovan
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, USA
| | | | - Micah Simmons
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - James H. Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ying Zhou
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Chongchong Xu
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Bing Bai
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, P. R. China
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jarek Meller
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Departments of Environmental Health, Electrical Engineering & Computing Systems and Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Zhexing Wen
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurology, Emory University School of Medicine, Atlanta, GA, USA
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25
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Sullivan CR, Mielnik CA, O'Donovan SM, Funk AJ, Bentea E, DePasquale EA, Alganem K, Wen Z, Haroutunian V, Katsel P, Ramsey AJ, Meller J, McCullumsmith RE. Connectivity Analyses of Bioenergetic Changes in Schizophrenia: Identification of Novel Treatments. Mol Neurobiol 2019; 56:4492-4517. [PMID: 30338483 PMCID: PMC7584383 DOI: 10.1007/s12035-018-1390-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/11/2018] [Indexed: 01/21/2023]
Abstract
We utilized a cell-level approach to examine glycolytic pathways in the DLPFC of subjects with schizophrenia (n = 16) and control (n = 16) and found decreased mRNA expression of glycolytic enzymes in pyramidal neurons, but not astrocytes. To replicate these novel bioenergetic findings, we probed independent datasets for bioenergetic targets and found similar abnormalities. Next, we used a novel strategy to build a schizophrenia bioenergetic profile by a tailored application of the Library of Integrated Network-Based Cellular Signatures data portal (iLINCS) and investigated connected cellular pathways, kinases, and transcription factors using Enrichr. Finally, with the goal of identifying drugs capable of "reversing" the bioenergetic schizophrenia signature, we performed a connectivity analysis with iLINCS and identified peroxisome proliferator-activated receptor (PPAR) agonists as promising therapeutic targets. We administered a PPAR agonist to the GluN1 knockdown model of schizophrenia and found it improved long-term memory. Taken together, our findings suggest that tailored bioinformatics approaches, coupled with the LINCS library of transcriptional signatures of chemical and genetic perturbagens, may be employed to identify novel treatment strategies for schizophrenia and related diseases.
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Affiliation(s)
| | - Catharine A Mielnik
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | | | - Adam J Funk
- Department of Neuroscience, University of Toledo, Toledo, OH, USA
| | - Eduard Bentea
- Neurosciences TA Biology, UCB BioPharma SPRL, Braine-l'Alleud, Belgium
| | - Erica A DePasquale
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Khaled Alganem
- Department of Neuroscience, University of Toledo, Toledo, OH, USA
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Vahram Haroutunian
- Department of Psychiatry and Neuroscience, The Icahn School of Medicine at Mount Sinai, Bronx, NY, USA
| | - Pavel Katsel
- Department of Psychiatry and Neuroscience, The Icahn School of Medicine at Mount Sinai, Bronx, NY, USA
| | - Amy J Ramsey
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jarek Meller
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Informatics, Nicolaus Copernicus University, Torun, Poland
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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26
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McGuire JL, Depasquale EA, Funk AJ, O'Donnovan SM, Hasselfeld K, Marwaha S, Hammond JH, Hartounian V, Meador-Woodruff JH, Meller J, McCullumsmith RE. Abnormalities of signal transduction networks in chronic schizophrenia. NPJ SCHIZOPHRENIA 2017; 3:30. [PMID: 28900113 PMCID: PMC5595970 DOI: 10.1038/s41537-017-0032-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 07/07/2017] [Accepted: 07/31/2017] [Indexed: 12/11/2022]
Abstract
Schizophrenia is a serious neuropsychiatric disorder characterized by disruptions of brain cell metabolism, microstructure, and neurotransmission. All of these processes require coordination of multiple kinase-mediated signaling events. We hypothesize that imbalances in kinase activity propagate through an interconnected network of intracellular signaling with potential to simultaneously contribute to many or all of the observed deficits in schizophrenia. We established a workflow distinguishing schizophrenia-altered kinases in anterior cingulate cortex using a previously published kinome array data set. We compared schizophrenia-altered kinases to haloperidol-altered kinases, and identified systems, functions, and regulators predicted using pathway analyses. We used kinase inhibitors with the kinome array to test hypotheses about imbalance in signaling and conducted preliminary studies of kinase proteins, phosphoproteins, and activity for kinases of interest. We investigated schizophrenia-associated single nucleotide polymorphisms in one of these kinases, AKT, for genotype-dependent changes in AKT protein or activity. Kinome analyses identified new kinases as well as some previously implicated in schizophrenia. These results were not explained by chronic antipsychotic treatment. Kinases identified in our analyses aligned with cytoskeletal arrangement and molecular trafficking. Of the kinases we investigated further, AKT and (unexpectedly) JNK, showed the most dysregulation in the anterior cingulate cortex of schizophrenia subjects. Changes in kinase activity did not correspond to protein or phosphoprotein levels. We also show that AKT single nucleotide polymorphism rs1130214, previously associated with schizophrenia, influenced enzyme activity but not protein or phosphoprotein levels. Our data indicate subtle changes in kinase activity and regulation across an interlinked kinase network, suggesting signaling imbalances underlie the core symptoms of schizophrenia. A study by US scientists indicates that changes in the activity of key signaling proteins may underlie core symptoms of schizophrenia. Protein kinases mediate the activation of intracellular signaling events and analyses of the kinome, the complete set of protein kinases encoded in the genome, previously revealed significant changes in phosphorylation patterns in postmortem brain tissue from patients with schizophrenia. Based on these findings, Jennifer McGuire at the University of Cincinnati and colleagues investigated the upstream regulation of these proteins. They identified both established and novel proteins associated with schizophrenia in the anterior cingulate cortex, with JNK and AKT activity being the most disrupted in schizophrenia patients. Their findings highlight how subtle changes in the activity of a small number of signaling proteins can propagate and have major consequences for mental health.
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Affiliation(s)
- Jennifer L McGuire
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA.
| | - Erica A Depasquale
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Adam J Funk
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - Sinead M O'Donnovan
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - Kathryn Hasselfeld
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
| | - Shruti Marwaha
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH, USA
| | - John H Hammond
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Vahram Hartounian
- Psychiatry & Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.,James J. Peters VA Medical Center, Mental Illness Research Education and Clinical Center (MIRECC), Bronx, NY, USA
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Jarek Meller
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Departments of Environmental Health, Electrical Engineering & Computing Systems and Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Robert E McCullumsmith
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA
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27
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Technological advances for interrogating the human kinome. Biochem Soc Trans 2017; 45:65-77. [PMID: 28202660 DOI: 10.1042/bst20160163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022]
Abstract
There is increasing appreciation among researchers and clinicians of the value of investigating biology and pathobiology at the level of cellular kinase (kinome) activity. Kinome analysis provides valuable opportunity to gain insights into complex biology (including disease pathology), identify biomarkers of critical phenotypes (including disease prognosis and evaluation of therapeutic efficacy), and identify targets for therapeutic intervention through kinase inhibitors. The growing interest in kinome analysis has fueled efforts to develop and optimize technologies that enable characterization of phosphorylation-mediated signaling events in a cost-effective, high-throughput manner. In this review, we highlight recent advances to the central technologies currently available for kinome profiling and offer our perspectives on the key challenges remaining to be addressed.
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28
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Fan LJ, Han HJ, Guan J, Zhang XW, Cui QH, Shen H, Shi C. Aberrantly expressed long noncoding RNAs in recurrent implantation failure: A microarray related study. Syst Biol Reprod Med 2017; 63:269-278. [PMID: 28441042 DOI: 10.1080/19396368.2017.1310329] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs longer than 200 nucleotides. They were long regarded as transcription noise for their low expression and non-protein coding features. Recent published reports indicate that lncRNAs are involved in virtually every aspect of human biology. We aimed to profile the endometrial lncRNA expression pattern in women with recurrent implantation failure (RIF) and predict the function of the genes of the dysregulated lncRNA transcripts. Endometrial samples (24) were collected during window of implantation (14 RIF women and 10 women who conceived after embryo transfer). For the microarray study, 7 RIF endometrium and 5 control endometrium were selected, and quantitative real-time PCR (RT-qPCR) was performed on the rest of the endometrial samples to validate the microarray results. After that, lncRNA-mRNA co-expression analysis, GO analysis, KEGG analysis, and lncRNA-transcript factor (TF) analysis were carried out to analyze the gene functions of the dysregulated lncRNA transcripts. We detected a total of 197 lncRNA transcripts that were dysregulated in RIF endometrium compared with the control group. The relative expression levels of eight selected lncRNA transcripts were validated by RT-qPCR and were in accordance with the microarray outcomes. GO and KEGG analyses revealed that the coexpressed mRNA transcripts were involved in pathways that may affect endometrial receptivity such as cell adhesion. The lncRNA target predictions provided potential TF targets of the dysregulated lncRNA transcripts. Our results indicate that lncRNA expression profiles of RIF endometrium were different from that of normal receptive endometrial, suggesting that lncRNAs may regulate endometrial receptivity. ABBREVIATIONS GO: Gene Oncology; GFs: growth factors; KEGG: Kyoto Encyclopedia of Genes and Genomes; lncRNAs: long noncoding RNAs; PCA3: prostate cancer antigen 3; RT-qPCR: quantitative real-time PCR; RIF: recurrent implantation failure; STK: serine/threonine kinase; TF: transcription factor; WOI: window of implantation.
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Affiliation(s)
- Li-Juan Fan
- a Department of Reproductive Medical Center , Peking University People's Hospital , Beijing , China
| | - Hong-Jing Han
- a Department of Reproductive Medical Center , Peking University People's Hospital , Beijing , China
| | - Jing Guan
- a Department of Reproductive Medical Center , Peking University People's Hospital , Beijing , China
| | - Xiao-Wei Zhang
- b Urology , Peking University People's Hospital , Beijing , China
| | - Qing-Hua Cui
- c Department of Biomedical Informatics , School of Basic Medical Sciences, Peking University , Beijing , China
| | - Huan Shen
- a Department of Reproductive Medical Center , Peking University People's Hospital , Beijing , China
| | - Cheng Shi
- a Department of Reproductive Medical Center , Peking University People's Hospital , Beijing , China
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29
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Kushima I, Aleksic B, Nakatochi M, Shimamura T, Shiino T, Yoshimi A, Kimura H, Takasaki Y, Wang C, Xing J, Ishizuka K, Oya-Ito T, Nakamura Y, Arioka Y, Maeda T, Yamamoto M, Yoshida M, Noma H, Hamada S, Morikawa M, Uno Y, Okada T, Iidaka T, Iritani S, Yamamoto T, Miyashita M, Kobori A, Arai M, Itokawa M, Cheng MC, Chuang YA, Chen CH, Suzuki M, Takahashi T, Hashimoto R, Yamamori H, Yasuda Y, Watanabe Y, Nunokawa A, Someya T, Ikeda M, Toyota T, Yoshikawa T, Numata S, Ohmori T, Kunimoto S, Mori D, Iwata N, Ozaki N. High-resolution copy number variation analysis of schizophrenia in Japan. Mol Psychiatry 2017; 22:430-440. [PMID: 27240532 DOI: 10.1038/mp.2016.88] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 12/30/2022]
Abstract
Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (<100 kb). Clinically significant CNVs were significantly more frequent in cases than in controls (odds ratio=3.04, P=9.3 × 10-9, 9.0% of cases). We confirmed a significant association of X-chromosome aneuploidies with SCZ and identified 11 de novo CNVs (e.g., MBD5 deletion) in cases. In patients with clinically significant CNVs, 41.7% had a history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.
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Affiliation(s)
- I Kushima
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.,Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - B Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Nakatochi
- Bioinformatics Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Shiino
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - A Yoshimi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - C Wang
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - J Xing
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - K Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Oya-Ito
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Maeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yamamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yoshida
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Noma
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Hamada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Iidaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Miyashita
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - A Kobori
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Arai
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Itokawa
- Center for Medical Cooperation, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M-C Cheng
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - Y-A Chuang
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - C-H Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - M Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - T Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - R Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - H Yamamori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Yasuda
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - A Nunokawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - M Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - T Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - T Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - S Numata
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Ohmori
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - S Kunimoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - D Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Brain and Mind Research Center, Nagoya University, Nagoya, Japan
| | - N Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - N Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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30
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Rosenberger AFN, Hilhorst R, Coart E, García Barrado L, Naji F, Rozemuller AJM, van der Flier WM, Scheltens P, Hoozemans JJM, van der Vies SM. Protein Kinase Activity Decreases with Higher Braak Stages of Alzheimer's Disease Pathology. J Alzheimers Dis 2016; 49:927-43. [PMID: 26519433 PMCID: PMC4927853 DOI: 10.3233/jad-150429] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alzheimer’s disease (AD) is characterized by a long pre-clinical phase (20–30 years), during which significant brain pathology manifests itself. Disease mechanisms associated with pathological hallmarks remain elusive. Most processes associated with AD pathogenesis, such as inflammation, synaptic dysfunction, and hyper-phosphorylation of tau are dependent on protein kinase activity. The objective of this study was to determine the involvement of protein kinases in AD pathogenesis. Protein kinase activity was determined in postmortem hippocampal brain tissue of 60 patients at various stages of AD and 40 non-demented controls (Braak stages 0-VI) using a peptide-based microarray platform. We observed an overall decrease of protein kinase activity that correlated with disease progression. The phosphorylation of 96.7% of the serine/threonine peptides and 37.5% of the tyrosine peptides on the microarray decreased significantly with increased Braak stage (p-value <0.01). Decreased activity was evident at pre-clinical stages of AD pathology (Braak I-II). Increased phosphorylation was not observed for any peptide. STRING analysis in combination with pathway analysis and identification of kinases responsible for peptide phosphorylation showed the interactions between well-known proteins in AD pathology, including the Ephrin-receptor A1 (EphA1), a risk gene for AD, and sarcoma tyrosine kinase (Src), which is involved in memory formation. Additionally, kinases that have not previously been associated with AD were identified, e.g., protein tyrosine kinase 6 (PTK6/BRK), feline sarcoma oncogene kinase (FES), and fyn-associated tyrosine kinase (FRK). The identified protein kinases are new biomarkers and potential drug targets for early (pre-clinical) intervention.
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Affiliation(s)
- Andrea F N Rosenberger
- Alzheimer Center & Department of Neurology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.,Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Riet Hilhorst
- PamGene International BV, 's-Hertogenbosch, The Netherlands
| | - Elisabeth Coart
- International Drug Development Institute, Louvain-la-Neuve, Belgium
| | | | - Faris Naji
- PamGene International BV, 's-Hertogenbosch, The Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center & Department of Neurology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.,Department of Epidemiology and Biostatistics, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Philip Scheltens
- Alzheimer Center & Department of Neurology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Jeroen J M Hoozemans
- Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Saskia M van der Vies
- Department of Pathology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
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31
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Dorsett CR, McGuire JL, Niedzielko TL, DePasquale EAK, Meller J, Floyd CL, McCullumsmith RE. Traumatic Brain Injury Induces Alterations in Cortical Glutamate Uptake without a Reduction in Glutamate Transporter-1 Protein Expression. J Neurotrauma 2016; 34:220-234. [PMID: 27312729 DOI: 10.1089/neu.2015.4372] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We hypothesize that the primary mechanism for removal of glutamate from the extracellular space is altered after traumatic brain injury (TBI). To evaluate this hypothesis, we initiated TBI in adult male rats using a 2.0 atm lateral fluid percussion injury (LFPI) model. In the ipsilateral cortex and hippocampus, we found no differences in expression of the primary glutamate transporter in the brain (GLT-1) 24 h after TBI. In contrast, we found a decrease in glutamate uptake in the cortex, but not the hippocampus, 24 h after injury. Because glutamate uptake is potently regulated by protein kinases, we assessed global serine-threonine protein kinase activity using a kinome array platform. Twenty-five kinome array peptide substrates were differentially phoshorylated between LFPI and controls in the cortex, whereas 19 peptide substrates were differentially phosphorylated in the hippocampus (fold change ≥ ± 1.15). We identified several kinases as likely to be involved in acute TBI, including protein kinase B (Akt) and protein kinase C (PKC), which are well-characterized modulators of GLT-1. Exploratory studies using an inhibitor of Akt suggest selective activation of kinases in LFPI versus controls. Ingenuity pathway analyses of implicated kinases from our network model found apoptosis and cell death pathways as top functions in acute LFPI. Taken together, our data suggest diminished activity of glutamate transporters in the prefrontal cortex, with no changes in protein expression of the primary glutamate transporter GLT-1, and global alterations in signaling networks that include serine-threonine kinases that are known modulators of glutamate transport activity.
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Affiliation(s)
- Christopher R Dorsett
- 1 Biological and Biomedical Sciences Doctoral Program, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Jennifer L McGuire
- 2 Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati , Cincinnati, Ohio
| | - Tracy L Niedzielko
- 3 Department of Physical Medicine and Rehabilitation, University of Alabama at Birmingham , Birmingham, Alabama
| | - Erica A K DePasquale
- 2 Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati , Cincinnati, Ohio
| | - Jaroslaw Meller
- 4 Departments of Environmental Health, Electrical Engineering & Computing Systems, and Biomedical Informatics, University of Cincinnati College of Medicine , Cincinnati, Ohio.,5 Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio
| | - Candace L Floyd
- 3 Department of Physical Medicine and Rehabilitation, University of Alabama at Birmingham , Birmingham, Alabama
| | - Robert E McCullumsmith
- 2 Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati , Cincinnati, Ohio
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Dussaq A, Anderson JC, Willey CD, Almeida JS. Mechanistic Parameterization of the Kinomic Signal in Peptide Arrays. ACTA ACUST UNITED AC 2016; 9:151-157. [PMID: 27601856 PMCID: PMC5010871 DOI: 10.4172/jpb.1000401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Kinases play a role in every cellular process involved in tumorigenesis ranging from proliferation, migration, and protein synthesis to DNA repair. While genetic sequencing has identified most kinases in the human genome, it does not describe the ‘kinome’ at the level of activity of kinases against their substrate targets. An attempt to address that limitation and give researchers a more direct view of cellular kinase activity is found in the PamGene PamChip® system, which records and compares the phosphorylation of 144 tyrosine or serine/threonine peptides as they are phosphorylated by cellular kinases. Accordingly, the kinetics of this time dependent kinomic signal needs to be well understood in order to transduce a parameter set into an accurate and meaningful mathematical model. Here we report the analysis and mathematical modeling of kinomic time series, which achieves a more accurate description of the accumulation of phosphorylated product than the current model, which assumes first order enzyme-substrate kinetics. Reproducibility of the proposed solution was of particular attention. Specifically, the non-linear parameterization procedure is delivered as a public open source web application where kinomic time series can be accurately decomposed into the model’s two parameter values measuring phosphorylation rate and capacity. The ability to deliver model parameterization entirely as a client side web application is an important result on its own given increasing scientific preoccupation with reproducibility. There is also no need for a potentially transitory and opaque server-side component maintained by the authors, nor of exchanging potentially sensitive data as part of the model parameterization process since the code is transferred to the browser client where it can be inspected and executed.
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Affiliation(s)
| | | | | | - Jonas S Almeida
- Biomedical Informatics Department, Stony Brook University, USA
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Anderson JC, Willey CD, Mehta A, Welaya K, Chen D, Duarte CW, Ghatalia P, Arafat W, Madan A, Sudarshan S, Naik G, Grizzle WE, Choueiri TK, Sonpavde G. High Throughput Kinomic Profiling of Human Clear Cell Renal Cell Carcinoma Identifies Kinase Activity Dependent Molecular Subtypes. PLoS One 2015; 10:e0139267. [PMID: 26406598 PMCID: PMC4583516 DOI: 10.1371/journal.pone.0139267] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/09/2015] [Indexed: 01/08/2023] Open
Abstract
Despite the widespread use of kinase-targeted agents in clear cell renal cell carcinoma (CC-RCC), comprehensive kinase activity evaluation (kinomic profiling) of these tumors is lacking. Thus, kinomic profiling of CC-RCC may assist in devising a classification system associated with clinical outcomes, and help identify potential therapeutic targets. Fresh frozen CC-RCC tumor lysates from 41 clinically annotated patients who had localized disease at diagnosis were kinomically profiled using the PamStation®12 high-content phospho-peptide substrate microarray system (PamGene International). Twelve of these patients also had matched normal kidneys available that were also profiled. Unsupervised hierarchical clustering and supervised comparisons based on tumor vs. normal kidney and clinical outcome (tumor recurrence) were performed and coupled with advanced network modeling and upstream kinase prediction methods. Unsupervised clustering analysis of localized CC-RCC tumors identified 3 major kinomic groups associated with inflammation (A), translation initiation (B), and immune response and cell adhesions (C) processes. Potential driver kinases implicated include PFTAIRE (PFTK1), PKG1, and SRC, which were identified in groups A, B, and C, respectively. Of the 9 patients who had tumor recurrence, only one was found in Group B. Supervised analysis showed decreased kinase activity of CDK1 and RSK1-4 substrates in those which progressed compared to others. Twelve tumors with matching normal renal tissue implicated increased PIM's and MAPKAPK's in tumors compared to adjacent normal renal tissue. As such, comprehensive kinase profiling of CC-RCC tumors could provide a functional classification strategy for patients with localized disease and identify potential therapeutic targets.
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Affiliation(s)
- Joshua C. Anderson
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Christopher D. Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amitkumar Mehta
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Karim Welaya
- Clinical Oncology Department, University of Alexandria, Alexandria, Egypt
| | - Dongquan Chen
- Division of Preventative Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Christine W. Duarte
- Center for Outcomes Research and Evaluation (CORE), Maine Medical Center Research Institute (MMCRI), Portland, Maine, United States of America
| | - Pooja Ghatalia
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Waleed Arafat
- Clinical Oncology Department, University of Alexandria, Alexandria, Egypt
| | - Ankit Madan
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Gurudatta Naik
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - William E. Grizzle
- Division of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Toni K. Choueiri
- Department of Medical Oncology, Kidney Cancer Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Guru Sonpavde
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Kinomic profiling of electromagnetic navigational bronchoscopy specimens: a new approach for personalized medicine. PLoS One 2014; 9:e116388. [PMID: 25549342 PMCID: PMC4280210 DOI: 10.1371/journal.pone.0116388] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 12/07/2014] [Indexed: 12/03/2022] Open
Abstract
Purpose Researchers are currently seeking relevant lung cancer biomarkers in order to make informed decisions regarding therapeutic selection for patients in so-called “precision medicine.” However, there are challenges to obtaining adequate lung cancer tissue for molecular analyses. Furthermore, current molecular testing of tumors at the genomic or transcriptomic level are very indirect measures of biological response to a drug, particularly for small molecule inhibitors that target kinases. Kinase activity profiling is therefore theorized to be more reflective of invivo biology than many current molecular analysis techniques. As a result, this study seeks to prove the feasibility of combining a novel minimally invasive biopsy technique that expands the number of lesions amenable for biopsy with subsequent exvivo kinase activity analysis. Methods Eight patients with lung lesions of varying location and size were biopsied using the novel electromagnetic navigational bronchoscopy (ENB) technique. Basal kinase activity (kinomic) profiles and exvivo interrogation of samples in combination with tyrosine kinase inhibitors erlotinib, crizotinib, and lapatinib were performed by PamStation 12 microarray analysis. Results Kinomic profiling qualitatively identified patient specific kinase activity profiles as well as patient and drug specific changes in kinase activity profiles following exposure to inhibitor. Thus, the study has verified the feasibility of ENB as a method for obtaining tissue in adequate quantities for kinomic analysis and has demonstrated the possible use of this tissue acquisition and analysis technique as a method for future study of lung cancer biomarkers. Conclusions We demonstrate the feasibility of using ENB-derived biopsies to perform kinase activity assessment in lung cancer patients.
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Podder A, Latha N. New Insights into Schizophrenia Disease Genes Interactome in the Human Brain: Emerging Targets and Therapeutic Implications in the Postgenomics Era. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:754-66. [DOI: 10.1089/omi.2014.0082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Avijit Podder
- Bioinformatics Infrastructure Facility, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Narayanan Latha
- Bioinformatics Infrastructure Facility, Sri Venkateswara College, University of Delhi, New Delhi, India
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