1
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Ruzicka WB, Mohammadi S, Fullard JF, Davila-Velderrain J, Subburaju S, Tso DR, Hourihan M, Jiang S, Lee HC, Bendl J, Voloudakis G, Haroutunian V, Hoffman GE, Roussos P, Kellis M. Single-cell multi-cohort dissection of the schizophrenia transcriptome. Science 2024; 384:eadg5136. [PMID: 38781388 DOI: 10.1126/science.adg5136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/21/2023] [Indexed: 05/25/2024]
Abstract
The complexity and heterogeneity of schizophrenia have hindered mechanistic elucidation and the development of more effective therapies. Here, we performed single-cell dissection of schizophrenia-associated transcriptomic changes in the human prefrontal cortex across 140 individuals in two independent cohorts. Excitatory neurons were the most affected cell group, with transcriptional changes converging on neurodevelopment and synapse-related molecular pathways. Transcriptional alterations included known genetic risk factors, suggesting convergence of rare and common genomic variants on neuronal population-specific alterations in schizophrenia. Based on the magnitude of schizophrenia-associated transcriptional change, we identified two populations of individuals with schizophrenia marked by expression of specific excitatory and inhibitory neuronal cell states. This single-cell atlas links transcriptomic changes to etiological genetic risk factors, contextualizing established knowledge within the human cortical cytoarchitecture and facilitating mechanistic understanding of schizophrenia pathophysiology and heterogeneity.
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Affiliation(s)
- W Brad Ruzicka
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shahin Mohammadi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jose Davila-Velderrain
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Neurogenomics Research Center, Human Technopole, 20157 Milan, Italy
| | - Sivan Subburaju
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Reed Tso
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
| | - Makayla Hourihan
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
| | - Shan Jiang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hao-Chih Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georgios Voloudakis
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Neurogenomics Research Center, Human Technopole, 20157 Milan, Italy
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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2
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Burrack N, Yitzhaky A, Mizrahi L, Wang M, Stern S, Hertzberg L. Altered Expression of PDE4 Genes in Schizophrenia: Insights from a Brain and Blood Sample Meta-Analysis and iPSC-Derived Neurons. Genes (Basel) 2024; 15:609. [PMID: 38790238 PMCID: PMC11121586 DOI: 10.3390/genes15050609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Schizophrenia symptomatology includes negative symptoms and cognitive impairment. Several studies have linked schizophrenia with the PDE4 family of enzymes due to their genetic association and function in cognitive processes such as long-term potentiation. We conducted a systematic gene expression meta-analysis of four PDE4 genes (PDE4A-D) in 10 brain sample datasets (437 samples) and three blood sample datasets (300 samples). Subsequently, we measured mRNA levels in iPSC-derived hippocampal dentate gyrus neurons generated from fibroblasts of three groups: healthy controls, healthy monozygotic twins (MZ), and their MZ siblings with schizophrenia. We found downregulation of PDE4B in brain tissues, further validated by independent data of the CommonMind consortium (515 samples). Interestingly, the downregulation signal was present in a subgroup of the patients, while the others showed no differential expression or even upregulation. Notably, PDE4A, PDE4B, and PDE4D exhibited upregulation in iPSC-derived neurons compared to healthy controls, whereas in blood samples, PDE4B was found to be upregulated while PDE4A was downregulated. While the precise mechanism and direction of altered PDE4 expression necessitate further investigation, the observed multilevel differential expression across the brain, blood, and iPSC-derived neurons compellingly suggests the involvement of PDE4 genes in the pathophysiology of schizophrenia.
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Affiliation(s)
- Nitzan Burrack
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84101, Israel;
- Clinical Research Center, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Liron Mizrahi
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3103301, Israel
| | - Meiyan Wang
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shani Stern
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3103301, Israel
| | - Libi Hertzberg
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- Shalvata Mental Health Center, Affiliated with the Faculty of Medicine, Tel-Aviv University, 13 Aliat Hanoar St., Hod Hasharon 45100, Israel
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3
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Miyano T, Mikkaichi T, Nakamura K, Yoshigae Y, Abernathy K, Ogura Y, Kiyosawa N. Circulating microRNA Profiles Identify a Patient Subgroup with High Inflammation and Severe Symptoms in Schizophrenia Experiencing Acute Psychosis. Int J Mol Sci 2024; 25:4291. [PMID: 38673876 PMCID: PMC11050142 DOI: 10.3390/ijms25084291] [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: 03/08/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Schizophrenia is a complex and heterogenous psychiatric disorder. This study aimed to demonstrate the potential of circulating microRNAs (miRNAs) as a clinical biomarker to stratify schizophrenia patients and to enhance understandings of their heterogenous pathophysiology. We measured levels of 179 miRNA and 378 proteins in plasma samples of schizophrenia patients experiencing acute psychosis and obtained their Positive and Negative Syndrome Scale (PANSS) scores. The plasma miRNA profile revealed three subgroups of schizophrenia patients, where one subgroup tended to have higher scores of all the PANSS subscales compared to the other subgroups. The subgroup with high PANSS scores had four distinctively downregulated miRNAs, which enriched 'Immune Response' according to miRNA set enrichment analysis and were reported to negatively regulate IL-1β, IL-6, and TNFα. The same subgroup had 22 distinctively upregulated proteins, which enriched 'Cytokine-cytokine receptor interaction' according to protein set enrichment analysis, and all the mapped proteins were pro-inflammatory cytokines. Hence, the subgroup is inferred to have comparatively high inflammation within schizophrenia. In conclusion, miRNAs are a potential biomarker that reflects both disease symptoms and molecular pathophysiology, and identify a patient subgroup with high inflammation. These findings provide insights for the precision medicinal strategies for anti-inflammatory treatments in the high-inflammation subgroup of schizophrenia.
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Affiliation(s)
- Takuya Miyano
- Translational Science Department II, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa, Tokyo 140-8710, Japan; (T.M.); (K.N.); (Y.Y.); (N.K.)
| | - Tsuyoshi Mikkaichi
- Translational Science Department II, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa, Tokyo 140-8710, Japan; (T.M.); (K.N.); (Y.Y.); (N.K.)
| | - Kouichi Nakamura
- Translational Science Department II, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa, Tokyo 140-8710, Japan; (T.M.); (K.N.); (Y.Y.); (N.K.)
| | - Yasushi Yoshigae
- Translational Science Department II, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa, Tokyo 140-8710, Japan; (T.M.); (K.N.); (Y.Y.); (N.K.)
| | - Kelly Abernathy
- Clinical Research Department, Sirtsei Pharmaceuticals, Inc., 3000 RDU Center Drive, Suite 130, Morrisville, NC 27560, USA;
| | - Yuji Ogura
- Translational Research Department, Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa, Tokyo 134-8630, Japan;
| | - Naoki Kiyosawa
- Translational Science Department II, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa, Tokyo 140-8710, Japan; (T.M.); (K.N.); (Y.Y.); (N.K.)
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4
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Larson KC, Martens LH, Marconi M, Dejesus C, Bruhn S, Miller TA, Tate B, Levenson JM. Preclinical translational platform of neuroinflammatory disease biology relevant to neurodegenerative disease. J Neuroinflammation 2024; 21:37. [PMID: 38297405 PMCID: PMC10832185 DOI: 10.1186/s12974-024-03029-3] [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: 08/23/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
Neuroinflammation is a key driver of neurodegenerative disease, however the tools available to model this disease biology at the systems level are lacking. We describe a translational drug discovery platform based on organotypic culture of murine cortical brain slices that recapitulate disease-relevant neuroinflammatory biology. After an acute injury response, the brain slices assume a chronic neuroinflammatory state marked by transcriptomic profiles indicative of activation of microglia and astrocytes and loss of neuronal function. Microglia are necessary for manifestation of this neuroinflammation, as depletion of microglia prior to isolation of the brain slices prevents both activation of astrocytes and robust loss of synaptic function genes. The transcriptomic pattern of neuroinflammation in the mouse platform is present in published datasets derived from patients with amyotrophic lateral sclerosis, Huntington's disease, and frontotemporal dementia. Pharmacological utility of the platform was validated by demonstrating reversal of microglial activation and the overall transcriptomic signature with transforming growth factor-β. Additional anti-inflammatory targets were screened and inhibitors of glucocorticoid receptors, COX-2, dihydrofolate reductase, and NLRP3 inflammasome all failed to reverse the neuroinflammatory signature. Bioinformatics analysis of the neuroinflammatory signature identified protein tyrosine phosphatase non-receptor type 11 (PTPN11/SHP2) as a potential target. Three structurally distinct inhibitors of PTPN11 (RMC-4550, TN0155, IACS-13909) reversed the neuroinflammatory disease signature. Collectively, these results highlight the utility of this novel neuroinflammatory platform for facilitating identification and validation of targets for neuroinflammatory neurodegenerative disease drug discovery.
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Affiliation(s)
- Kelley C Larson
- Vigil Neuroscience, Watertown, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Lauren H Martens
- , Neumora Therapeutics, Watertown, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Michael Marconi
- Department of Molecular Pathology, Massachusetts General Hospital, Boston, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Christopher Dejesus
- Atalanta Therapeutics, Boston, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Suzanne Bruhn
- Charcot-Marie-Tooth Association, Glenolden, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Thomas A Miller
- Walden Biosciences, Cambridge, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Barbara Tate
- FARA, Homestead, USA
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA
| | - Jonathan M Levenson
- FireCyte Therapeutics, Beverly, USA.
- Tiaki Therapeutics, Inc., c/o Dementia Discovery Fund, 201 Washington Street, 39th Floor, Boston, MA, 02108, USA.
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5
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Shamir A, Yitzhaky A, Segev A, Haroutunian V, Katsel P, Hertzberg L. Up-Regulation of S100 Gene Family in Brain Samples of a Subgroup of Individuals with Schizophrenia: Meta-analysis. Neuromolecular Med 2023; 25:388-401. [PMID: 37005977 DOI: 10.1007/s12017-023-08743-4] [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: 12/01/2022] [Accepted: 03/12/2023] [Indexed: 04/04/2023]
Abstract
The S100 proteins family is known to affect neuroinflammation and astrocyte activation, which have been suggested to be contributors to the pathogenesis of schizophrenia. We conducted a systematic meta-analysis of S100 genes differential expression in postmortem samples of patients with schizophrenia vs. healthy controls, following the commonly used Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Twelve microarray datasets met the inclusion criteria (overall 511 samples, 253 schizophrenia and 258 controls were analyzed). Nine out of 21 genes were significantly up-regulated or with tendency for up-regulation. A per-sample fold change analysis indicated that the S100 genes' up-regulation was concentrated in a subgroup of the patients. None of the genes have been found to be down-regulated. ANXA3, which encodes Annexin 3 protein and was associated with neuroinflammation, was up-regulated and positively correlated with the S100 genes' expression pattern. In addition, astrocytes and endothelial cell markers were significantly correlated with S100A8 expression. S100 correlation with ANXA3 and endothelial cell markers suggests that the up-regulation we detected reflects increased inflammation. However, it might also reflect astrocytes abundance or activation. The fact that S100 proteins were shown to be up-regulated in blood samples and other body fluids of patients with schizophrenia suggests a potential role as biomarkers, which might help disease subtyping, and the development of etiological treatments for immune dysregulation in schizophrenia.
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Affiliation(s)
- Anat Shamir
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Aviv Segev
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
- Shalvata Mental Health Center, 13 Aliat Hanoar St, 45100, Hod Hasharon, Israel
| | - Vahram Haroutunian
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry (MIRECC), James J Peters VA Medical Center, Bronx, NY, USA
| | - Pavel Katsel
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Libi Hertzberg
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel.
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
- Shalvata Mental Health Center, 13 Aliat Hanoar St, 45100, Hod Hasharon, Israel.
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6
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Mekiten O, Yitzhaky A, Gould N, Rosenblum K, Hertzberg L. Ribosome subunits are upregulated in brain samples of a subgroup of individuals with schizophrenia: A systematic gene expression meta-analysis. J Psychiatr Res 2023; 164:372-381. [PMID: 37413782 DOI: 10.1016/j.jpsychires.2023.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023]
Abstract
One of the new theories accounting for the underlying pathophysiology of schizophrenia is excitation/inhibition imbalance. Interestingly, perturbation in protein synthesis machinery as well as oxidative stress can lead to excitation/inhibition imbalance. We thus performed a systematic meta-analysis of the expression of 79 ribosome subunit genes and two oxidative-stress related genes, HIF1A and NQO1, in brain samples of individuals with schizophrenia vs. healthy controls. We integrated 12 gene expression datasets, following the PRISMA guidelines (overall 511 samples, 253 schizophrenia and 258 controls). Five ribosome subunit genes were significantly upregulated in a subgroup of the patients with schizophrenia, while 24 (30%) showed a tendency for upregulation. HIF1A and NQO1 were also found to be significantly upregulated. Moreover, HIF1A and NQO1 showed positive correlation with the expression of the upregulated ribosome subunit genes. Our results, together with previous findings, suggest a possible role for altered mRNA translation in the pathogenesis of schizophrenia, in association with markers of increased oxidative stress in a subgroup of patients. Further studies should define whether the upregulation of ribosome subunits result in altered mRNA translation, which proteins are modulated and how it characterizes a subgroup of the patients with schizophrenia.
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Affiliation(s)
- Ori Mekiten
- Faculty of Medicine, Tel-Aviv University, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Nathaniel Gould
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Kobi Rosenblum
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel; Center for Gene Manipulation in the Brain, University of Haifa, Haifa, Israel
| | - Libi Hertzberg
- Faculty of Medicine, Tel-Aviv University, Israel; Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel; Shalvata Mental Health Center, Israel.
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7
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Miyahara K, Hino M, Shishido R, Nagaoka A, Izumi R, Hayashi H, Kakita A, Yabe H, Tomita H, Kunii Y. Identification of schizophrenia symptom-related gene modules by postmortem brain transcriptome analysis. Transl Psychiatry 2023; 13:144. [PMID: 37142572 PMCID: PMC10160042 DOI: 10.1038/s41398-023-02449-8] [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: 01/13/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Schizophrenia is a multifactorial disorder, the genetic architecture of which remains unclear. Although many studies have examined the etiology of schizophrenia, the gene sets that contribute to its symptoms have not been fully investigated. In this study, we aimed to identify each gene set associated with corresponding symptoms of schizophrenia using the postmortem brains of 26 patients with schizophrenia and 51 controls. We classified genes expressed in the prefrontal cortex (analyzed by RNA-seq) into several modules by weighted gene co-expression network analysis (WGCNA) and examined the correlation between module expression and clinical characteristics. In addition, we calculated the polygenic risk score (PRS) for schizophrenia from Japanese genome-wide association studies, and investigated the association between the identified gene modules and PRS to evaluate whether genetic background affected gene expression. Finally, we conducted pathway analysis and upstream analysis using Ingenuity Pathway Analysis to clarify the functions and upstream regulators of symptom-related gene modules. As a result, three gene modules generated by WGCNA were significantly correlated with clinical characteristics, and one of these showed a significant association with PRS. Genes belonging to the transcriptional module associated with PRS significantly overlapped with signaling pathways of multiple sclerosis, neuroinflammation, and opioid use, suggesting that these pathways may also be profoundly implicated in schizophrenia. Upstream analysis indicated that genes in the detected module were profoundly regulated by lipopolysaccharides and CREB. This study identified schizophrenia symptom-related gene sets and their upstream regulators, revealing aspects of the pathophysiology of schizophrenia and identifying potential therapeutic targets.
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Affiliation(s)
- Kazusa Miyahara
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Mizuki Hino
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Risa Shishido
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Ryuta Izumi
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hideki Hayashi
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Tohoku University Hospital, Miyagi, Japan
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Miyagi, Japan
| | - Yasuto Kunii
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan.
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8
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Vera-Montecinos A, Rodríguez-Mias R, Vila È, Villén J, Ramos B. Analysis of networks in the dorsolateral prefrontal cortex in chronic schizophrenia: Relevance of altered immune response. Front Pharmacol 2023; 14:1003557. [PMID: 37033658 PMCID: PMC10076656 DOI: 10.3389/fphar.2023.1003557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
The dorsolateral prefrontal cortex (DLPFC) has a crucial role in cognitive functioning and negative symptoms in schizophrenia. However, limited information of altered protein networks is available in this region in schizophrenia. We performed a proteomic analysis using single-shot liquid chromatography-tandem mass spectrometry of grey matter of postmortem DLPFC in chronic schizophrenia subjects (n = 20) and unaffected subjects (n = 20) followed by bioinformatic analysis to identify altered protein networks in schizophrenia (PXD024939 identifier in ProteomeXchange repository). Our results displayed a proteome profile in the DLPFC of 1989 proteins. 43 proteins were found significantly altered in schizophrenia. Analysis of this panel showed an enrichment of biological processes implicated in vesicle-mediated transport, processing and antigen presentation via MHC class II, intracellular transport and selenium metabolism. The enriched identified pathways were MHC class II antigen presentation, vesicle-mediated transport, Golgi ER retrograde transport, Nef mediated CD8 downregulation and the immune system. All these enriched categories were found to be downregulated. Furthermore, our network analyses showed crosstalk between proteins involved in MHC class II antigen presentation, membrane trafficking, Golgi-to-ER retrograde transport, Nef-mediated CD8 downregulation and the immune system with only one module built by 13 proteins. RAB7A showed eight interactions with proteins of all these pathways. Our results provide an altered molecular network involved in immune response in the DLPFC in schizophrenia with a central role of RAB7A. These results suggest that RAB7A or other proteins of this network could be potential targets for novel pharmacological strategies in schizophrenia for improving cognitive and negative symptoms.
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Affiliation(s)
- América Vera-Montecinos
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Sant Boi de Llobregat, Spain
| | - Ricard Rodríguez-Mias
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA, United States
| | - Èlia Vila
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Sant Boi de Llobregat, Spain
| | - Judit Villén
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA, United States
| | - Belén Ramos
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Sant Boi de Llobregat, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM (Biomedical Network Research Center of Mental Health), Ministry of Economy, Industry and Competitiveness, Institute of Health Carlos III, Madrid, Spain
- Department de Bioquímica i Biología Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Facultat de Medicina, Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
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9
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Segev S, Yitzhaky A, Ben Shachar D, Hertzberg L. VDAC genes down-regulation in brain samples of individuals with schizophrenia is revealed by a systematic meta-analysis. Neurosci Res 2023:S0168-0102(23)00022-6. [PMID: 36717018 DOI: 10.1016/j.neures.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 01/29/2023]
Abstract
Mitochondrial dysfunction was shown to be involved in schizophrenia pathophysiology. Abnormal energy states can lead to alterations in neural function and thereby to the cognitive and behavioral aberrations characteristics of schizophrenia. Voltage-dependent anion-selective channels (VDAC) are located in the outer mitochondrial membrane and are involved in mitochondrial energy production. Only few studies explored VDAC genes' expression in schizophrenia, and their results were not consistent. We conducted a systematic meta-analysis of ten brain samples gene expression datasets (overall 368 samples, 179 schizophrenia, 189 controls). In addition, we conducted a meta-analysis of three blood samples datasets (overall 300 samples, 167 schizophrenia, 133 controls). Pairwise correlation analysis was conducted between the VDAC and proteasome subunit genes' expression patterns. VDAC1, VDAC2 and VDAC3 showed significant down-regulation in brain samples of patients with schizophrenia. They also showed significant positive correlations with the proteasome subunit genes' expression levels. Our findings suggest that VDAC genes might play a role in mitochondrial dysfunction in schizophrenia. VDAC1 was down-regulated also in blood samples, which suggests its potential role as a biomarker for schizophrenia. The correlation with proteasome subunits, which were previously shown to be down-regulated in a subgroup of the patients, suggests that our findings might characterize a subgroup of the patients. This direction has the potential to lead to patients' stratification and more precisely-targeted therapy and necessitates further study.
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Affiliation(s)
- Shaked Segev
- Sackler School of Medicine, Tel-Aviv University, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Dorit Ben Shachar
- Psychobiology Research Lab, Department of Neuroscience, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Israel
| | - Libi Hertzberg
- Sackler School of Medicine, Tel-Aviv University, Israel; Shalvata Mental Health Center, Israel; Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
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10
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Shriebman Y, Yitzhaky A, Kosloff M, Hertzberg L. Gene expression meta-analysis in patients with schizophrenia reveals up-regulation of RGS2 and RGS16 in Brodmann Area 10. Eur J Neurosci 2023; 57:360-372. [PMID: 36443250 DOI: 10.1111/ejn.15876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/10/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022]
Abstract
Regulator of G-protein signalling (RGS) proteins inhibit signalling by G-protein-coupled receptors (GPCRs). GPCRs mediate the functions of several important neurotransmitters and serve as targets of many anti-psychotics. RGS2, RGS4, RGS5 and RGS16 are located on chromosome 1q23.3-31, a locus found to be associated with schizophrenia. Although previous gene expression analysis detected down-regulation of RGS4 expression in brain samples of patients with schizophrenia, the results were not consistent. In the present study, we performed a systematic meta-analysis of differential RGS2, RGS4, RGS5 and RGS16 expression in Brodmann Area 10 (BA10) samples of patients with schizophrenia and from healthy controls. Two microarray datasets met the inclusion criteria (overall, 41 schizophrenia samples and 38 controls were analysed). RGS2 and RGS16 were found to be up-regulated in BA10 samples of individuals with schizophrenia, whereas no differential expression of RGS4 and RGS5 was detected. Analysis of dorso-lateral prefrontal cortex samples of the CommonMind Consortium (258 schizophrenia samples vs. 279 controls) further validated the results. Given their central role in inactivating G-protein-coupled signalling pathways, our results suggest that differential gene expression might lead to enhanced inactivation of G-protein signalling in schizophrenia. This, in turn, suggests that additional studies are needed to further explore the consequences of the differential expression we detected, this time at the protein and functional levels.
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Affiliation(s)
- Yaen Shriebman
- Shalvata Mental Health Center, affiliated with the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Mickey Kosloff
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Libi Hertzberg
- Shalvata Mental Health Center, affiliated with the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
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11
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Zhao Q, Cao H, Zhang W, Li S, Xiao Y, Tamminga CA, Keshavan MS, Pearlson GD, Clementz BA, Gershon ES, Hill SK, Keedy SK, Ivleva EI, Lencer R, Sweeney JA, Gong Q, Lui S. A subtype of institutionalized patients with schizophrenia characterized by pronounced subcortical and cognitive deficits. Neuropsychopharmacology 2022; 47:2024-2032. [PMID: 35260788 PMCID: PMC9556672 DOI: 10.1038/s41386-022-01300-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/28/2022] [Accepted: 02/19/2022] [Indexed: 02/05/2023]
Abstract
Some patients with schizophrenia have severe cognitive impairment and functional deficits that require long-term institutional care. The patterns of brain-behavior alterations in these individuals, and their differences from patients living successfully in the community, remain poorly understood. Previous cognition-based studies for stratifying schizophrenia patients highlight the importance of subcortical structures in the context of illness heterogeneity. In the present study, subcortical volumes from 96 institutionalized patients with long-term schizophrenia were evaluated using cluster analysis to test for heterogeneity. These data were compared to those from two groups of community-dwelling individuals with schizophrenia for comparison purposes, including 68 long-term ill and 126 first-episode individuals. A total of 290 demographically matched healthy participants were included as normative references at a 1:1 ratio for each patient sample. A subtype of institutionalized patients was identified based on their pattern of subcortical alterations. Using a machine learning algorithm developed to discriminate the two groups of institutionalized patients, all three patient samples were found to have similar rates of patients assigned to the two subtypes (approximately 50% each). In institutionalized patients, only the subtype with the identified pattern of subcortical alterations had greater neocortical and cognitive abnormalities than those in the similarity classified community-dwelling patients with long-term illness. Thus, for the subtype of patients with a distinctive pattern of subcortical alterations, when the distinct pattern of subcortical alterations is present and particularly severe, it is associated with cognitive impairments that may contribute to persistent disability and institutionalization.
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Affiliation(s)
- Qiannan Zhao
- Huaxi MR Research Center, Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
- Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, Sichuan Province, China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Hengyi Cao
- Huaxi MR Research Center, Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY, USA
| | - Wenjing Zhang
- Huaxi MR Research Center, Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
- Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, Sichuan Province, China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Siyi Li
- Huaxi MR Research Center, Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
- Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, Sichuan Province, China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Yuan Xiao
- Huaxi MR Research Center, Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
- Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, Sichuan Province, China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Matcheri S Keshavan
- Department of Psychiatry, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Godfrey D Pearlson
- Departments of Psychiatry and Neurobiology, Yale University and Olin Neuropsychiatric Research Center, Hartford, CT, USA
| | - Brett A Clementz
- Department of Psychology, University of Georgia, Athens, GA, USA
| | - Elliot S Gershon
- Department of Psychiatry, University of Chicago, Chicago, IL, USA
| | - Scot Kristian Hill
- Department of Psychology, Rosalind Franklin University of Medicine and Science, Chicago, IL, USA
| | - Sarah K Keedy
- Department of Psychiatry, University of Chicago, Chicago, IL, USA
| | - Elena I Ivleva
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rebekka Lencer
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - John A Sweeney
- Huaxi MR Research Center, Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Qiyong Gong
- Huaxi MR Research Center, Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China.
- Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, Sichuan Province, China.
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China.
| | - Su Lui
- Huaxi MR Research Center, Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China.
- Research Unit of Psychoradiology, Chinese Academy of Medical Sciences, Chengdu, Sichuan Province, China.
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China.
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12
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Batiuk MY, Tyler T, Dragicevic K, Mei S, Rydbirk R, Petukhov V, Deviatiiarov R, Sedmak D, Frank E, Feher V, Habek N, Hu Q, Igolkina A, Roszik L, Pfisterer U, Garcia-Gonzalez D, Petanjek Z, Adorjan I, Kharchenko PV, Khodosevich K. Upper cortical layer-driven network impairment in schizophrenia. SCIENCE ADVANCES 2022; 8:eabn8367. [PMID: 36223459 PMCID: PMC9555788 DOI: 10.1126/sciadv.abn8367] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/24/2022] [Indexed: 05/31/2023]
Abstract
Schizophrenia is one of the most widespread and complex mental disorders. To characterize the impact of schizophrenia, we performed single-nucleus RNA sequencing (snRNA-seq) of >220,000 neurons from the dorsolateral prefrontal cortex of patients with schizophrenia and matched controls. In addition, >115,000 neurons were analyzed topographically by immunohistochemistry. Compositional analysis of snRNA-seq data revealed a reduction in abundance of GABAergic neurons and a concomitant increase in principal neurons, most pronounced for upper cortical layer subtypes, which was substantiated by histological analysis. Many neuronal subtypes showed extensive transcriptomic changes, the most marked in upper-layer GABAergic neurons, including down-regulation in energy metabolism and up-regulation in neurotransmission. Transcription factor network analysis demonstrated a developmental origin of transcriptomic changes. Last, Visium spatial transcriptomics further corroborated upper-layer neuron vulnerability in schizophrenia. Overall, our results point toward general network impairment within upper cortical layers as a core substrate associated with schizophrenia symptomatology.
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Affiliation(s)
- Mykhailo Y. Batiuk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Teadora Tyler
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Katarina Dragicevic
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shenglin Mei
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Rasmus Rydbirk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Viktor Petukhov
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ruslan Deviatiiarov
- The National Center for Personalized Medicine of Endocrine Diseases, Moscow 115478, Russia
- Kazan Federal University, Kazan 420043, Russia
| | - Dora Sedmak
- Croatian Institute for Brain Research and Center of Excellence for Basic, Clinical and Translational Neuroscience, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Erzsebet Frank
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Virginia Feher
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Nikola Habek
- Croatian Institute for Brain Research and Center of Excellence for Basic, Clinical and Translational Neuroscience, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Igolkina
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- St. Petersburg Polytechnical University, St. Petersburg 195251, Russia
| | - Lilla Roszik
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Diego Garcia-Gonzalez
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Zdravko Petanjek
- Croatian Institute for Brain Research and Center of Excellence for Basic, Clinical and Translational Neuroscience, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Istvan Adorjan
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Peter V. Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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13
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Almodóvar-Payá C, Guardiola-Ripoll M, Giralt-López M, Gallego C, Salgado-Pineda P, Miret S, Salvador R, Muñoz MJ, Lázaro L, Guerrero-Pedraza A, Parellada M, Carrión MI, Cuesta MJ, Maristany T, Sarró S, Fañanás L, Callado LF, Arias B, Pomarol-Clotet E, Fatjó-Vilas M. NRN1 Gene as a Potential Marker of Early-Onset Schizophrenia: Evidence from Genetic and Neuroimaging Approaches. Int J Mol Sci 2022; 23:ijms23137456. [PMID: 35806464 PMCID: PMC9267632 DOI: 10.3390/ijms23137456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 12/10/2022] Open
Abstract
Included in the neurotrophins family, the Neuritin 1 gene (NRN1) has emerged as an attractive candidate gene for schizophrenia (SZ) since it has been associated with the risk for the disorder and general cognitive performance. In this work, we aimed to further investigate the association of NRN1 with SZ by exploring its role on age at onset and its brain activity correlates. First, we developed two genetic association analyses using a family-based sample (80 early-onset (EO) trios (offspring onset ≤ 18 years) and 71 adult-onset (AO) trios) and an independent case–control sample (120 healthy subjects (HS), 87 EO and 138 AO patients). Second, we explored the effect of NRN1 on brain activity during a working memory task (N-back task; 39 HS, 39 EO and 39 AO; matched by age, sex and estimated IQ). Different haplotypes encompassing the same three Single Nucleotide Polymorphisms(SNPs, rs3763180–rs10484320–rs4960155) were associated with EO in the two samples (GCT, TCC and GTT). Besides, the GTT haplotype was associated with worse N-back task performance in EO and was linked to an inefficient dorsolateral prefrontal cortex activity in subjects with EO compared to HS. Our results show convergent evidence on the NRN1 association with EO both from genetic and neuroimaging approaches, highlighting the role of neurotrophins in the pathophysiology of SZ.
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Affiliation(s)
- Carmen Almodóvar-Payá
- FIDMAG Germanes Hospitalàries Research Foundation, 08830 Sant Boi de Llobregat, Barcelona, Spain; (C.A.-P.); (M.G.-R.); (P.S.-P.); (R.S.); (A.G.-P.); (S.S.)
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
| | - Maria Guardiola-Ripoll
- FIDMAG Germanes Hospitalàries Research Foundation, 08830 Sant Boi de Llobregat, Barcelona, Spain; (C.A.-P.); (M.G.-R.); (P.S.-P.); (R.S.); (A.G.-P.); (S.S.)
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
| | - Maria Giralt-López
- Departament de Psiquiatria, Hospital Universitari Germans Trias i Pujol (HUGTP), 08916 Badalona, Barcelona, Spain;
- Departament de Psiquiatria i Medicina Legal, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Carme Gallego
- Department of Cell Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Barcelona, Spain;
| | - Pilar Salgado-Pineda
- FIDMAG Germanes Hospitalàries Research Foundation, 08830 Sant Boi de Llobregat, Barcelona, Spain; (C.A.-P.); (M.G.-R.); (P.S.-P.); (R.S.); (A.G.-P.); (S.S.)
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
| | - Salvador Miret
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
- Centre de Salut Mental d’Adults de Lleida, Servei de Psiquiatria, Salut Mental i Addiccions, Hospital Universitari Santa Maria de Lleida, 25198 Lleida, Lleida, Spain
- Institut de Recerca Biomèdica (IRB), 25198 Lleida, Lleida, Spain
| | - Raymond Salvador
- FIDMAG Germanes Hospitalàries Research Foundation, 08830 Sant Boi de Llobregat, Barcelona, Spain; (C.A.-P.); (M.G.-R.); (P.S.-P.); (R.S.); (A.G.-P.); (S.S.)
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
| | - María J. Muñoz
- Complex Assistencial en Salut Mental Benito Menni, 08830 Sant Boi de Llobregat, Barcelona, Spain;
| | - Luisa Lázaro
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic de Barcelona, 08036 Barcelona, Barcelona, Spain
- Departament de Medicina, Universitat de Barcelona (UB), 08036 Barcelona, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Barcelona, Spain
| | - Amalia Guerrero-Pedraza
- FIDMAG Germanes Hospitalàries Research Foundation, 08830 Sant Boi de Llobregat, Barcelona, Spain; (C.A.-P.); (M.G.-R.); (P.S.-P.); (R.S.); (A.G.-P.); (S.S.)
- Complex Assistencial en Salut Mental Benito Menni, 08830 Sant Boi de Llobregat, Barcelona, Spain;
| | - Mara Parellada
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
- Servicio de Psiquiatría del Niño y del Adolescente, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Gregorio Marañón (IiSGM), 28007 Madrid, Madrid, Spain
- Departamento de Psiquiatría, Facultad de Medicina, Universidad Complutense, 28040 Madrid, Madrid, Spain
| | | | - Manuel J. Cuesta
- Servicio de Psiquiatría, Hospital Universitario de Navarra, 31008 Pamplona, Navarra, Spain;
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), 31008 Pamplona, Navarra, Spain
| | - Teresa Maristany
- Departament de Diagnòstic per la Imatge, Hospital Sant Joan de Déu Fundació de Recerca, 08950 Esplugues de Llobregat, Barcelona, Spain;
| | - Salvador Sarró
- FIDMAG Germanes Hospitalàries Research Foundation, 08830 Sant Boi de Llobregat, Barcelona, Spain; (C.A.-P.); (M.G.-R.); (P.S.-P.); (R.S.); (A.G.-P.); (S.S.)
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
| | - Lourdes Fañanás
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
- Departament de Biologia Evolutiva, Ecología i Ciències Ambientals, Universitat de Barcelona (UB), 08028 Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Barcelona, Spain
| | - Luis F. Callado
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
- Department of Pharmacology, University of the Basque Country, UPV/EHU, 48940 Leioa, Bizkaia, Spain
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Bárbara Arias
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
- Departament de Biologia Evolutiva, Ecología i Ciències Ambientals, Universitat de Barcelona (UB), 08028 Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Barcelona, Spain
| | - Edith Pomarol-Clotet
- FIDMAG Germanes Hospitalàries Research Foundation, 08830 Sant Boi de Llobregat, Barcelona, Spain; (C.A.-P.); (M.G.-R.); (P.S.-P.); (R.S.); (A.G.-P.); (S.S.)
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
- Correspondence: (E.P.-C.); (M.F.-V.)
| | - Mar Fatjó-Vilas
- FIDMAG Germanes Hospitalàries Research Foundation, 08830 Sant Boi de Llobregat, Barcelona, Spain; (C.A.-P.); (M.G.-R.); (P.S.-P.); (R.S.); (A.G.-P.); (S.S.)
- Instituto de Salud Carlos III, Biomedical Research Network in Mental Health (CIBERSAM), 28029 Madrid, Madrid, Spain; (S.M.); (L.L.); (M.P.); (L.F.); (L.F.C.); (B.A.)
- Departament de Biologia Evolutiva, Ecología i Ciències Ambientals, Universitat de Barcelona (UB), 08028 Barcelona, Barcelona, Spain
- Correspondence: (E.P.-C.); (M.F.-V.)
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14
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Childers E, Bowen EFW, Rhodes CH, Granger R. Immune-Related Genomic Schizophrenic Subtyping Identified in DLPFC Transcriptome. Genes (Basel) 2022; 13:genes13071200. [PMID: 35885983 PMCID: PMC9319783 DOI: 10.3390/genes13071200] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/26/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Well-documented evidence of the physiologic, genetic, and behavioral heterogeneity of schizophrenia suggests that diagnostic subtyping may clarify the underlying pathobiology of the disorder. Recent studies have demonstrated that increased inflammation may be a prominent feature of a subset of schizophrenics. However, these findings are inconsistent, possibly due to evaluating schizophrenics as a single group. In this study, we segregated schizophrenic patients into two groups (“Type 1”, “Type 2”) by their gene expression in the dorsolateral prefrontal cortex and explored biological differences between the subgroups. The study included post-mortem tissue samples that were sequenced in multiple, publicly available gene datasets using different sequencing methods. To evaluate the role of inflammation, the expression of genes in multiple components of neuroinflammation were examined: complement cascade activation, glial cell activation, pro-inflammatory mediator secretion, blood–brain barrier (BBB) breakdown, chemokine production and peripheral immune cell infiltration. The Type 2 schizophrenics showed widespread abnormal gene expression across all the neuroinflammation components that was not observed in Type 1 schizophrenics. Our results demonstrate the importance of separating schizophrenic patients into their molecularly defined subgroups and provide supporting evidence for the involvement of the immune-related pathways in a schizophrenic subset.
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Affiliation(s)
- Eva Childers
- Dartmouth College, Hanover, NH 03755, USA; (E.C.); (E.F.W.B.)
| | | | | | - Richard Granger
- Dartmouth College, Hanover, NH 03755, USA; (E.C.); (E.F.W.B.)
- Correspondence:
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15
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Going deep into schizophrenia with artificial intelligence. Schizophr Res 2022; 245:122-140. [PMID: 34103242 DOI: 10.1016/j.schres.2021.05.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/30/2022]
Abstract
Despite years of research, the mechanisms governing the onset, relapse, symptomatology, and treatment of schizophrenia (SZ) remain elusive. The lack of appropriate analytic tools to deal with the heterogeneity and complexity of SZ may be one of the reasons behind this situation. Deep learning, a subfield of artificial intelligence (AI) inspired by the nervous system, has recently provided an accessible way of modeling and analyzing complex, high-dimensional, nonlinear systems. The unprecedented accuracy of deep learning algorithms in classification and prediction tasks has revolutionized a wide range of scientific fields and is rapidly permeating SZ research. Deep learning has the potential of becoming a valuable aid for clinicians in the prediction, diagnosis, and treatment of SZ, especially in combination with principles from Bayesian statistics. Furthermore, deep learning could become a powerful tool for uncovering the mechanisms underlying SZ thanks to a growing number of techniques designed for improving model interpretability and causal reasoning. The purpose of this article is to introduce SZ researchers to the field of deep learning and review its latest applications in SZ research. In general, existing studies have yielded impressive results in classification and outcome prediction tasks. However, methodological concerns related to the assessment of model performance in several studies, the widespread use of small training datasets, and the little clinical value of some models suggest that some of these results should be taken with caution.
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16
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Chand GB, Jiang H, Miller JP, Rhodes CH, Tu Z, Wong DF. Differential Sphingosine-1-Phosphate Receptor-1 Protein Expression in the Dorsolateral Prefrontal Cortex Between Schizophrenia Type 1 and Type 2. Front Psychiatry 2022; 13:827981. [PMID: 35350429 PMCID: PMC8957823 DOI: 10.3389/fpsyt.2022.827981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/03/2022] [Indexed: 11/25/2022] Open
Abstract
Understanding the etiology and treatment approaches in schizophrenia is challenged in part by the heterogeneity of this disorder. One encouraging progress is the growing evidence that there are subtypes of schizophrenia. Recent in vitro findings of messenger ribonucleic acid (mRNA) gene expression on postmortem dorsolateral prefrontal cortex (DLPFC) showed that schizophrenia has two subtypes, those with a relatively normal DLPFC transcriptome (Type 1) and those with differentially expressed genes (Type 2). Sphingosine-1-phosphate receptor-1 (S1PR1) is one of the genes that was highly upregulated in Type 2 compared to Type 1 and controls. The impact of that finding is limited because it only can be confirmed through analysis of autopsy tissue, and the clinical characteristics such as symptoms severity or illness duration except for cause of death was not available from that Medical Examiner based autopsy study. However, S1PR1 has great potential because it is a target gene that can be accessed via positron emission tomography (PET) in vivo using specific radioligands (starting with [11C]CS1P1) successfully developed at our center in human brain imaging. As a preliminary study to validate this PET target in schizophrenia, S1PR1 protein expression was assessed by receptor autoradiography (ARG) using [3H]CS1P1 and immunohistochemistry (IHC) in the DLPFC from patients with schizophrenia classified as Type 1 or Type 2 based on their DLPFC transcriptomes and from controls. Our analyses demonstrate that ARG S1PR1 protein expression is significantly higher in Type 2 compared to Type 1 (p < 0.05) and controls (p < 0.05), which was consistent with previous mRNA S1PR1. These findings support the possibility that PET S1PR1 can be used as a future imaging biomarker to distinguish these subgroups of schizophrenic patients during life with obvious implications for both patient management and the design of clinical trials to validate novel pharmacologic therapies.
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Affiliation(s)
- Ganesh B. Chand
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Hao Jiang
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, United States
| | - J. Philip Miller
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
| | | | - Zhude Tu
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Dean Foster Wong
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, United States
- Department of Psychiatry, Neuroscience, and Neurology, Washington University School of Medicine, St. Louis, MO, United States
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Gao Y, Li Y, Li S, Liang X, Ren Z, Yang X, Zhang B, Hu Y, Yang X. Systematic discovery of signaling pathways linking immune activation to schizophrenia. iScience 2021; 24:103209. [PMID: 34746692 PMCID: PMC8551081 DOI: 10.1016/j.isci.2021.103209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/21/2021] [Accepted: 09/29/2021] [Indexed: 11/06/2022] Open
Abstract
Immune activation has been shown to play a critical role in the development of schizophrenia; however its underlying mechanism remains unknown. Our report demonstrates a high-quality protein interaction network for schizophrenia (SCZ Network), constructed using our “neighborhood walk” approach in combination with “random walk with restart”. The spatiotemporal expression pattern of the genes in this disease network revealed two developmental stages sensitive to perturbation by immune activation: mid-to late gestation, and adolescence. Furthermore, we induced immune activation at these stages in mice, carried out transcriptome sequencing on the mouse brains, and illustrated clear potential molecular pathways and key regulators correlating maternal immune activation during gestation and an increased risk for schizophrenia after a second immune activation at puberty. This work provides not only valuable resources for the study on molecular mechanisms underlying schizophrenia, but also a systematic strategy for the discovery of molecular pathways of complex mental disorders. A high-quality molecular network for schizophrenia (SCZ Network) A landscape of molecular pathways linking immune activation and schizophrenia The spatiotemporal network dynamics revealing stages susceptible to immune activation Identification of the molecular pathways and regulators in the immune-activated brain
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Affiliation(s)
- Yue Gao
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence and Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yanjun Li
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence and Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - ShuangYan Li
- Department of Psychiatry, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaozhen Liang
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhonglu Ren
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xiaoxue Yang
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Bin Zhang
- Department of Psychiatry, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xinping Yang
- Center for Genetics and Developmental Systems Biology, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence and Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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Hertzberg L, Maggio N, Muler I, Yitzhaky A, Majer M, Haroutunian V, Zuk O, Katsel P, Domany E, Weiser M. Comprehensive Gene Expression Analysis Detects Global Reduction of Proteasome Subunits in Schizophrenia. Schizophr Bull 2021; 47:785-795. [PMID: 33141894 PMCID: PMC8084431 DOI: 10.1093/schbul/sbaa160] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND The main challenge in the study of schizophrenia is its high heterogeneity. While it is generally accepted that there exist several biological mechanisms that may define distinct schizophrenia subtypes, they have not been identified yet. We performed comprehensive gene expression analysis to search for molecular signals that differentiate schizophrenia patients from healthy controls and examined whether an identified signal was concentrated in a subgroup of the patients. METHODS Transcriptome sequencing of 14 superior temporal gyrus (STG) samples of subjects with schizophrenia and 15 matched controls from the Stanley Medical Research Institute (SMRI) was performed. Differential expression and pathway enrichment analysis results were compared to an independent cohort. Replicability was tested on 6 additional independent datasets. RESULTS The 2 STG cohorts showed high replicability. Pathway enrichment analysis of the down-regulated genes pointed to proteasome-related pathways. Meta-analysis of differential expression identified down-regulation of 12 of 39 proteasome subunit genes in schizophrenia. The signal of proteasome subunits down-regulation was replicated in 6 additional datasets (overall 8 cohorts with 267 schizophrenia and 266 control samples, from 5 brain regions). The signal was concentrated in a subgroup of patients with schizophrenia. CONCLUSIONS We detected global down-regulation of proteasome subunits in a subgroup of patients with schizophrenia. We hypothesize that the down-regulation of proteasome subunits leads to proteasome dysfunction that causes accumulation of ubiquitinated proteins, which has been recently detected in a subgroup of schizophrenia patients. Thus, down-regulation of proteasome subunits might define a biological subtype of schizophrenia.
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Affiliation(s)
- Libi Hertzberg
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
- Shalvata Mental Health Center, Affiliated to the Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nicola Maggio
- Department of Neurology, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Department of Neurology and Neurosurgery, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Inna Muler
- Childhood Leukemia Research Institute and the Department of Pediatric Hemato-Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Majer
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, The Mount Sinai School of Medicine, New York, NY
- Department of Psychiatry, James J Peters VA Medical Center, Bronx, NY
| | - Or Zuk
- Department of Statistics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Pavel Katsel
- Departments of Psychiatry and Neuroscience, The Mount Sinai School of Medicine, New York, NY
| | - Eytan Domany
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Mark Weiser
- Department of Psychiatry, Chaim Sheba Medical Center, Ramat-Gan and the Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
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19
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Afridi R, Seol S, Kang HJ, Suk K. Brain-immune interactions in neuropsychiatric disorders: Lessons from transcriptome studies for molecular targeting. Biochem Pharmacol 2021; 188:114532. [PMID: 33773976 DOI: 10.1016/j.bcp.2021.114532] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022]
Abstract
Understanding the pathophysiological mechanisms of neuropsychiatric disorders has been a challenging quest for neurobiologists. Recent years have witnessed enormous technological advances in the field of neuroimmunology, blurring boundaries between the central nervous system and the periphery. Consequently, the discipline has expanded to cover interactions between the nervous and immune systems in health and diseases. The complex interplay between the peripheral and central immune pathways in neuropsychiatric disorders has recently been documented in various studies, but the genetic determinants remain elusive. Recent transcriptome studies have identified dysregulated genes involved in peripheral immune cell activation, blood-brain barrier integrity, glial cell activation, and synaptic plasticity in major depressive disorder, bipolar disorder, autism spectrum disorder, and schizophrenia. Herein, the key transcriptomic techniques applied in investigating differentially expressed genes and pathways responsible for altered brain-immune interactions in neuropsychiatric disorders are discussed. The application of transcriptomics that can aid in identifying molecular targets in various neuropsychiatric disorders is highlighted.
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Affiliation(s)
- Ruqayya Afridi
- Department of Pharmacology, Brain Science & Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sihwan Seol
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hyo Jung Kang
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea.
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science & Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
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20
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Stertz L, Di Re J, Pei G, Fries GR, Mendez E, Li S, Smith-Callahan L, Raventos H, Tipo J, Cherukuru R, Zhao Z, Liu Y, Jia P, Laezza F, Walss-Bass C. Convergent genomic and pharmacological evidence of PI3K/GSK3 signaling alterations in neurons from schizophrenia patients. Neuropsychopharmacology 2021; 46:673-682. [PMID: 33288841 PMCID: PMC8027596 DOI: 10.1038/s41386-020-00924-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
Human-induced pluripotent stem cells (hiPSCs) allow for the establishment of brain cellular models of psychiatric disorders that account for a patient's genetic background. Here, we conducted an RNA-sequencing profiling study of hiPSC-derived cell lines from schizophrenia (SCZ) subjects, most of which are from a multiplex family, from the population isolate of the Central Valley of Costa Rica. hiPSCs, neural precursor cells, and cortical neurons derived from six healthy controls and seven SCZ subjects were generated using standard methodology. Transcriptome from these cells was obtained using Illumina HiSeq 2500, and differential expression analyses were performed using DESeq2 (|fold change|>1.5 and false discovery rate < 0.3), in patients compared to controls. We identified 454 differentially expressed genes in hiPSC-derived neurons, enriched in pathways including phosphoinositide 3-kinase/glycogen synthase kinase 3 (PI3K/GSK3) signaling, with serum-glucocorticoid kinase 1 (SGK1), an inhibitor of glycogen synthase kinase 3β, as part of this pathway. We further found that pharmacological inhibition of downstream effectors of the PI3K/GSK3 pathway, SGK1 and GSK3, induced alterations in levels of neurite markers βIII tubulin and fibroblast growth factor 12, with differential effects in patients compared to controls. While demonstrating the utility of hiPSCs derived from multiplex families to identify significant cell-specific gene network alterations in SCZ, these studies support a role for disruption of PI3K/GSK3 signaling as a risk factor for SCZ.
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Affiliation(s)
- Laura Stertz
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jessica Di Re
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Gabriel R Fries
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Emily Mendez
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Shenglan Li
- Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Laura Smith-Callahan
- Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Henriette Raventos
- Centro de Investigacion en Biologia Celular y Molecular, Universidad de Costa Rica, San Jose, Costa Rica
| | - Jerricho Tipo
- School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Rohan Cherukuru
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Zhongming Zhao
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ying Liu
- Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Fernanda Laezza
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Consuelo Walss-Bass
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
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21
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Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. Transl Psychiatry 2019; 9:256. [PMID: 31624234 PMCID: PMC6797775 DOI: 10.1038/s41398-019-0596-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
Both heritability and environment contribute to risk for schizophrenia. However, the molecular mechanisms of interactions between genetic and non-genetic factors remain unclear. Epigenetic regulation of neuronal genome may be a presumable mechanism in pathogenesis of schizophrenia. Here, we performed analysis of open chromatin landscape of gene promoters in prefrontal cortical (PFC) neurons from schizophrenic patients. We cataloged cell-type-based epigenetic signals of transcriptional start sites (TSS) marked by histone H3-K4 trimethylation (H3K4me3) across the genome in PFC from multiple schizophrenia subjects and age-matched control individuals. One of the top-ranked chromatin alterations was found in the major histocompatibility (MHC) locus on chromosome 6 highlighting the overlap between genetic and epigenetic risk factors in schizophrenia. The chromosome conformation capture (3C) analysis in human brain cells revealed the architecture of multipoint chromatin interactions between the schizophrenia-associated genetic and epigenetic polymorphic sites and distantly located HLA-DRB5 and BTNL2 genes. In addition, schizophrenia-specific chromatin modifications in neurons were particularly prominent for non-coding RNA genes, including an uncharacterized LINC01115 gene and recently identified BNRNA_052780. Notably, protein-coding genes with altered epigenetic state in schizophrenia are enriched for oxidative stress and cell motility pathways. Our results imply the rare individual epigenetic alterations in brain neurons are involved in the pathogenesis of schizophrenia.
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