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Hagihara H, Shoji H, Hattori S, Sala G, Takamiya Y, Tanaka M, Ihara M, Shibutani M, Hatada I, Hori K, Hoshino M, Nakao A, Mori Y, Okabe S, Matsushita M, Urbach A, Katayama Y, Matsumoto A, Nakayama KI, Katori S, Sato T, Iwasato T, Nakamura H, Goshima Y, Raveau M, Tatsukawa T, Yamakawa K, Takahashi N, Kasai H, Inazawa J, Nobuhisa I, Kagawa T, Taga T, Darwish M, Nishizono H, Takao K, Sapkota K, Nakazawa K, Takagi T, Fujisawa H, Sugimura Y, Yamanishi K, Rajagopal L, Hannah ND, Meltzer HY, Yamamoto T, Wakatsuki S, Araki T, Tabuchi K, Numakawa T, Kunugi H, Huang FL, Hayata-Takano A, Hashimoto H, Tamada K, Takumi T, Kasahara T, Kato T, Graef IA, Crabtree GR, Asaoka N, Hatakama H, Kaneko S, Kohno T, Hattori M, Hoshiba Y, Miyake R, Obi-Nagata K, Hayashi-Takagi A, Becker LJ, Yalcin I, Hagino Y, Kotajima-Murakami H, Moriya Y, Ikeda K, Kim H, Kaang BK, Otabi H, Yoshida Y, Toyoda A, Komiyama NH, Grant SGN, Ida-Eto M, Narita M, Matsumoto KI, Okuda-Ashitaka E, Ohmori I, Shimada T, Yamagata K, Ageta H, Tsuchida K, Inokuchi K, Sassa T, Kihara A, Fukasawa M, Usuda N, Katano T, Tanaka T, Yoshihara Y, Igarashi M, Hayashi T, Ishikawa K, Yamamoto S, Nishimura N, Nakada K, Hirotsune S, Egawa K, Higashisaka K, Tsutsumi Y, Nishihara S, Sugo N, Yagi T, Ueno N, Yamamoto T, Kubo Y, Ohashi R, Shiina N, Shimizu K, Higo-Yamamoto S, Oishi K, Mori H, Furuse T, Tamura M, Shirakawa H, Sato DX, Inoue YU, Inoue T, Komine Y, Yamamori T, Sakimura K, Miyakawa T. Large-scale animal model study uncovers altered brain pH and lactate levels as a transdiagnostic endophenotype of neuropsychiatric disorders involving cognitive impairment. eLife 2024; 12:RP89376. [PMID: 38529532 DOI: 10.7554/elife.89376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
Increased levels of lactate, an end-product of glycolysis, have been proposed as a potential surrogate marker for metabolic changes during neuronal excitation. These changes in lactate levels can result in decreased brain pH, which has been implicated in patients with various neuropsychiatric disorders. We previously demonstrated that such alterations are commonly observed in five mouse models of schizophrenia, bipolar disorder, and autism, suggesting a shared endophenotype among these disorders rather than mere artifacts due to medications or agonal state. However, there is still limited research on this phenomenon in animal models, leaving its generality across other disease animal models uncertain. Moreover, the association between changes in brain lactate levels and specific behavioral abnormalities remains unclear. To address these gaps, the International Brain pH Project Consortium investigated brain pH and lactate levels in 109 strains/conditions of 2294 animals with genetic and other experimental manipulations relevant to neuropsychiatric disorders. Systematic analysis revealed that decreased brain pH and increased lactate levels were common features observed in multiple models of depression, epilepsy, Alzheimer's disease, and some additional schizophrenia models. While certain autism models also exhibited decreased pH and increased lactate levels, others showed the opposite pattern, potentially reflecting subpopulations within the autism spectrum. Furthermore, utilizing large-scale behavioral test battery, a multivariate cross-validated prediction analysis demonstrated that poor working memory performance was predominantly associated with increased brain lactate levels. Importantly, this association was confirmed in an independent cohort of animal models. Collectively, these findings suggest that altered brain pH and lactate levels, which could be attributed to dysregulated excitation/inhibition balance, may serve as transdiagnostic endophenotypes of debilitating neuropsychiatric disorders characterized by cognitive impairment, irrespective of their beneficial or detrimental nature.
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Affiliation(s)
- Hideo Hagihara
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Hirotaka Shoji
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Satoko Hattori
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Giovanni Sala
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Yoshihiro Takamiya
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Mika Tanaka
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Masafumi Ihara
- Department of Neurology, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Mihiro Shibutani
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Kei Hori
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Akito Nakao
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masayuki Matsushita
- Department of Molecular Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Anja Urbach
- Department of Neurology, Jena University Hospital, Jena, Germany
| | - Yuta Katayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Shota Katori
- Laboratory of Mammalian Neural Circuits, National Institute of Genetics, Mishima, Japan
| | - Takuya Sato
- Laboratory of Mammalian Neural Circuits, National Institute of Genetics, Mishima, Japan
| | - Takuji Iwasato
- Laboratory of Mammalian Neural Circuits, National Institute of Genetics, Mishima, Japan
| | - Haruko Nakamura
- Department of Molecular Pharmacology and Neurobiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshio Goshima
- Department of Molecular Pharmacology and Neurobiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Matthieu Raveau
- Laboratory for Neurogenetics, RIKEN Center for Brain Science, Wako, Japan
| | - Tetsuya Tatsukawa
- Laboratory for Neurogenetics, RIKEN Center for Brain Science, Wako, Japan
| | - Kazuhiro Yamakawa
- Laboratory for Neurogenetics, RIKEN Center for Brain Science, Wako, Japan
- Department of Neurodevelopmental Disorder Genetics, Institute of Brain Sciences, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Noriko Takahashi
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Physiology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Haruo Kasai
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Tokyo, Japan
| | - Johji Inazawa
- Research Core, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ikuo Nobuhisa
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tetsushi Kagawa
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tetsuya Taga
- Department of Stem Cell Regulation, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mohamed Darwish
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Department of Behavioral Physiology, Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
| | | | - Keizo Takao
- Department of Behavioral Physiology, Graduate School of Innovative Life Science, University of Toyama, Toyama, Japan
- Department of Behavioral Physiology, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Kiran Sapkota
- Department of Neuroscience, Southern Research, Birmingham, United States
| | - Kazutoshi Nakazawa
- Department of Neuroscience, Southern Research, Birmingham, United States
| | - Tsuyoshi Takagi
- Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Haruki Fujisawa
- Department of Endocrinology, Diabetes and Metabolism, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Yoshihisa Sugimura
- Department of Endocrinology, Diabetes and Metabolism, School of Medicine, Fujita Health University, Toyoake, Japan
| | - Kyosuke Yamanishi
- Department of Neuropsychiatry, Hyogo Medical University School of Medicine, Nishinomiya, Japan
| | - Lakshmi Rajagopal
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Nanette Deneen Hannah
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Herbert Y Meltzer
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, United States
| | - Tohru Yamamoto
- Department of Molecular Neurobiology, Faculty of Medicine, Kagawa University, Kita-gun, Japan
| | - Shuji Wakatsuki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Katsuhiko Tabuchi
- Department of Molecular & Cellular Physiology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Tadahiro Numakawa
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
- Department of Psychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Freesia L Huang
- Program of Developmental Neurobiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Atsuko Hayata-Takano
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
- Department of Pharmacology, Graduate School of Dentistry, Osaka University, Suita, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Japan
- Division of Bioscience, Institute for Datability Science, Osaka University, Suita, Japan
- Transdimensional Life Imaging Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Molecular Pharmaceutical Science, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kota Tamada
- RIKEN Brain Science Institute, Wako, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
| | - Toru Takumi
- RIKEN Brain Science Institute, Wako, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Japan
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Japan
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Isabella A Graef
- Department of Pathology, Stanford University School of Medicine, Stanford, United States
| | - Gerald R Crabtree
- Department of Pathology, Stanford University School of Medicine, Stanford, United States
| | - Nozomi Asaoka
- Department of Pharmacology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hikari Hatakama
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Shuji Kaneko
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Takao Kohno
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Mitsuharu Hattori
- Department of Biomedical Science, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Yoshio Hoshiba
- Laboratory of Medical Neuroscience, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Ryuhei Miyake
- Laboratory for Multi-scale Biological Psychiatry, RIKEN Center for Brain Science, Wako, Japan
| | - Kisho Obi-Nagata
- Laboratory for Multi-scale Biological Psychiatry, RIKEN Center for Brain Science, Wako, Japan
| | - Akiko Hayashi-Takagi
- Laboratory of Medical Neuroscience, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
- Laboratory for Multi-scale Biological Psychiatry, RIKEN Center for Brain Science, Wako, Japan
| | - Léa J Becker
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Ipek Yalcin
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France
| | - Yoko Hagino
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | | | - Yuki Moriya
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kazutaka Ikeda
- Addictive Substance Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hyopil Kim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, United States
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Hikari Otabi
- College of Agriculture, Ibaraki University, Ami, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yuta Yoshida
- College of Agriculture, Ibaraki University, Ami, Japan
| | - Atsushi Toyoda
- College of Agriculture, Ibaraki University, Ami, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Ibaraki University Cooperation between Agriculture and Medical Science (IUCAM), Ibaraki, Japan
| | - Noboru H Komiyama
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Seth G N Grant
- Genes to Cognition Program, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michiru Ida-Eto
- Department of Developmental and Regenerative Medicine, Mie University, Graduate School of Medicine, Tsu, Japan
| | - Masaaki Narita
- Department of Developmental and Regenerative Medicine, Mie University, Graduate School of Medicine, Tsu, Japan
| | - Ken-Ichi Matsumoto
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, Izumo, Japan
| | - Emiko Okuda-Ashitaka
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka, Japan
| | - Iori Ohmori
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Tadayuki Shimada
- Child Brain Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kanato Yamagata
- Child Brain Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiroshi Ageta
- Division for Therapies Against Intractable Diseases, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Kunihiro Tsuchida
- Division for Therapies Against Intractable Diseases, Center for Medical Science, Fujita Health University, Toyoake, Japan
| | - Kaoru Inokuchi
- Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
- Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
- Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency (JST), University of Toyama, Toyama, Japan
| | - Takayuki Sassa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Motoaki Fukasawa
- Department of Anatomy II, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nobuteru Usuda
- Department of Anatomy II, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tayo Katano
- Department of Medical Chemistry, Kansai Medical University, Hirakata, Japan
| | - Teruyuki Tanaka
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Yoshihara
- Laboratory for Systems Molecular Ethology, RIKEN Center for Brain Science, Wako, Japan
| | - Michihiro Igarashi
- Department of Neurochemistry and Molecular Cell Biology, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- Transdiciplinary Research Program, Niigata University, Niigata, Japan
| | - Takashi Hayashi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Kaori Ishikawa
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Satoshi Yamamoto
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd, Fujisawa, Japan
| | - Naoya Nishimura
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd, Fujisawa, Japan
| | - Kazuto Nakada
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Japan
| | - Shinji Hirotsune
- Department of Genetic Disease Research, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Kiyoshi Egawa
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Kazuma Higashisaka
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Yasuo Tsutsumi
- Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Shoko Nishihara
- Glycan & Life Systems Integration Center (GaLSIC), Soka University, Tokyo, Japan
| | - Noriyuki Sugo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Takeshi Yagi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Naoto Ueno
- Laboratory of Morphogenesis, National Institute for Basic Biology, Okazaki, Japan
| | - Tomomi Yamamoto
- Division of Biophysics and Neurobiology, National Institute for Physiological Sciences, Okazaki, Japan
| | - Yoshihiro Kubo
- Division of Biophysics and Neurobiology, National Institute for Physiological Sciences, Okazaki, Japan
| | - Rie Ohashi
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
| | - Kimiko Shimizu
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
| | - Sayaka Higo-Yamamoto
- Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Katsutaka Oishi
- Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- School of Integrative and Global Majors (SIGMA), University of Tsukuba, Tsukuba, Japan
| | - Hisashi Mori
- Department of Molecular Neuroscience, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Tamio Furuse
- Mouse Phenotype Analysis Division, Japan Mouse Clinic, RIKEN BioResource Research Center (BRC), Tsukuba, Japan
| | - Masaru Tamura
- Mouse Phenotype Analysis Division, Japan Mouse Clinic, RIKEN BioResource Research Center (BRC), Tsukuba, Japan
| | - Hisashi Shirakawa
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Daiki X Sato
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Yuriko Komine
- Young Researcher Support Group, Research Enhancement Strategy Office, National Institute for Basic Biology, National Institute of Natural Sciences, Okazaki, Japan
- Division of Brain Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Tetsuo Yamamori
- Division of Brain Biology, National Institute for Basic Biology, Okazaki, Japan
- Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, Wako, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Japan
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Liu S, Zhang L, Fan X, Wang G, Liu Q, Yang Y, Shao M, Song M, Li W, Lv L, Su X. Lactate levels in the brain and blood of schizophrenia patients: A systematic review and meta-analysis. Schizophr Res 2024; 264:29-38. [PMID: 38086110 DOI: 10.1016/j.schres.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/06/2023] [Accepted: 11/28/2023] [Indexed: 03/01/2024]
Abstract
BACKGROUND The pathophysiological mechanisms of schizophrenia are still unclear. Converging evidence suggests that energy metabolism abnormalities are involved in schizophrenia, and support its role in the pathophysiology of this disease. Lactate plays an important role in energy metabolism. Many studies have reported changes in the levels of lactate in the brain and serum of schizophrenia patients; however, the results from these studies are not consistent. To overcome this limitation, the goal of the present meta-analysis is to analyze the changes in lactate levels in the brain and blood of schizophrenia patients. METHODS For this systematic review and meta-analysis, we performed a thorough search of relevant literature in the English language, using the MEDLINE, Cochrane, and Embase databases. RESULTS In the present meta-analysis, 20 studies were scrutinized, including 13 studies on brain lactate levels, which involved 322 schizophrenia patients and 324 healthy individuals as controls. 7 studies on blood lactate levels, involving 234 schizophrenia patients and 238 healthy individuals, were also included. Brain lactate levels were elevated in schizophrenia patients, both in vivo and in post-mortem studies. Nevertheless, blood lactate levels in schizophrenia patients have revealed no statistically significant difference, as compared with control individuals. CONCLUSIONS In comparison with healthy individuals, schizophrenia patients had higher lactate levels in the brain, rather than in the blood. These findings suggest independent regulatory mechanisms of lactate levels in the brain and peripheral tissues. Abnormal lactate metabolism in the brain may be an important pathological mechanism in schizophrenia.
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Affiliation(s)
- Senqi Liu
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China
| | - Luwen Zhang
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China; International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Xiaoyun Fan
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China
| | - Guanyu Wang
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China
| | - Qing Liu
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China; International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Yongfeng Yang
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China; International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Minglong Shao
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China; International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Meng Song
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China; International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Wenqiang Li
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China; International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Luxian Lv
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China; International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China.
| | - Xi Su
- Department of Psychiatry, Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China; Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China; International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China.
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Menéndez-Valle I, Cachán-Vega C, Boga JA, González-Blanco L, Antuña E, Potes Y, Caballero B, Vega-Naredo I, Saiz P, Bobes J, García-Portilla P, Coto-Montes A. Differential Cellular Interactome in Schizophrenia and Bipolar Disorder-Discriminatory Biomarker Role. Antioxidants (Basel) 2023; 12:1948. [PMID: 38001801 PMCID: PMC10669042 DOI: 10.3390/antiox12111948] [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: 09/29/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Schizophrenia (SCH) and bipolar disorder (BD) are two of the most important psychiatric pathologies due to their high population incidence and disabling power, but they also present, mainly in their debut, high clinical similarities that make their discrimination difficult. In this work, the differential oxidative stress, present in both disorders, is shown as a concatenator of the systemic alterations-both plasma and erythrocyte, and even at the level of peripheral blood mononuclear cells (PBMC)-in which, for the first time, the different affectations that both disorders cause at the level of the cellular interactome were observed. A marked erythrocyte antioxidant imbalance only present in SCH generalizes to oxidative damage at the plasma level and shows a clear impact on cellular involvement. From the alteration of protein synthesis to the induction of death by apoptosis, including proteasomal damage, mitochondrial imbalance, and autophagic alteration, all the data show a greater cellular affectation in SCH than in BD, which could be linked to increased oxidative stress. Thus, patients with SCH in our study show increased endoplasmic reticulum (ER)stress that induces increased proteasomal activity and a multifactorial response to misfolded proteins (UPR), which, together with altered mitochondrial activity, generating free radicals and leading to insufficient energy production, is associated with defective autophagy and ultimately leads the cell to a high apoptotic predisposition. In BD, however, oxidative damage is much milder and without significant activation of survival mechanisms or inhibition of apoptosis. These clear differences identified at the molecular and cellular level between the two disorders, resulting from progressive afflictions in which oxidative stress can be both a cause and a consequence, significantly improve the understanding of both disorders to date and are essential for the development of targeted and preventive treatments.
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Affiliation(s)
- Iván Menéndez-Valle
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Servicio de Inmunología, Hospital Universitario Central de Asturias (HUCA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
| | - Cristina Cachán-Vega
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Department of Cell Biology and Morphology, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
| | - José Antonio Boga
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
| | - Laura González-Blanco
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra. AS-267, 33300 Villaviciosa, Asturias, Spain
| | - Eduardo Antuña
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Department of Cell Biology and Morphology, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
| | - Yaiza Potes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Department of Cell Biology and Morphology, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
| | - Beatriz Caballero
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Department of Cell Biology and Morphology, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
| | - Ignacio Vega-Naredo
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Department of Cell Biology and Morphology, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
| | - Pilar Saiz
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Departament of Medicine, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
| | - Julio Bobes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Departament of Medicine, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
| | - Paz García-Portilla
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Departament of Medicine, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
| | - Ana Coto-Montes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario, s/n, 33011 Oviedo, Asturias, Spain
- Instituto de Neurociencias (INEUROPA), University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
- Department of Cell Biology and Morphology, Faculty of Medicine, University of Oviedo, Julián Clavería, s/n, 33006 Oviedo, Asturias, Spain
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Miyahara K, Hino M, Yu Z, Ono C, Nagaoka A, Hatano M, Shishido R, Yabe H, Tomita H, Kunii Y. The influence of tissue pH and RNA integrity number on gene expression of human postmortem brain. Front Psychiatry 2023; 14:1156524. [PMID: 37520228 PMCID: PMC10379646 DOI: 10.3389/fpsyt.2023.1156524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Evaluating and controlling confounders are necessary when investigating molecular pathogenesis using human postmortem brain tissue. Particularly, tissue pH and RNA integrity number (RIN) are valuable indicators for controlling confounders. However, the influences of these indicators on the expression of each gene in postmortem brain have not been fully investigated. Therefore, we aimed to assess these effects on gene expressions of human brain samples. Methods We isolated total RNA from occipital lobes of 13 patients with schizophrenia and measured the RIN and tissue pH. Gene expression was analyzed and gene sets affected by tissue pH and RIN were identified. Moreover, we examined the functions of these genes by enrichment analysis and upstream regulator analysis. Results We identified 2,043 genes (24.7%) whose expressions were highly correlated with pH; 3,004 genes (36.3%) whose expressions were highly correlated with RIN; and 1,293 genes (15.6%) whose expressions were highly correlated with both pH and RIN. Genes commonly affected by tissue pH and RIN were highly associated with energy production and the immune system. In addition, genes uniquely affected by tissue pH were highly associated with the cell cycle, whereas those uniquely affected by RIN were highly associated with RNA processing. Conclusion The current study elucidated the influence of pH and RIN on gene expression profiling and identified gene sets whose expressions were affected by tissue pH or RIN. These findings would be helpful in the control of confounders for future postmortem brain studies.
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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
| | - Zhiqian Yu
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Chiaki Ono
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Masataka Hatano
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Risa Shishido
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Psychiatry, Tohoku University Hospital, Sendai, 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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5
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Tosoni G, Ayyildiz D, Bryois J, Macnair W, Fitzsimons CP, Lucassen PJ, Salta E. Mapping human adult hippocampal neurogenesis with single-cell transcriptomics: Reconciling controversy or fueling the debate? Neuron 2023; 111:1714-1731.e3. [PMID: 37015226 DOI: 10.1016/j.neuron.2023.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/06/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
The notion of exploiting the regenerative potential of the human brain in physiological aging or neurological diseases represents a particularly attractive alternative to conventional strategies for enhancing or restoring brain function. However, a major first question to address is whether the human brain does possess the ability to regenerate. The existence of human adult hippocampal neurogenesis (AHN) has been at the center of a fierce scientific debate for many years. The advent of single-cell transcriptomic technologies was initially viewed as a panacea to resolving this controversy. However, recent single-cell RNA sequencing studies in the human hippocampus yielded conflicting results. Here, we critically discuss and re-analyze previously published AHN-related single-cell transcriptomic datasets. We argue that, although promising, the single-cell transcriptomic profiling of AHN in the human brain can be confounded by methodological, conceptual, and biological factors that need to be consistently addressed across studies and openly discussed within the scientific community.
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Affiliation(s)
- Giorgia Tosoni
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands
| | - Dilara Ayyildiz
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands
| | - Julien Bryois
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Will Macnair
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center, CH-4070, Basel, Switzerland
| | - Carlos P Fitzsimons
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
| | - Paul J Lucassen
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands; Center for Urban Mental Health, University of Amsterdam, 1098 SM, Amsterdam, the Netherlands
| | - Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, 1105 BA, Amsterdam, the Netherlands.
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6
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Abouhashem AS, Singh K, Srivastava R, Liu S, Mathew-Steiner SS, Gu X, Kacar S, Hagar A, Sandusky GE, Roy S, Wan J, Sen CK. The Prolonged Terminal Phase of Human Life Induces Survival Response in the Skin Transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540715. [PMID: 37292819 PMCID: PMC10245562 DOI: 10.1101/2023.05.15.540715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Human death marks the end of organismal life under conditions such that the components of the human body continue to be alive. Such postmortem cellular survival depends on the nature (Hardy scale of slow-fast death) of human death. Slow and expected death typically results from terminal illnesses and includes a prolonged terminal phase of life. As such organismal death process unfolds, do cells of the human body adapt for postmortem cellular survival? Organs with low energy cost-of-living, such as the skin, are better suited for postmortem cellular survival. In this work, the effect of different durations of terminal phase of human life on postmortem changes in cellular gene expression was investigated using RNA sequencing data of 701 human skin samples from the Genotype-Tissue Expression (GTEx) database. Longer terminal phase (slow-death) was associated with a more robust induction of survival pathways (PI3K-Akt signaling) in postmortem skin. Such cellular survival response was associated with the upregulation of embryonic developmental transcription factors such as FOXO1 , FOXO3 , ATF4 and CEBPD . Upregulation of PI3K-Akt signaling was independent of sex or duration of death-related tissue ischemia. Analysis of single nucleus RNA-seq of post-mortem skin tissue specifically identified the dermal fibroblast compartment to be most resilient as marked by adaptive induction of PI3K-Akt signaling. In addition, slow death also induced angiogenic pathways in the dermal endothelial cell compartment of postmortem human skin. In contrast, specific pathways supporting functional properties of the skin as an organ were downregulated following slow death. Such pathways included melanogenesis and those representing the skin extracellular matrix (collagen expression and metabolism). Efforts to understand the significance of death as a biological variable (DABV) in influencing the transcriptomic composition of surviving component tissues has far-reaching implications including rigorous interpretation of experimental data collected from the dead and mechanisms involved in transplant-tissue obtained from dead donors.
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Hagihara H, Murano T, Miyakawa T. The gene expression patterns as surrogate indices of pH in the brain. Front Psychiatry 2023; 14:1151480. [PMID: 37200901 PMCID: PMC10185791 DOI: 10.3389/fpsyt.2023.1151480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/11/2023] [Indexed: 05/20/2023] Open
Abstract
Hydrogen ion (H+) is one of the most potent intrinsic neuromodulators in the brain in terms of concentration. Changes in H+ concentration, expressed as pH, are thought to be associated with various biological processes, such as gene expression, in the brain. Accumulating evidence suggests that decreased brain pH is a common feature of several neuropsychiatric disorders, including schizophrenia, bipolar disorder, autism spectrum disorder, and Alzheimer's disease. However, it remains unclear whether gene expression patterns can be used as surrogates for pH changes in the brain. In this study, we performed meta-analyses using publicly available gene expression datasets to profile the expression patterns of pH-associated genes, whose expression levels were correlated with brain pH, in human patients and mouse models of major central nervous system (CNS) diseases, as well as in mouse cell-type datasets. Comprehensive analysis of 281 human datasets from 11 CNS disorders revealed that gene expression associated with decreased pH was over-represented in disorders including schizophrenia, bipolar disorder, autism spectrum disorders, Alzheimer's disease, Huntington's disease, Parkinson's disease, and brain tumors. Expression patterns of pH-associated genes in mouse models of neurodegenerative disease showed a common time course trend toward lower pH over time. Furthermore, cell type analysis identified astrocytes as the cell type with the most acidity-related gene expression, consistent with previous experimental measurements showing a lower intracellular pH in astrocytes than in neurons. These results suggest that the expression pattern of pH-associated genes may be a surrogate for the state- and trait-related changes in pH in brain cells. Altered expression of pH-associated genes may serve as a novel molecular mechanism for a more complete understanding of the transdiagnostic pathophysiology of neuropsychiatric and neurodegenerative disorders.
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Almeida D, Turecki G. Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection. Methods 2022; 207:3-10. [PMID: 36064002 DOI: 10.1016/j.ymeth.2022.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptome of a cell constitutes an essential piece of cellular identity and contributes to the multifaceted complexity and heterogeneity of cell-types within the mammalian brain. Thus, while a wealth of studies have investigated transcriptomic alterations underlying the pathophysiology of diseases of the brain, their use of bulk-tissue homogenates makes it difficult to tease apart whether observed differences are explained by disease state or cellular composition. Cell-type-specific enrichment strategies are, therefore, crucial in the context of gene expression profiling. Laser capture microdissection (LCM) is one such strategy that allows for the capture of specific cell-types, or regions of interest, under microscopic visualization. In this review, we focus on using LCM for cell-type specific gene expression profiling in post-mortem human brain samples. We begin with a discussion of various LCM systems, followed by a walk-through of each step in the LCM to gene expression profiling workflow and a description of some of the limitations associated with LCM. Throughout the review, we highlight important considerations when using LCM with post-mortem human brain samples. Whenever applicable, commercially available kits that have proven successful in the context of LCM with post-mortem human brain samples are described.
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Affiliation(s)
- Daniel Almeida
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3; Department of Psychiatry, McGill University, Montreal, QC, Canada, H3A 1A1.
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Gomez Rueda H, Bustillo J. Brain differential gene expression and blood cross-validation of a molecular signature of patients with major depressive disorder. Psychiatr Genet 2022; 32:105-115. [PMID: 35030558 PMCID: PMC9071037 DOI: 10.1097/ypg.0000000000000309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 11/15/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The agreement between clinicians diagnosing major depressive disorder (MDD) is poor. The objective of this study was to identify a reproducible and robust gene expression marker capable of differentiating MDD from healthy control (HC) subjects. MATERIALS AND METHODS Brain and blood gene expression datasets were searched, which included subjects with MDD and HC. The largest database including different areas of brain samples (GSE80655) was used to identify an initial gene expression marker. Tests of robustness and reproducibility were then implemented in 13 brain and 7 blood independent datasets. Correlations between expression in brain and blood samples were also examined. Finally, an enrichment analysis to explore the marker biological meaning was completed. RESULTS Twenty-eight genes were differentially expressed in GSE80655, of which 23 were critical to differentiate MDD from HC. The accuracy obtained using the 23 genes was 0.77 and 0.8, before and after the forward selection model, respectively. The gene marker's robustness and reproducibility were between the range of 0.46 and 0.63 in the other brain datasets and between 0.45 and 0.78 for the blood datasets. Brain and blood expression tended to correlate in some samples. Thirteen of the 23 genes were related to stress and immune response. CONCLUSION A 23 gene expression marker was able to distinguish subjects with MDD from HC, with adequate reproducibility and low robustness in the independent databases investigated. This gene set was similarly expressed in the brain and blood and involved genes related to stress and immune response.
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Affiliation(s)
- Hugo Gomez Rueda
- Department of Psychiatry and Behavioral Sciences, University of New Mexico Health Sciences Center
| | - Juan Bustillo
- Department of Psychiatry and Behavioral Sciences, University of New Mexico Health Sciences Center
- Department of Neurosciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
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10
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Willsey HR, Willsey AJ, Wang B, State MW. Genomics, convergent neuroscience and progress in understanding autism spectrum disorder. Nat Rev Neurosci 2022; 23:323-341. [PMID: 35440779 PMCID: PMC10693992 DOI: 10.1038/s41583-022-00576-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/31/2022]
Abstract
More than a hundred genes have been identified that, when disrupted, impart large risk for autism spectrum disorder (ASD). Current knowledge about the encoded proteins - although incomplete - points to a very wide range of developmentally dynamic and diverse biological processes. Moreover, the core symptoms of ASD involve distinctly human characteristics, presenting challenges to interpreting evolutionarily distant model systems. Indeed, despite a decade of striking progress in gene discovery, an actionable understanding of pathobiology remains elusive. Increasingly, convergent neuroscience approaches have been recognized as an important complement to traditional uses of genetics to illuminate the biology of human disorders. These methods seek to identify intersection among molecular-level, cellular-level and circuit-level functions across multiple risk genes and have highlighted developing excitatory neurons in the human mid-gestational prefrontal cortex as an important pathobiological nexus in ASD. In addition, neurogenesis, chromatin modification and synaptic function have emerged as key potential mediators of genetic vulnerability. The continued expansion of foundational 'omics' data sets, the application of higher-throughput model systems and incorporating developmental trajectories and sex differences into future analyses will refine and extend these results. Ultimately, a systems-level understanding of ASD genetic risk holds promise for clarifying pathobiology and advancing therapeutics.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA.
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11
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Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain. Nat Neurosci 2022; 25:306-316. [PMID: 35260865 DOI: 10.1038/s41593-022-01022-8] [Citation(s) in RCA: 152] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples.
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12
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Xicota L, De Toma I, Maffioletti E, Pisanu C, Squassina A, Baune BT, Potier MC, Stacey D, Dierssen M. Recommendations for pharmacotranscriptomic profiling of drug response in CNS disorders. Eur Neuropsychopharmacol 2022; 54:41-53. [PMID: 34743061 DOI: 10.1016/j.euroneuro.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 08/16/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022]
Abstract
Pharmacotranscriptomics is a still very new field of research that has just begun to flourish and promises to enable target discovery, inform biomarker and evaluate drug efficacy beyond pharmacogenomics. The aim of this review is to provide a critical overview of the biological foundations of transcriptomics, methodological approaches to transcriptomic studies, and their advantages and limitations. We present the different RNA species (rRNAs, tRNAs, mtRNAs, snRNAs, scRNAs, mRNAs, ncRNAs, LINE and SINE transcripts, circular RNAs, piRNAs, miRNAs, snoRNAs) and their potential for pharmacotranscriptomic studies as markers to predict treatment response in neurological and psychiatric disorders. We also review the accessible sources of RNA in patients peripheral blood cells (including platelets), plasma, microvesicles, exosomes, apoptotic bodies, and how those affect the integrity and relative abundances of RNAs and reflect the situation in the Central Nervous System (CNS). Finally, we discuss the suitability and indications of different techniques, such as microarrays and RNA-sequencing (RNA-Seq) techniques to understand gene expression differences or to reveal variation in expression levels of coding and non-coding genes. We conclude with some recommendations for future directions, e.g., gaps of knowledge and particular RNAs/tissues that have been overlooked.
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Affiliation(s)
- Laura Xicota
- Paris Brain Institute, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Ilario De Toma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elisabetta Maffioletti
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy; Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Bernhard T Baune
- Department of Psychiatry, University of Muenster, Muenster, Germany; Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Marie Claude Potier
- Paris Brain Institute, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - David Stacey
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom of Great Britain and Northern Ireland United Kingdom
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Biomedical Research Networking Center on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain.
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13
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Zaccaria A, Antinori P, Licker V, Kövari E, Lobrinus JA, Burkhard PR. Multiomic Analyses of Dopaminergic Neurons Isolated from Human Substantia Nigra in Parkinson's Disease: A Descriptive and Exploratory Study. Cell Mol Neurobiol 2021; 42:2805-2818. [PMID: 34528139 PMCID: PMC9561004 DOI: 10.1007/s10571-021-01146-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/02/2021] [Indexed: 11/21/2022]
Abstract
Dopaminergic neurons (DA) of the substantia nigra pars compacta (SNpc) selectively and progressively degenerate in Parkinson’s disease (PD). Until now, molecular analyses of DA in PD have been limited to genomic or transcriptomic approaches, whereas, to the best of our knowledge, no proteomic or combined multiomic study examining the protein profile of these neurons is currently available. In this exploratory study, we used laser capture microdissection to extract regions from DA in 10 human SNpc obtained at autopsy in PD patients and control subjects. Extracted RNA and proteins were identified by RNA sequencing and nanoliquid chromatography–mass spectrometry, respectively, and the differential expression between PD and control group was assessed. Qualitative analyses confirmed that the microdissection protocol preserves the integrity of our samples and offers access to specific molecular pathways. This multiomic analysis highlighted differential expression of 52 genes and 33 proteins, including molecules of interest already known to be dysregulated in PD, such as LRP2, PNMT, CXCR4, MAOA and CBLN1 genes, or the Aldehyde dehydrogenase 1 protein. On the other hand, despite the same samples were used for both analyses, correlation between RNA and protein expression was low, as exemplified by the CST3 gene encoding for the cystatin C protein. This is the first exploratory study analyzing both gene and protein expression of laser-dissected neuronal parts from SNpc in PD. Data are available via ProteomeXchange with identifier PXD024748 and via GEO with identifier GSE 169755.
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Affiliation(s)
- Affif Zaccaria
- Neuroproteomics Group, University Medical Center, Faculty of Medicine, Geneva University, Geneva, Switzerland.
| | - Paola Antinori
- Neuroproteomics Group, University Medical Center, Faculty of Medicine, Geneva University, Geneva, Switzerland
| | - Virginie Licker
- Neuroproteomics Group, University Medical Center, Faculty of Medicine, Geneva University, Geneva, Switzerland
| | - Enikö Kövari
- Department of Psychiatry, Geneva University Hospitals, Geneva, Switzerland
| | | | - Pierre R Burkhard
- Neuroproteomics Group, University Medical Center, Faculty of Medicine, Geneva University, Geneva, Switzerland.,Department of Neurology, Geneva University Hospitals, Geneva, Switzerland
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14
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Xia J, Xue X, Liu W, Qi Z, Liu W. The Role of Fgf9 in the Antidepressant Effects of Exercise and Fluoxetine in Chronic Unpredictable Mild Stress Mice. Psychosom Med 2021; 83:795-804. [PMID: 33938506 DOI: 10.1097/psy.0000000000000953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE The neurotrophic hypothesis of depression posits that stress and depression decrease neurotrophic factor expression in brain, whereas antidepressants and exercise can contribute to the blockade of stress effects and produce antidepressant effects. Fibroblast growth factor 9 (FGF9), a member of the fibroblast growth factor (FGF) family, has been reported to be dysregulated in depression. The present study aimed to determine whether and how Fgf9 mediates the antidepressant effects of fluoxetine and exercise in chronic unpredictable mild stress (CUMS) mice. METHODS Male C57BL/6 mice were exposed to CUMS for 7 weeks. From the fourth week, CUMS-exposed mice were subjected to fluoxetine treatment or swimming exercise for 4 weeks. Forced swim test, tail suspension test, and hole-board test were used to assess behaviors of mice. Real-time polymerase chain reaction was used to examine hippocampal messenger RNA levels of Fgf9, Fgf2, FgfR1, FgfR2, and FgfR3. Western blotting was used to examine the protein levels of Fgf9, protein kinase B (Akt), and phosphorylation of Akt at Ser473 in mouse hippocampus. RESULTS Our results demonstrated that CUMS induced depression-like behaviors, which were reversed by fluoxetine treatment and swimming exercise. Moreover, we found that CUMS resulted in a dysregulation of Fgf9, Fgf2, and FgfR2 expression, whereas fluoxetine and swimming restored the FGF expression in CUMS-exposed mice. An analysis of the proteins suggests that the antidepressant effects of fluoxetine and exercise in CUMS-exposed mice were associated with ameliorated Fgf9/Akt signaling. CONCLUSIONS Our findings have demonstrated that swimming exercise mimics the antidepressant effects of fluoxetine by regulating Fgf9 in CUMS-exposed mice, which may offer new mechanism-based therapeutic targets for depression.
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Affiliation(s)
- Jie Xia
- From the Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education (Xia, Xue, Wenbin Liu, Qi, Weina Liu), College of Physical Education and Health (Xia, Wenbin Liu, Qi, Weina Liu), East China Normal University; and Key Laboratory of Exercise and Health Sciences of Ministry of Education (Xue), Shanghai University of Sport, Shanghai, China
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15
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Decreased Brain pH and Pathophysiology in Schizophrenia. Int J Mol Sci 2021; 22:ijms22168358. [PMID: 34445065 PMCID: PMC8395078 DOI: 10.3390/ijms22168358] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 12/26/2022] Open
Abstract
Postmortem studies reveal that the brain pH in schizophrenia patients is lower than normal. The exact cause of this low pH is unclear, but increased lactate levels due to abnormal energy metabolism appear to be involved. Schizophrenia patients display distinct changes in mitochondria number, morphology, and function, and such changes promote anaerobic glycolysis, elevating lactate levels. pH can affect neuronal activity as H+ binds to numerous proteins in the nervous system and alters the structure and function of the bound proteins. There is growing evidence of pH change associated with cognition, emotion, and psychotic behaviors. Brain has delicate pH regulatory mechanisms to maintain normal pH in neurons/glia and extracellular fluid, and a change in these mechanisms can affect, or be affected by, neuronal activities associated with schizophrenia. In this review, we discuss the current understanding of the cause and effect of decreased brain pH in schizophrenia based on postmortem human brains, animal models, and cellular studies. The topic includes the factors causing decreased brain pH in schizophrenia, mitochondria dysfunction leading to altered energy metabolism, and pH effects on the pathophysiology of schizophrenia. We also review the acid/base transporters regulating pH in the nervous system and discuss the potential contribution of the major transporters, sodium hydrogen exchangers (NHEs), and sodium-coupled bicarbonate transporters (NCBTs), to schizophrenia.
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Dai J, Chen Y, Dai R, Jiang Y, Tian J, Liu S, Xu M, Li M, Zhou J, Liu C, Chen C. Agonal Factors Distort Gene-Expression Patterns in Human Postmortem Brains. Front Neurosci 2021; 15:614142. [PMID: 33841074 PMCID: PMC8027124 DOI: 10.3389/fnins.2021.614142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/16/2021] [Indexed: 01/01/2023] Open
Abstract
Agonal factors, the conditions that occur just prior to death, can impact the molecular quality of postmortem brains, influencing gene expression results. Our study used gene expression data of 262 samples from ROSMAP with the detailed terminal state recorded for each donor, such as fever, infection, and unconsciousness. Fever and infection were the primary contributors to brain gene expression changes, brain cell-type-specific gene expression, and cell proportion changes. Furthermore, we also found that previous studies of gene expression in postmortem brains were confounded by agonal factors. Therefore, correction for agonal factors is important in the step of data preprocessing. Our analyses revealed fever and infection contributing to gene expression changes in postmortem brains and emphasized the necessity of study designs that document and account for agonal factors.
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Affiliation(s)
- Jiacheng Dai
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Chen
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Rujia Dai
- Upstate Medical University, Syracuse, NY, United States
| | - Yi Jiang
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jianghua Tian
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Sihan Liu
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Meng Xu
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Miao Li
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jiaqi Zhou
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chunyu Liu
- Department of Psychiatry, Upstate Medical University, Syracuse, NY, United States
| | - Chao Chen
- Center for Medical Genetics, Department of Psychiatry, School of Life Sciences, National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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17
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Antunes ASLM, de Almeida V, Crunfli F, Carregari VC, Martins-de-Souza D. Proteomics for Target Identification in Psychiatric and Neurodegenerative Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1286:251-264. [PMID: 33725358 DOI: 10.1007/978-3-030-55035-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Psychiatric and neurodegenerative disorders such as schizophrenia (SCZ), Parkinson's disease (PD), and Alzheimer's disease (AD) continue to grow around the world with a high impact on health, social, and economic outcomes for the patient and society. Despite efforts, the etiology and pathophysiology of these disorders remain unclear. Omics technologies have contributed to the understanding of the molecular mechanisms that underlie these complex disorders and have suggested novel potential targets for treatment and diagnostics. Here, we have highlighted the unique and common pathways shared between SCZ, PD, and AD and highlight the main proteomic findings over the last 5 years using in vitro models, postmortem brain samples, and cerebrospinal fluid (CSF) or blood of patients. These studies have identified possible therapeutic targets and disease biomarkers. Further studies including target validation, the use of large sample sizes, and the integration of omics findings with bioinformatics tools are required to provide a better comprehension of pharmacological targets.
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Affiliation(s)
- André S L M Antunes
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
| | - Valéria de Almeida
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Victor C Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria, Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil
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18
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Swaab DF, Bao AM. Matching of the postmortem hypothalamus from patients and controls. HANDBOOK OF CLINICAL NEUROLOGY 2021; 179:141-156. [PMID: 34225959 DOI: 10.1016/b978-0-12-819975-6.00007-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The quality of postmortem hypothalamus research depends strongly on a thorough clinical investigation and documentation of the patient's disorder and therapies. In addition, a systematic and professional neuropathological investigation of the entire brain of both the cases and the controls is absolutely crucial. In the experience of the Netherlands Brain Bank (NBB), about 20% of the clinical neurological diagnoses, despite being made in first rate clinics, have to be revised or require extra diagnoses after a complete and thorough neuropathologic review by the NBB. The neuropathology examination may reveal for instance that the elderly "controls" already have preclinical neurodegenerative alterations. In postmortem studies, the patient and control groups must be matched for as many as possible of the known confounding factors. This is necessary to make the groups as similar as possible, except for the topic being investigated. Confounding factors are present (i) before, (ii) during, and (iii) after death. They are, respectively: (i) genetic background, systemic diseases, duration and gravity of illness, medicines and addictive compounds used, age, sex, gender identity, sexual orientation, clock- and seasonal time of death, and lateralization; (ii) agonal state, stress of dying; and (iii) postmortem delay, freezing procedures, fixation, and storage time. Agonal state is generally estimated by measuring the pH of the brain. However, there are disorders in which pH is lower as a part of the disease process. Because of the large number of potentially confounding factors that differ according to, for instance, brain area and disease, a brain bank should have a large number of controls at its disposal for appropriate matching. If matching fails for some confounders, the influence of the confounders may be determined by statistical methods, such as analysis of variance or the regression models.
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Affiliation(s)
- Dick F Swaab
- Department Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.
| | - Ai-Min Bao
- Department of Neurobiology and Department of Neurology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China
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19
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Pruett BS, Meador-Woodruff JH. Evidence for altered energy metabolism, increased lactate, and decreased pH in schizophrenia brain: A focused review and meta-analysis of human postmortem and magnetic resonance spectroscopy studies. Schizophr Res 2020; 223:29-42. [PMID: 32958361 DOI: 10.1016/j.schres.2020.09.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/21/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Though the pathophysiology of schizophrenia remains poorly understood, altered brain energy metabolism is increasingly implicated. Here, we conduct meta-analyses of the available human studies measuring lactate or pH in schizophrenia brain and discuss the accumulating evidence for increased lactate and decreased pH in schizophrenia brain and evidence linking these to negative and cognitive symptom severity. Meta-analysis of six postmortem studies revealed a significant increase in lactate in schizophrenia brain while meta-analysis of 14 magnetic resonance spectroscopy studies did not reveal a significant change in brain pH in schizophrenia. However, only five of these studies were likely sufficiently powered to detect differences in brain pH, and meta-analysis of these five studies found a nonsignificant decrease in pH in schizophrenia brain. Next, we discuss evidence for altered brain energy metabolism in schizophrenia and how this may underlie a buildup of lactate and decreased pH. This alteration, similar to the Warburg effect extensively described in cancer biology, involves diminished tricarboxylic acid cycle and oxidative phosphorylation along with a shift toward increased reliance on glycolysis for energy production. We then explore the role that mitochondrial dysfunction, oxidative stress, and hypoxia-related changes in gene expression likely play in this shift in brain energy metabolism and address the functional consequences of lowered brain pH in schizophrenia including alterations in neurotransmitter regulation, mRNA stability, and overall patterns of gene expression. Finally, we discuss how altered energy metabolism in schizophrenia brain may serve as an effective target in the treatment of this illness.
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Affiliation(s)
- Brandon S Pruett
- University of Alabama at Birmingham, Birmingham, AL, United States of America.
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20
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Lendor S, Olkowicz M, Boyaci E, Yu M, Diwan M, Hamani C, Palmer M, Reyes-Garcés N, Gómez-Ríos GA, Pawliszyn J. Investigation of Early Death-Induced Changes in Rat Brain by Solid Phase Microextraction via Untargeted High Resolution Mass Spectrometry: In Vivo versus Postmortem Comparative Study. ACS Chem Neurosci 2020; 11:1827-1840. [PMID: 32407623 DOI: 10.1021/acschemneuro.0c00270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Analysis of brain samples obtained postmortem remains a standard approach in neuroscience, despite often being suboptimal for inferring roles of small molecules in the pathophysiology of brain diseases. Sample collection and preservation further hinders conclusive interpretation of biomarker analysis in autopsy samples. We investigate purely death-induced changes affecting rat hippocampus in the first hour of postmortem interval (PMI) by means of untargeted liquid chromatography-mass spectrometry-based metabolomics. The unique possibility of sampling the same brain area of each animal both in vivo and postmortem was enabled by employing solid phase microextraction (SPME) probes. Four millimeter probes coated with mixed mode extraction phase were used to sample awake, freely roaming animals, with 2 more sampling events performed after death. Significant changes in brain neurochemistry were found to occur as soon as 30 min after death, further progressing with increasing PMI, evidenced by relative changes in levels of metabolites and lipids. These included species from several distinct groups, which can be classified as engaged in energy metabolism-related processes, signal transduction, neurotransmission, or inflammatory response. Additionally, we perform thorough analysis of interindividual variability in response to death, which provides insights into how this aspect can obscure conclusions drawn from an untargeted study at single metabolite and pathway level. The results suggest high demand for systematic studies examining the PMI time course with in vivo sampling as a starting point to eliminate artifacts in the form of neurochemical changes assumed to occur in vivo.
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Affiliation(s)
- Sofia Lendor
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Mariola Olkowicz
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Ezel Boyaci
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Miao Yu
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Mustansir Diwan
- Neuroimaging Research Section, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario M5T 1R8, Canada
| | - Clement Hamani
- Neuroimaging Research Section, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario M5T 1R8, Canada
| | - Michael Palmer
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Nathaly Reyes-Garcés
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - German Augusto Gómez-Ríos
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
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Selvaraj K, Manickam N, Kumaran E, Thangadurai K, Elumalai G, Sekar A, Radhakrishnan RK, Kandasamy M. Deterioration of neuroregenerative plasticity in association with testicular atrophy and dysregulation of the hypothalamic-pituitary-gonadal (HPG) axis in Huntington's disease: A putative role of the huntingtin gene in steroidogenesis. J Steroid Biochem Mol Biol 2020; 197:105526. [PMID: 31715317 DOI: 10.1016/j.jsbmb.2019.105526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 12/22/2022]
Abstract
Huntington's disease (HD) is an autosomal dominant progressive neurodegenerative disorder mainly affecting the structure and functions of the striatum, cerebral cortex and hippocampus leading to movement disorders, cognitive dysfunctions and emotional disturbances. The onset of HD has been linked to a pathogenic CAG repeat expansion in the huntingtin (HTT) gene that encodes for the polyglutamine (polyQ) stretches in the huntingtin (Htt) protein. Notably, the neuropathogenic events of the mutant HTT gene appear to be primed during adulthood and magnified along the ageing process. While the normal Htt protein is vital for the neuronal differentiation and neuroprotection, experimental HD models and postmortem human HD brains have been characterized by neurodegeneration and defects in neuroregenerative plasticity in the basal ganglia and limbic system including the hippocampus. Besides gonadal dysfunctions, reduced androgen levels and abnormal hypothalamic-pituitary-gonadal (HPG) axis have increasingly been evident in HD. Recently, ageing-related changes in levels of steroid sex hormones have been proposed to play a detrimental effect on the regulation of hippocampal neurogenesis in the adult brain. Considering its adult-onset nature, a potential relationship between dysregulation in the synthesis of sex steroid hormones and the pathogenesis of the mutant HTT gene appears to be an important clinical issue in HD. While the hippocampus and testis are the major sites of steroidogenesis, the presence of Htt in both areas is conclusively evident. Hence, the expression of the normal HTT gene may take part in the steroidogenic events in aforementioned organs in the physiological state, whereas the mutant HTT gene may cause defects in steroidogenesis in HD. Therefore, this review article comprehends the potential relationship between the gonadal dysfunctions and abnormal hippocampal plasticity in HD and represents a hypothesis for the putative role of the HTT gene in the regulation of steroidogenesis in gonads and in the brain.
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Affiliation(s)
- Kaviya Selvaraj
- School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Nivethitha Manickam
- Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Elamathi Kumaran
- School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Kayalvizhi Thangadurai
- Department of Bio-Medical Science, Bharathidasan University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Gokul Elumalai
- Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Aravinthan Sekar
- Department of Biotechnology, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Risna Kanjirassery Radhakrishnan
- Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Mahesh Kandasamy
- School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India; Laboratory of Stem Cells and Neuroregeneration, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India; Faculty Recharge Programme, University Grants Commission (UGC-FRP), New Delhi, India.
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22
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Ono CT, Yu Z, Kikuchi Y, Kunii Y, Hino M, Matsumoto J, Nagaoka A, Ito J, Iwasaki Y, Hagihara H, Miyakawa T, Yoshida M, Saito Y, Niwa SI, Yabe H, Kakita A, Tomita H. Minimal amount of tissue-based pH measurement to improve quality control in neuropsychiatric post-mortem brain studies. Psychiatry Clin Neurosci 2019; 73:566-573. [PMID: 31102310 DOI: 10.1111/pcn.12863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 12/23/2022]
Abstract
AIM Tissue pH and RNA integrity are crucial quality-control indicators of human post-mortem brain tissues in the identification of the pathogeneses of neuropsychiatric disorders, but pH has not been measured as often due to limitations in the amount of tissue available. This study was designed to develop and validate a protocol for tissue pH evaluation using a minimal amount of human post-mortem tissues. METHODS A procedure that included a proper ratio of brain tissue weight to water for homogenization and the duration of homogenization was designed based on preliminary experiments using mouse brain tissues. The minimal (10 mg) and typical (100 mg) amounts of post-mortem brain tissue from 52 subjects were homogenized in 5 volumes (50 μL/10 mg tissue) and 10 volumes (1000 μL/100 mg tissue) of nuclease-free water and subjected to pH measurements using an InLab Ultra micro pH electrode. RESULTS The pH values based on the new protocol using a minimal amount of tissue significantly correlated with measurements of the standard protocol (r2 = 0.86). The correlation coefficients of the pH values between gray and white matter of the same brain region, and the values between different brain regions were 0.73 and 0.54, respectively. CONCLUSION The proposed protocol used one-tenth of the tissue amount of current standard protocol and enabled us to evaluate the exact quality of post-mortem brain tissue subjected to subsequent analyses. The application of this protocol may improve the detection of biological phenomena of interest in post-mortem brain studies by diminishing confounding factors.
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Affiliation(s)
- Chiaki T Ono
- Department of Disaster Psychiatry, International Research Institute of Disaster Psychiatry, Tohoku University, Sendai, Japan
| | - Zhiqian Yu
- Department of Disaster Psychiatry, International Research Institute of Disaster Psychiatry, Tohoku University, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Disaster Psychiatry, International Research Institute of Disaster Psychiatry, Tohoku University, Sendai, Japan
| | - Yasuto Kunii
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan.,Department of Psychiatry, Aizu Medical Center, Fukushima Medical University, Fukushima, Japan
| | - Mizuki Hino
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Junya Matsumoto
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Junko Ito
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yasushi Iwasaki
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Hideo Hagihara
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Yuko Saito
- Department of Pathology and Laboratory Medicine, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Shin-Ichi Niwa
- Department of Psychiatry, Aizu Medical Center, Fukushima Medical University, Fukushima, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hiroaki Tomita
- Department of Disaster Psychiatry, International Research Institute of Disaster Psychiatry, Tohoku University, Sendai, Japan
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Puthumana JS, Regenold WT. Glucose-6-phosphate dehydrogenase activity in bipolar disorder and schizophrenia: Relationship to mitochondrial impairment. J Psychiatr Res 2019; 112:99-103. [PMID: 30875545 DOI: 10.1016/j.jpsychires.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/15/2019] [Accepted: 03/04/2019] [Indexed: 12/15/2022]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) is the first and rate-limiting enzyme of the pentose phosphate pathway that is essential to maintaining cellular redox balance. G6PD is especially plentiful in brain, and its deficiency has been linked to mood and psychotic disorders. We measured G6PD activity spectrophotometrically in four groups of 15 parietal somatosensory association cortex [Brodmann area (BA) 7] tissue samples (N = 60) from individuals with bipolar disorder (BPD); nonpsychotic unipolar major depression (UPD); schizophrenia (SCZ), and controls without psychiatric illness (CON). We report for the first time brain G6PD activity levels in these disorders. G6PD activity did not differ by brain group. In BPD and SCZ brains, however, it correlated significantly and inversely with percent of hexokinase 1 (HK1) in the tissue homogenate mitochondrial fraction as determined previously in another set of tissue samples obtained from the same brains and brain region. The correlation in SCZ brains lost statistical significance after controlling for brain pH. This finding indicates a positive relationship in BPD brains between G6PD activity and HK1 mitochondrial detachment, an indicator of mitochondrial impairment associated with increased mitochondrial generation of reactive oxygen species. We speculate that this relationship could be evidence that G6PD activity is proportionate to and may be a compensatory response to oxidative stress in the BA7 region of BPD brains. Future research should focus on clarifying the relationships among G6PD activity, markers of oxidative stress, brain pH, and evidence of mitochondrial impairment, particularly HK1 mitochondrial detachment, in brains of individuals with G6PD deficiency, BPD and SCZ.
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Affiliation(s)
- Joseph S Puthumana
- University of Maryland School of Medicine, 655 W Baltimore Street, Baltimore, MD, 21201, USA.
| | - William T Regenold
- University of Maryland School of Medicine, Department of Psychiatry, 22 S. Greene St, Baltimore, MD, 21201, USA.
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24
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Yoshimi A, Yamada S, Kunimoto S, Aleksic B, Hirakawa A, Ohashi M, Matsumoto Y, Hada K, Itoh N, Arioka Y, Kimura H, Kushima I, Nakamura Y, Shiino T, Mori D, Tanaka S, Hamada S, Noda Y, Nagai T, Yamada K, Ozaki N. Proteomic analysis of lymphoblastoid cell lines from schizophrenic patients. Transl Psychiatry 2019; 9:126. [PMID: 31011151 PMCID: PMC6476876 DOI: 10.1038/s41398-019-0461-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/28/2019] [Accepted: 03/12/2019] [Indexed: 11/09/2022] Open
Abstract
Although a number of studies have identified several convincing candidate genes or molecules, the pathophysiology of schizophrenia (SCZ) has not been completely elucidated. Therapeutic optimization based on pathophysiology should be performed as early as possible to improve functional outcomes and prognosis; to detect useful biomarkers for SCZ, which reflect pathophysiology and can be utilized for timely diagnosis and effective therapy. To explore biomarkers for SCZ, we employed fluorescence two-dimensional differential gel electrophoresis (2D-DIGE) of lymphoblastoid cell lines (LCLs) (1st sample set: 30 SCZ and 30 CON). Differentially expressed proteins were sequenced by liquid chromatography tandem-mass spectrometry (LC-MS/MS) and identified proteins were confirmed by western blotting (WB) (1st and 2nd sample set: 60 SCZ and 60 CON). Multivariate logistic regression analysis was performed to identify an optimal combination of biomarkers to create a prediction model for SCZ. Twenty protein spots were differentially expressed between SCZ and CON in 2D-DIGE analysis and 22 unique proteins were identified by LC-MS/MS. Differential expression of eight of 22 proteins was confirmed by WB. Among the eight candidate proteins (HSPA4L, MX1, GLRX3, UROD, MAPRE1, TBCB, IGHM, and GART), we successfully constructed logistic regression models comprised of 4- and 6-markers with good discriminative ability between SCZ and CON. In both WB and gene expression analysis of LCL, MX1 showed reproducibly significant associations. Moreover, Mx1 and its related proinflamatory genes (Mx2, Il1b, and Tnf) were also up-regulated in poly I:C-treated mice. Differentially expressed proteins might be associated with molecular pathophysiology of SCZ, including dysregulation of immunological reactions and potentially provide diagnostic and prognostic biomarkers.
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Affiliation(s)
- Akira Yoshimi
- grid.259879.8Division of Clinical Sciences and Neuropsychopharmacology, Faculty and Graduate School of Pharmacy, Meijo University, Nagoya, 468-8503 Japan ,0000 0001 0943 978Xgrid.27476.30Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan ,0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Shinnosuke Yamada
- grid.259879.8Division of Clinical Sciences and Neuropsychopharmacology, Faculty and Graduate School of Pharmacy, Meijo University, Nagoya, 468-8503 Japan ,0000 0001 0943 978Xgrid.27476.30Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Shohko Kunimoto
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
| | - Akihiro Hirakawa
- 0000 0001 2151 536Xgrid.26999.3dDepartment of Biostatistics and Bioinformatics, Graduate School of Medicine, University of Tokyo, Tokyo, 113-0033 Japan
| | - Mitsuki Ohashi
- grid.259879.8Division of Clinical Sciences and Neuropsychopharmacology, Faculty and Graduate School of Pharmacy, Meijo University, Nagoya, 468-8503 Japan
| | - Yurie Matsumoto
- grid.259879.8Division of Clinical Sciences and Neuropsychopharmacology, Faculty and Graduate School of Pharmacy, Meijo University, Nagoya, 468-8503 Japan ,0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Kazuhiro Hada
- 0000 0001 0943 978Xgrid.27476.30Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Norimichi Itoh
- 0000 0001 0943 978Xgrid.27476.30Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Yuko Arioka
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan ,0000 0004 0569 8970grid.437848.4Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, 466-8550 Japan
| | - Hiroki Kimura
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan ,0000 0004 0569 8970grid.437848.4Department of Psychiatry, Nagoya University Hospital, Nagoya, 466-8550 Japan
| | - Itaru Kushima
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan ,0000 0004 0569 8970grid.437848.4Department of Psychiatry, Nagoya University Hospital, Nagoya, 466-8550 Japan ,0000 0001 0943 978Xgrid.27476.30Institute for Advanced Research, Nagoya University, Nagoya, 464-8601 Japan
| | - Yukako Nakamura
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Tomoko Shiino
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan ,0000 0000 9832 2227grid.416859.7Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, 187-8553 Japan
| | - Daisuke Mori
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan ,0000 0001 0943 978Xgrid.27476.30Brain and Mind Research Center, Nagoya University, Nagoya, 466-8550 Japan
| | - Satoshi Tanaka
- 0000 0004 0569 8970grid.437848.4Department of Psychiatry, Nagoya University Hospital, Nagoya, 466-8550 Japan
| | - Shuko Hamada
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Yukihiro Noda
- grid.259879.8Division of Clinical Sciences and Neuropsychopharmacology, Faculty and Graduate School of Pharmacy, Meijo University, Nagoya, 468-8503 Japan ,0000 0001 0943 978Xgrid.27476.30Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan ,0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Taku Nagai
- 0000 0001 0943 978Xgrid.27476.30Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Kiyofumi Yamada
- 0000 0001 0943 978Xgrid.27476.30Department of Neuropsychopharmacology and Hospital Pharmacy, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan
| | - Norio Ozaki
- 0000 0001 0943 978Xgrid.27476.30Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, 466-8550 Japan ,0000 0004 0569 8970grid.437848.4Department of Psychiatry, Nagoya University Hospital, Nagoya, 466-8550 Japan
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25
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Abstract
An autopsy is a specialized surgical procedure consisting of external and internal examination of a deceased individual for the purposes of documenting abnormalities and determining or confirming medical diagnoses that may have contributed to their death. One of the benefits of an autopsy is the opportunity to collect and store biospecimens for the purposes of biobanking. This chapter outlines the procedures necessary to procure, store, and utilize biospecimens obtained during an autopsy. With the emergence of molecular diagnostics, this chapter also discusses factors that influence the integrity of autopsy biospecimens prior to procurement. These include the postmortem interval, as well as premortem factors such as the patient's agonal state, biospecimen temperature, and pH.
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26
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Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Losada PM, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science 2018; 362:eaat8127. [PMID: 30545856 PMCID: PMC6443102 DOI: 10.1126/science.aat8127] [Citation(s) in RCA: 677] [Impact Index Per Article: 112.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022]
Abstract
Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.
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Affiliation(s)
- Michael J. Gandal
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Evi Hadjimichael
- Department of Psychiatry, and Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rebecca L. Walker
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chao Chen
- The School of Life Science, Central South University, Changsha, Hunan 410078, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, Hunan, China
| | - Shuang Liu
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Hyejung Won
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Merina Varghese
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongjun Wang
- The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Annie W. Shieh
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jillian Haney
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Sepideh Parhami
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Judson Belmont
- Department of Psychiatry, and Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minsoo Kim
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Patricia Moran Losada
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Justyna Mleczko
- Departments of Medicine and Cardiology, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Xia
- The School of Life Science, Central South University, Changsha, Hunan 410078, China
| | - Rujia Dai
- The School of Life Science, Central South University, Changsha, Hunan 410078, China
| | - Daifeng Wang
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Yucheng T. Yang
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Min Xu
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Kenneth Fish
- Departments of Medicine and Cardiology, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick R. Hof
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Fishberg Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Dominic Fitzgerald
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Kevin White
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago IL 60637
- Tempus Labs, Inc. Chicago IL 60654
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Mette A. Peters
- CNS Data Coordination group, Sage Bionetworks, Seattle, WA 98109, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry and Computer Science, Yale University, New Haven, CT, USA
| | - Chunyu Liu
- The School of Life Science, Central South University, Changsha, Hunan 410078, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Dalila Pinto
- Department of Psychiatry, and Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel H. Geschwind
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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27
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Inference of cell type content from human brain transcriptomic datasets illuminates the effects of age, manner of death, dissection, and psychiatric diagnosis. PLoS One 2018; 13:e0200003. [PMID: 30016334 PMCID: PMC6049916 DOI: 10.1371/journal.pone.0200003] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/18/2018] [Indexed: 01/01/2023] Open
Abstract
Psychiatric illness is unlikely to arise from pathology occurring uniformly across all cell types in affected brain regions. Despite this, transcriptomic analyses of the human brain have typically been conducted using macro-dissected tissue due to the difficulty of performing single-cell type analyses with donated post-mortem brains. To address this issue statistically, we compiled a database of several thousand transcripts that were specifically-enriched in one of 10 primary cortical cell types in previous publications. Using this database, we predicted the relative cell type content for 833 human cortical samples using microarray or RNA-Seq data from the Pritzker Consortium (GSE92538) or publicly-available databases (GSE53987, GSE21935, GSE21138, CommonMind Consortium). These predictions were generated by averaging normalized expression levels across transcripts specific to each cell type using our R-package BrainInABlender (validated and publicly-released on github). Using this method, we found that the principal components of variation in the datasets strongly correlated with the predicted neuronal/glial content of the samples. This variability was not simply due to dissection–the relative balance of brain cell types appeared to be influenced by a variety of demographic, pre- and post-mortem variables. Prolonged hypoxia around the time of death predicted increased astrocytic and endothelial gene expression, illustrating vascular upregulation. Aging was associated with decreased neuronal gene expression. Red blood cell gene expression was reduced in individuals who died following systemic blood loss. Subjects with Major Depressive Disorder had decreased astrocytic gene expression, mirroring previous morphometric observations. Subjects with Schizophrenia had reduced red blood cell gene expression, resembling the hypofrontality detected in fMRI experiments. Finally, in datasets containing samples with especially variable cell content, we found that controlling for predicted sample cell content while evaluating differential expression improved the detection of previously-identified psychiatric effects. We conclude that accounting for cell type can greatly improve the interpretability of transcriptomic data.
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28
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White K, Yang P, Li L, Farshori A, Medina AE, Zielke HR. Effect of Postmortem Interval and Years in Storage on RNA Quality of Tissue at a Repository of the NIH NeuroBioBank. Biopreserv Biobank 2018; 16:148-157. [PMID: 29498539 PMCID: PMC5906728 DOI: 10.1089/bio.2017.0099] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Brain tissue from 1068 donors was analyzed for RNA quality as a function of postmortem interval (PMI) and years in storage. Approximately 83% of the cortical and cerebellar samples had an RNA integrity number (RIN) of 6 or greater, indicating their likely suitability for real-time quantitative polymerase chain reaction research. The average RIN value was independent of the PMI, up to at least 36 hours. The RNA quality for specific donated brains could not be predicted based on the PMI. Individual samples with a low PMI could have a poor RIN value, while a sample with a PMI over 36 hours may have a high RIN value. The RIN values for control brain donors, all of whom died suddenly and unexpectedly, were marginally higher than for individuals with clinical brain disorders. Polymerase chain reaction (PCR) analysis of samples confirmed that RIN values were more critical than PMI for determining suitability of tissue for molecular biological studies and samples should be matched by their RIN values rather than PMI. Importantly, PCR analysis established that tissue stored up to 23 years at −80°C yielded high-quality RNA. These results confirm that postmortem human brain tissue collected by brain and tissue banks over decades can serve as high quality material for the study of human disorders.
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Affiliation(s)
- Kimberly White
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
| | - Peixin Yang
- 2 Department of Obstetrics and Gynecology, University of Maryland School of Medicine , Baltimore, Maryland
| | - Ling Li
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland.,3 Office of the Chief Medical Examiner, Baltimore, Maryland
| | - Amna Farshori
- 4 Degree Program in Osteopathic Medicine, Edward Via College of Osteopathic Medicine , Blacksburg, Virginia
| | - Alexandre E Medina
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
| | - Horst Ronald Zielke
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
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29
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Hagihara H, Catts VS, Katayama Y, Shoji H, Takagi T, Huang FL, Nakao A, Mori Y, Huang KP, Ishii S, Graef IA, Nakayama KI, Shannon Weickert C, Miyakawa T. Decreased Brain pH as a Shared Endophenotype of Psychiatric Disorders. Neuropsychopharmacology 2018; 43:459-468. [PMID: 28776581 PMCID: PMC5770757 DOI: 10.1038/npp.2017.167] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/14/2017] [Accepted: 08/01/2017] [Indexed: 01/25/2023]
Abstract
Although the brains of patients with schizophrenia and bipolar disorder exhibit decreased brain pH relative to those of healthy controls upon postmortem examination, it remains controversial whether this finding reflects a primary feature of the diseases or is a result of confounding factors such as medication and agonal state. To date, systematic investigation of brain pH has not been undertaken using animal models that can be studied without confounds inherent in human studies. In the present study, we first reevaluated the pH of the postmortem brains of patients with schizophrenia and bipolar disorder by conducting a meta-analysis of existing data sets from 10 studies. We then measured pH, lactate levels, and related metabolite levels in brain homogenates from five neurodevelopmental mouse models of psychiatric disorders, including schizophrenia, bipolar disorder, and autism spectrum disorder. All mice were drug naive with the same agonal state, postmortem interval, and age within each strain. Our meta-analysis revealed that brain pH was significantly lower in patients with schizophrenia and bipolar disorder than in control participants, even when a few potential confounding factors (postmortem interval, age, and history of antipsychotic use) were considered. In animal experiments, we observed significantly lower pH and higher lactate levels in the brains of model mice relative to controls, as well as a significant negative correlation between pH and lactate levels. Our findings suggest that lower pH associated with increased lactate levels is not a mere artifact, but rather implicated in the underlying pathophysiology of schizophrenia and bipolar disorder.
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Affiliation(s)
- Hideo Hagihara
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Vibeke S Catts
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW, Australia,School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Yuta Katayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hirotaka Shoji
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Tsuyoshi Takagi
- Institute for Developmental Research, Aichi Human Service Center, Kasugai, Japan,RIKEN Tsukuba Institute, Tsukuba, Japan
| | - Freesia L Huang
- Program of Developmental Neurobiology, National Institute of Child Health and Human Development, National Institute of Health, Bethesda, MD, USA
| | - Akito Nakao
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kuo-Ping Huang
- Program of Developmental Neurobiology, National Institute of Child Health and Human Development, National Institute of Health, Bethesda, MD, USA
| | | | - Isabella A Graef
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Cynthia Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW, Australia,School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan,Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan, Tel: +81 562 93 9376, Fax: +81 562 92 5382, E-mail:
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Ramirez EPC, Keller CE, Vonsattel JP. The New York Brain Bank of Columbia University: practical highlights of 35 years of experience. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:105-118. [PMID: 29496134 DOI: 10.1016/b978-0-444-63639-3.00008-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The New York Brain Bank processes brains and organs of clinically well-characterized patients with age-related neurodegenerative diseases, and for comparison, from individuals without neurologic or psychiatric impairments. The donors, either patients or individuals, were evaluated at healthcare facilities of the Columbia University of New York. Each source brain yields four categories of samples: fresh frozen blocks and crushed parenchyma, and formalin-fixed wet blocks and histology sections. A source brain is thoroughly evaluated to determine qualitatively and quantitatively any changes it might harbor using conventional neuropathologic techniques. The clinical and pathologic diagnoses are integrated to determine the distributive diagnosis assigned to the samples obtained from a source brain. The gradual standardization of the protocol was developed in 1981 in response to the evolving requirements of basic investigations on neurodegeneration. The methods assimilate long-standing experience from multiple centers. The resulting and current protocol includes a constant central core applied to all brains with conditional flexibility around it. The New York Brain Bank is an integral part of the department of pathology, where the expertise, teaching duties, and hardware are shared. Since details of the protocols are available online, this chapter focuses on practical issues in professionalizing brain banking.
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Affiliation(s)
- Etty Paola Cortes Ramirez
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States; New York Brain Bank, Children's Hospital, New York, NY, United States
| | | | - Jean Paul Vonsattel
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States; New York Brain Bank, Children's Hospital, New York, NY, United States; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States.
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The art of matching brain tissue from patients and controls for postmortem research. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:197-217. [PMID: 29496142 DOI: 10.1016/b978-0-444-63639-3.00015-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The quality of postmortem research depends strongly on a thorough clinical investigation and documentation of the patient's disorder and therapies. In addition, a systematic and professional neuropathologic investigation of both cases and controls is absolutely crucial. In the experience of the Netherlands Brain Bank (NBB), about 20% of clinical neurologic diagnoses, despite being made in first-rate clinics, have to be revised or require an extra diagnosis after a complete and thorough review by the NBB. The neuropathology examination may reveal for instance that the "controls" already have preclinical neurodegenerative alterations. In postmortem studies the patient and control groups must be matched for as many of the known confounding factors as possible. This is necessary to make the groups as similar as possible, except for the topic being investigated. Confounding factors are present before, during, and after death. They are respectively: (1) genetic background, systemic diseases, duration and gravity of illness, medicines and addictive compounds used, age, sex, gender identity, sexual orientation, circadian and seasonal fluctuations, lateralization; (2) agonal state, stress of dying; and (3) postmortem delay, freezing procedures, fixation and storage time. Consequently, a brain bank should have a large number of controls at its disposal for appropriate matching. If matching fails for some confounders, then their influence may be determined by statistical methods such as analysis of variance or regression models.
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Miller JA, Guillozet-Bongaarts A, Gibbons LE, Postupna N, Renz A, Beller AE, Sunkin SM, Ng L, Rose SE, Smith KA, Szafer A, Barber C, Bertagnolli D, Bickley K, Brouner K, Caldejon S, Chapin M, Chua ML, Coleman NM, Cudaback E, Cuhaciyan C, Dalley RA, Dee N, Desta T, Dolbeare TA, Dotson NI, Fisher M, Gaudreault N, Gee G, Gilbert TL, Goldy J, Griffin F, Habel C, Haradon Z, Hejazinia N, Hellstern LL, Horvath S, Howard K, Howard R, Johal J, Jorstad NL, Josephsen SR, Kuan CL, Lai F, Lee E, Lee F, Lemon T, Li X, Marshall DA, Melchor J, Mukherjee S, Nyhus J, Pendergraft J, Potekhina L, Rha EY, Rice S, Rosen D, Sapru A, Schantz A, Shen E, Sherfield E, Shi S, Sodt AJ, Thatra N, Tieu M, Wilson AM, Montine TJ, Larson EB, Bernard A, Crane PK, Ellenbogen RG, Keene CD, Lein E. Neuropathological and transcriptomic characteristics of the aged brain. eLife 2017; 6. [PMID: 29120328 PMCID: PMC5679757 DOI: 10.7554/elife.31126] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/22/2017] [Indexed: 12/11/2022] Open
Abstract
As more people live longer, age-related neurodegenerative diseases are an increasingly important societal health issue. Treatments targeting specific pathologies such as amyloid beta in Alzheimer’s disease (AD) have not led to effective treatments, and there is increasing evidence of a disconnect between traditional pathology and cognitive abilities with advancing age, indicative of individual variation in resilience to pathology. Here, we generated a comprehensive neuropathological, molecular, and transcriptomic characterization of hippocampus and two regions cortex in 107 aged donors (median = 90) from the Adult Changes in Thought (ACT) study as a freely-available resource (http://aging.brain-map.org/). We confirm established associations between AD pathology and dementia, albeit with increased, presumably aging-related variability, and identify sets of co-expressed genes correlated with pathological tau and inflammation markers. Finally, we demonstrate a relationship between dementia and RNA quality, and find common gene signatures, highlighting the importance of properly controlling for RNA quality when studying dementia.
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Affiliation(s)
| | | | - Laura E Gibbons
- Department of Medicine, University of Washington, Seattle, United States
| | - Nadia Postupna
- Department of Pathology, University of Washington, Seattle, United States
| | - Anne Renz
- Kaiser Permanente Washington Health Research Institute, Seattle, United States
| | - Allison E Beller
- Department of Pathology, University of Washington, Seattle, United States
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, United States
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, United States
| | - Shannon E Rose
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, United States
| | - Chris Barber
- Allen Institute for Brain Science, Seattle, United States
| | | | | | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, United States
| | | | - Mike Chapin
- Allen Institute for Brain Science, Seattle, United States
| | - Mindy L Chua
- Department of Pathology, University of Washington, Seattle, United States
| | - Natalie M Coleman
- Department of Pathology, University of Washington, Seattle, United States
| | - Eiron Cudaback
- Department of Pathology, University of Washington, Seattle, United States
| | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, United States
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, United States
| | - Tim A Dolbeare
- Allen Institute for Brain Science, Seattle, United States
| | | | - Michael Fisher
- Allen Institute for Brain Science, Seattle, United States
| | | | - Garrett Gee
- Allen Institute for Brain Science, Seattle, United States
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, United States
| | - Fiona Griffin
- Allen Institute for Brain Science, Seattle, United States
| | - Caroline Habel
- Allen Institute for Brain Science, Seattle, United States
| | - Zeb Haradon
- Allen Institute for Brain Science, Seattle, United States
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, United States
| | - Leanne L Hellstern
- Department of Pathology, University of Washington, Seattle, United States
| | - Steve Horvath
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Kim Howard
- Department of Pathology, University of Washington, Seattle, United States
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, United States
| | - Justin Johal
- Allen Institute for Brain Science, Seattle, United States
| | - Nikolas L Jorstad
- Department of Pathology, University of Washington, Seattle, United States
| | - Samuel R Josephsen
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Florence Lai
- Allen Institute for Brain Science, Seattle, United States
| | - Eric Lee
- Allen Institute for Brain Science, Seattle, United States
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, United States
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, United States
| | - Xianwu Li
- Department of Pathology, University of Washington, Seattle, United States
| | - Desiree A Marshall
- Department of Pathology, University of Washington, Seattle, United States
| | - Jose Melchor
- Allen Institute for Brain Science, Seattle, United States
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, United States
| | | | | | - Elizabeth Y Rha
- Department of Pathology, University of Washington, Seattle, United States
| | - Samantha Rice
- Department of Pathology, University of Washington, Seattle, United States
| | - David Rosen
- Allen Institute for Brain Science, Seattle, United States
| | - Abharika Sapru
- Department of Pathology, University of Washington, Seattle, United States
| | - Aimee Schantz
- Department of Pathology, University of Washington, Seattle, United States
| | - Elaine Shen
- Allen Institute for Brain Science, Seattle, United States
| | - Emily Sherfield
- Department of Pathology, University of Washington, Seattle, United States
| | - Shu Shi
- Allen Institute for Brain Science, Seattle, United States
| | - Andy J Sodt
- Allen Institute for Brain Science, Seattle, United States
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, United States
| | - Angela M Wilson
- Department of Pathology, University of Washington, Seattle, United States
| | - Thomas J Montine
- Department of Pathology, University of Washington, Seattle, United States
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, United States
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, United States
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, United States
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, United States
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, United States
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, United States
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Abstract
PURPOSE OF REVIEW Posttraumatic stress disorder (PTSD) is characterized by hyperarousal and recurrent stressful memories after an emotionally traumatic event. Extensive research has been conducted to identify the neurobiological determinants that underlie the pathophysiology of PTSD. In this review, we examine evidence regarding the molecular and cellular pathophysiology of PTSD focusing on two primary brain regions: the vmPFC and the amygdala. RECENT FINDINGS This discussion includes a review of the molecular alterations related to PTSD, focusing mainly on changes to glucocorticoid receptor signaling. We also examine postmortem gene expression studies that have been conducted to date and the molecular changes that have been observed in peripheral blood studies of PTSD patients. Causal, mechanistic evidence is difficult to obtain in human studies, so we also review preclinical models of PTSD. Integration of peripheral blood and postmortem studies with preclinical models of PTSD has begun to reveal the molecular changes occurring in patients with PTSD. These findings indicate that the pathophysiology of PTSD includes disruption of glucocorticoid signaling and inflammatory systems and occurs at the level of altered gene expression. We will assess the impact of these findings on the future of PTSD molecular research.
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Affiliation(s)
- Matthew J Girgenti
- Department of Psychiatry, Laboratory of Molecular Psychiatry, Center for Genes and Behavior, Yale University School of Medicine, New Haven, CT, 06508, USA
| | - Brendan D Hare
- Department of Psychiatry, Laboratory of Molecular Psychiatry, Center for Genes and Behavior, Yale University School of Medicine, New Haven, CT, 06508, USA
| | - Sriparna Ghosal
- Department of Psychiatry, Laboratory of Molecular Psychiatry, Center for Genes and Behavior, Yale University School of Medicine, New Haven, CT, 06508, USA
| | - Ronald S Duman
- Department of Psychiatry, Laboratory of Molecular Psychiatry, Center for Genes and Behavior, Yale University School of Medicine, New Haven, CT, 06508, USA.
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Antipsychotic-induced Hdac2 transcription via NF-κB leads to synaptic and cognitive side effects. Nat Neurosci 2017; 20:1247-1259. [PMID: 28783139 DOI: 10.1038/nn.4616] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022]
Abstract
Antipsychotic drugs remain the standard for schizophrenia treatment. Despite their effectiveness in treating hallucinations and delusions, prolonged exposure to antipsychotic medications leads to cognitive deficits in both schizophrenia patients and animal models. The molecular mechanisms underlying these negative effects on cognition remain to be elucidated. Here we demonstrate that chronic antipsychotic drug exposure increases nuclear translocation of NF-κB in both mouse and human frontal cortex, a trafficking event triggered via 5-HT2A-receptor-dependent downregulation of the NF-κB repressor IκBα. This upregulation of NF-κB activity led to its increased binding at the Hdac2 promoter, thereby augmenting Hdac2 transcription. Deletion of HDAC2 in forebrain pyramidal neurons prevented the negative effects of antipsychotic treatment on synaptic remodeling and cognition. Conversely, virally mediated activation of NF-κB signaling decreased cortical synaptic plasticity via HDAC2. Together, these observations may aid in developing therapeutic strategies to improve the outcome of schizophrenia treatment.
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Normal Striatal Vesicular Acetylcholine Transporter Expression in Tourette Syndrome. eNeuro 2017; 4:eN-NWR-0178-17. [PMID: 28791334 PMCID: PMC5547197 DOI: 10.1523/eneuro.0178-17.2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/28/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022] Open
Abstract
Considerable prior work suggests basal ganglia dysfunction in Tourette syndrome (TS). Analysis of a small number of postmortem specimens suggests deficits of some striatal interneuron populations, including striatal cholinergic interneurons. To assess the integrity of striatal cholinergic interneurons in TS, we used [18F]FEOBV positron emission tomography (PET) to quantify striatal vesicular acetylcholine transporter (VAChT) expression, a measure of cholinergic terminal density, in human TS and control subjects. We found no evidence of striatal cholinergic deficits. Discrepant imaging and postmortem analysis results may reflect agonal or postmortem changes, medication effects, or significant disease heterogeneity.
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Abstract
BACKGROUND Psychiatric disorders are multigenic diseases with complex etiology that contribute significantly to human morbidity and mortality. Although clinically distinct, several disorders share many symptoms, suggesting common underlying molecular changes exist that may implicate important regulators of pathogenesis and provide new therapeutic targets. METHODS We performed RNA sequencing on tissue from the anterior cingulate cortex, dorsolateral prefrontal cortex, and nucleus accumbens from three groups of 24 patients each diagnosed with schizophrenia, bipolar disorder, or major depressive disorder, and from 24 control subjects. We identified differentially expressed genes and validated the results in an independent cohort. Anterior cingulate cortex samples were also subjected to metabolomic analysis. ChIP-seq data were used to characterize binding of the transcription factor EGR1. RESULTS We compared molecular signatures across the three brain regions and disorders in the transcriptomes of post-mortem human brain samples. The most significant disease-related differences were in the anterior cingulate cortex of schizophrenia samples compared to controls. Transcriptional changes were assessed in an independent cohort, revealing the transcription factor EGR1 as significantly down-regulated in both cohorts and as a potential regulator of broader transcription changes observed in schizophrenia patients. Additionally, broad down-regulation of genes specific to neurons and concordant up-regulation of genes specific to astrocytes was observed in schizophrenia and bipolar disorder patients relative to controls. Metabolomic profiling identified disruption of GABA levels in schizophrenia patients. CONCLUSIONS We provide a comprehensive post-mortem transcriptome profile of three psychiatric disorders across three brain regions. We highlight a high-confidence set of independently validated genes differentially expressed between schizophrenia and control patients in the anterior cingulate cortex and integrate transcriptional changes with untargeted metabolite profiling.
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A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer's Disease, Glioblastoma and Lung cancer. Sci Rep 2017; 7:4474. [PMID: 28667284 PMCID: PMC5493619 DOI: 10.1038/s41598-017-04400-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/25/2017] [Indexed: 11/27/2022] Open
Abstract
Epidemiological studies indicate that patients suffering from Alzheimer’s disease have a lower risk of developing lung cancer, and suggest a higher risk of developing glioblastoma. Here we explore the molecular scenarios that might underlie direct and inverse co-morbidities between these diseases. Transcriptomic meta-analyses reveal significant numbers of genes with inverse patterns of expression in Alzheimer’s disease and lung cancer, and with similar patterns of expression in Alzheimer’s disease and glioblastoma. These observations support the existence of molecular substrates that could at least partially account for these direct and inverse co-morbidity relationships. A functional analysis of the sets of deregulated genes points to the immune system, up-regulated in both Alzheimer’s disease and glioblastoma, as a potential link between these two diseases. Mitochondrial metabolism is regulated oppositely in Alzheimer’s disease and lung cancer, indicating that it may be involved in the inverse co-morbidity between these diseases. Finally, oxidative phosphorylation is a good candidate to play a dual role by decreasing or increasing the risk of lung cancer and glioblastoma in Alzheimer’s disease.
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38
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Warden AS, Mayfield RD. Gene expression profiling in the human alcoholic brain. Neuropharmacology 2017; 122:161-174. [PMID: 28254370 DOI: 10.1016/j.neuropharm.2017.02.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 01/12/2023]
Abstract
Long-term alcohol use causes widespread changes in gene expression in the human brain. Aberrant gene expression changes likely contribute to the progression from occasional alcohol use to alcohol use disorder (including alcohol dependence). Transcriptome studies have identified individual gene candidates that are linked to alcohol-dependence phenotypes. The use of bioinformatics techniques to examine expression datasets has provided novel systems-level approaches to transcriptome profiling in human postmortem brain. These analytical advances, along with recent developments in next-generation sequencing technology, have been instrumental in detecting both known and novel coding and non-coding RNAs, alternative splicing events, and cell-type specific changes that may contribute to alcohol-related pathologies. This review offers an integrated perspective on alcohol-responsive transcriptional changes in the human brain underlying the regulatory gene networks that contribute to alcohol dependence. This article is part of the Special Issue entitled "Alcoholism".
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Affiliation(s)
- Anna S Warden
- Institute for Neuroscience, The University of Texas at Austin, 1 University Station, C7000, Austin, TX 78712, USA; Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA.
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Morris G, Walder K, McGee SL, Dean OM, Tye SJ, Maes M, Berk M. A model of the mitochondrial basis of bipolar disorder. Neurosci Biobehav Rev 2017; 74:1-20. [DOI: 10.1016/j.neubiorev.2017.01.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 01/08/2017] [Accepted: 01/10/2017] [Indexed: 12/11/2022]
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40
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Azevedo JA, Carter BS, Meng F, Turner DL, Dai M, Schatzberg AF, Barchas JD, Jones EG, Bunney WE, Myers RM, Akil H, Watson SJ, Thompson RC. The microRNA network is altered in anterior cingulate cortex of patients with unipolar and bipolar depression. J Psychiatr Res 2016; 82:58-67. [PMID: 27468165 PMCID: PMC5026930 DOI: 10.1016/j.jpsychires.2016.07.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 11/26/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs acting as post-transcriptional regulators of gene expression. Though implicated in multiple CNS disorders, miRNAs have not been examined in any psychiatric disease state in anterior cingulate cortex (AnCg), a brain region centrally involved in regulating mood. We performed qPCR analyses of 29 miRNAs previously implicated in psychiatric illness (major depressive disorder (MDD), bipolar disorder (BP) and/or schizophrenia (SZ)) in AnCg of patients with MDD and BP versus controls. miR-132, miR-133a and miR-212 were initially identified as differentially expressed in BP, miR-184 in MDD and miR-34a in both MDD and BP (although none survived multiple correction testing and must be considered preliminary). In silico target prediction algorithms identified putative targets of differentially expressed miRNAs. Nuclear Co-Activator 1 (NCOA1), Nuclear Co-Repressor 2 (NCOR2) and Phosphodiesterase 4B (PDE4B) were selected based upon predicted targeting by miR-34a (with NCOR2 and PDE4B both targeted by miR-184) and published relevance to psychiatric illness. Luciferase assays identified PDE4B as a target of miR-34a and miR-184, while NCOA1 and NCOR2 were targeted by miR-34a and 184, respectively. qPCR analyses were performed to determine whether changes in miRNA levels correlated with mRNA levels of validated targets. NCOA1 showed an inverse correlation with miR-34a in BP, while NCOR2 demonstrated a positive correlation. In sum, this is the first study to demonstrate miRNA changes in AnCg in psychiatric illness and validate miR-34a as differentially expressed in CNS in MDD. These findings support a mechanistic role for miRNAs in the regulation of stress-responsive genes disrupted in psychiatric illness.
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Affiliation(s)
- Joshua A Azevedo
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Bradley S Carter
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Neuroscience Program, Oberlin College, Science Center A261, 119 Woodland St., Oberlin, OH, 44074, USA
| | - Fan Meng
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - David L Turner
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Department of Biological Chemistry, University of Michigan, 5301 MSRB III, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Manhong Dai
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA
| | - Alan F Schatzberg
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, 401 Quarry Rd, Stanford, CA, 94305, USA
| | - Jack D Barchas
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, Weill Cornell Medical College, 525 East 68th Street, New York, NY, 10065, USA
| | - Edward G Jones
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Center for Neuroscience, University of California - Davis, 1544 Newton Court, Davis, CA, 95618, USA
| | - William E Bunney
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Psychiatry and Human Behavior, University of California - Irvine, 101 The City Dr S, Orange, CA, 92868, USA
| | - Richard M Myers
- Pritzker Neuropsychiatric Disorders Research Consortium, USA; Hudson Alpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Huda Akil
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - Stanley J Watson
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA
| | - Robert C Thompson
- Molecular and Behavioral Neuroscience Institute, University of Michigan, 205 Zina Pitcher Pl, Ann Arbor, MI, 48109, USA; Neuroscience Graduate Program, University of Michigan, 4137 Undergraduate Science Building (USB), 204 Washtenaw Avenue, Ann Arbor, MI, 48109, USA; Pritzker Neuropsychiatric Disorders Research Consortium, USA; Department of Psychiatry, University of Michigan, 530 Church St, Ann Arbor, MI, 48109, USA.
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Hughey JJ, Butte AJ. Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans. J Biol Rhythms 2016; 31:588-597. [PMID: 27702781 PMCID: PMC5105327 DOI: 10.1177/0748730416668049] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The daily timing of mammalian physiology is coordinated by circadian clocks throughout the body. Although measurements of clock gene expression indicate that these clocks in mice are normally in phase with each other, the situation in humans remains unclear. We used publicly available data from five studies, comprising over 1000 samples, to compare the phasing of circadian gene expression in human brain and human blood. Surprisingly, after controlling for age, clock gene expression in brain was phase-delayed by ~8.5 h relative to that of blood. We then examined clock gene expression in two additional human organs and in organs from nine other mammalian species, as well as in the suprachiasmatic nucleus (SCN). In most tissues outside the SCN, the expression of clock gene orthologs showed a phase difference of ~12 h between diurnal and nocturnal species. The exception to this pattern was human brain, whose phasing resembled that of the SCN. Our results highlight the value of a multi-tissue, multi-species meta-analysis, and have implications for our understanding of the human circadian system.
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Affiliation(s)
- Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, California
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42
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Bakulski KM, Halladay A, Hu VW, Mill J, Fallin MD. Epigenetic Research in Neuropsychiatric Disorders: the "Tissue Issue". Curr Behav Neurosci Rep 2016; 3:264-274. [PMID: 28093577 DOI: 10.1007/s40473-016-0083-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Evidence has linked neuropsychiatric disorders with epigenetic marks as either a biomarker of disease, biomarker of exposure, or mechanism of disease processes. Neuropsychiatric epidemiologic studies using either target brain tissue or surrogate blood tissue each have methodological challenges and distinct advantages. RECENT FINDINGS Brain tissue studies are challenged by small sample sizes of cases and controls, incomplete phenotyping, post-mortem timing, and cellular heterogeneity, but the use of a primary disease relevant tissue is critical. Blood-based studies have access to much larger sample sizes and more replication opportunities, as well as the potential for longitudinal measurements, both prior to onset and during the course of treatments. Yet, blood studies also are challenged by cell-type heterogeneity, and many question the validity of using peripheral tissues as a brain biomarker. Emerging evidence suggests that these limitations to blood-based epigenetic studies are surmountable, but confirmation in target tissue remains important. SUMMARY Epigenetic mechanisms have the potential to help elucidate biology connecting experiential risk factors with neuropsychiatric disease manifestation. Cross-tissue studies as well as advanced epidemiologic methods should be employed to more effectively conduct neuropsychiatric epigenetic research.
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Affiliation(s)
- Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Alycia Halladay
- Autism Science Foundation, New York City, New York, USA; Department of Pharmacology and Toxicology, Rutgers University, New Brunswick, New Jersey, USA
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK; Institute for Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Abstract
The etiology and pathophysiology of schizophrenia and related mental disorders such as bipolar disorder and major depression remain largely unclear. Recent advances in mRNA profiling techniques made it possible to perform genome-wide gene expression analysis in a hypothesis-free manner. It was thought that this large-scale data mining approach would reveal unknown molecular cascades involved in mental disorders. Contrary to this initial expectation, however, DNA microarray results in psychiatric fields have been notoriously discordant. Here the authors review the findings of DNA microarray analysis, focusing on systematic gene expression changes in schizophrenia, as well as alterations in the expression of specific genes, that have been reported and replicated. The authors also address the probable causes for the discordance among studies, possible ways to solve the problem, and their preferred approach for data interpretation.
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Affiliation(s)
- Kazuya Iwamoto
- Laboratory for Molecular Dynamics of Mental Disorders, Brain Science Institute, RIKEN, Saitama, Japan.
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Walker DG, Whetzel AM, Serrano G, Sue LI, Lue LF, Beach TG. Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program. Cell Tissue Bank 2016; 17:361-75. [PMID: 27083469 DOI: 10.1007/s10561-016-9555-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 04/07/2016] [Indexed: 11/25/2022]
Abstract
Many factors affect the integrity of messenger RNA from human autopsy tissues including postmortem interval (PMI) between death and tissue preservation and the pre-mortem agonal and disease states. In this communication, we describe RNA isolation and characterization of 389 samples from 18 different tissues from elderly donors who were participants in a rapid whole-body autopsy program located in Sun City, Arizona ( www.brainandbodydonationprogram.org ). Most tissues were collected within a PMI of 2-6 h (median 3.15 h; N = 455), but for this study, tissue from cases with longer PMIs (1.25-29.25 h) were included. RNA quality was assessed by RNA integrity number (RIN) and total yield (ng RNA/mg tissue). RIN correlated with PMI for heart (r = -0.531, p = 0.009) and liver (r = -558, p = 0.0017), while RNA yield correlated with PMI for colon (r = -485, p = 0.016) and skin (r = -0.460, p = 0.031). RNAs with the lowest integrity were from skin and cervix where 22.7 and 31.4 % of samples respectively failed to produce intact RNA; by contrast all samples from esophagus, lymph node, jejunum, lung, stomach, submandibular gland and kidney produced RNA with measurable RINs. Expression levels in heart RNA of 4 common housekeeping normalization genes showed significant correlations of Ct values with RIN, but only one gene, glyceraldehyde-3 phosphate dehydrogenase, showed a correlation of Ct with PMI. There were no correlations between RIN values obtained for liver, adrenal, cervix, esophagus and lymph node and those obtained from corresponding brain samples. We show that high quality RNA can be produced from most human autopsy tissues, though with significant differences between tissues and donors. The RNA stability and yield did not depend solely on PMI; other undetermined factors are involved, but these do not include the age of the donor.
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Affiliation(s)
- Douglas G Walker
- Banner Sun Health Research Institute, Sun City, AZ, USA.
- Laboratory of Neuroinflammation, Biodesign Neurodegenerative Disease Research Center, Arizona State University, Room 538, School of Life Sciences - E Wing, 427 E. Tyler Mall, Tempe, AZ, 85287, USA.
| | | | - Geidy Serrano
- Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Lucia I Sue
- Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Lih-Fen Lue
- Laboratory of Neuroinflammation, Biodesign Neurodegenerative Disease Research Center, Arizona State University, Room 538, School of Life Sciences - E Wing, 427 E. Tyler Mall, Tempe, AZ, 85287, USA
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Gillio-Meina C, Zielke HR, Fraser DD. Translational Research in Pediatrics IV: Solid Tissue Collection and Processing. Pediatrics 2016; 137:peds.2015-0490. [PMID: 26659457 DOI: 10.1542/peds.2015-0490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 11/24/2022] Open
Abstract
Solid tissues are critical for child-health research. Specimens are commonly obtained at the time of biopsy/surgery or postmortem. Research tissues can also be obtained at the time of organ retrieval for donation or from tissue that would otherwise have been discarded. Navigating the ethics of solid tissue collection from children is challenging, and optimal handling practices are imperative to maximize tissue quality. Fresh biopsy/surgical specimens can be affected by a variety of factors, including age, gender, BMI, relative humidity, freeze/thaw steps, and tissue fixation solutions. Postmortem tissues are also vulnerable to agonal factors, body storage temperature, and postmortem intervals. Nonoptimal tissue handling practices result in nucleotide degradation, decreased protein stability, artificial posttranslational protein modifications, and altered lipid concentrations. Tissue pH and tryptophan levels are 2 methods to judge the quality of solid tissue collected for research purposes; however, the RNA integrity number, together with analyses of housekeeping genes, is the new standard. A comprehensive clinical data set accompanying all tissue samples is imperative. In this review, we examined: the ethical standards relating to solid tissue procurement from children; potential sources of solid tissues; optimal practices for solid tissue processing, handling, and storage; and reliable markers of solid tissue quality.
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Affiliation(s)
- Carolina Gillio-Meina
- Translational Research Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | | | - Douglas D Fraser
- Translational Research Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada; Centre for Critical Illness Research, Critical Care Medicine and Pediatrics, Clinical Neurologic Sciences, and Physiology and Pharmacology, Western University, London, Ontario, Canada
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Distinctive transcriptome alterations of prefrontal pyramidal neurons in schizophrenia and schizoaffective disorder. Mol Psychiatry 2015; 20:1397-405. [PMID: 25560755 PMCID: PMC4492919 DOI: 10.1038/mp.2014.171] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/14/2014] [Accepted: 11/12/2014] [Indexed: 12/12/2022]
Abstract
Schizophrenia is associated with alterations in working memory that reflect dysfunction of dorsolateral prefrontal cortex (DLPFC) circuitry. Working memory depends on the activity of excitatory pyramidal cells in DLPFC layer 3 and, to a lesser extent, in layer 5. Although many studies have profiled gene expression in DLPFC gray matter in schizophrenia, little is known about cell-type-specific transcript expression in these two populations of pyramidal cells. We hypothesized that interrogating gene expression, specifically in DLPFC layer 3 or 5 pyramidal cells, would reveal new and/or more robust schizophrenia-associated differences that would provide new insights into the nature of pyramidal cell dysfunction in the illness. We also sought to determine the impact of other variables, such as a diagnosis of schizoaffective disorder or medication use at the time of death, on the patterns of gene expression in pyramidal neurons. Individual pyramidal cells in DLPFC layers 3 or 5 were captured by laser microdissection from 36 subjects with schizophrenia or schizoaffective disorder and matched normal comparison subjects. The mRNA from cell collections was subjected to transcriptome profiling by microarray followed by quantitative PCR validation. Expression of genes involved in mitochondrial (MT) or ubiquitin-proteasome system (UPS) functions were markedly downregulated in the patient group (P-values for MT-related and UPS-related pathways were <10(-7) and <10(-5), respectively). MT-related gene alterations were more prominent in layer 3 pyramidal cells, whereas UPS-related gene alterations were more prominent in layer 5 pyramidal cells. Many of these alterations were not present, or found to a lesser degree, in samples of DLPFC gray matter from the same subjects, suggesting that they are pyramidal cell specific. Furthermore, these findings principally reflected alterations in the schizophrenia subjects were not present or present to a lesser degree in the schizoaffective disorder subjects (diagnosis of schizoaffective disorder was the most significant covariate, P<10(-6)) and were not attributable to factors frequently comorbid with schizophrenia. In summary, our findings reveal expression deficits in MT- and UPS-related genes specific to layer 3 and/or layer 5 pyramidal cells in the DLPFC of schizophrenia subjects. These cell type-specific transcriptome signatures are not characteristic of schizoaffective disorder, providing a potential molecular-cellular basis of differences in clinical phenotypes.
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Bagewadi S, Adhikari S, Dhrangadhariya A, Irin AK, Ebeling C, Namasivayam AA, Page M, Hofmann-Apitius M, Senger P. NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. Database (Oxford) 2015; 2015:bav099. [PMID: 26475471 PMCID: PMC4608514 DOI: 10.1093/database/bav099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 09/07/2015] [Accepted: 09/10/2015] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer's disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html.
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Affiliation(s)
- Shweta Bagewadi
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany,
| | - Subash Adhikari
- Department of Chemistry, South University of Science and Technology of China, No 1088, Xueyuan Road, Xili, Shenzhen, China
| | - Anjani Dhrangadhariya
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany
| | - Afroza Khanam Irin
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany
| | - Christian Ebeling
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany
| | - Aishwarya Alex Namasivayam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg and
| | - Matthew Page
- Translational Bioinformatics, UCB Pharma, 216 Bath Rd, Slough SL1 3WE, United Kingdom
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany, Rheinische Friedrich-Wilhelms-Universitaet Bonn, Bonn-Aachen International Center for Information Technology, 53113, Bonn, Germany
| | - Philipp Senger
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53754 Sankt Augustin, Germany,
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48
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Abstract
Both gene expression profiling in postmortem human brain and studies using animal models have implicated the fibroblast growth factor (FGF) family in affect regulation and suggest a potential role in the pathophysiology of major depressive disorder (MDD). FGF2, the most widely characterized family member, is down-regulated in the depressed brain and plays a protective role in rodent models of affective disorders. By contrast, using three microarray analyses followed by quantitative RT-PCR confirmation, we show that FGF9 expression is up-regulated in the hippocampus of individuals with MDD, and that FGF9 expression is inversely related to the expression of FGF2. Because little is known about FGF9's function in emotion regulation, we used animal models to shed light on its potential role in affective function. We found that chronic social defeat stress, an animal model recapitulating some aspects of MDD, leads to a significant increase in hippocampal FGF9 expression, paralleling the elevations seen in postmortem human brain tissue. Chronic intracerebroventricular administration of FGF9 increased both anxiety- and depression-like behaviors. In contrast, knocking down FGF9 expression in the dentate gyrus of the hippocampus using a lentiviral vector produced a decrease in FGF9 expression and ameliorated anxiety-like behavior. Collectively, these results suggest that high levels of hippocampal FGF9 play an important role in the development or expression of mood and anxiety disorders. We propose that the relative levels of FGF9 in relation to other members of the FGF family may prove key to understanding vulnerability or resilience in affective disorders.
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Beach TG, Adler CH, Sue LI, Serrano G, Shill HA, Walker DG, Lue L, Roher AE, Dugger BN, Maarouf C, Birdsill AC, Intorcia A, Saxon-Labelle M, Pullen J, Scroggins A, Filon J, Scott S, Hoffman B, Garcia A, Caviness JN, Hentz JG, Driver-Dunckley E, Jacobson SA, Davis KJ, Belden CM, Long KE, Malek-Ahmadi M, Powell JJ, Gale LD, Nicholson LR, Caselli RJ, Woodruff BK, Rapscak SZ, Ahern GL, Shi J, Burke AD, Reiman EM, Sabbagh MN. Arizona Study of Aging and Neurodegenerative Disorders and Brain and Body Donation Program. Neuropathology 2015; 35:354-89. [PMID: 25619230 DOI: 10.1111/neup.12189] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/11/2014] [Indexed: 12/13/2022]
Abstract
The Brain and Body Donation Program (BBDP) at Banner Sun Health Research Institute (http://www.brainandbodydonationprogram.org) started in 1987 with brain-only donations and currently has banked more than 1600 brains. More than 430 whole-body donations have been received since this service was commenced in 2005. The collective academic output of the BBDP is now described as the Arizona Study of Aging and Neurodegenerative Disorders (AZSAND). Most BBDP subjects are enrolled as cognitively normal volunteers residing in the retirement communities of metropolitan Phoenix, Arizona. Specific recruitment efforts are also directed at subjects with Alzheimer's disease, Parkinson's disease and cancer. The median age at death is 82. Subjects receive standardized general medical, neurological, neuropsychological and movement disorders assessments during life and more than 90% receive full pathological examinations by medically licensed pathologists after death. The Program has been funded through a combination of internal, federal and state of Arizona grants as well as user fees and pharmaceutical industry collaborations. Subsets of the Program are utilized by the US National Institute on Aging Arizona Alzheimer's Disease Core Center and the US National Institute of Neurological Disorders and Stroke National Brain and Tissue Resource for Parkinson's Disease and Related Disorders. Substantial funding has also been received from the Michael J. Fox Foundation for Parkinson's Research. The Program has made rapid autopsy a priority, with a 3.0-hour median post-mortem interval for the entire collection. The median RNA Integrity Number (RIN) for frozen brain and body tissue is 8.9 and 7.4, respectively. More than 2500 tissue requests have been served and currently about 200 are served annually. These requests have been made by more than 400 investigators located in 32 US states and 15 countries. Tissue from the BBDP has contributed to more than 350 publications and more than 200 grant-funded projects.
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Affiliation(s)
- Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Lucia I Sue
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Geidy Serrano
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Holly A Shill
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - LihFen Lue
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Alex E Roher
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Chera Maarouf
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Alex C Birdsill
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | - Joel Pullen
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Jessica Filon
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Sarah Scott
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Angelica Garcia
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | | | | | - Kathryn J Davis
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Kathy E Long
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | - Lisa D Gale
- Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | | | | | | | | | - Jiong Shi
- Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Anna D Burke
- Banner Alzheimer Institute, Phoenix, Arizona, USA
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Mucci NR, Moore HM, Brigham LE, Goldthwaite CA, Little AR, Lockhart NC, Scott MP, Struewing JP, Vincent SL, Compton CC. Meeting research needs with postmortem biospecimen donation: summary of recommendations for postmortem recovery of normal human biospecimens for research. Biopreserv Biobank 2014; 11:77-82. [PMID: 24845428 DOI: 10.1089/bio.2012.0063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Normal human tissues, bodily fluids, and other biospecimens of known quality are essential for research to understand the development of cancer and other diseases and to develop new diagnostics and therapies. However, obtaining normal biospecimens appropriate for contemporary large-scale molecular and genomic research is one of the most challenging biospecimen acquisition problems for scientists and biospecimen resources that support research. Recognizing this challenge, the U.S. National Cancer Institute recently convened a series of workshops and meetings focused on the acquisition of normal tissues for research and produced an extensive document, Recommendations for Postmortem Recovery of Normal Human Biospecimens for Research. This article summarizes these recommendations, addressing key ethical, operational, and scientific elements for collecting normal reference biospecimens from postmortem donors in the U.S. Awareness of these recommendations can foster more effective collaborations and mitigate potential logistical challenges, while promoting postmortem biospecimen donation options for families and increasing the availability of high quality normal biospecimens for research. The recommendations have been put into practice in the collection of normal human biospecimens for the NIH Genotype-Tissue Expression Program (GTEx), a pilot study of human gene expression and regulation in multiple tissues which will provide valuable insights into the mechanisms of gene regulation and, in the future, its disease-related perturbations (http://commonfund.nih.gov/GTEx/).
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