1
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Bellon A. Comparing stem cells, transdifferentiation and brain organoids as tools for psychiatric research. Transl Psychiatry 2024; 14:127. [PMID: 38418498 PMCID: PMC10901833 DOI: 10.1038/s41398-024-02780-8] [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: 04/17/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 03/01/2024] Open
Abstract
The inaccessibility of neurons coming directly from patients has hindered our understanding of mental illnesses at the cellular level. To overcome this obstacle, six different cellular approaches that carry the genetic vulnerability to psychiatric disorders are currently available: Olfactory Neuroepithelial Cells, Mesenchymal Stem Cells, Pluripotent Monocytes, Induced Pluripotent Stem Cells, Induced Neuronal cells and more recently Brain Organoids. Here we contrast advantages and disadvantages of each of these six cell-based methodologies. Neuronal-like cells derived from pluripotent monocytes are presented in more detail as this technique was recently used in psychiatry for the first time. Among the parameters used for comparison are; accessibility, need for reprograming, time to deliver differentiated cells, differentiation efficiency, reproducibility of results and cost. We provide a timeline on the discovery of these cell-based methodologies, but, our main goal is to assist researchers selecting which cellular approach is best suited for any given project. This manuscript also aims to help readers better interpret results from the published literature. With this goal in mind, we end our work with a discussion about the differences and similarities between cell-based techniques and postmortem research, the only currently available tools that allow the study of mental illness in neurons or neuronal-like cells coming directly from patients.
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Affiliation(s)
- Alfredo Bellon
- Penn State Hershey Medical Center, Department of Psychiatry and Behavioral Health, Hershey, PA, USA.
- Penn State Hershey Medical Center, Department of Pharmacology, Hershey, PA, USA.
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2
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Sahay S, Devine EA, McCullumsmith RE, O’Donovan SM. Adenosine Receptor mRNA Expression in Frontal Cortical Neurons in Schizophrenia. Cells 2023; 13:32. [PMID: 38201235 PMCID: PMC10778287 DOI: 10.3390/cells13010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Schizophrenia is a devastating neuropsychiatric disorder associated with the dysregulation of glutamate and dopamine neurotransmitter systems. The adenosine system is an important neuroregulatory system in the brain that modulates glutamate and dopamine signaling via the ubiquitously expressed adenosine receptors; however, adenosine A1 and A2A receptor (A1R and A2AR) mRNA expression is poorly understood in specific cell subtypes in the frontal cortical brain regions implicated in this disorder. In this study, we assayed A1R and A2AR mRNA expression via qPCR in enriched populations of pyramidal neurons, which were isolated from postmortem anterior cingulate cortex (ACC) tissue from schizophrenia (n = 20) and control (n = 20) subjects using laser microdissection (LMD). A1R expression was significantly increased in female schizophrenia subjects compared to female control subjects (t(13) = -4.008, p = 0.001). A1R expression was also significantly decreased in female control subjects compared to male control subjects, suggesting sex differences in basal A1R expression (t(17) = 2.137, p = 0.047). A significant, positive association was found between dementia severity (clinical dementia rating (CDR) scores) and A2AR mRNA expression (Spearman's r = 0.424, p = 0.009). A2AR mRNA expression was significantly increased in unmedicated schizophrenia subjects, suggesting that A2AR expression may be normalized by chronic antipsychotic treatment (F(1,14) = 9.259, p = 0.009). Together, these results provide novel insights into the neuronal expression of adenosine receptors in the ACC in schizophrenia and suggest that receptor expression changes may be sex-dependent and associated with cognitive decline in these subjects.
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Affiliation(s)
- Smita Sahay
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (S.S.); (R.E.M.)
| | - Emily A. Devine
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Robert E. McCullumsmith
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (S.S.); (R.E.M.)
- Neuroscience Institute Promedica, Toledo, OH 43606, USA
| | - Sinead M. O’Donovan
- Department of Neurosciences, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA; (S.S.); (R.E.M.)
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3
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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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4
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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: 149] [Impact Index Per Article: 74.5] [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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5
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Highet B, Parker R, Faull RLM, Curtis MA, Ryan B. RNA Quality in Post-mortem Human Brain Tissue Is Affected by Alzheimer's Disease. Front Mol Neurosci 2022; 14:780352. [PMID: 34992523 PMCID: PMC8724529 DOI: 10.3389/fnmol.2021.780352] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Gene expression studies of human post-mortem brain tissue are useful for understanding the pathogenesis of neurodegenerative disease. These studies rely on the assumption that RNA quality is consistent between disease and neurologically normal cases; however, previous studies have suggested that RNA quality may be affected by neurodegenerative disease. Here, we compared RNA quality in human post-mortem brain tissue between neurologically normal cases (n = 14) and neurodegenerative disease cases (Alzheimer’s disease n = 10; Parkinson’s disease n = 11; and Huntington’s disease n = 9) in regions affected by pathology and regions that are relatively devoid of pathology. We identified a statistically significant decrease in RNA integrity number (RIN) in Alzheimer’s disease tissue relative to neurologically normal tissue (mixed effects model, p = 0.04). There were no statistically significant differences between neurologically normal cases and Parkinson’s disease or Huntington’s disease cases. Next, we investigated whether total RNA quality affected mRNA quantification, by correlating RIN with qPCR threshold cycle (CT). CT values for all six genes investigated were strongly correlated with RIN (p < 0.05, Pearson correlation); this effect was only partially mitigated by normalization to RPL30. Our results indicate that RNA quality is decreased in Alzheimer’s disease tissue. We recommend that RIN should be considered when this tissue is used in gene expression analyses.
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Affiliation(s)
- Blake Highet
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Remai Parker
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Richard L M Faull
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Maurice A Curtis
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Brigid Ryan
- Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.,Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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6
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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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7
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Kim S, Webster MJ. The Stanley Neuropathology Consortium Integrative Database (SNCID) for Psychiatric Disorders. Neurosci Bull 2018; 35:277-282. [PMID: 30484114 DOI: 10.1007/s12264-018-0314-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sanghyeon Kim
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Maree J Webster
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD, 20850, USA.
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8
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Xu X, Stoyanova EI, Lemiesz AE, Xing J, Mash DC, Heintz N. Species and cell-type properties of classically defined human and rodent neurons and glia. eLife 2018; 7:e37551. [PMID: 30320555 PMCID: PMC6188473 DOI: 10.7554/elife.37551] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression and epigenetic events in specific cell types in a range of species, including postmortem human brain. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping and immunofluorescence localization. Studies of sixteen human postmortem brains revealed gender specific transcriptional differences, cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event evident in three donor samples. Our data establish a comprehensive approach for analysis of molecular events associated with specific circuits and cell types in a wide variety of human conditions.
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Affiliation(s)
- Xiao Xu
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Elitsa I Stoyanova
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Agata E Lemiesz
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Jie Xing
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
| | - Deborah C Mash
- Miller School of MedicineUniversity of MiamiMiamiUnited States
| | - Nathaniel Heintz
- Laboratory of Molecular BiologyHoward Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
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9
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Weickert CS, Rothmond DA, Purves-Tyson TD. Considerations for optimal use of postmortem human brains for molecular psychiatry: lessons from schizophrenia. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:221-235. [PMID: 29496143 DOI: 10.1016/b978-0-444-63639-3.00016-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Schizophrenia is a disabling disease impacting millions of people around the world, for which there is no known cure. Current antipsychotic treatments for schizophrenia mainly target psychotic symptoms, do little to ameliorate social or cognitive deficits, have side-effects that cause weight gain, and diabetes and 30% of people do not respond. Thus, better therapeutics for schizophrenia aimed at the route biologic changes are needed and discovering the underlying neurobiology is key to this quest. Postmortem brain studies provide the most direct and detailed way to determine the pathophysiology of schizophrenia. This chapter outlines steps that can be taken to ensure the best-quality molecular data from postmortem brain tissue are obtained. In this chapter, we also discuss targeted and high-throughput methods for examining gene and protein expression and some of the strengths and limitations of each method. We briefly consider why gene and protein expression changes may not always concur within brain tissue. We conclude that postmortem brain research that investigates gene and protein expression in well-characterized and matched brain cohorts provides an important foundation to be considered when interpreting data obtained from studies of living schizophrenia patients.
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Affiliation(s)
- Cynthia Shannon Weickert
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia; Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, Australia.
| | - Debora A Rothmond
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, Australia
| | - Tertia D Purves-Tyson
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia; Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, Australia
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10
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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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11
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Sonntag KC, Woo TUW. Laser microdissection and gene expression profiling in the human postmortem brain. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:263-272. [PMID: 29496145 DOI: 10.1016/b978-0-444-63639-3.00018-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Laser microdissection in combination with gene expression profiling using postmortem human brain tissue provides a powerful approach to interrogating cell type-specific pathologies within neural circuits that are known to be dysfunctional in neuropsychiatric disorders. The success of these experiments critically depends on a number of factors, such as the cellular purity of the sample, the quality of the RNA, the methodologies of data normalization and computational data analysis, and how data are interpreted. Data obtained from these experiments should be validated at the protein level. Furthermore, from the perspective of disease mechanism discovery, it would be ideal to investigate whether manipulation of the expression of genes identified as differentially expressed can rescue or ameliorate the neurobiologic or behavioral phenotypes associated with the specific disease. Thus, the ultimate value of this approach rests upon the fact that the generation of novel disease-related pathophysiologic hypotheses may lead to deeper understanding of disease mechanisms and possible development of effective targeted treatments.
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Affiliation(s)
- Kai-Christian Sonntag
- Laboratory for Translational Research on Neurodegeneration, Belmont, MA, United States; Department of Psychiatry, Harvard Medical School, Boston, MA, United States
| | - Tsung-Ung W Woo
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, MA, United States; Department of Psychiatry, Harvard Medical School, Boston, MA, United States.
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12
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Kramvis I, Mansvelder HD, Meredith RM. Neuronal life after death: electrophysiologic recordings from neurons in adult human brain tissue obtained through surgical resection or postmortem. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:319-333. [PMID: 29496151 DOI: 10.1016/b978-0-444-63639-3.00022-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recordings from fresh human brain slices derived from surgically resected brain tissue are being used to unravel mechanisms underlying human neurophysiology and for the evaluation of potential therapeutic targets and compounds. Data resulting from these studies provide unique insights into physiologic properties of human neuronal microcircuits. However, substantial limitations still remain with this approach. First, the tissue is always resected from patients, never from healthy controls. Second, the patient population undergoing brain surgery with tissue resection is limited to epilepsy and tumor patients - never from patients with other neurologic disorders. Third, the vast majority of tissue resected is limited largely to temporal cortex and hippocampus, occasionally amygdala. Therefore, the possibility to study brain tissue: (1) from healthy controls; (2) from patients with different neuropathologies; (3) from different brain areas; and (4) from a wide spectrum of ages only exists through autopsy-derived brain tissue. Here we describe methods and results from physiologic recordings of adult human neurons and microcircuits in both surgically derived brain tissue as well as in tissue derived from autopsies. We define postmortem time windows during which physiologic recordings could match data obtained from surgical tissue.
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Affiliation(s)
- Ioannis Kramvis
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, The Netherlands.
| | - Rhiannon M Meredith
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, The Netherlands
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13
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Mighdoll MI, Hyde TM. Brain donation at autopsy: clinical characterization and toxicologic analyses. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:143-154. [PMID: 29496137 DOI: 10.1016/b978-0-444-63639-3.00011-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The study of postmortem human brain tissue is central to the advancement of neurobiologic studies of psychiatric and neurologic illnesses, particularly the study of brain-specific isoforms and molecules. Due to tissue demands, especially pertaining to brain regions strongly implicated in the pathophysiology of neuropsychiatric disorders, the success and future of this research depend on the availability of high-quality brain specimens from large numbers of subjects, including nonpsychiatric controls, both of which may be obtained from brain banks. In this chapter, we elaborate on the need for and acquisition of well-curated and properly diagnosed postmortem human brains, relying upon our experience with the Human Brain and Tissue Repository located at the Lieber Institute for Brain Development in Baltimore, MD. We explain the advantages of sourcing postmortem human tissue from medical examiner offices, which provide access to cases of all ages, both with and without central nervous system disorders. Neuropathology analyses and toxicologic screenings, along with autopsy reports and extensive interviews with family members and treating physicians, are invaluable to the diagnoses of postmortem cases. Ultimately, the study of psychiatric and neurologic disorders is the study of brain disease, and accordingly, there is no substitution for human brain tissue.
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Affiliation(s)
- Michelle I Mighdoll
- Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Abstract
The National PTSD Brain Bank (NPBB) is a brain tissue biorepository established to support research on the causes, progression, and treatment of PTSD. It is a six-part consortium led by VA's National Center for PTSD with participating sites at VA medical centers in Boston, MA; Durham, NC; Miami, FL; West Haven, CT; and White River Junction, VT along with the Uniformed Services University of Health Sciences. It is also well integrated with VA's Boston-based brain banks that focus on Alzheimer's disease, ALS, chronic traumatic encephalopathy, and other neurological disorders. This article describes the organization and operations of NPBB with specific attention to: tissue acquisition, tissue processing, diagnostic assessment, maintenance of a confidential data biorepository, adherence to ethical standards, governance, accomplishments to date, and future challenges. Established in 2014, NPBB has already acquired and distributed brain tissue to support research on how PTSD affects brain structure and function.
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15
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Decreased NOX2 expression in the brain of patients with bipolar disorder: association with valproic acid prescription and substance abuse. Transl Psychiatry 2017; 7:e1206. [PMID: 28809856 PMCID: PMC5611741 DOI: 10.1038/tp.2017.175] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/05/2017] [Accepted: 06/13/2017] [Indexed: 12/19/2022] Open
Abstract
Neuroinflammation and increased oxidative stress are believed to contribute to the development of psychiatric diseases. Animal studies have implicated NADPH oxidases (NOX) as relevant sources of reactive oxygen species in the brain. We have analyzed the expression of NOX isoforms in post-mortem brain samples from patients with psychiatric disorders (schizophrenia, bipolar disorder) and non-psychiatric subjects. Two collections from the Stanley Medical Research Institute were studied: the Array Collection (RNA, 35 individuals per group), and a neuropathology consortium collection (paraffin-embedded sections, 15 individuals per group). Quantitative PCR analysis revealed expression of NOX2 and NOX4 in prefrontal cortex. No impact of psychiatric disease on NOX4 levels was detected. Remarkably, the expression of NOX2 was specifically decreased in prefrontal and cingulate cortices of bipolar patients, as compared with controls and schizophrenic patients. NOX2 expression was not statistically associated with demographic parameters and post-mortem interval, but correlated with brain pH. Immunostaining demonstrated that NOX2 was predominantly expressed in microglia, which was corroborated by a decrease in the microglial markers CD68 and CD11b in the cingulate cortex of bipolar disorder patients. The analysis of potentially confounding parameters showed association of valproic acid prescription and heavy substance abuse with lower levels of NOX2. Taken together, we did not observe changes of NOX2 in schizophrenic patients, but a marked decrease of microglial markers and NOX2 in the brain of bipolar patients. This might be an underlying feature of bipolar disorder and/or a consequence of valproic acid treatment and substance abuse.
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16
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Palmer-Aronsten B, Sheedy D, McCrossin T, Kril J. An International Survey of Brain Banking Operation and Characterization Practices. Biopreserv Biobank 2016; 14:464-469. [PMID: 27399803 DOI: 10.1089/bio.2016.0003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Brain banks continue to make a major contribution to the study of neurological and psychiatric disorders. The current complexity and scope of research heighten the need for well-characterized cases and the demand for larger cohorts and necessitate strategies, such as the establishment of bank networks based in regional areas. While individual brain banks have developed protocols that meet researchers' needs within the confines of resources and funding, to further promote collaboration, standardization and scientific validity and understanding of the current protocols of participating banks are required. A survey was sent to brain banks, identified by an Internet search, to investigate operational protocols, case characterization, cohort management, data collection, standardization, and degree of collaboration between banks. The majority of the 24 banks that returned the survey have been established for more than 20 years, and most are affiliated with a regional network. While prospective donor programs were the primary source of donation, the data collected on donors varied. Longitudinal information assists case characterization and enhances the analysis capabilities of research. However, acquiring this information depended on the availability of qualified staff. Respondents indicated a high level of importance for standardization, but only 8 of 24 considered this occurred between banks. Standard diagnostic criteria were not achieved in the classification of controls, and some banks relied on the researcher to indicate the criteria for classification of controls. Although the capacity to collaborate with other banks was indicated by 16 of 24 banks, this occurred infrequently. Engagement of all brain banks to participate toward a consensus of diagnostic tools, especially for controls, will strengthen collaboration.
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Affiliation(s)
- Beatrix Palmer-Aronsten
- 1 NSW Brain Tissue Resource Centre, Charles Perkins Centre, and Discipline of Pathology, Sydney Medical School, University of Sydney , Sydney, Australia .,2 Schizophrenia Research Institute , Randwick, Australia
| | - Donna Sheedy
- 1 NSW Brain Tissue Resource Centre, Charles Perkins Centre, and Discipline of Pathology, Sydney Medical School, University of Sydney , Sydney, Australia
| | - Toni McCrossin
- 1 NSW Brain Tissue Resource Centre, Charles Perkins Centre, and Discipline of Pathology, Sydney Medical School, University of Sydney , Sydney, Australia
| | - Jillian Kril
- 1 NSW Brain Tissue Resource Centre, Charles Perkins Centre, and Discipline of Pathology, Sydney Medical School, University of Sydney , Sydney, Australia
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17
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Sonntag KC, Tejada G, Subburaju S, Berretta S, Benes FM, Woo TUW. Limited predictability of postmortem human brain tissue quality by RNA integrity numbers. J Neurochem 2016; 138:53-9. [PMID: 27062510 DOI: 10.1111/jnc.13637] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 12/19/2022]
Abstract
The RNA integrity number (RIN) is often considered to be a critical measure of the quality of postmortem human brains. However, it has been suggested that RINs do not necessarily reflect the availability of intact mRNA. Using the Agilent bioanalyzer and qRT-PCR, we explored whether RINs provide a meaningful way of assessing mRNA degradation and integrity in human brain samples by evaluating the expression of 3'-5' mRNA sequences of the cytochrome C-1 (CYC1) gene. Analysis of electropherograms showed that RINs were not consistently correlated with RNA or cDNA profiles and appeared to be poor predictors of overall cDNA quality. Cycle thresholds from qRT-PCR analysis to quantify the amount of CYC1 mRNA revealed positive correlations of RINs with amplification of full-length transcripts, despite the variable degree of linear degradation along the 3'-5' sequence. These data demonstrate that in postmortem human brain tissue the RIN is an indicator of mRNA quantity independent of degradation, but does not predict mRNA integrity, suggesting that RINs provide an incomplete measure of brain tissue quality. Quality assessment of postmortem human brains by RNA integrity numbers (RINs) may be misleading, as they do not measure intact mRNAs. We show that the RIN is an indicator of mRNA quantity independent of degradation, but does not predict mRNA integrity, suggesting that RINs provide an incomplete measure of brain tissue quality. Our results resolve controversial assumption on interpreting quality assessments of human postmortem brains by RINs.
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Affiliation(s)
- Kai-C Sonntag
- Division of Basic Neuroscience, Department of Psychiatry, Harvard Brain Tissue Resource Center, McLean Hospital/Harvard Medical School, Belmont, Massachusetts, USA
| | - George Tejada
- Division of Basic Neuroscience, Department of Psychiatry, Harvard Brain Tissue Resource Center, McLean Hospital/Harvard Medical School, Belmont, Massachusetts, USA
| | - Sivan Subburaju
- Division of Basic Neuroscience, Department of Psychiatry, Harvard Brain Tissue Resource Center, McLean Hospital/Harvard Medical School, Belmont, Massachusetts, USA
| | - Sabina Berretta
- Division of Basic Neuroscience, Department of Psychiatry, Harvard Brain Tissue Resource Center, McLean Hospital/Harvard Medical School, Belmont, Massachusetts, USA
| | - Francine M Benes
- Division of Basic Neuroscience, Department of Psychiatry, Harvard Brain Tissue Resource Center, McLean Hospital/Harvard Medical School, Belmont, Massachusetts, USA
| | - Tsung-Ung W Woo
- Division of Basic Neuroscience, Department of Psychiatry, Harvard Brain Tissue Resource Center, McLean Hospital/Harvard Medical School, Belmont, Massachusetts, USA
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18
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Kimoto S, Glausier JR, Fish KN, Volk DW, Bazmi HH, Arion D, Datta D, Lewis DA. Reciprocal Alterations in Regulator of G Protein Signaling 4 and microRNA16 in Schizophrenia. Schizophr Bull 2016; 42:396-405. [PMID: 26424323 PMCID: PMC4753606 DOI: 10.1093/schbul/sbv139] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
N-methyl-d-aspartate receptor (NMDAR) hypofunction in the dorsolateral prefrontal cortex (DLPFC) has been implicated in the pathology of schizophrenia. NMDAR activity is negatively regulated by some G protein-coupled receptors (GPCRs). Signaling through these GPCRs is reduced by Regulator of G protein Signaling 4 (RGS4). Thus, lower levels of RGS4 would enhance GPCR-mediated reductions in NMDAR activity and could contribute to NMDAR hypofunction in schizophrenia. In this study, we quantified RGS4 mRNA and protein levels at several levels of resolution in the DLPFC from subjects with schizophrenia and matched healthy comparison subjects. To investigate molecular mechanisms that could contribute to altered RGS4 levels, we quantified levels of small noncoding RNAs, known as microRNAs (miRs), which regulate RGS4 mRNA integrity after transcription. RGS4 mRNA and protein levels were significantly lower in schizophrenia subjects and were positively correlated across all subjects. The RGS4 mRNA deficit was present in pyramidal neurons of DLPFC layers 3 and 5 of the schizophrenia subjects. In contrast, levels of miR16 were significantly higher in the DLPFC of schizophrenia subjects, and higher miR16 levels predicted lower RGS4 mRNA levels. These findings provide convergent evidence of lower RGS4 mRNA and protein levels in schizophrenia that may result from increased expression of miR16. Given the role of RGS4 in regulating GPCRs, and consequently the strength of NMDAR signaling, these findings could contribute to the molecular substrate for NMDAR hypofunction in DLPFC pyramidal cells in schizophrenia.
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Affiliation(s)
- Sohei Kimoto
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA; Department of Psychiatry, Nara Medical University, Nara, Japan
| | - Jill R Glausier
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | - Kenneth N Fish
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | - David W Volk
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | - H Holly Bazmi
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | - Dominique Arion
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | - Dibyadeep Datta
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA; Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA
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19
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El-Kashef N, Gomes I, Mercer-Chalmers-Bender K, Schneider PM, Rothschild MA, Juebner M. Validation of adequate endogenous reference genes for reverse transcription-qPCR studies in human post-mortem brain tissue of SIDS cases. Forensic Sci Med Pathol 2015; 11:517-29. [DOI: 10.1007/s12024-015-9717-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2015] [Indexed: 01/04/2023]
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20
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Berretta S, Heckers S, Benes FM. Searching human brain for mechanisms of psychiatric disorders. Implications for studies on schizophrenia. Schizophr Res 2015; 167:91-7. [PMID: 25458567 PMCID: PMC4427537 DOI: 10.1016/j.schres.2014.10.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 12/14/2022]
Abstract
In the past 25years, research on the human brain has been providing a clear path toward understanding the pathophysiology of psychiatric illnesses. The successes that have been accrued are matched by significant difficulties identifying and controlling a large number of potential confounding variables. By systematically and effectively accounting for unwanted variance in data from imaging and postmortem human brain studies, meaningful and reliable information regarding the pathophysiology of human brain disorders can be obtained. This perspective paper focuses on postmortem investigations to discuss some of the most challenging sources of variance, including diagnosis, comorbidity, substance abuse and pharmacological treatment, which confound investigations of the human brain.
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Affiliation(s)
- Sabina Berretta
- Translational Neuroscience Laboratory, McLean Hospital, 115 Mill St., Belmont, MA 02478, USA; Department of Psychiatry, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA; Program in Neuroscience, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA.
| | - Stephan Heckers
- Department of Psychiatry, Vanderbilt University. 161 21st Ave S. #T1217 Nashville, TN, USA
| | - Francine M. Benes
- Dept. of Psychiatry, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA,Program in Neuroscience, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA,Program in Structural and Molecular Neuroscience, 115 Mill St. Belmont MA, 02478, USA
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21
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Abstract
Postmortem brain research is invaluable to the study of neurologic and neuropsychiatric disorders, including Alzheimer disease, schizophrenia, and major depression. A major confounder in molecular studies using human brain tissue is postmortem interval (i.e. the amount of time between a subject's death and processing of tissue). We examined the integrity of biomolecules that were of interest to molecular studies of neurologic disorders, including RNA, microRNA, histone modifications, and proteins, at various postmortem intervals in an animal model to assess their robustness and suitability for experimentation. Sprague-Dawley rats were selected as model and subjected to 2 conditions: a variable postmortem interval at room temperature and a fixed time of 24 hours at 4°C, which simulates the period commonly spent in the morgue before brain collection. Eight time points were investigated. MicroRNA was impressively resistant to postmortem intervals; methylated histone modifications showed a threshold between 72 and 96 hours, mirroring results from histone proteins at 72 hours. RNA degradation was transcript-specific, with housekeeping genes being more robust than genes with lower expression. Our results suggest that molecules commonly investigated in genetic and epigenetic studies were highly stable through the postmortem intervals investigated. These results support the continued use of postmortem tissue for neuropsychiatric research.
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22
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Ferrer I. Selection of controls in the study of human neurodegenerative diseases in old age. J Neural Transm (Vienna) 2014; 122:941-7. [DOI: 10.1007/s00702-014-1287-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 07/24/2014] [Indexed: 12/13/2022]
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23
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Kohen R, Dobra A, Tracy JH, Haugen E. Transcriptome profiling of human hippocampus dentate gyrus granule cells in mental illness. Transl Psychiatry 2014; 4:e366. [PMID: 24594777 PMCID: PMC3966046 DOI: 10.1038/tp.2014.9] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/06/2014] [Indexed: 12/20/2022] Open
Abstract
This study is, to the best of our knowledge, the first application of whole transcriptome sequencing (RNA-seq) to cells isolated from postmortem human brain by laser capture microdissection. We investigated the transcriptome of dentate gyrus (DG) granule cells in postmortem human hippocampus in 79 subjects with mental illness (schizophrenia, bipolar disorder, major depression) and nonpsychiatric controls. We show that the choice of normalization approach for analysis of RNA-seq data had a strong effect on results; under our experimental conditions a nonstandard normalization method gave superior results. We found evidence of disrupted signaling by miR-182 in mental illness. This was confirmed using a novel method of leveraging microRNA genetic variant information to indicate active targeting. In healthy subjects and those with bipolar disorder, carriers of a high- vs those with a low-expressing genotype of miR-182 had different levels of miR-182 target gene expression, indicating an active role of miR-182 in shaping the DG transcriptome for those subject groups. By contrast, comparing the transcriptome between carriers of different genotypes among subjects with major depression and schizophrenia suggested a loss of DG miR-182 signaling in these conditions.
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Affiliation(s)
- R Kohen
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA,Department of Psychiatry and Behavioral Sciences, University of Washington, 1959 Pacific Avenue NE, Seattle, WA 98195-6560, USA. E-mail:
| | - A Dobra
- Department of Statistics, University of Washington, Seattle, WA, USA,Department of Biobehavioral Nursing and Health Systems, University of Washington, Seattle, WA, USA,Center for Statistics and The Social Sciences, University of Washington, Seattle, WA, USA
| | - J H Tracy
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - E Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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24
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Aktas B, Sun H, Yao H, Shi W, Hubbard R, Zhang Y, Jiang T, Ononye SN, Wali VB, Pusztai L, Symmans WF, Hatzis C. Global gene expression changes induced by prolonged cold ischemic stress and preservation method of breast cancer tissue. Mol Oncol 2014; 8:717-27. [PMID: 24602449 DOI: 10.1016/j.molonc.2014.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/17/2014] [Accepted: 02/05/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Tissue handling can alter global gene expression potentially affecting the analytical performance of genomic signatures, but such effects have not been systematically evaluated. METHODS Tissue samples from 11 previously untreated breast tumors were minced and aliquots were either snap frozen or placed in RNAlater immediately or after 20, 40, 60, 120 or 180 min at room temperature. RNA was profiled on Affymetrix HG-U133A arrays. We used probe-set-wise hierarchical models to evaluate the effect of preservation method on transcript expression and linear mixed effects models to assess the effect of cold ischemic delay on the expression of individual probe sets. Gene set enrichment analysis identified pathways overrepresented in the affected transcripts. We combined the levels of 41 most sensitive transcripts to develop an index of ischemic stress. RESULTS Concordance in global gene expression between the baseline and 40 min delay was higher for samples preserved in RNAlater (average concordance correlation coefficient CCC = 0.92 compared to 0.88 for snap frozen). Overall, 481 transcripts (3%) were significantly affected by the preservation method, most of them involved in processes important in cancer. Prolonged cold ischemic delay of up to 3 h induced marginal global gene expression changes (average CCC = 0.90 between baseline and 3 h delay). However 41 transcripts were significantly affected by cold ischemic delay. Among the induced transcripts were stress response genes, apoptotic response genes; among the downregulated were genes involved in metabolism, protein processing and cell cycle regulation. An index combining the expression levels of these genes was proportional to the cold ischemic delay. CONCLUSIONS Prolonged cold ischemia induces significant transcriptional changes in a small subset of transcripts in the tissue. Furthermore, the expression level of about 3% of the transcripts is affected by the preservation method. These sensitive transcripts should not be included in genomic signatures for more reliable analytical performance.
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Affiliation(s)
- Bilge Aktas
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Hongxia Sun
- Department of Pathology, UT M.D. Anderson Cancer Center, P.O. Box 85, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, UT M.D. Anderson Cancer Center, P.O. Box 301402, Houston, TX 77230, USA
| | - Weiwei Shi
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Rebekah Hubbard
- Department of Pathology, UT M.D. Anderson Cancer Center, P.O. Box 85, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Ya Zhang
- Department of Pathology, UT M.D. Anderson Cancer Center, P.O. Box 85, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Tingting Jiang
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Sophia N Ononye
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Vikram B Wali
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Lajos Pusztai
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - W Fraser Symmans
- Department of Pathology, UT M.D. Anderson Cancer Center, P.O. Box 85, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Christos Hatzis
- Section of Medical Oncology, Yale Cancer Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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McCullumsmith RE, Hammond JH, Shan D, Meador-Woodruff JH. Postmortem brain: an underutilized substrate for studying severe mental illness. Neuropsychopharmacology 2014; 39:65-87. [PMID: 24091486 PMCID: PMC3857666 DOI: 10.1038/npp.2013.239] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 02/08/2023]
Abstract
We propose that postmortem tissue is an underutilized substrate that may be used to translate genetic and/or preclinical studies, particularly for neuropsychiatric illnesses with complex etiologies. Postmortem brain tissues from subjects with schizophrenia have been extensively studied, and thus serve as a useful vehicle for illustrating the challenges associated with this biological substrate. Schizophrenia is likely caused by a combination of genetic risk and environmental factors that combine to create a disease phenotype that is typically not apparent until late adolescence. The complexity of this illness creates challenges for hypothesis testing aimed at understanding the pathophysiology of the illness, as postmortem brain tissues collected from individuals with schizophrenia reflect neuroplastic changes from a lifetime of severe mental illness, as well as treatment with antipsychotic medications. While there are significant challenges with studying postmortem brain, such as the postmortem interval, it confers a translational element that is difficult to recapitulate in animal models. On the other hand, data derived from animal models typically provide specific mechanistic and behavioral measures that cannot be generated using human subjects. Convergence of these two approaches has led to important insights for understanding molecular deficits and their causes in this illness. In this review, we discuss the problem of schizophrenia, review the common challenges related to postmortem studies, discuss the application of biochemical approaches to this substrate, and present examples of postmortem schizophrenia studies that illustrate the role of the postmortem approach for generating important new leads for understanding the pathophysiology of severe mental illness.
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Affiliation(s)
| | - John H Hammond
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Dan Shan
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
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26
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Williams G. SPIEDw: a searchable platform-independent expression database web tool. BMC Genomics 2013; 14:765. [PMID: 24199845 PMCID: PMC4046673 DOI: 10.1186/1471-2164-14-765] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 10/28/2013] [Indexed: 12/16/2022] Open
Abstract
Background SPIEDw is a web tool designed to facilitate fast and simple quantitative querying of publically available gene expression data. The resource is motivated by the observation that transcriptional profiles can serve as effective means of comparing biological states across a wide set of experiments. Results Gene expression data for over 200,000 experiments across multiple species and platforms have been collected into a searchable database. The new resource is a development of the previously published SPIED, which was designed to be downloaded and queried locally with SPIED software. SPIEDw features three significant improvements over the original version. Firstly, the number of experiments covered has been doubled and now includes Agilent and Illumina technologies. Secondly, SPIEDw has an enhanced search algorithm for speedy web-based querying and lastly an abridged dataset comprising the most regulated genes has been included for a speedier search and searching for enrichment of gene sets. Conclusions SPIEDw is simple to use, not requiring any expertise in microarray analysis, and the output straightforward to interpret. It is hoped that this will open up gene expression data mining to the wider research community. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-765) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gareth Williams
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London SE1 1UL, UK.
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27
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Musella V, Verderio P, Reid JF, Pizzamiglio S, Gariboldi M, Callari M, Massimo M, De Cecco L, Veneroni S, Pierotti MA, Daidone MG. Effects of warm ischemic time on gene expression profiling in colorectal cancer tissues and normal mucosa. PLoS One 2013; 8:e53406. [PMID: 23308215 PMCID: PMC3538764 DOI: 10.1371/journal.pone.0053406] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 11/30/2012] [Indexed: 01/09/2023] Open
Abstract
Background Genome-wide gene expression analyses of tumors are a powerful tool to identify gene signatures associated with biologically and clinically relevant characteristics and for several tumor types are under clinical validation by prospective trials. However, handling and processing of clinical specimens may significantly affect the molecular data obtained from their analysis. We studied the effects of tissue handling time on gene expression in human normal and tumor colon tissues undergoing routine surgical procedures. Methods RNA extracted from specimens of 15 patients at four time points (for a total of 180 samples) after surgery was analyzed for gene expression on high-density oligonucleotide microarrays. A mixed-effects model was used to identify probes with different expression means across the four different time points. The p-values of the model were adjusted with the Bonferroni method. Results Thirty-two probe sets associated with tissue handling time in the tumor specimens, and thirty-one in the normal tissues, were identified. Most genes exhibited moderate changes in expression over the time points analyzed; however four of them were oncogenes, and two confirmed the effect of tissue handling by independent validation. Conclusions Our results suggest that a critical time point for tissue handling in colon seems to be 60 minutes at room temperature. Although the number of time-dependent genes we identified was low, the three genes that already showed changes at this time point in tumor samples were all oncogenes, hence recommending standardization of tissue-handling protocols and effort to reduce the time from specimen removal to snap freezing accounting for warm ischemia in this tumor type.
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Affiliation(s)
- Valeria Musella
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Verderio
- Unit of Medical Statistics and Biometry, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - James Francis Reid
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Molecular Genetics of Cancer, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy
| | - Sara Pizzamiglio
- Unit of Medical Statistics and Biometry, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Manuela Gariboldi
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Molecular Genetics of Cancer, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy
| | - Maurizio Callari
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Milione Massimo
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvia Veneroni
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Maria Grazia Daidone
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- * E-mail:
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Wong J, Rothmond DA, Webster MJ, Shannon Weickert C. Increases in two truncated TrkB isoforms in the prefrontal cortex of people with schizophrenia. Schizophr Bull 2013; 39:130-40. [PMID: 21795612 PMCID: PMC3523916 DOI: 10.1093/schbul/sbr070] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The truncated brain-derived neurotrophic factor (BDNF) receptors (truncated TrkB [TrkB-TK-] and sarc homology containing TrkB [TrkB-Shc]) are alternative transcripts of the full-length TrkB receptor (TrkB-TK+) that produce isoforms capable of binding to BDNF but not being able to mediate the classic neurotrophic response via tyrosine kinase signaling. We hypothesized that in the dorsolateral prefrontal cortex (DLPFC) of people with schizophrenia, truncated TrkB receptors (TK- and Shc) would be altered and may contribute to deficits in BDNF function. Using a large cohort of controls and schizophrenics (n = 72/72), we measured mRNA expression of the full-length TrkB receptor, TrkB-TK+ and the truncated TrkB receptors, TrkB-TK- and TrkB-Shc, by quantitative real-time polymerase chain reaction and protein expression by western blotting. We found highly significant increases in mRNA expression of both truncated TrkB receptor isoforms in people with schizophrenia. When we examined the full-length TrkB-TK+:truncated TrkB ratios, we observed significant decreases in schizophrenia both on the mRNA and protein level. We found a slight reduction in TrkB-TK+ mRNA and a significant reduction in TrkB-TK+ protein expression in schizophrenia, which was evident in females. No gender-specific changes were found for the truncated TrkB receptors. Diagnostic changes in TrkB-TK+ mRNA and protein may be subtle and/or gender-specific, whereas changes in TrkB-TK- and TrkB-Shc expression are robust and may generalize to both males and females with schizophrenia. Increased truncated TrkB receptors may contribute to reduced overall BDNF/tyrosine receptor kinase B (TrkB) signaling and lead to reduced neuronal plasticity in the DLPFC in schizophrenia suggesting that therapies aimed at ameliorating neurotrophin deficits may need to consider blocking excessive truncated TrkB function.
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Affiliation(s)
- Jenny Wong
- Schizophrenia Research Institute, Sydney, Australia,Neuroscience Research Australia, Randwick, Australia,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Debora A. Rothmond
- Schizophrenia Research Institute, Sydney, Australia,Neuroscience Research Australia, Randwick, Australia
| | - Maree J. Webster
- Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD
| | - Cynthia Shannon Weickert
- Schizophrenia Research Institute, Sydney, Australia,Neuroscience Research Australia, Randwick, Australia,School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia,To whom correspondence should be addressed; Macquarie Group Foundation Chair of Schizophrenia Research, Neuroscience Research Australia, Barker Street, Randwick, New South Wales, 2031, Australia; tel: +61-2-9399-1117, fax: +61-2-9399-1005, e-mail:
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29
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Williams G. A searchable cross-platform gene expression database reveals connections between drug treatments and disease. BMC Genomics 2012; 13:12. [PMID: 22233519 PMCID: PMC3305579 DOI: 10.1186/1471-2164-13-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 01/10/2012] [Indexed: 11/29/2022] Open
Abstract
Background Transcriptional data covering multiple platforms and species is collected and processed into a searchable platform independent expression database (SPIED). SPIED consists of over 100,000 expression fold profiles defined independently of control/treatment assignment and mapped to non-redundant gene lists. The database is thus searchable with query profiles defined over genes alone. The motivation behind SPIED is that transcriptional profiles can be quantitatively compared and ranked and thus serve as effective surrogates for comparing the underlying biological states across multiple experiments. Results Drug perturbation, cancer and neurodegenerative disease derived transcriptional profiles are shown to be effective descriptors of the underlying biology as they return related drugs and pathologies from SPIED. In the case of Alzheimer's disease there is high transcriptional overlap with other neurodegenerative conditions and rodent models of neurodegeneration and nerve injury. Combining the query signature with correlating profiles allows for the definition of a tight neurodegeneration signature that successfully highlights many neuroprotective drugs in the Broad connectivity map. Conclusions Quantitative querying of expression data from across the totality of deposited experiments is an effective way of discovering connections between different biological systems and in particular that between drug action and biological disease state. Examples in cancer and neurodegenerative conditions validate the utility of SPIED.
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Affiliation(s)
- Gareth Williams
- Wolfson Centre for Age-Related Diseases, King's College London, London Bridge, London SE1 1UL, UK.
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30
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Sherwood KR, Head MW, Walker R, Smith C, Ironside JW, Fazakerley JK. RNA integrity in post mortem human variant Creutzfeldt-Jakob disease (vCJD) and control brain tissue. Neuropathol Appl Neurobiol 2011; 37:633-42. [DOI: 10.1111/j.1365-2990.2011.01162.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Moore HM, Kelly AB, Jewell SD, McShane LM, Clark DP, Greenspan R, Hayes DF, Hainaut P, Kim P, Mansfield E, Potapova O, Riegman P, Rubinstein Y, Seijo E, Somiari S, Watson P, Weier HU, Zhu C, Vaught J. Biospecimen reporting for improved study quality (BRISQ). J Proteome Res 2011; 10:3429-38. [PMID: 21574648 PMCID: PMC3169291 DOI: 10.1021/pr200021n] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human biospecimens are subject to a number of different collection, processing, and storage factors that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research utilizing human tissues, it is critical that information regarding the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications around biospecimen-related research and help reassure patient contributors and the advocacy community that the contributions are valued and respected.
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Affiliation(s)
- Helen M Moore
- Office of Biorepositories and Biospecimen Research, National Cancer Institute, Bethesda, Maryland, USA
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Sheedy D, Harding A, Say M, Stevens J, Kril JJ. Histological assessment of cerebellar granule cell layer in postmortem brain; a useful marker of tissue integrity? Cell Tissue Bank 2011; 13:521-7. [PMID: 21710172 DOI: 10.1007/s10561-011-9265-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/20/2011] [Indexed: 11/25/2022]
Abstract
Tissue quality control measures are routinely performed in brain banks with the assessment of brain pH being the most common measure. In some brain banks the assessment of the RNA integrity number is also performed, although this requires access to specialised equipment and is more expensive. The aim of this study is to determine if there is a correlation between the visual assessment of cerebellar granule cell integrity and brain pH or RIN. One hundred and five consecutive cases from the NSW Tissue Resource Centre, Sydney, Australia were accessed. The cerebrum was hemisected and one hemisphere sliced parasagittally at approximately 1-2 cm intervals and frozen. The other hemisphere was fixed in 15% buffered formalin for 2-3 weeks. The contralateral cerebellar hemisphere was preserved in the same manner as the cerebral hemisphere. Samples of fixed tissue were embedded in paraffin, 7 μm sections cut and stained routinely with hematoxylin and eosin. The granular cell layer (GCL) was assessed microscopically to determine the degree of autolytic degradation. Degradation was graded as nil, mild, moderate or severe. Brain tissue pH and RIN were measured using standardised protocols. This study showed that both brain pH and RIN significantly correlated with the severity of the degradation of the cerebellar granule cell layer. This additional screening tool can be performed during routine histological review of the cerebellar tissue to assess the suitability for further investigation of tissue quality.
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Affiliation(s)
- Donna Sheedy
- Discipline of Pathology, The University of Sydney, Sydney, NSW 2006, Australia
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Sheedy D, Say M, Stevens J, Harper CG, Kril JJ. Influence of liver pathology on markers of postmortem brain tissue quality. Alcohol Clin Exp Res 2011; 36:55-60. [PMID: 21689123 DOI: 10.1111/j.1530-0277.2011.01580.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Postmortem brain tissue provides an important resource to investigate various brain disorders, including those resulting from the effects of alcohol abuse. Unlike the traditionally recognized confounders to tissue quality (e.g., coma, hypoxia), our understanding of the effects of liver disease is incomplete. The aim of this study was to determine the effects of liver pathology, and in particular cirrhosis resulting in hepatic encephalopathy (HE), on 2 postmortem brain tissue quality markers, brain pH and RNA integrity. METHODS We measured tissue quality markers in a cohort of alcohol abuse and control cases collected by the NSW Tissue Resource Centre. Cerebellar tissue was used to evaluate both brain pH and RNA quality (as indicated by the RNA integrity number: RIN). A histological assessment was performed on each case to exclude coexisting pathologies (e.g., cerebrovascular disease, hypoxic encephalopathy, neurodegenerative disease) and to assess the presence or absence of HE. Autopsy reports were reviewed for liver pathology and toxicology. RESULTS Analysis revealed that cases of alcohol abuse had a lower mean (±SD) brain pH, 6.46 (±0.3) as compared with the control mean 6.64 (±0.2). The mean RIN for the alcohol abuse group was 6.97 (±1.3) and controls 7.66 (±0.5). The severity of liver pathology affected both brain pH (p < 0.0001) and RIN (p < 0.0001). The comparison between cirrhotic cases highlighted increased degradation of RNA in cases with cirrhosis resulting in HE (p = 0.0095). A similar effect was seen on brain pH (p = 0.0019). CONCLUSIONS The results show that the presence of cirrhosis and, more so, HE reduces the pH and RIN of postmortem brain tissue.
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Affiliation(s)
- Donna Sheedy
- Discipline of Pathology, Sydney Medical School, The University of Sydney, NSW, Australia
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34
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Koppelkamm A, Vennemann B, Lutz-Bonengel S, Fracasso T, Vennemann M. RNA integrity in post-mortem samples: influencing parameters and implications on RT-qPCR assays. Int J Legal Med 2011; 125:573-80. [PMID: 21584656 DOI: 10.1007/s00414-011-0578-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 04/29/2011] [Indexed: 01/27/2023]
Abstract
Messenger RNA (mRNA) profiling in post-mortem human tissue might reveal information about gene expression at the time point of death or close to it. When working with post-mortem human tissue, one is confronted with a natural RNA degradation caused by several parameters which are not yet fully understood. The aims of the present study were to analyse the influence of impaired RNA integrity on the reliability of quantitative gene expression data and to identify ante- and post-mortem parameters that might lead to reduced RNA integrities in post-mortem human brain, cardiac muscle and skeletal muscle tissues. Furthermore, this study determined the impact of several parameters like type of tissue, age at death, gender and body mass index (BMI), as well as duration of agony, cause of death and post-mortem interval on the RNA integrity. The influence of RNA integrity on the reliability of quantitative gene expression data was analysed by generating degradation profiles for three gene transcripts. Based on the deduced cycle of quantification data, this study shows that reverse transcription quantitative polymerase chain reaction (RT-qPCR) performance is affected by impaired RNA integrity. Depending on the transcript and tissue type, a shift in cycle threshold values of up to two cycles was observed. Determining RNA integrity number of 136 post-mortem samples revealed significantly different RNA qualities among the three tissue types with brain revealing significantly lower integrities compared to skeletal and cardiac muscle. The body mass index was found to influence RNA integrity in skeletal muscle tissue (M. iliopsoas). Samples originating from deceased with a BMI > 25 were of significantly lower integrity compared to samples from normal weight donors. Correct data normalisation was found to partly diminish the effects caused by impaired RNA quality. Nevertheless, it can be concluded that in post-mortem tissue with low RNA integrity numbers, the detection of large differences in gene expression activities might still be possible, whereas small expression differences are prone to misinterpretation due to degradation. Thus, when working with post-mortem samples, we recommend generating degradation profiles for all transcripts of interest in order to reveal detection limits of RT-qPCR assays.
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Affiliation(s)
- Antje Koppelkamm
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, 79104 Freiburg, Germany
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35
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Moore HM, Kelly A, Jewell SD, McShane LM, Clark DP, Greenspan R, Hainaut P, Hayes DF, Kim P, Mansfield E, Potapova O, Riegman P, Rubinstein Y, Seijo E, Somiari S, Watson P, Weier HU, Zhu C, Vaught J. Biospecimen Reporting for Improved Study Quality. Biopreserv Biobank 2011; 9:57-70. [PMID: 21826252 DOI: 10.1089/bio.2010.0036] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 01/11/2011] [Indexed: 01/07/2023] Open
Abstract
Human biospecimens are subject to a number of different collection, processing, and storage factors that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research utilizing human tissues, it is critical that information regarding the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The Biospecimen Reporting for Improved Study Quality guidelines are proposed as an important and timely resource tool to strengthen communication and publications around biospecimen-related research and help reassure patient contributors and the advocacy community that the contributions are valued and respected.
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36
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Deep-Soboslay A, Benes FM, Haroutunian V, Ellis JK, Kleinman JE, Hyde TM. Psychiatric brain banking: three perspectives on current trends and future directions. Biol Psychiatry 2011; 69:104-12. [PMID: 20673875 PMCID: PMC3105380 DOI: 10.1016/j.biopsych.2010.05.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/12/2010] [Accepted: 05/14/2010] [Indexed: 12/31/2022]
Abstract
Postmortem human brain tissue is critical for advancing neurobiological studies of psychiatric illness, particularly for identifying brain-specific transcripts and isoforms. State-of-the-art methods and recommendations for maintaining psychiatric brain banks are discussed in three disparate collections, the National Institute of Mental Health Brain Tissue Collection, the Harvard Brain Tissue Resource Center, and the Mount Sinai School of Medicine Alzheimer's Disease and Schizophrenia Brain Bank. While the National Institute of Mental Health Brain Tissue Collection obtains donations from medical examiners and focuses on clinical diagnosis, toxicology, and building life span control cohorts, the Harvard Brain Tissue Resource Center is designed as a repository to collect large-volume, high-quality brain tissue from community-based donors across a nationwide network, placing emphasis on the accessibility of tissue and related data to research groups worldwide. The Mount Sinai School of Medicine Alzheimer's Disease and Schizophrenia Brain Bank has shown that prospective recruitment is a successful approach to tissue donation, placing particular emphasis on clinical diagnosis through antemortem contact with donors, as well as stereological tissue sampling methods for neuroanatomical studies and frozen tissue sampling approaches that enable multiple assessments (e.g., RNA, DNA, protein, enzyme activity, binding) of the same tissue block. Promising scientific approaches for elucidating the molecular and cellular pathways in brain that may contribute to schizophrenia are briefly discussed. Despite different perspectives from three established brain collections, there is consensus that varied networking strategies, rigorous tissue and clinical characterization, sample and data accessibility, and overall adaptability are integral to the success of psychiatric brain banking.
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Affiliation(s)
- Amy Deep-Soboslay
- Section on Neuropathology, Clinical Brain Disorders Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Francine M. Benes
- Harvard Brain Tissue Resource Center, Program in Structural and Molecular Neuroscience, McLean Hospital, Belmont, MA, USA
| | - Vahram Haroutunian
- The Mount Sinai School of Medicine Alzheimer's Disease and Schizophrenia Brain Bank, New York, NY, USA
| | - Justin K. Ellis
- Section on Neuropathology, Clinical Brain Disorders Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Joel E. Kleinman
- Section on Neuropathology, Clinical Brain Disorders Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Thomas M. Hyde
- Section on Neuropathology, Clinical Brain Disorders Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
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McCullumsmith RE, Meador-Woodruff JH. Novel approaches to the study of postmortem brain in psychiatric illness: old limitations and new challenges. Biol Psychiatry 2011; 69:127-33. [PMID: 21094488 DOI: 10.1016/j.biopsych.2010.09.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 09/14/2010] [Accepted: 09/27/2010] [Indexed: 11/29/2022]
Abstract
Biological psychiatry has made significant advances through the development of postmortem studies, animal models, and studies with living humans. Although these approaches each have advantages and disadvantages, the postmortem field is undergoing a significant shift toward more complex and informative methodologies. In the first part of this review, we summarize the long-standing methodologic challenges facing this field. In the second part of the article, we discuss the innovative approaches being used for postmortem studies, including laser capture microdissection and subcellular fractionization. These techniques will permit scientists working in the postmortem field to ask and answer the largest possible questions, providing new targets for drug discovery and improved treatments for severe mental illness.
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Affiliation(s)
- Robert E McCullumsmith
- Department of Psychiatry and Behavioral Neurobiology, Universityof Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294, USA.
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38
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Tunbridge EM, Eastwood SL, Harrison PJ. Changed relative to what? Housekeeping genes and normalization strategies in human brain gene expression studies. Biol Psychiatry 2011; 69:173-9. [PMID: 20673871 DOI: 10.1016/j.biopsych.2010.05.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/25/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022]
Abstract
Many studies in biological psychiatry compare the abundance of individual messenger RNAs between cases and control subjects or, more recently, between genotype groups. Most utilize some form of normalization procedure, usually expressing the transcript(s) of interest relative to that of a housekeeping gene or genes (also called reference genes), to overcome various sources of experimental error. Indeed, normalization is such a standard procedure that its purpose, principles, and limitations are sometimes overlooked, and some papers lack sufficient information as to its implementation. Here, we review the rationales for normalization and argue that in well-conducted psychiatric gene expression studies using human brain tissue, it is reducing intersubject variability rather than experimental error that is the major benefit of normalization. We also review the conceptual and empirical basis for the category of housekeeping genes-i.e., genes with a ubiquitous and invariant expression. We conclude that the evidence is against any such simple categorization and that a more pragmatic, less dogmatic, approach to the selection and implementation of reference genes is required, which takes into account the particular issues that pertain to human brain tissue studies. This pragmatism extends to the issue of whether normalization should be to one or multiple reference genes. We end by making several recommendations toward a more flexible, transparent, and comprehensive approach to data presentation and analysis. We illustrate the review with examples from studies of schizophrenia and mood disorder.
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Affiliation(s)
- Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom
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Harrison PJ, Laatikainen LM, Tunbridge EM, Eastwood SL. Human brain weight is correlated with expression of the 'housekeeping genes' beta-2-microglobulin (β2M) and TATA-binding protein (TBP). Neuropathol Appl Neurobiol 2011; 36:498-504. [PMID: 20831744 DOI: 10.1111/j.1365-2990.2010.01098.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
AIMS Many variables affect mRNA measurements in post mortem human brain tissue. Brain weight has not hitherto been considered to be such a factor. This study examined whether there is any relationship between brain weight and mRNA abundance. METHODS We investigated quantitative real-time RT-PCR data for five 'housekeeping genes' using the 104 adult brains of the Stanley Microarray Consortium series. Eleven data sets were analysed, from cerebellum, hippocampus, and anterior cingulate cortex. We used a specified sequence of correlations, partial correlations and multiple regression analyses. RESULTS Brain weight correlated with the 'raw' (i.e. non-normalized) data for two mRNAs, β2-microglobulin and TATA-binding protein, measured in cerebellum and hippocampus, respectively. In hippocampus, the geometric mean of three housekeeping gene transcripts also correlated with brain weight. The correlations were significant after adjusting for age, sex and other confounders, and the effect of brain weight was confirmed using multiple regression. No correlations with brain weight were seen in the anterior cingulate cortex, nor for the other mRNAs examined. CONCLUSIONS The findings were not anticipated; they need replication in another brain series, and a more systematic survey is indicated. In the interim, we suggest that quantitative gene expression studies in human brain should inspect for a potential influence of brain weight, especially as the affected transcripts are commonly used as reference genes for normalization purposes in studies of neurological and psychiatric disorders. The relationship of brain weight with β2-microglobulin mRNA may reflect the roles of major histocompatibility complex class I genes in synapse formation and plasticity.
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Affiliation(s)
- P J Harrison
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK.
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40
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Effects of antemortem and postmortem variables on human brain mRNA quality: a BrainNet Europe study. J Neuropathol Exp Neurol 2010; 69:70-81. [PMID: 20010301 DOI: 10.1097/nen.0b013e3181c7e32f] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Well-characterized and preserved human brain tissue that is prepared and stored in brain banks is an essential resource for research in neurological diseases. This study examined the quality of human brain postmortem tissue from multiple laboratories within the BrainNet Europe brain bank network to identify all possible confounding variables and determine how they may affect RNA quality. Antemortem and postmortem information was retrospectively collected for a large cohort of samples. Total RNA was isolated from anatomically defined brain regions using a standardized procedure; RNA quality was assessed using an Agilent 2100 Bioanalyzer. No significant difference in RNA quality was observed in 6 different brain regions. RNA quality deteriorated with increasing numbers of antemortem events such as hospitalization, coma, respiratory illness, and the use of artificial ventilation; accumulation of such events was associated with elevated hypoxia-inducible factor 1 alpha mRNA expression. Brain pH was found to be a good indicator of RNA quality. There was no correlation of postmortem delay with cerebrospinal fluid pH or RNA quality overall, but some individual RNAs decreased in quality with antemortem events and with postmortem delay. RNA quality did not affect total RNA yield. Determining the factors that are best predictors of RNA quality can help brain banks with selection criteria for storing high-quality brain tissue for research.
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Weickert CS, Sheedy D, Rothmond DA, Dedova I, Fung S, Garrick T, Wong J, Harding AJ, Sivagnanansundaram S, Hunt C, Duncan C, Sundqvist N, Tsai SY, Anand J, Draganic D, Harper C. Selection of Reference Gene Expression in a Schizophrenia Brain Cohort. Aust N Z J Psychiatry 2010; 44:59-70. [PMID: 20073568 PMCID: PMC2950262 DOI: 10.3109/00048670903393662] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE In order to conduct postmortem human brain research into the neuropatho-logical basis of schizophrenia, it is critical to establish cohorts that are well-characterized and well-matched. The aim of the present study was therefore to determine if specimen characteristics including: diagnosis, age, postmortem interval (PMI), brain acidity (pH), and/or the agonal state of the subject at death related to RNA quality, and to determine the most appropriate reference gene mRNAs. METHODS A matched cohort was selected of 74 subjects (schizophrenia/schizoaffective disorder, n = 37; controls, n = 37). Middle frontal gyrus tissue was pulverized, tissue pH was measured, RNA isolated for cDNA from each case, and RNA integrity number (RIN) measurements were assessed. Using quantitative reverse transcription-polymerase chain reaction, nine housekeeper genes were measured and a geomean calculated per case in each diagnostic group. RESULTS The RINs were very good (mean = 7.3) and all nine housekeeper control genes were significantly correlated with RIN. Seven of nine housekeeper genes were also correlated with pH; two clinical variables, agonal state and duration of illness, did have an effect on some control mRNAs. No major impact of PMI or freezer time on housekeeper mRNAs was detected. The results show that people with schizophrenia had significantly less PPIA and SDHA mRNA and tended to have less GUSB and B2M mRNA, suggesting that these control genes may not be good candidates for normalization. CONCLUSIONS In the present cohort <10% variability in RINs was detected and the diagnostic groups were well matched overall. The cohort was adequately powered (0.80-0.90) to detect mRNA differences (25%) due to disease. The study suggests that multiple factors should be considered in mRNA expression studies of human brain tissues. When schizophrenia cases are adequately matched to control cases subtle differences in gene expression can be reliably detected.
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Affiliation(s)
- Cynthia Shannon Weickert
- Schizophrenia Research Institute, Sydney, AU,School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Donna Sheedy
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Debora A. Rothmond
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Irina Dedova
- Schizophrenia Research Institute, Sydney, AU,New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Samantha Fung
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, AU
| | - Therese Garrick
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Jenny Wong
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, AU
| | - Antony J. Harding
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Sinthuja Sivagnanansundaram
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Clare Hunt
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Carlotta Duncan
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Nina Sundqvist
- Schizophrenia Research Institute, Sydney, AU,New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | - Shan-Yuan Tsai
- Schizophrenia Research Institute, Sydney, AU,Schizophrenia Research Laboratory, Prince of Wales Medical Research Institute, Randwick, AU
| | - Jasna Anand
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
| | | | - Clive Harper
- New South Wales Tissue Resource Centre, Department of Pathology, School of Medical Sciences, University of Sydney, AU
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42
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Thellin O, ElMoualij B, Heinen E, Zorzi W. A decade of improvements in quantification of gene expression and internal standard selection. Biotechnol Adv 2009; 27:323-33. [PMID: 19472509 DOI: 10.1016/j.biotechadv.2009.01.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Major improvements have been made in mRNA quantification and internal standard selection over the last decade. Our aim in this paper is to present the main developments that are of interest for practical laboratory work, contrasting the situation as it is now with the one of ten years ago, and presenting some excellent examples of what can be done today. Specifically, we will mainly discuss Real-Time RT-PCR major improvements that have been performed in the following areas: the most commonly used quantification techniques, the mathematical and software tools created to help researchers in their work on internal standard selection, the availability of detection chemistries and technical information and of commercial tools and services. In addition to mRNA quantification, we will also discuss some aspects of non-coding RNA and protein quantification. In addition to technical improvements, the development of international cooperation and the creation of technical databases are likely to represent a major tool for the future in the standardization of gene expression quantification.
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Affiliation(s)
- Olivier Thellin
- Service of Human Histology/CRPP, University of Liege, 1 Avenue de l'Hopital, 4000 Liege, Belgium
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43
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Dedova I, Harding A, Sheedy D, Garrick T, Sundqvist N, Hunt C, Gillies J, Harper CG. The importance of brain banks for molecular neuropathological research: The New South Wales Tissue Resource Centre experience. Int J Mol Sci 2009; 10:366-384. [PMID: 19333451 PMCID: PMC2662458 DOI: 10.3390/ijms10010366] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 01/14/2009] [Accepted: 01/22/2009] [Indexed: 12/28/2022] Open
Abstract
New developments in molecular neuropathology have evoked increased demands for postmortem human brain tissue. The New South Wales Tissue Resource Centre (TRC) at The University of Sydney has grown from a small tissue collection into one of the leading international brain banking facilities, which operates with best practice and quality control protocols. The focus of this tissue collection is on schizophrenia and allied disorders, alcohol use disorders and controls. This review highlights changes in TRC operational procedures dictated by modern neuroscience, and provides examples of applications of modern molecular techniques to study the neuropathogenesis of many different brain disorders.
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Affiliation(s)
- Irina Dedova
- Schizophrenia Research Institute, Sydney, NSW 2010, Australia
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Antony Harding
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Donna Sheedy
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Therese Garrick
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Nina Sundqvist
- Schizophrenia Research Institute, Sydney, NSW 2010, Australia
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Clare Hunt
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Juliette Gillies
- Schizophrenia Research Institute, Sydney, NSW 2010, Australia
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
| | - Clive G Harper
- The New South Wales Tissue Resource Centre, Discipline of Pathology, The University of Sydney, NSW 2006, Australia
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44
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Sheedy D, Garrick T, Dedova I, Hunt C, Miller R, Sundqvist N, Harper C. An Australian Brain Bank: a critical investment with a high return! Cell Tissue Bank 2008; 9:205-16. [PMID: 18543078 PMCID: PMC3391553 DOI: 10.1007/s10561-008-9076-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 05/18/2008] [Indexed: 11/26/2022]
Abstract
Research into neuropsychiatric disorders, including alcohol-related problems, is limited in part by the lack of appropriate animal models. However, the development of new technologies in pathology and molecular biology means that many more questions can be addressed using appropriately stored human brain tissues. The New South Wales Tissue Resource Centre (TRC) in the University of Sydney (Australia) is a human brain bank that can provide tissues to the neuroscience research community studying alcohol-related brain disorders, schizophrenia, depression and bipolar disorders. Carefully standardised operational protocols and integrated information systems means that the TRC can provide high quality, accurately characterised, tissues for research. A recent initiative, the pre-mortem donor program called "Using our Brains", encourages individuals without neuropsychiatric illness to register as control donors, a critical group for all research. Community support for this program is strong with over 2,000 people registering their interest. Discussed herein are the protocols pertaining to this multifaceted facility and the benefits of investment, both scientific and financial, to neuroscience researchers and the community at large.
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Affiliation(s)
- D Sheedy
- Discipline of Pathology, University of Sydney, Sydney, NSW 2006, Australia.
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Ferrer I, Martinez A, Boluda S, Parchi P, Barrachina M. Brain banks: benefits, limitations and cautions concerning the use of post-mortem brain tissue for molecular studies. Cell Tissue Bank 2008; 9:181-94. [DOI: 10.1007/s10561-008-9077-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2008] [Accepted: 05/18/2008] [Indexed: 11/30/2022]
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Bell JE, Alafuzoff I, Al-Sarraj S, Arzberger T, Bogdanovic N, Budka H, Dexter DT, Falkai P, Ferrer I, Gelpi E, Gentleman SM, Giaccone G, Huitinga I, Ironside JW, Klioueva N, Kovacs GG, Meyronet D, Palkovits M, Parchi P, Patsouris E, Reynolds R, Riederer P, Roggendorf W, Seilhean D, Schmitt A, Schmitz P, Streichenberger N, Schwalber A, Kretzschmar H. Management of a twenty-first century brain bank: experience in the BrainNet Europe consortium. Acta Neuropathol 2008; 115:497-507. [PMID: 18365220 DOI: 10.1007/s00401-008-0360-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 02/28/2008] [Accepted: 02/28/2008] [Indexed: 10/22/2022]
Abstract
Collections of human postmortem brains gathered in brain banks have underpinned many significant developments in the understanding of central nervous system (CNS) disorders and continue to support current research. Unfortunately, the worldwide decline in postmortem examinations has had an adverse effect on research tissue procurement, particularly from control cases (non-diseased brains). Recruitment to brain donor programmes partially addresses this problem and has been successful for dementing and neurodegenerative conditions. However, the collection of brains from control subjects, particularly from younger individuals, and from CNS disorders of sudden onset, remains a problem. Brain banks need to adopt additional strategies to circumvent such shortages. The establishment of brain bank networks allows data on, and access to, control cases and unusual CNS disorders to be shared, providing a larger resource for potential users. For the brain banks themselves, inclusion in a network fosters the sharing of protocols and development of best practice and quality control. One aspect of this collective experience concerns brain bank management, excellence in which is a prerequisite not only for gaining the trust of potential donors and of society in general, but also for ensuring equitable distribution to researchers of high quality tissue samples. This review addresses the legal, ethical and governance issues, tissue quality, and health and safety aspects of brain bank management and data management in a network, as well as the needs of users, brain bank staffing, donor programs, funding issues and public relations. Recent developments in research methodology present new opportunities for researchers who use brain tissue samples, but will require brain banks to adopt more complex protocols for tissue collection, preparation and storage, with inevitable cost implications for the future.
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Gründemann J, Schlaudraff F, Haeckel O, Liss B. Elevated alpha-synuclein mRNA levels in individual UV-laser-microdissected dopaminergic substantia nigra neurons in idiopathic Parkinson's disease. Nucleic Acids Res 2008; 36:e38. [PMID: 18332041 PMCID: PMC2367701 DOI: 10.1093/nar/gkn084] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The presynaptic protein α-synuclein is involved in several neurodegenerative diseases, including Parkinson's disease (PD). In rare familial forms of PD, causal mutations (PARK1) as well as multiplications (PARK4) of the α-synuclein gene have been identified. In sporadic, idiopathic PD, abnormal accumulation and deposition of α-synuclein might also cause degeneration of dopaminergic midbrain neurons, the clinically most relevant neuronal population in PD. Thus, cell-specific quantification of α-synuclein expression-levels in dopaminergic neurons from idiopathic PD patients in comparison to controls would provide essential information about contributions of α-synuclein to the etiology of PD. However, a number of previous studies addressing this question at the tissue-level yielded varying results regarding α-synuclein expression. To increase specificity, we developed a cell-specific approach for mRNA quantification that also took into account the important issue of variable RNA integrities of the individual human postmortem brain samples. We demonstrate that PCR –amplicon size can confound quantitative gene-expression analysis, in particular of partly degraded RNA. By combining optimized UV-laser microdissection- and quantitative RT–PCR-techniques with suitable PCR assays, we detected significantly elevated α-synuclein mRNA levels in individual, surviving neuromelanin- and tyrosine hydroxylase-positive substantia nigra dopaminergic neurons from idiopathic PD brains compared to controls. These results strengthen the pathophysiologic role of transcriptional dysregulation of the α-synuclein gene in sporadic PD.
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Affiliation(s)
- Jan Gründemann
- Molecular Neurobiology, Department of Physiology, Philipps-University Marburg, Deutschhausstrasse 2, 35037 Marburg, Germany
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Guilarte TR, Hammoud DA, McGlothan JL, Caffo BS, Foss CA, Kozikowski AP, Pomper MG. Dysregulation of glutamate carboxypeptidase II in psychiatric disease. Schizophr Res 2008; 99:324-32. [PMID: 18191545 PMCID: PMC2287371 DOI: 10.1016/j.schres.2007.11.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 10/30/2007] [Accepted: 11/05/2007] [Indexed: 11/30/2022]
Abstract
Experimental evidence is beginning to converge on an important role for dysregulation of glutamate carboxypeptidase II (GCPII) in schizophrenia. The goal of this study was to determine GCPII levels in postmortem brain specimens of patients with schizophrenia, bipolar disorder or unipolar depression and age-matched control subjects. We used N-[N-(S)-1,3-dicarboxypropyl]carbamoyl]-S-3-[(125)I]iodo-l-tyrosine ([(125)I]DCIT), a high-affinity radioligand for GCPII, to probe for GCPII expression in prefrontal cortex (PFC) and mesial temporal lobe, two brain regions implicated in the pathophysiology of schizophrenia. We found that GCPII levels measured by [(125)I]DCIT quantitative autoradiography were significantly lower in the PFC and entorhinal cortex in patients with schizophrenia compared to age-matched controls. Patients with bipolar disorder also expressed significantly lower GCPII levels in PFC than controls. The decrease in [(125)I]DCIT binding in schizophrenia and bipolar disorder remained significant after adjusting for drug abuse. A significant difference in GCPII levels was also observed between schizophrenia relative to bipolar disorder and depressed subjects in the hippocampus-stratum lucidum and between schizophrenia and bipolar in the CA2 region of the hippocampus, with bipolar and depressed subjects expressing higher levels of GCPII than subjects with schizophrenia. These differences in hippocampal GCPII levels may implicate differences in the etiologies of these mental disorders. In summary, this study demonstrates a regional dysregulation of GCPII expression in the brain of patients with schizophrenia and other psychiatric disorders and supports a hypoglutamatergic state of the former illness. GCPII may represent a viable therapeutic target for intervention in psychiatric disease.
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Affiliation(s)
- Tomás R. Guilarte
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Dima A. Hammoud
- Department of Radiology, Johns Hopkins Medical Institutions, Baltimore, MD 21231
| | - Jennifer L. McGlothan
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Brian S. Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | | | | | - Martin G. Pomper
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205,Department of Radiology, Johns Hopkins Medical Institutions, Baltimore, MD 21231
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Millar T, Walker R, Arango JC, Ironside JW, Harrison DJ, MacIntyre DJ, Blackwood D, Smith C, Bell JE. Tissue and organ donation for research in forensic pathology: the MRC Sudden Death Brain and Tissue Bank. J Pathol 2008; 213:369-75. [PMID: 17990279 DOI: 10.1002/path.2247] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Novel methodological approaches to the investigation of brain and non-central nervous system disorders have led to increased demand for well-characterized, high quality human tissue samples, particularly from control cases. In the setting of the new Human Tissue legislation, we sought to determine whether relatives who have been suddenly bereaved are willing to grant authorization for research use of post mortem tissue samples and organs in sufficient numbers to support the establishment of a brain and tissue bank based in the forensic service. Research authorization was sought from families on the day prior to forensic post mortem examination followed up by written confirmation. We have to date selected individuals who have died suddenly (age range 1-89 years) and who were likely to have normal brains or who had displayed symptoms of a CNS disorder of interest to researchers, including psychiatric disorders. One hundred and eleven families have been approached during the first 2 years of this project. Research use of tissue samples was authorized by 96% of families and 17% agreed to whole brain donation. Audit of families' experience does not suggest that they are further distressed by being approached. Respondents expressed a clear view that the opportunity for research donation should be open to all bereaved families. Despite the sometimes long post mortem intervals, the quality of tissue samples is good, as assessed by a range of markers including Agilent BioAnalyzer quantification of RNA integrity (mean value 6.4). We conclude that the vast majority of families are willing to support research use of post mortem tissues even in the context of sudden bereavement and despite previous adverse publicity. The potential for acquisition of normal CNS and non-CNS tissues and of various hard-to-get CNS disorders suggests that efforts to access the forensic post mortem service for research material are eminently worthwhile.
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Affiliation(s)
- T Millar
- Neuropathology Unit, University of Edinburgh, Alexander Donald Building, Western General Hospital, Edinburgh, EH4 2XU, UK
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