1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Pietersen CY, Mauney SA, Kim SS, Lim MP, Rooney RJ, Goldstein JM, Petryshen TL, Seidman LJ, Shenton ME, McCarley RW, Sonntag KC, Woo TUW. Molecular profiles of pyramidal neurons in the superior temporal cortex in schizophrenia. J Neurogenet 2014; 28:53-69. [PMID: 24702465 PMCID: PMC4196521 DOI: 10.3109/01677063.2014.882918] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 01/09/2014] [Indexed: 12/22/2022]
Abstract
Disrupted synchronized oscillatory firing of pyramidal neuronal networks in the cerebral cortex in the gamma frequency band (i.e., 30-100 Hz) mediates many of the cognitive deficits and symptoms of schizophrenia. In fact, the density of dendritic spines and the average somal area of pyramidal neurons in layer 3 of the cerebral cortex, which mediate both long-range (associational) and local (intrinsic) corticocortical connections, are decreased in subjects with this illness. To explore the molecular pathophysiology of pyramidal neuronal dysfunction, we extracted ribonucleic acid (RNA) from laser-captured pyramidal neurons from layer 3 of Brodmann's area 42 of the superior temporal gyrus (STG) from postmortem brains from schizophrenia and normal control subjects. We then profiled the messenger RNA (mRNA) expression of these neurons, using microarray technology. We identified 1331 mRNAs that were differentially expressed in schizophrenia, including genes that belong to the transforming growth factor beta (TGF-β) and the bone morphogenetic proteins (BMPs) signaling pathways. Disturbances of these signaling mechanisms may in part contribute to the altered expression of other genes found to be differentially expressed in this study, such as those that regulate extracellular matrix (ECM), apoptosis, and cytoskeletal and synaptic plasticity. In addition, we identified 10 microRNAs (miRNAs) that were differentially expressed in schizophrenia; enrichment analysis of their predicted gene targets revealed signaling pathways and gene networks that were found by microarray to be dysregulated, raising an interesting possibility that dysfunction of pyramidal neurons in schizophrenia may in part be mediated by a concerted dysregulation of gene network functions as a result of the altered expression of a relatively small number of miRNAs. Taken together, findings of this study provide a neurobiological framework within which specific hypotheses about the molecular mechanisms of pyramidal cell dysfunction in schizophrenia can be formulated.
Collapse
Affiliation(s)
- Charmaine Y. Pietersen
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah A. Mauney
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
| | - Susie S. Kim
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
| | - Maribel P. Lim
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
| | | | - Jill M. Goldstein
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Tracey L. Petryshen
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Larry J. Seidman
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Martha E. Shenton
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Robert W. McCarley
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Psychiatry, Veterans Affairs Boston Healthcare System, Brockton, Massachusetts, USA
| | - Kai-C. Sonntag
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, McLean Hospital, Belmont, Massachusetts, USA
| | - Tsung-Ung W. Woo
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| |
Collapse
|
4
|
Onwuameze OE, Nam K, Epping EA, Wassink TH, Ziebell S, Andreasen NC, Ho BC. MAPK14 and CNR1 gene variant interactions: effects on brain volume deficits in schizophrenia patients with marijuana misuse. Psychol Med 2013; 43:619-631. [PMID: 22850347 PMCID: PMC3847818 DOI: 10.1017/s0033291712001559] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Adolescent marijuana use is associated with increased risk for schizophrenia. We previously reported that marijuana misuse in conjunction with specific cannabinoid receptor 1 (CNR1) genetic variants (rs12720071-G-allele carriers) contributed to white-matter (WM) brain volume deficits in schizophrenia patients. In this study, we assessed the influence of another cannabinoid-related gene, mitogen-activated protein kinase 14 (MAPK14), and potential MAPK14-CNR1 gene-gene interactions in conferring brain volume abnormalities among schizophrenia patients with marijuana abuse/dependence. MAPK14 encodes a member of the MAPK family involved in diverse cellular processes, including CNR1-induced apoptosis. METHOD We genotyped 235 schizophrenia patients on nine MAPK14 tag single nucleotide polymorphisms (tSNPs). Approximately one quarter of the sample had marijuana abuse or dependence. Differential effects of MAPK14 tSNPs on brain volumes across patients with versus without marijuana abuse/dependence were examined using ANCOVA. RESULTS Of the MAPK14 tSNPs, only rs12199654 had significant genotype effects and genotype × marijuana misuse interaction effects on WM volumes. rs12199654-A homozygotes with marijuana abuse/dependence had significantly smaller total cerebral and lobar WM volumes. The effects of MAPK14 rs12199654 on WM volume deficits remained significant even after controlling for the CNR1 rs12720071 genotype. There were significant main effects of the MAPK14 CNR1 diplotype and diplotype × marijuana interaction on WM brain volumes, with both genetic variants having additive contributions to WM volume deficits only in patients with marijuana misuse. CONCLUSIONS Given that CNR1-induced apoptosis is preceded by increased MAPK phosphorylation, our study suggests that potential MAPK14-CNR1 gene-gene interactions may mediate brain morphometric features in schizophrenia patients with heavy marijuana use.
Collapse
Affiliation(s)
- O. E. Onwuameze
- Department of Psychiatry, Southern Illinois University Medical School, Springfield, IL, USA
| | - K.W. Nam
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - E. A. Epping
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - T. H. Wassink
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - S. Ziebell
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - N. C. Andreasen
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - B.-C. Ho
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| |
Collapse
|
5
|
Harvey PD. Cognitive impairment in schizophrenia: profile, course, and neurobiological determinants. HANDBOOK OF CLINICAL NEUROLOGY 2012; 106:433-45. [PMID: 22608636 DOI: 10.1016/b978-0-444-52002-9.00025-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Philip D Harvey
- Department of Psychiatry and Behavioural Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.
| |
Collapse
|
6
|
Benes FM, Lim B, Matzilevich D, Subburaju S, Walsh JP. Circuitry-based gene expression profiles in GABA cells of the trisynaptic pathway in schizophrenics versus bipolars. Proc Natl Acad Sci U S A 2008; 105:20935-40. [PMID: 19104056 PMCID: PMC2606901 DOI: 10.1073/pnas.0810153105] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Indexed: 01/22/2023] Open
Abstract
Significant reductions in GABAergic cell numbers and/or activity have been demonstrated in the hippocampus of subjects with schizophrenia and bipolar disorder. To understand how different subpopulations of interneurons are regulated, laser microdissection and gene expression profiling have been used to "deconstruct" the trisynaptic pathway, so that subtypes of GABA cells could be defined by their location in various layers of CA3/2 and CA1. The results suggest that the cellular endophenotypes for SZ and BD may be determined by multiple factors that include unique susceptibility genes for the respective disorders and altered integration among hippocampal GABA cells with extrinsic and intrinsic afferent fiber systems. The extensive and intricate data that has come from this study has provided insights into how a complex circuit, like the trisynaptic pathway, may be regulated in human hippocampus in both health and disease.
Collapse
Affiliation(s)
- Francine M Benes
- Program in Structural and Molecular Neuroscience, McLean Hospital, Belmont, MA 02478, USA.
| | | | | | | | | |
Collapse
|