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Dundar B, Agac B, Alzayadneh E, Tashjian R, Conway KS. The presence of shrunken neurons with pyknotic nuclei in the dentate nucleus is a common postmortem change associated with autolysis of the cerebellar granular cell layer. FREE NEUROPATHOLOGY 2024; 5:5-13. [PMID: 38803422 PMCID: PMC11129276 DOI: 10.17879/freeneuropathology-2024-5398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/03/2024] [Indexed: 05/29/2024]
Affiliation(s)
- Bilge Dundar
- Mayo Clinic, Department of Pathology, Rochester, MN, USA
| | - Busranur Agac
- Washington University in St. Louis, Department of Neurology, St. Louis, MO, USA
| | - Eyas Alzayadneh
- University of Iowa, Department of Pathology, Iowa City, IA, USA
| | - Randy Tashjian
- University of Michigan, Department of Pathology, Ann Arbor, MI, USA
| | - Kyle S. Conway
- University of Michigan, Department of Pathology, Ann Arbor, MI, USA
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Miyahara K, Hino M, Yu Z, Ono C, Nagaoka A, Hatano M, Shishido R, Yabe H, Tomita H, Kunii Y. The influence of tissue pH and RNA integrity number on gene expression of human postmortem brain. Front Psychiatry 2023; 14:1156524. [PMID: 37520228 PMCID: PMC10379646 DOI: 10.3389/fpsyt.2023.1156524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Evaluating and controlling confounders are necessary when investigating molecular pathogenesis using human postmortem brain tissue. Particularly, tissue pH and RNA integrity number (RIN) are valuable indicators for controlling confounders. However, the influences of these indicators on the expression of each gene in postmortem brain have not been fully investigated. Therefore, we aimed to assess these effects on gene expressions of human brain samples. Methods We isolated total RNA from occipital lobes of 13 patients with schizophrenia and measured the RIN and tissue pH. Gene expression was analyzed and gene sets affected by tissue pH and RIN were identified. Moreover, we examined the functions of these genes by enrichment analysis and upstream regulator analysis. Results We identified 2,043 genes (24.7%) whose expressions were highly correlated with pH; 3,004 genes (36.3%) whose expressions were highly correlated with RIN; and 1,293 genes (15.6%) whose expressions were highly correlated with both pH and RIN. Genes commonly affected by tissue pH and RIN were highly associated with energy production and the immune system. In addition, genes uniquely affected by tissue pH were highly associated with the cell cycle, whereas those uniquely affected by RIN were highly associated with RNA processing. Conclusion The current study elucidated the influence of pH and RIN on gene expression profiling and identified gene sets whose expressions were affected by tissue pH or RIN. These findings would be helpful in the control of confounders for future postmortem brain studies.
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Affiliation(s)
- Kazusa Miyahara
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Mizuki Hino
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Zhiqian Yu
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Chiaki Ono
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Masataka Hatano
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Risa Shishido
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Psychiatry, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Yasuto Kunii
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
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Man's best friend in life and death: scientific perspectives and challenges of dog brain banking. GeroScience 2021; 43:1653-1668. [PMID: 33970413 PMCID: PMC8492856 DOI: 10.1007/s11357-021-00373-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
Biobanking refers to the systematic collection, storage, and distribution of pre- or post-mortem biological samples derived from volunteer donors. The demand for high-quality human specimens is clearly demonstrated by the number of newly emerging biobanking facilities and large international collaborative networks. Several animal species are relevant today in medical research; therefore, similar initiatives in comparative physiology could be fruitful. Dogs, in particular, are gaining increasing attention in translational research on complex phenomena, like aging, cancer, and neurodegenerative diseases. Therefore, biobanks gathering and storing dog biological materials together with related data could play a vital role in translational and veterinary research projects. To achieve these aims, a canine biobank should meet the same standards in sample quality and data management as human biobanks and should rely on well-designed collaborative networks between different professionals and dog owners. While efforts to create dog biobanks could face similar financial and technical challenges as their human counterparts, they can widen the spectrum of successful collaborative initiatives towards a better picture of dogs’ physiology, disease, evolution, and translational potential. In this review, we provide an overview about the current state of dog biobanking and introduce the “Canine Brain and Tissue Bank” (CBTB)—a new, large-scale collaborative endeavor in the field.
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Correlation of cerebellar granular layer autolysis with ante-mortem systemic acid-base status. Cell Tissue Bank 2021; 22:505-509. [PMID: 33523332 DOI: 10.1007/s10561-021-09900-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 01/15/2021] [Indexed: 10/22/2022]
Abstract
Research in neuroscience relies heavily upon postmortem human brain tissue. Cerebellar granular layer autolysis (GLA) is a surrogate marker for the quality of such tissue and suitability for molecular analysis. GLA is associated with reduced brain tissue pH. The aim of this study was to assess correlation of GLA with premortem systemic acid-base status. This is a retrospective study in which 62 consecutive adult autopsy cases were included. Sections of cerebellum were reviewed microscopically for presence of GLA. Autolysis was graded as negative, grade 1, grade 2, and grade 3. Medical records were reviewed for arterial blood gas analysis. Postmortem interval was recorded. 23 of 62 cases showed GLA. Of the 23 patients with autolysis, 22 were acidotic and 1 was alkalotic. Of these 23 cases, 15 had metabolic acidosis, 4 had respiratory acidosis, 3 had combined acidosis and 1 had respiratory alkalosis. There was no statistically significant difference in postmortem interval between the two groups. 10 cases with grade 3 autolysis had mean pH of 7.13, 7 cases with grade 2 autolysis had mean pH of 7.23 and in 6 cases with grade 1 autolysis the mean pH was 7.2. Overall, the mean pH in patients with GLA was 7.19, and in the non-autolytic cases the mean pH was 7.28 (P < 0.05). There was no correlation between the degree of acidosis and severity of autolysis. GLA is associated with premortem systemic acidosis, and premortem systemic alkalosis is associated with the absence of GLA. Premortem acid-base status may serve as an additional quality indicator for assessment of tissue for research.
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Akinyemi RO, Salami A, Akinyemi J, Ojagbemi A, Olopade F, Coker M, Farombi T, Nweke M, Arulogun O, Jegede A, Owolabi M, Kalaria RN, Ogunniyi A. Brain banking in low and middle-income countries: Raison D'être for the Ibadan Brain Ageing, Dementia And Neurodegeneration (IBADAN) Brain Bank Project. Brain Res Bull 2018; 145:136-141. [PMID: 30149197 DOI: 10.1016/j.brainresbull.2018.08.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/15/2018] [Accepted: 08/21/2018] [Indexed: 02/08/2023]
Abstract
Brain banks are biorepositories of central nervous system (CNS) tissue including fixed and frozen whole brains, brain biopsies and spinal cord, as well as body fluids comprising the cerebrospinal fluid (CSF) and blood stored for research purposes. Though several independent brain banks exist in high income countries, only five low- and middle - income countries (LMIC) have brain banks. The African continent is yet to establish a formalized brain bank despite its huge human genomic diversity, ageing of her populations with concomitant increases in ageing - associated brain disorders and differential phenotypic expression and outcomes of brain disorders. Cellular and molecular clinicopathological studies are vital to shaping our understanding of the interaction between racial (genetic) and geographical (environmental) factors in the natural history and mechanisms of disease, and unravelling frameworks of diagnostic biomarkers, and new therapeutic and preventative interventions. The Ibadan Brain Ageing, Dementia And Neurodegeneration (IBADAN) Brain Bank, the first organized brain tissue biorepository in sub - Saharan Africa, is set up to accrue, process and store unique brain tissues for future research into a broad spectrum of neurological and psychiatric disorders. The potential unique discoveries and research breakthroughs will benefit people of African ancestry and other ancestral populations.
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Affiliation(s)
- Rufus O Akinyemi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria.
| | - Ayodeji Salami
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Joshua Akinyemi
- Department of Epidemiology and Medical Statistics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Akin Ojagbemi
- Department of Psychiatry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Funmi Olopade
- Department of Anatomy, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Motunrayo Coker
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Temitope Farombi
- Chief Tony Anenih Geriatric Centre, University College Hospital, Ibadan, Nigeria
| | - Michael Nweke
- Department of Pathology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oyedunni Arulogun
- Department of Health Education and Promotion, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ayodele Jegede
- Department of Sociology, Faculty of the Social Sciences, University of Ibadan, Ibadan, Nigeria
| | - Mayowa Owolabi
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Rajesh N Kalaria
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Adesola Ogunniyi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria; Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
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Fan J, Khanin R, Sakamoto H, Zhong Y, Michael C, Pena D, Javier B, Wood LD, Iacobuzio-Donahue CA. Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program. Oncotarget 2018; 7:66906-66921. [PMID: 27602498 PMCID: PMC5341846 DOI: 10.18632/oncotarget.11836] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/31/2016] [Indexed: 12/18/2022] Open
Abstract
The last decade has seen a marked rise in the use of cancer tissues obtained from research autopsies. Such resources have been invaluable for studying cancer evolution or the mechanisms of therapeutic resistance to targeted therapies. Degradation of biomolecules is a potential challenge to usage of cancer tissues obtained in the post-mortem setting and remains incompletely studied. We analysed the nucleic acid quality in 371 different frozen tissue samples collected from 80 patients who underwent a research autopsy, including eight normal tissue types, primary and metastatic tumors. Our results indicate that RNA integrity number (RIN) of normal tissues decline with the elongation of post-mortem interval (PMI) in a tissue-type specific manner. Unlike normal tissues, the RNA quality of cancer tissues is highly variable with respect to post-mortem interval. The kinetics of DNA damage also has tissue type-specific features. Moreover, while DNA degradation is an indicator of low RNA quality, the converse is not true. Finally, we show that despite RIN values as low as 5.0, robust data can be obtained by RNA sequencing that reliably discriminates expression signatures.
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Affiliation(s)
- Jun Fan
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Raya Khanin
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hitomi Sakamoto
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yi Zhong
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chelsea Michael
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Derwin Pena
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Breanna Javier
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Laura D Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
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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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Bolbanabad HM, Anvari E, Rezai MJ, Moayeri A, Kaffashian MR. Amelioration of cerebellar dysfunction in rats following postnatal ethanol exposure using low-intensity pulsed ultrasound. J Chem Neuroanat 2017; 81:71-75. [DOI: 10.1016/j.jchemneu.2017.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/06/2017] [Accepted: 02/06/2017] [Indexed: 10/20/2022]
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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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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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