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Hao J, Wang M, Liu J, Yusufu M, Cao K, Fu J. Alteration of Neurotrophic Factors and Innervation in Extraocular Muscles of Individuals With Concomitant Esotropia. Invest Ophthalmol Vis Sci 2024; 65:1. [PMID: 38441891 PMCID: PMC10916883 DOI: 10.1167/iovs.65.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
Purpose To determine whether neurotrophic factors and innervation in extraocular muscles (EOMs) were altered in different types of concomitant esotropia, and to explore the possible association between neurotrophic factors and innervation of EOMs in humans. Methods Patients with concomitant esotropia who required strabismus surgery were recruited from January to December 2022. Lateral rectus EOMs were obtained from patients, and controls were obtained from deceased organ donors. Immunofluorescence (IF) was performed to detect innervation of EOMs (neurofilament and synaptophysin), and immunohistochemistry (IHC) was used to detect the neurotrophic factors insulin-like growth factor-1 (IGF-1), brain-derived neurotrophic factor (BDNF), glial cell-derived neurotrophic factor (GDNF), and neurotrophin-3 (NT-3). The positive IHC results were further verified using western blotting (WB). One-way ANOVA followed by a Dunnett's multiple comparison post hoc test was used for continuous variables and the χ2 test for categorical variables. Spearman correlation analysis was used for the correlation analysis. Results We collected lateral rectus EOM samples from acute and chronic types of concomitant esotropia and controls. Consistent with IHC, WB showed that IGF-1 was significantly increased in patients with acute acquired comitant esotropia or essential infantile esotropia compared with controls. In IF, synaptophysins were significantly increased only in acute acquired comitant esotropia compared with controls. Furthermore, Spearman correlation analysis showed that the correlation between IGF-1 and synaptophysin was borderline (P = 0.057) for patients with acute acquired comitant esotropia. Conclusions Our study highlights the role of IGF-1 and altered innervation of EOMs in acute acquired comitant esotropia, suggesting that an effect of increased IGF-1 on nerve innervation may temporarily cause a compensatory increase in the strength of lateral rectus muscles.
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Affiliation(s)
- Jie Hao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Ophthalmology & Visual Sciences, Beijing, China
| | - Meixu Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Ophthalmology & Visual Sciences, Beijing, China
| | - Jiawen Liu
- Industrial Engineering and Operations Research, University of California, Berkeley, California, United States
| | - Mayinuer Yusufu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
- Department of Surgery (Ophthalmology), The University of Melbourne, Melbourne, Australia
| | - Kai Cao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Ophthalmology & Visual Sciences, Beijing, China
| | - Jing Fu
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Ophthalmology & Visual Sciences, Beijing, China
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Janković T, Pilipović K. Single Versus Repetitive Traumatic Brain Injury: Current Knowledge on the Chronic Outcomes, Neuropathology and the Role of TDP-43 Proteinopathy. Exp Neurobiol 2023; 32:195-215. [PMID: 37749924 PMCID: PMC10569144 DOI: 10.5607/en23008] [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: 02/16/2023] [Revised: 07/18/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023] Open
Abstract
Traumatic brain injury (TBI) is one of the most important causes of death and disability in adults and thus an important public health problem. Following TBI, secondary pathophysiological processes develop over time and condition the development of different neurodegenerative entities. Previous studies suggest that neurobehavioral changes occurring after a single TBI are the basis for the development of Alzheimer's disease, while repetitive TBI is considered to be a contributing factor for chronic traumatic encephalopathy development. However, pathophysiological processes that determine the evolvement of a particular chronic entity are still unclear. Human post-mortem studies have found combinations of amyloid, tau, Lewi bodies, and TAR DNA-binding protein 43 (TDP-43) pathologies after both single and repetitive TBI. This review focuses on the pathological changes of TDP-43 after single and repetitive brain traumas. Numerous studies have shown that TDP-43 proteinopathy noticeably occurs after repetitive head trauma. A relatively small number of available preclinical research on single brain injury are not in complete agreement with the results from the human samples, which makes it difficult to draw specific conclusions. Also, as TBI is considered a heterogeneous type of injury, different experimental trauma models and injury intensities may cause differences in the cascade of secondary injury, which should be considered in future studies. Experimental and post-mortem studies of TDP-43 pathobiology should be carried out, preferably in the same laboratories, to determine its involvement in the development of neurodegenerative conditions after one and repetitive TBI, especially in the context of the development of new therapeutic options.
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Affiliation(s)
- Tamara Janković
- Department of Basic and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Rijeka, Rijeka 51000, Croatia
| | - Kristina Pilipović
- Department of Basic and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Rijeka, Rijeka 51000, Croatia
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Sabbir MG, Swanson M, Speth RC, Albensi BC. Hippocampal versus cortical deletion of cholinergic receptor muscarinic 1 in mice differentially affects post-translational modifications and supramolecular assembly of respiratory chain-associated proteins, mitochondrial ultrastructure, and respiration: implications in Alzheimer's disease. Front Cell Dev Biol 2023; 11:1179252. [PMID: 37293125 PMCID: PMC10246746 DOI: 10.3389/fcell.2023.1179252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction: In a previous retrospective study using postmortem human brain tissues, we demonstrated that loss of Cholinergic Receptor Muscarinic 1 (CHRM1) in the temporal cortex of a subset of Alzheimer's patients was associated with poor survival, whereas similar loss in the hippocampus showed no such association. Mitochondrial dysfunction underlies Alzheimer's pathogenesis. Therefore, to investigate the mechanistic basis of our findings, we evaluated cortical mitochondrial phenotypes in Chrm1 knockout (Chrm1-/-) mice. Cortical Chrm1 loss resulted in reduced respiration, reduced supramolecular assembly of respiratory protein complexes, and caused mitochondrial ultrastructural abnormalities. These mouse-based findings mechanistically linked cortical CHRM1 loss with poor survival of Alzheimer's patients. However, evaluation of the effect of Chrm1 loss on mouse hippocampal mitochondrial characteristics is necessary to fully understand our retrospective human tissue-based observations. This is the objective of this study. Methods: Enriched hippocampal and cortical mitochondrial fractions (EHMFs/ECMFs, respectively) derived from wild-type and Chrm1-/- mice were used to measure respiration by quantifying real-time oxygen consumption, supramolecular assembly of oxidative phosphorylation (OXPHOS)-associated proteins by blue native polyacrylamide gel electrophoresis, post-translational modifications (PTMs) by isoelectric focusing (IEF), and mitochondrial ultrastructure by electron microscopy. Results: In contrast to our previous observations in Chrm1-/- ECMFs, EHMFs of Chrm1-/- mice significantly increased respiration with a concomitant increase in the supramolecular assembly of OXPHOS-associated proteins, specifically Atp5a and Uqcrc2, with no mitochondrial ultrastructural alterations. IEF of ECMFs and EHMFs from Chrm1-/- mice showed a decrease and an increase, respectively in a negatively charged (pH∼3) fraction of Atp5a relative to the wild-type mice, with a corresponding decrease or increase in the supramolecular assembly of Atp5a and respiration indicating a tissue-specific signaling effect. Discussion: Our findings indicate that loss of Chrm1 in the cortex causes structural, and physiological alterations to mitochondria that compromise neuronal function, whereas Chrm1 loss in the hippocampus may benefit neuronal function by enhancing mitochondrial function. This brain region-specific differential effect of Chrm1 deletion on mitochondrial function supports our human brain region-based findings and Chrm1-/- mouse behavioral phenotypes. Furthermore, our study indicates that Chrm1-mediated brain region-specific differential PTMs of Atp5a may alter complex-V supramolecular assembly which in turn regulates mitochondrial structure-function.
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Affiliation(s)
- Mohammad Golam Sabbir
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
- Alzo Biosciences Inc., San Diego, CA, United States
- Canadian Centre for Agri-Food Research in Health and Medicine, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
- Barry & Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Mamiko Swanson
- Alzo Biosciences Inc., San Diego, CA, United States
- Barry & Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Robert C. Speth
- Barry & Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- Department of Pharmacology and Physiology, School of Medicine, Georgetown University, Washington, DC, United States
| | - Benedict C. Albensi
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
- Barry & Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL, United States
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB, Canada
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Braccagni G, Scheggi S, Bortolato M. Elevated levels of serotonin 5-HT 2A receptors in the orbitofrontal cortex of antisocial individuals. Eur Arch Psychiatry Clin Neurosci 2023; 273:411-425. [PMID: 36094569 PMCID: PMC10831872 DOI: 10.1007/s00406-022-01480-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022]
Abstract
Antisocial behavior (ASB) is characterized by frequent violations of the rights and properties of others, as well as aggressive conduct. While ample evidence points to a critical role of serotonin in the emotional modulation of social responses, the implication of this neurotransmitter in ASB is unclear. Here, we performed the first-ever postmortem analysis of serotonergic markers in the orbitofrontal cortex (OFC) of male subjects with ASB (n = 9). We focused on this brain region, given its well-recognized role in social response and ASB pathophysiology. Given that all individuals also had a substance use disorder (SUD) diagnosis, two age-matched control groups were used: SUD only and unaffected controls. Tissues were processed for immunoblotting analyses on eight key serotonergic targets: tryptophan hydroxylase 2 (TPH2), the rate-limiting enzyme of brain serotonin synthesis; serotonin transporter (SERT), the primary carrier for serotonin uptake; monoamine oxidase A (MAOA), the primary enzyme for serotonin catabolism; and five serotonin receptors previously shown to influence social behavior: 5-HT1A, 5-HT1B, 5-HT2A, 5-HT2C, and 5-HT4. Our analyses documented a significant increase in 5-HT2A receptor levels in the ASB + SUD group compared to SUD-only controls. Furthermore, TPH2 levels were significantly reduced in the SUD group (including SUD only and ASB + SUD) compared to unaffected controls. No difference was detected in the expression of any other serotonergic target. These results are in keeping with previous evidence showing high 5-HT2A receptor binding in the OFC of pathologically aggressive individuals and point to this molecule as a potential target for ASB treatment.
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Affiliation(s)
- Giulia Braccagni
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, L.S. Skaggs Hall, Room 3916, 30 S 2000 E, Salt Lake City, UT, 84112, USA
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Simona Scheggi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Marco Bortolato
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, L.S. Skaggs Hall, Room 3916, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
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Huang AW, Janssen PML. The Case for, and Challenges of, Human Cardiac Tissue in Advancing Phosphoprotein Research. Front Physiol 2022; 13:853511. [PMID: 35399265 PMCID: PMC8984461 DOI: 10.3389/fphys.2022.853511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
Cardiovascular disease (CVD) and stroke affect over 92 million Americans and account for nearly 1 out of 3 deaths in the US. The use of animal models in cardiovascular research has led to considerable advances in treatment and in our understanding of the pathophysiology of many CVDs. Still, animals may not fully recapitulate human disease states; species differences have long been postulated to be one of the main reasons for a failure of translation between animals and humans in drug discovery and development. Indeed, it has become increasingly clear over the past few decades that to answer certain biomedical questions, like the physiological mechanisms that go awry in many human CVDs, animal tissues may not always be the best option to use. While human cardiac tissue has long been used for laboratory research, published findings often contradict each other, leading to difficulties in interpretation. Current difficulties in utilizing human cardiac tissue include differences in acquisition time, varying tissue procurement protocols, and the struggle to define a human “control” sample. With the tremendous emphasis on translational research that continues to grow, research studies using human tissues are becoming more common. This mini review will discuss advantages, disadvantages, and considerations of using human cardiac tissue in the study of CVDs, paying specific attention to the study of phosphoproteins.
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Leslie SN, Kanyo J, Datta D, Wilson RS, Zeiss C, Duque A, Lam TT, Arnsten AFT, Nairn AC. Simple, Single-Shot Phosphoproteomic Analysis of Heat-Stable Tau Identifies Age-Related Changes in pS235- and pS396-Tau Levels in Non-human Primates. Front Aging Neurosci 2021; 13:767322. [PMID: 34867294 PMCID: PMC8637411 DOI: 10.3389/fnagi.2021.767322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Age is the most significant risk factor for Alzheimer's disease (AD), and understanding its role in specific aspects of AD pathology will be critical for therapeutic development. Neurofibrillary tangles composed of hyperphosphorylated tau are a quintessential hallmark of AD. To study age-related changes in tau phosphorylation, we developed a simple, antibody-free approach for single shot analysis of tau phosphorylation across the entire protein by liquid-chromatography tandem mass spectrometry. This methodology is species independent; thus, while initially developed in a rodent model, we utilized this technique to analyze 36 phosphorylation sites on rhesus monkey tau from the prefrontal cortex (PFC), a region vulnerable to AD-linked degeneration. Data are available via ProteomeXchange with identifier PXD027971. We identified novel, age-related changes in tau phosphorylation in the rhesus monkey PFC and analyzed patterns of phosphorylation change across domains of the protein. We confirmed a significant increase and positive correlation with age of phosphorylated serine 235 tau and phosphorylated serine 396 tau levels in an expanded cohort of 14 monkeys. Histology showed robust labeling for tau phosphorylated at these sites in vulnerable layer III pyramidal cells in the PFC. The results presented in this study suggest an important role of the natural aging process in tau phosphorylation in rhesus monkey.
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Affiliation(s)
- Shannon N. Leslie
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven, CT, United States
- Interdepartmental Neuroscience Program, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Dibyadeep Datta
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Rashaun S. Wilson
- Keck MS & Proteomics Resource, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Caroline Zeiss
- Department of Comparative Medicine, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Alvaro Duque
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - TuKiet T. Lam
- Keck MS & Proteomics Resource, Yale School of Medicine, Yale University, New Haven, CT, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Amy F. T. Arnsten
- Department of Neuroscience, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Angus C. Nairn
- Department of Psychiatry, Yale School of Medicine, Yale University, New Haven, CT, United States
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Molecular Pathways Involved in Frontotemporal Lobar Degeneration with TDP-43 Proteinopathy: What Can We Learn from Proteomics? Int J Mol Sci 2021; 22:ijms221910298. [PMID: 34638637 PMCID: PMC8508653 DOI: 10.3390/ijms221910298] [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: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) is a neurodegenerative disorder clinically characterized by behavioral, language, and motor symptoms, with major impact on the lives of patients and their families. TDP-43 proteinopathy is the underlying neuropathological substrate in the majority of cases, referred to as FTLD-TDP. Several genetic causes have been identified, which have revealed some components of its pathophysiology. However, the exact mechanisms driving FTLD-TDP remain largely unknown, forestalling the development of therapies. Proteomic approaches, in particular high-throughput mass spectrometry, hold promise to help elucidate the pathogenic molecular and cellular alterations. In this review, we describe the main findings of the proteomic profiling studies performed on human FTLD-TDP brain tissue. Subsequently, we address the major biological pathways implicated in FTLD-TDP, by reviewing these data together with knowledge derived from genomic and transcriptomic literature. We illustrate that an integrated perspective, encompassing both proteomic, genetic, and transcriptomic discoveries, is vital to unravel core disease processes, and to enable the identification of disease biomarkers and therapeutic targets for this devastating disorder.
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Fan Y, Nirujogi RS, Garrido A, Ruiz-Martínez J, Bergareche-Yarza A, Mondragón-Rezola E, Vinagre-Aragón A, Croitoru I, Gorostidi Pagola A, Paternain Markinez L, Alcalay R, Hickman RA, Düring J, Gomes S, Pratuseviciute N, Padmanabhan S, Valldeoriola F, Pérez Sisqués L, Malagelada C, Ximelis T, Molina Porcel L, Martí MJ, Tolosa E, Alessi DR, Sammler EM. R1441G but not G2019S mutation enhances LRRK2 mediated Rab10 phosphorylation in human peripheral blood neutrophils. Acta Neuropathol 2021; 142:475-494. [PMID: 34125248 PMCID: PMC8357670 DOI: 10.1007/s00401-021-02325-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022]
Abstract
Heterozygous gain-of-kinase function variants in LRRK2 (leucine-rich repeat kinase 2) cause 1-2% of all cases of Parkinson's disease (PD) albeit with incomplete and age-dependent penetrance. All pathogenic LRRK2 mutations reside within the two catalytic domains of LRRK2-either in its kinase domain (e.g. G2019S) with modest effect or its ROC-COR GTPase domain (e.g. R1441G/H) with large effect on LRRK2 kinase activity. We have previously reported assays to interrogate LRRK2 kinase pathway activity in human bio-samples measuring phosphorylation of its endogenous substrate Rab10, that mirrors LRRK2 kinase activation status. Here, we isolated neutrophils from fresh peripheral blood from 101 participants including 42 LRRK2 mutation carriers (21 with the G2019S and 21 with the R1441G mutations), 27 patients with idiopathic PD, and 32 controls. Using a dual approach, LRRK2 dependent Rab10 phosphorylation at Threonine 73 (pRab10Thr73) was measured by quantitative multiplexed immunoblotting for pRab10Thr73/total Rab10 as well as targeted mass-spectrometry for absolute pRab10Thr73 occupancy. We found a significant over fourfold increase in pRab10Thr73 phosphorylation in carriers of the LRRK2 R1441G mutation irrespective of clinical disease status. The effect of the LRRK2 G2019S mutation did not reach statistical significance. Furthermore, we show that LRRK2 phosphorylation at Serine 935 is not a marker for LRRK2 kinase activity in human neutrophils. When analysing pRab10Thr73 phosphorylation in post-mortem brain samples, we observed overall high variability irrespective of clinical and LRRK2 mutation status and attributed this mainly to the adverse effect of the peri- and post-mortem period on the stability of posttranslational modifications such as protein phosphorylation. Overall, in vivo LRRK2 dependent pRab10Thr73 phosphorylation in human peripheral blood neutrophils is a specific, robust and promising biomarker for significant LRRK2 kinase hyperactivation, as with the LRRK2 R1441G mutation. Additional readouts and/or assays may be needed to increase sensitivity to detect modest LRRK2 kinase activation, as with the LRRK2 G2019S mutation. Our assays could be useful for patient stratification and target engagement studies for LRRK2 kinase inhibitors.
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Affiliation(s)
- Ying Fan
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Raja S Nirujogi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Alicia Garrido
- Parkinson's Disease and Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Javier Ruiz-Martínez
- Group of Neurodegenerative Diseases, Biodonostia Research Institute, San Sebastian, Spain
| | | | | | - Ana Vinagre-Aragón
- Group of Neurodegenerative Diseases, Biodonostia Research Institute, San Sebastian, Spain
| | - Ioana Croitoru
- Group of Neurodegenerative Diseases, Biodonostia Research Institute, San Sebastian, Spain
| | - Ana Gorostidi Pagola
- Group of Neurodegenerative Diseases, Biodonostia Research Institute, San Sebastian, Spain
| | | | - Roy Alcalay
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Richard A Hickman
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jonas Düring
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Sara Gomes
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Neringa Pratuseviciute
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | | | - Francesc Valldeoriola
- Parkinson's Disease and Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Leticia Pérez Sisqués
- Departament de Biomedicina, Facultat de Medicina I Ciències de La Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Malagelada
- Departament de Biomedicina, Facultat de Medicina I Ciències de La Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Teresa Ximelis
- Neurological Tissue Bank of the Biobanc-Hospital Clinic-Institut D'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Molina Porcel
- Neurological Tissue Bank of the Biobanc-Hospital Clinic-Institut D'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic, Institut D'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Maria José Martí
- Parkinson's Disease and Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Eduardo Tolosa
- Parkinson's Disease and Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Dario R Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Esther M Sammler
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK.
- Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
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Shinohara M, Hirokawa J, Shimodaira A, Tashiro Y, Suzuki K, Gheni G, Fukumori A, Matsubara T, Morishima M, Saito Y, Murayama S, Sato N. ELISA Evaluation of Tau Accumulation in the Brains of Patients with Alzheimer Disease. J Neuropathol Exp Neurol 2021; 80:652-662. [PMID: 34283221 DOI: 10.1093/jnen/nlab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite the routine use of sandwich enzyme-linked immunosorbent assays (ELISAs) for quantifying tau levels in CSF and plasma, tau accumulations in the brains of patients with Alzheimer disease (AD) have rarely been evaluated by this method. Thus, by introducing several tau ELISAs that target different epitopes, we evaluated accumulated tau levels in postmortem brains depending on disease stage, brain areas, and other AD-related changes. Notably, tau levels in insoluble fraction determined by each ELISAs differ depending on the epitopes of antibodies: non-AD control samples yield relatively high signals when an antibody against the N-terminal region of tau is used. On the other hand, ELISAs combining antibodies against the later-middle to C-terminal regions of tau produced substantially increased signals from AD samples, compared to those from non-AD controls. Such ELISAs better distinguish AD and non-AD controls, and the results are more closely associated with Braak neurofibrillary tangles stage, Aβ accumulation, and glial markers. Moreover, these ELISAs can reflect the pattern of tau spread across brain regions. In conclusion, Tau ELISAs that combine antibodies against the later-middle to C-terminal regions of tau can better reflect neuropathological tau accumulation, which would enable to evaluate tau accumulation in the brain at a biochemical level.
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Affiliation(s)
- Mitsuru Shinohara
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Junko Hirokawa
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Akemi Shimodaira
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Yoshitaka Tashiro
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Kaoru Suzuki
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Ghupurjan Gheni
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Akio Fukumori
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Tomoyasu Matsubara
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Maho Morishima
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Yuko Saito
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Shigeo Murayama
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
| | - Naoyuki Sato
- From the Department of Aging Neurobiology, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan (MS, JH, AS, YT, KS, GG, AF, NS).,Department of Aging Neurobiology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan (MS, AF, NS).,Department of Pharmacotherapeutics II, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan (AF).,Department of Neuropathology (The Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Itabashi, Tokyo, Japan (TM, MM, YS, SM).,Brain Bank for Neurodevelopmental, Neurological and Psychiatric Disorders, United Graduate School of Child Development, Osaka University, Suita, Osaka, Japan (SM)
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10
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Grimm R. How Modern Mass Spectrometry Can Solve Ancient Questions: A Multi-Omics Study of the Stomach Content of the Oldest Human Ice Mummy, the 5300-Year-Old Iceman or Oetzi. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2261:1-12. [PMID: 33420980 DOI: 10.1007/978-1-0716-1186-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the past 40 years, mass spectrometry has seen a stunning development regarding increased sensitivity, resolution, and accuracy, especially for biomolecule analysis. These days without any doubt mass spectrometry is the most powerful analytical tool as a standalone technique or in conjunction with separation techniques such as high-performance liquid chromatography (HPLC), gas chromatography (GC), or capillary electrophoresis (CE). It is literally used to analyze any kind of small or large molecules ranging from basic elements to metabolites, pesticides, toxins, small or large molecule drugs, oligonucleotides, peptides, proteins, and many other molecule classes.Here, various modern mass spectrometry techniques such as LC-MS , GC-MS, ICP-MS, and elemental bio-imaging are briefly described how they were used for the first complex multi-omics study of the oldest human ice mummy, the 5300-year-old Iceman or Oetzi. The study comprised of mass spectrometry-driven proteomics (protein profiling and characterization), metabolomics, lipidomics, glycomics, and metallomics.
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11
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Dienel GA. Stop the rot. Enzyme inactivation at brain harvest prevents artifacts: A guide for preservation of the in vivo concentrations of brain constituents. J Neurochem 2021; 158:1007-1031. [PMID: 33636013 DOI: 10.1111/jnc.15293] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 12/25/2022]
Abstract
Post-mortem metabolism is widely recognized to cause rapid and prolonged changes in the concentrations of multiple classes of compounds in brain, that is, they are labile. Post-mortem changes from levels in living brain include components of pathways of metabolism of glucose and energy compounds, amino acids, lipids, signaling molecules, neuropeptides, phosphoproteins, and proteins. Methods that stop enzyme activity at brain harvest were developed almost 50 years ago and have been extensively used in studies of brain functions and diseases. Unfortunately, these methods are not commonly used to harvest brain tissue for mass spectrometry-based metabolomic studies or for imaging mass spectrometry studies (IMS, also called mass spectrometry imaging, MSI, or matrix-assisted laser desorption/ionization-MSI, MALDI-MSI). Instead these studies commonly kill animals, decapitate, dissect out brain and regions of interest if needed, then 'snap' freeze the tissue to stop enzymatic activity after harvest, with post-mortem intervals typically ranging from ~0.5 to 3 min. To increase awareness of the importance of stopping metabolism at harvest and preventing the unnecessary complications of not doing so, this commentary provides examples of labile metabolites and the magnitudes of their post-mortem changes in concentrations during brain harvest. Brain harvest methods that stop metabolism at harvest eliminate post-mortem enzymatic activities and can improve characterization of normal and diseased brain. In addition, metabolomic studies would be improved by reporting absolute units of concentration along with normalized peak areas or fold changes. Then reported values can be evaluated and compared with the extensive neurochemical literature to help prevent reporting of artifactual data.
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Affiliation(s)
- Gerald A Dienel
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Cell Biology and Physiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
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12
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Concepcion FA, Khan MN, Ju Wang JD, Wei AD, Ojemann JG, Ko AL, Shi Y, Eng JK, Ramirez JM, Poolos NP. HCN Channel Phosphorylation Sites Mapped by Mass Spectrometry in Human Epilepsy Patients and in an Animal Model of Temporal Lobe Epilepsy. Neuroscience 2021; 460:13-30. [PMID: 33571596 DOI: 10.1016/j.neuroscience.2021.01.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
Because hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels modulate the excitability of cortical and hippocampal principal neurons, these channels play a key role in the hyperexcitability that occurs during the development of epilepsy after a brain insult, or epileptogenesis. In epileptic rats generated by pilocarpine-induced status epilepticus, HCN channel activity is downregulated by two main mechanisms: a hyperpolarizing shift in gating and a decrease in amplitude of the current mediated by HCN channels, Ih. Because these mechanisms are modulated by various phosphorylation signaling pathways, we hypothesized that phosphorylation changes occur at individual HCN channel amino acid residues (phosphosites) during epileptogenesis. We collected CA1 hippocampal tissue from male Sprague Dawley rats made epileptic by pilocarpine-induced status epilepticus, and age-matched naïve controls. We also included resected human brain tissue containing epileptogenic zones (EZs) where seizures arise for comparison to our chronically epileptic rats. After enrichment for HCN1 and HCN2 isoforms by immunoprecipitation and trypsin in-gel digestion, the samples were analyzed by mass spectrometry. We identified numerous phosphosites from HCN1 and HCN2 channels, representing a novel survey of phosphorylation sites within HCN channels. We found high levels of HCN channel phosphosite homology between humans and rats. We also identified a novel HCN1 channel phosphosite S791, which underwent significantly increased phosphorylation during the chronic epilepsy stage. Heterologous expression of a phosphomimetic mutant, S791D, replicated a hyperpolarizing shift in Ih gating seen in neurons from chronically epileptic rats. These results show that HCN1 channel phosphorylation is altered in epilepsy and may be of pathogenic importance.
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Affiliation(s)
- F A Concepcion
- Department of Neurology and Regional Epilepsy Center, University of Washington, Seattle, WA, United States
| | - M N Khan
- Department of Neurology and Regional Epilepsy Center, University of Washington, Seattle, WA, United States
| | - J-D Ju Wang
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, United States
| | - A D Wei
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, United States
| | - J G Ojemann
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, United States; Department of Neurological Surgery, University of Washington, Seattle, WA, United States
| | - A L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, United States
| | - Y Shi
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, United States
| | - J K Eng
- Proteomics Resource, University of Washington, Seattle, WA, United States
| | - J-M Ramirez
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, United States; Department of Neurological Surgery, University of Washington, Seattle, WA, United States
| | - N P Poolos
- Department of Neurology and Regional Epilepsy Center, University of Washington, Seattle, WA, United States.
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13
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De Santis D, Rossini L, Tassi L, Didato G, Tringali G, Cossu M, Bramerio M, Padelli F, Regondi MC, Colciaghi F, Aronica E, Spreafico R, Garbelli R. pCREB expression in human tissues from epilepsy surgery. Epilepsia 2020; 61:1240-1252. [PMID: 32463128 DOI: 10.1111/epi.16549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/29/2020] [Indexed: 02/01/2023]
Abstract
OBJECTIVE Activity-dependent changes have been reported in animal models and in human epileptic specimens and could potentially be used as tissue biomarkers to evaluate the propensity of a tissue to generate seizure activity. In this context, cAMP-response element binding protein (CREB) activation was specifically reported in human epileptic foci and related mainly to interictal spike activity. To get further insights into CREB activation in human epilepsy, we analyzed pCREB expression on brain tissue samples from patients who underwent surgery for drug-resistant focal epilepsy, correlating this expression with intracranial stereo-electroencephalography (SEEG) recording in a subgroup. METHODS Neocortical specimens from patients with neuropathological diagnosis of no lesion (cryptogenic), malformations of cortical development,mainly type II focal cortical dysplasia (FCD), and hippocampi with and without hippocampal sclerosis have been analyzed by immunohistochemistry. Peritumoral cortex from non-epileptic patients and autoptic samples were used as controls, whereas rat brains were used to test possible loss of pCREB antigenicity due to fixation procedures and postmortem delay. RESULTS pCREB was consistently expressed in layer II neuronal nuclei in regions with normal cortical lamination both in epileptic and non-epileptic surgical tissues. In patients with SEEG recordings, this anatomical pattern was unrelated to the presence of interictal spike activity. Conversely, in the core of type II FCD, as well as in other developmental malformations, pCREB was scattered without any laminar specificity. Furthermore, quantitative data did not reveal significant differences between epileptic and non-epileptic tissues, except for an increased immunoreactivity in the core of type IIB FCD lesion related mainly to reactive glial and balloon cells. SIGNIFICANCE The present data argue against the reliability of pCREB immunohistochemistry as a marker of epileptic focus but underscores its layer-related expression, suggesting a potential application in the study of malformations of cortical development, a wide range of diseases arising from perturbations of normal brain development.
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Affiliation(s)
- Dalia De Santis
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Laura Rossini
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Laura Tassi
- Claudio Munari Epilepsy Surgery Center, Niguarda Hospital, Milan, Italy
| | - Giuseppe Didato
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giovanni Tringali
- Neurosurgery Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Massimo Cossu
- Claudio Munari Epilepsy Surgery Center, Niguarda Hospital, Milan, Italy
| | | | - Francesco Padelli
- Scientific Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | | | - Francesca Colciaghi
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Aronica
- Department of (Neuro) Pathology, University of Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Roberto Spreafico
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Rita Garbelli
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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14
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Andrade NS, Ramic M, Esanov R, Liu W, Rybin MJ, Gaidosh G, Abdallah A, Del’Olio S, Huff TC, Chee NT, Anatha S, Gendron TF, Wahlestedt C, Zhang Y, Benatar M, Mueller C, Zeier Z. Dipeptide repeat proteins inhibit homology-directed DNA double strand break repair in C9ORF72 ALS/FTD. Mol Neurodegener 2020; 15:13. [PMID: 32093728 PMCID: PMC7041170 DOI: 10.1186/s13024-020-00365-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The C9ORF72 hexanucleotide repeat expansion is the most common known genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two fatal age-related neurodegenerative diseases. The C9ORF72 expansion encodes five dipeptide repeat proteins (DPRs) that are produced through a non-canonical translation mechanism. Among the DPRs, proline-arginine (PR), glycine-arginine (GR), and glycine-alanine (GA) are the most neurotoxic and increase the frequency of DNA double strand breaks (DSBs). While the accumulation of these genotoxic lesions is increasingly recognized as a feature of disease, the mechanism(s) of DPR-mediated DNA damage are ill-defined and the effect of DPRs on the efficiency of each DNA DSB repair pathways has not been previously evaluated. METHODS AND RESULTS Using DNA DSB repair assays, we evaluated the efficiency of specific repair pathways, and found that PR, GR and GA decrease the efficiency of non-homologous end joining (NHEJ), single strand annealing (SSA), and microhomology-mediated end joining (MMEJ), but not homologous recombination (HR). We found that PR inhibits DNA DSB repair, in part, by binding to the nucleolar protein nucleophosmin (NPM1). Depletion of NPM1 inhibited NHEJ and SSA, suggesting that NPM1 loss-of-function in PR expressing cells leads to impediments of both non-homologous and homology-directed DNA DSB repair pathways. By deleting NPM1 sub-cellular localization signals, we found that PR binds NPM1 regardless of the cellular compartment to which NPM1 was directed. Deletion of the NPM1 acidic loop motif, known to engage other arginine-rich proteins, abrogated PR and NPM1 binding. Using confocal and super-resolution immunofluorescence microscopy, we found that levels of RAD52, a component of the SSA repair machinery, were significantly increased iPSC neurons relative to isogenic controls in which the C9ORF72 expansion had been deleted using CRISPR/Cas9 genome editing. Western analysis of post-mortem brain tissues confirmed that RAD52 immunoreactivity is significantly increased in C9ALS/FTD samples as compared to controls. CONCLUSIONS Collectively, we characterized the inhibitory effects of DPRs on key DNA DSB repair pathways, identified NPM1 as a facilitator of DNA repair that is inhibited by PR, and revealed deficits in homology-directed DNA DSB repair pathways as a novel feature of C9ORF72-related disease.
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Affiliation(s)
- Nadja S. Andrade
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
| | - Melina Ramic
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
| | - Rustam Esanov
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
| | - Wenjun Liu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL 33136 USA
| | - Mathew J. Rybin
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
| | - Gabriel Gaidosh
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136 USA
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136 USA
| | - Abbas Abdallah
- Department of Neurology, University of Massachusetts Medical School, Worchester, MA USA
| | - Samuel Del’Olio
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
| | - Tyler C. Huff
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136 USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1601 NW 12th Ave, Miami, FL. 33136 USA
| | - Nancy T. Chee
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
| | - Sadhana Anatha
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
| | - Tania F. Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224 USA
| | - Claes Wahlestedt
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
| | - Yanbin Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave, Miami, FL 33136 USA
| | - Michael Benatar
- Department of Neurology, University of Miami Miller School of Medicine, 115 NW 14th St.,, Miami, FL 33136 USA
| | - Christian Mueller
- Department of Neurology, University of Massachusetts Medical School, Worchester, MA USA
- Department of Pediatrics and Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA USA
| | - Zane Zeier
- Department of Psychiatry & Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Biomedical Research Building Room 413, Florida, Miami 33136 USA
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15
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Besnard A, Langberg T, Levinson S, Chu D, Vicidomini C, Scobie KN, Dwork AJ, Arango V, Rosoklija GB, Mann JJ, Hen R, Leonardo ED, Boldrini M, Sahay A. Targeting Kruppel-like Factor 9 in Excitatory Neurons Protects against Chronic Stress-Induced Impairments in Dendritic Spines and Fear Responses. Cell Rep 2019; 23:3183-3196. [PMID: 29898391 PMCID: PMC7453932 DOI: 10.1016/j.celrep.2018.05.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 04/09/2018] [Accepted: 05/14/2018] [Indexed: 11/01/2022] Open
Abstract
Stress exposure is associated with the pathogenesis of psychiatric disorders, including post-traumatic stress disorder (PTSD) and major depressive disorder (MDD). Here, we show in rodents that chronic stress exposure rapidly and transiently elevates hippocampal expression of Kruppel-like factor 9 (Klf9). Inducible genetic silencing of Klf9 expression in excitatory forebrain neurons in adulthood prior to, but not after, onset of stressor prevented chronic restraint stress (CRS)-induced potentiation of contextual fear acquisition in female mice and chronic corticosterone (CORT) exposure-induced fear generalization in male mice. Klf9 silencing prevented chronic CORT and CRS induced enlargement of dendritic spines in the ventral hippocampus of male and female mice, respectively. KLF9 mRNA density was increased in the anterior dentate gyrus of women, but not men, with more severe recent stressful life events and increased mortality. Thus, Klf9 functions as a stress-responsive transcription factor that mediates circuit and behavioral resilience in a sex-specific manner.
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Affiliation(s)
- Antoine Besnard
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Tomer Langberg
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Sally Levinson
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Duong Chu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Cinzia Vicidomini
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Kimberly N Scobie
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Divisions of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY 10032, USA; Macedonian Academy of Sciences & Arts, Skopje 1000, Republic of Macedonia
| | - Victoria Arango
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA; Divisions of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Gorazd B Rosoklija
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA; Divisions of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY 10032, USA; Macedonian Academy of Sciences & Arts, Skopje 1000, Republic of Macedonia
| | - J John Mann
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA; Divisions of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY 10032, USA
| | - René Hen
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA; Department of Neuroscience, Columbia University Medical Center, New York, NY 10032, USA; Department of Pharmacology, Columbia University Medical Center, New York, NY 10032, USA; Division of Integrative Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA
| | - E David Leonardo
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA
| | - Maura Boldrini
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA; Divisions of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Amar Sahay
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA; BROAD Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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16
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Tobin MK, Musaraca K, Disouky A, Shetti A, Bheri A, Honer WG, Kim N, Dawe RJ, Bennett DA, Arfanakis K, Lazarov O. Human Hippocampal Neurogenesis Persists in Aged Adults and Alzheimer's Disease Patients. Cell Stem Cell 2019; 24:974-982.e3. [PMID: 31130513 DOI: 10.1016/j.stem.2019.05.003] [Citation(s) in RCA: 331] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/23/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022]
Abstract
Whether hippocampal neurogenesis persists throughout life in the human brain is not fully resolved. Here, we demonstrate that hippocampal neurogenesis is persistent through the tenth decade of life and is detectable in patients with mild cognitive impairments and Alzheimer's disease. In a cohort of 18 participants with a mean age of 90.6 years, Nestin+Sox2+ neural progenitor cells (NPCs) and DCX+ neuroblasts and immature neurons were detected, but their numbers greatly varied between participants. Nestin+ cells localize in the anterior hippocampus, and NPCs, neuroblasts, and immature neurons are evenly distributed along the anterior to posterior axis. The number of DCX+PCNA+ cells is reduced in mild cognitive impairments, and higher numbers of neuroblasts are associated with better cognitive status. The number of DCX+PCNA+ cells correlates with functional interactions between presynaptic SNARE proteins. Our results suggest that hippocampal neurogenesis persists in the aged and diseased human brain and that it is possibly associated with cognition.
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Affiliation(s)
- Matthew K Tobin
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA
| | - Kianna Musaraca
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA
| | - Ahmed Disouky
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA
| | - Aashutosh Shetti
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA
| | - Abdullah Bheri
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA
| | - William G Honer
- Department of Psychiatry, The University of British Columbia, Vancouver, BC, Canada
| | - Namhee Kim
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Robert J Dawe
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Diagnostic Radiology, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Konstantinos Arfanakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA; Department of Diagnostic Radiology, Rush University Medical Center, Chicago, IL, USA; Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Orly Lazarov
- Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA.
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17
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Boldrini M, Galfalvy H, Dwork AJ, Rosoklija GB, Trencevska-Ivanovska I, Pavlovski G, Hen R, Arango V, Mann JJ. Resilience Is Associated With Larger Dentate Gyrus, While Suicide Decedents With Major Depressive Disorder Have Fewer Granule Neurons. Biol Psychiatry 2019; 85:850-862. [PMID: 30819514 PMCID: PMC6830307 DOI: 10.1016/j.biopsych.2018.12.022] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 12/28/2018] [Accepted: 12/28/2018] [Indexed: 01/04/2023]
Abstract
BACKGROUND Early life adversity (ELA) increases major depressive disorder (MDD) and suicide risk and potentially affects dentate gyrus (DG) plasticity. We reported smaller DG and fewer granular neurons (GNs) in MDD. ELA effects on DG plasticity in suicide decedents with MDD (MDDSui) and resilient subjects (ELA history without MDD or suicide) are unknown. METHODS We quantified neural progenitor cells (NPCs), GNs, glia, and DG volume in whole hippocampus postmortem in four groups of drug-free, neuropathology-free subjects (N = 52 total): psychological autopsy-defined MDDSui and control subjects with and without ELA (before 15 years of age). RESULTS ELA was associated with larger DG (p < .0001) and trending fewer NPCs (p = .0190) only in control subjects in whole DG, showing no effect on NPCs and DG volume in MDDSui. ELA exposure was associated with more GNs (p = .0003) and a trend for more glia (p = .0160) in whole DG in MDDSui and control subjects. MDDSui without ELA had fewer anterior and mid DG GNs (p < .0001), fewer anterior DG NPCs (p < .0001), and smaller whole DG volume (p = .0005) compared with control subjects without ELA. In MDDSui, lower Global Assessment Scale score correlated with fewer GNs and smaller DG. CONCLUSIONS Resilience to ELA involves a larger DG, perhaps related to more neurogenesis depleting NPCs, and because mature GNs and glia numbers do not differ in the resilient group, perhaps there are effects on process extension and synaptic load that can be examined in future studies. In MDDSui without ELA, smaller DG volume, with fewer GNs and NPCs, suggests less neurogenesis and/or more apoptosis and dendrite changes.
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Affiliation(s)
- Maura Boldrini
- Department of Psychiatry, Columbia University, New York State Psychiatric Institute, New York, New York; Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, New York.
| | - Hanga Galfalvy
- Department of Psychiatry, New York State Psychiatric Institute, New York, New York; Department of Biostatistics, New York State Psychiatric Institute, New York
| | - Andrew J. Dwork
- Department of Psychiatry, New York State Psychiatric Institute, New York, New York; Department of Pathology and Cell Biology, New York State Psychiatric Institute, New York, New York; Columbia University, Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, New York; Division of Integrative Neuroscience, New York State Psychiatric Institute, New York, New York
| | - Gorazd B. Rosoklija
- Department of Psychiatry, New York State Psychiatric Institute, New York, New York; Columbia University, Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, New York; Division of Integrative Neuroscience, New York State Psychiatric Institute, New York, New York; Macedonian Academy of Sciences and Arts, Ss. Cyril and Methodius University, Skopje, Macedonia
| | | | - Goran Pavlovski
- Institute for Forensic Medicine, Ss. Cyril and Methodius University, Skopje, Macedonia
| | - René Hen
- Department of Psychiatry, New York State Psychiatric Institute, New York, New York; Department of Neuroscience, New York State Psychiatric Institute, New York, New York; Department of Pharmacology, New York State Psychiatric Institute, New York, New York; Division of Integrative Neuroscience, New York State Psychiatric Institute, New York, New York
| | - Victoria Arango
- Department of Psychiatry, New York State Psychiatric Institute, New York, New York; Columbia University, Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, New York
| | - J. John Mann
- Department of Psychiatry, New York State Psychiatric Institute, New York, New York; Columbia University, Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, New York
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18
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Wu C, Huang BE, Chen G, Lovenberg TW, Pocalyko DJ, Yao X. Integrative Analysis of DiseaseLand Omics Database for Disease Signatures and Treatments: A Bipolar Case Study. Front Genet 2019; 10:396. [PMID: 31114610 PMCID: PMC6503737 DOI: 10.3389/fgene.2019.00396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 04/11/2019] [Indexed: 11/13/2022] Open
Abstract
Transcriptomics technologies such as next-generation sequencing and microarray platforms provide exciting opportunities for improving diagnosis and treatment of complex diseases. Transcriptomics studies often share similar hypotheses, but are carried out on different platforms, in different conditions, and with different analysis approaches. These factors, in addition to small sample sizes, can result in a lack of reproducibility. A clear understanding and unified picture of many complex diseases are still elusive, highlighting an urgent need to effectively integrate multiple transcriptomic studies for disease signatures. We have integrated more than 3,000 high-quality transcriptomic datasets in oncology, immunology, neuroscience, cardiovascular and metabolic disease, and from both public and internal sources (DiseaseLand database). We established a systematic data integration and meta-analysis approach, which can be applied in multiple disease areas to create a unified picture of the disease signature and prioritize drug targets, pathways, and compounds. In this bipolar case study, we provided an illustrative example using our approach to combine a total of 30 genome-wide gene expression studies using postmortem human brain samples. First, the studies were integrated by extracting raw FASTQ or CEL files, then undergoing the same procedures for preprocessing, normalization, and statistical inference. Second, both p-value and effect size based meta-analysis algorithms were used to identify a total of 204 differentially expressed (DE) genes (FDR < 0.05) genes in the prefrontal cortex. Among these were BDNF, VGF, WFS1, DUSP6, CRHBP, MAOA, and RELN, which have previously been implicated in bipolar disorder. Finally, pathway enrichment analysis revealed a role for GPCR, MAPK, immune, and Reelin pathways. Compound profiling analysis revealed MAPK and other inhibitors may modulate the DE genes. The ability to robustly combine and synthesize the information from multiple studies enables a more powerful understanding of this complex disease.
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Affiliation(s)
- Chun Wu
- Computational Sciences, Discovery Sciences, Janssen Research & Development, LLC, Spring House, PA, United States
| | - Bevan E Huang
- Computational Sciences, Discovery Sciences, Janssen Research & Development, LLC, Spring House, PA, United States
| | - Guang Chen
- Neuroscience Therapeutic Area, Janssen Research & Development, LLC, La Jolla, CA, United States
| | - Timothy W Lovenberg
- Neuroscience Therapeutic Area, Janssen Research & Development, LLC, La Jolla, CA, United States
| | - David J Pocalyko
- Computational Sciences, Discovery Sciences, Janssen Research & Development, LLC, Spring House, PA, United States
| | - Xiang Yao
- Computational Sciences, Discovery Sciences, Janssen Research & Development, LLC, La Jolla, CA, United States
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19
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Castellani RJ, Perry G. Tau Biology, Tauopathy, Traumatic Brain Injury, and Diagnostic Challenges. J Alzheimers Dis 2019; 67:447-467. [PMID: 30584140 PMCID: PMC6398540 DOI: 10.3233/jad-180721] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2018] [Indexed: 12/12/2022]
Abstract
There is considerable interest in the pathobiology of tau protein, given its potential role in neurodegenerative diseases and aging. Tau is an important microtubule associated protein, required for the assembly of tubulin into microtubules and maintaining structural integrity of axons. Tau has other diverse cellular functions involving signal transduction, cellular proliferation, developmental neurobiology, neuroplasticity, and synaptic activity. Alternative splicing results in tau isoforms with differing microtubule binding affinity, differing representation in pathological inclusions in certain disease states, and differing roles in developmental biology and homeostasis. Tau haplotypes confer differing susceptibility to neurodegeneration. Tau phosphorylation is a normal metabolic process, critical in controlling tau's binding to microtubules, and is ongoing within the brain at all times. Tau may be hyperphosphorylated, and may aggregate as detectable fibrillar deposits in tissues, in both aging and neurodegenerative disease. The hypothesis that p-tau is neurotoxic has prompted constructs related to isomers, low-n assembly intermediates or oligomers, and the "tau prion". Human postmortem studies have elucidated broad patterns of tauopathy, with tendencies for those patterns to differ as a function of disease phenotype. However, there is extensive overlap, not only between genuine neurodegenerative diseases, but also between aging and disease. Recent studies highlight uniqueness to pathological patterns, including a pattern attributed to repetitive head trauma, although clinical correlations have been elusive. The diagnostic process for tauopathies and neurodegenerative diseases in general is challenging in many respects, and may be particularly problematic for postmortem evaluation of former athletes and military service members.
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Affiliation(s)
- Rudy J. Castellani
- Departments of Pathology and Neuroscience, West Virginia University School of Medicine, Morgantown, WV, USA
| | - George Perry
- College of Sciences, University of Texas, San Antonio, San Antonio, TX, USA
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20
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Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018; 142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.
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21
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Ponath G, Lincoln MR, Levine-Ritterman M, Park C, Dahlawi S, Mubarak M, Sumida T, Airas L, Zhang S, Isitan C, Nguyen TD, Raine CS, Hafler DA, Pitt D. Enhanced astrocyte responses are driven by a genetic risk allele associated with multiple sclerosis. Nat Commun 2018; 9:5337. [PMID: 30559390 PMCID: PMC6297228 DOI: 10.1038/s41467-018-07785-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/24/2018] [Indexed: 12/22/2022] Open
Abstract
Epigenetic annotation studies of genetic risk variants for multiple sclerosis (MS) implicate dysfunctional lymphocytes in MS susceptibility; however, the role of central nervous system (CNS) cells remains unclear. We investigated the effect of the risk variant, rs7665090G, located near NFKB1, on astrocytes. We demonstrated that chromatin is accessible at the risk locus, a prerequisite for its impact on astroglial function. The risk variant was associated with increased NF-κB signaling and target gene expression, driving lymphocyte recruitment, in cultured human astrocytes and astrocytes within MS lesions, and with increased lesional lymphocytic infiltrates and lesion sizes. Thus, our study establishes a link between genetic risk for MS (rs7665090G) and dysfunctional astrocyte responses associated with increased CNS access for peripheral immune cells. MS may therefore result from variant-driven dysregulation of the peripheral immune system and of the CNS, where perturbed CNS cell function aids in establishing local autoimmune inflammation. It is unclear if multiple sclerosis (MS) genetic susceptibility can be mediated through perturbations of CNS-intrinsic pathways. Authors show that the rs7665090 risk variant is associated with astrocyte responses that enhance lymphocyte recruitment, and with increased lymphocyte infiltration and lesion sizes in MS lesions.
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Affiliation(s)
- Gerald Ponath
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Matthew R Lincoln
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06511, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, 02141, USA
| | | | - Calvin Park
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Somiah Dahlawi
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Mayyan Mubarak
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Tomokazu Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06511, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, 02141, USA
| | - Laura Airas
- Division of Clinical Neurosciences, University of Turku, Turku, 20520, Finland
| | - Shun Zhang
- Department of Radiology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Cigdem Isitan
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Thanh D Nguyen
- Department of Radiology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Cedric S Raine
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06511, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, 02141, USA
| | - David Pitt
- Department of Neurology, Yale School of Medicine, New Haven, CT, 06511, USA.
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22
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Wilson RS, Nairn AC. Cell-Type-Specific Proteomics: A Neuroscience Perspective. Proteomes 2018; 6:51. [PMID: 30544872 PMCID: PMC6313874 DOI: 10.3390/proteomes6040051] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022] Open
Abstract
Cell-type-specific analysis has become a major focus for many investigators in the field of neuroscience, particularly because of the large number of different cell populations found in brain tissue that play roles in a variety of developmental and behavioral disorders. However, isolation of these specific cell types can be challenging due to their nonuniformity and complex projections to different brain regions. Moreover, many analytical techniques used for protein detection and quantitation remain insensitive to the low amounts of protein extracted from specific cell populations. Despite these challenges, methods to improve proteomic yield and increase resolution continue to develop at a rapid rate. In this review, we highlight the importance of cell-type-specific proteomics in neuroscience and the technical difficulties associated. Furthermore, current progress and technological advancements in cell-type-specific proteomics research are discussed with an emphasis in neuroscience.
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Affiliation(s)
- Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, 300 George St., New Haven, CT 06511, USA.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
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23
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Hermann D, Hirth N, Reimold M, Batra A, Smolka MN, Hoffmann S, Kiefer F, Noori HR, Sommer WH, Reischl G, la Fougère C, Mann K, Spanagel R, Hansson AC. Low μ-Opioid Receptor Status in Alcohol Dependence Identified by Combined Positron Emission Tomography and Post-Mortem Brain Analysis. Neuropsychopharmacology 2017; 42:606-614. [PMID: 27510425 PMCID: PMC5240173 DOI: 10.1038/npp.2016.145] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/20/2022]
Abstract
Blockade of the μ-opioid receptor (MOR) by naltrexone reduces relapse risk in a subpopulation of alcohol-dependent patients. Previous positron-emission-tomography (PET) studies using the MOR ligand [11C]carfentanil have found increased MOR availability in abstinent alcoholics, which may reflect either increased MOR expression or lower endogenous ligand concentration. To differentiate between both effects, we investigated two cohorts of alcoholic subjects using either post-mortem or clinical PET analysis. Post-mortem brain tissue of alcohol-dependent subjects and controls (N=43/group) was quantitatively analyzed for MOR ([3H]DAMGO)-binding sites and OPRM1 mRNA in striatal regions. [11C]carfentanil PET was performed in detoxified, medication free alcohol-dependent patients (N=38), followed by a randomized controlled study of naltrexone versus placebo and follow-up for 1 year (clinical trial number: NCT00317031). Because the functional OPRM1 variant rs1799971:A>G affects the ligand binding, allele carrier status was considered in the analyses. MOR-binding sites were reduced by 23-51% in post-mortem striatal tissue of alcoholics. In the PET study, a significant interaction of OPRM1 genotype, binding potential (BPND) for [11C]carfentanil in the ventral striatum, and relapse risk was found. Particularly in G-allele carriers, lower striatal BPND was associated with a higher relapse risk. Interestingly, this effect was more pronounced in the naltrexone treatment group. Reduced MOR is interpreted as a neuroadaptation to an alcohol-induced release of endogenous ligands in patients with severe alcoholism. Low MOR availability may explain the ineffectiveness of naltrexone treatment in this subpopulation. Finally, low MOR-binding sites are proposed as a molecular marker for a negative disease course.
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Affiliation(s)
- Derik Hermann
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany,Central Institute of Mental Health (ZI), Square J5, Mannheim 68159, Germany, Tel: +49 621 1703 6293 or +49 621 1703 3522, Fax: 49 621 17036255,E-mail: or
| | - Natalie Hirth
- Institute of Psychopharmacology, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias Reimold
- Department of Nuclear Medicine, University of Tübingen, Tübingen, Germany
| | - Anil Batra
- Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Michael N Smolka
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany,Department of Psychiatry and Psychotherapy, Technische Universität Dresden, Dresden, Germany
| | - Sabine Hoffmann
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Falk Kiefer
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hamid R Noori
- Institute of Psychopharmacology, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Wolfgang H Sommer
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany,Institute of Psychopharmacology, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gerald Reischl
- Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
| | | | - Karl Mann
- Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Rainer Spanagel
- Institute of Psychopharmacology, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anita C Hansson
- Institute of Psychopharmacology, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany,Central Institute of Mental Health (ZI), Square J5, Mannheim 68159, Germany, Tel: +49 621 1703 6293 or +49 621 1703 3522, Fax: 49 621 17036255,E-mail: or
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24
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Abstract
The ability to adequately measure the phosphorylation state of a protein has major biological as well as clinical relevance. Due to its variable nature, reversible protein phosphorylations are sensitive to changes in the tissue environment. StabilizorTM T1 is a system for rapid inactivation of enzymatic activity in biological samples. Enzyme inactivation is accomplished using thermal denaturation in a rapid, homogeneous, and reproducible fashion without the need of added chemical inhibitors. Using pCREB(Ser133) as a model system, the applicability of the Stabilizor system to preserve a rapidly lost phosphorylation is shown.
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25
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Hino M, Kunii Y, Matsumoto J, Wada A, Nagaoka A, Niwa SI, Takahashi H, Kakita A, Akatsu H, Hashizume Y, Yamamoto S, Yabe H. Decreased VEGFR2 expression and increased phosphorylated Akt1 in the prefrontal cortex of individuals with schizophrenia. J Psychiatr Res 2016; 82:100-8. [PMID: 27484635 DOI: 10.1016/j.jpsychires.2016.07.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/21/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022]
Abstract
The Akt signaling pathway involves various cellular processes and depends on extracellular stimuli. Since Akt signaling participates in cytoprotection, synapse plasticity, axon extension, and neurotransmission in the nervous system, alteration in Akt signaling might be a potential cause of schizophrenia. In this study, we performed multiplex fluorescent bead based immunoassays for members of the Akt signaling pathway in postmortem brains of controls and patients with schizophrenia. Vascular endothelial growth factor receptor 2 (VEGFR2/KDR) was significantly decreased in the prefrontal cortex (PFC) of patients with schizophrenia, and the expression level of VEGFR2 was inversely correlated with the positive symptom subscale of the Diagnostic Instrument for Brain Studies (DIBS) in patients with schizophrenia. There was also an increase in phosphorylated Akt1 in the PFC in the patients, though the ratio of phospho/total Akt1 is not significantly different. In the nucleus accumbens (NAcc) there was no significant difference in expression and phosphorylation levels of Akt signaling proteins. Genetic analysis revealed a significant correlation of a SNP of KDR (rs7692791) with ERK1/2 and Akt1 phospho/total rates. Since VEGFR2 participates in angiogenesis and neurotrophic activation, either or both functions might be responsible for onset of schizophrenia.
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Affiliation(s)
- Mizuki Hino
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan.
| | - Yasuto Kunii
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Junya Matsumoto
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Akira Wada
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Atsuko Nagaoka
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Shin-Ichi Niwa
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan; Department of Psychiatry, Aizu Medical Center, School of Medicine, Fukushima Medical University, 969-3492 Fukushima, Japan
| | - Hitoshi Takahashi
- Department of Pathology, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathological Neuroscience, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Hiroyasu Akatsu
- Department of Community-based Medical Education/Department of Community-based Medicine, Nagoya City University Graduate School of Medical Science, Japan; Choju Medical Institute, Fukushimura Hospital, 441-8124, Aichi, Japan
| | - Yoshio Hashizume
- Choju Medical Institute, Fukushimura Hospital, 441-8124, Aichi, Japan
| | - Sakon Yamamoto
- Choju Medical Institute, Fukushimura Hospital, 441-8124, Aichi, Japan
| | - Hirooki Yabe
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
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26
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Sokoloff AJ, Douglas M, Rahnert JA, Burkholder T, Easley KA, Luo Q. Absence of morphological and molecular correlates of sarcopenia in the macaque tongue muscle styloglossus. Exp Gerontol 2016; 84:40-48. [PMID: 27566374 DOI: 10.1016/j.exger.2016.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Equivocal decline of tongue muscle performance with age is compatible with resistance of the tongue to sarcopenia, the loss of muscle volume and function that typically occurs with aging. To test this possibility we characterized anatomical and molecular indices of sarcopenia in the macaque tongue muscle styloglossus (SG). METHODS We quantified myosin heavy chain (MHC), muscle fiber MHC phenotype and size and total and phosphorylated growth- and atrophy-related proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), immunoblot and immunohistochemistry (IHC) in the SG in twenty-four macaque monkeys (Macaca rhesus, age range 9months to 31years) categorized into Young (<8years of age), Middle-aged (15-21years of age) and Old (>22years of age) groups. RESULTS In Young, Middle and Old age groups, by SDS-PAGE MHCI comprised ~1/3 and MHCII ~2/3 of total MHC. MHCI relative frequency was lower and MHCII higher in Middle versus Young (p=0.0099) and Middle versus Old (p=0.052). Relative frequencies of MHC fiber phenotype were not different by age but were different by phenotype (rates 233, 641 and 111 per 1000 fibers for MHCI, MHCII and MHCI-II respectively, p=0.03). Few or no fibers were positive for developmental MHC. Mean cross-sectional area (CSA) was not different among the three age groups for MHCII and MHCI-II; however MHCI fibers tended to be larger in Middle versus Old and Young (mean=2257μm2,1917μm2 (p=0.05) and 1704μm2 (p=0.06), respectively). For each age group, mean CSA increased across MHC phenotype (lowest mean CSA for MHCI and highest mean CSA for MHCII). Spearman analysis demonstrated age-related increases in total p70 ribosomal protein S6 kinase (P70), phosphorylated P70421/424, phosphorylated P38 mitogen-activated protein kinase and muscle atrophy F-Box, a trend to age-related decrease in total extracellular signal-regulated kinase (ERK), and no age-related change in total protein kinase B (Akt/PKB), phosphorylated Akt, phosphorylated ERK, phosphorylated c-Jun N-terminal kinase (JNK46) and phosphorylated P70389. CONCLUSION Common anatomical and molecular indices of sarcopenia are absent in our sample of macaque SG. Relative frequencies of MHCII protein and phenotype are preserved with age. Although MAFbx expression increases with age, this is not associated with fiber atrophy, perhaps reflecting compensatory growth signaling by p70. The resistant nature of the styloglossus muscle to sarcopenia may be related to routine activation of tongue muscles in respiration and swallowing and the preservation of hypoglossal motoneuron number with age.
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Affiliation(s)
- Alan J Sokoloff
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, United States.
| | - Megan Douglas
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, United States
| | - Jill A Rahnert
- School of Applied Physiology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Thomas Burkholder
- School of Applied Physiology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Kirk A Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Qingwei Luo
- Department of Physiology, Emory University School of Medicine, Atlanta, GA, United States
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Ferrari F, Villa RF. The Neurobiology of Depression: an Integrated Overview from Biological Theories to Clinical Evidence. Mol Neurobiol 2016; 54:4847-4865. [DOI: 10.1007/s12035-016-0032-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 08/01/2016] [Indexed: 12/21/2022]
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Blair JA, Wang C, Hernandez D, Siedlak SL, Rodgers MS, Achar RK, Fahmy LM, Torres SL, Petersen RB, Zhu X, Casadesus G, Lee HG. Individual Case Analysis of Postmortem Interval Time on Brain Tissue Preservation. PLoS One 2016; 11:e0151615. [PMID: 26982086 PMCID: PMC4794172 DOI: 10.1371/journal.pone.0151615] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/01/2016] [Indexed: 11/19/2022] Open
Abstract
At autopsy, the time that has elapsed since the time of death is routinely documented and noted as the postmortem interval (PMI). The PMI of human tissue samples is a parameter often reported in research studies and comparable PMI is preferred when comparing different populations, i.e., disease versus control patients. In theory, a short PMI may alleviate non-experimental protein denaturation, enzyme activity, and other chemical changes such as the pH, which could affect protein and nucleic acid integrity. Previous studies have compared PMI en masse by looking at many different individual cases each with one unique PMI, which may be affected by individual variance. To overcome this obstacle, in this study human hippocampal segments from the same individuals were sampled at different time points after autopsy creating a series of PMIs for each case. Frozen and fixed tissue was then examined by Western blot, RT-PCR, and immunohistochemistry to evaluate the effect of extended PMI on proteins, nucleic acids, and tissue morphology. In our results, immunostaining profiles for most proteins remained unchanged even after PMI of over 50 h, yet by Western blot distinctive degradation patterns were observed in different protein species. Finally, RNA integrity was lower after extended PMI; however, RNA preservation was variable among cases suggesting antemortem factors may play a larger role than PMI in protein and nucleic acid integrity.
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Affiliation(s)
- Jeffrey A. Blair
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
| | - Chunyu Wang
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Damarys Hernandez
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sandra L. Siedlak
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mark S. Rodgers
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Rojan K. Achar
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Lara M. Fahmy
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sandy L. Torres
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Robert B. Petersen
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (HL); (XZ); (GC)
| | - Gemma Casadesus
- Department of Biological Sciences and School of Biomedical Sciences, Kent State University, Kent, Ohio, United States of America
- * E-mail: (HL); (XZ); (GC)
| | - Hyoung-gon Lee
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (HL); (XZ); (GC)
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Bennike TB, Kastaniegaard K, Padurariu S, Gaihede M, Birkelund S, Andersen V, Stensballe A. Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples. EUPA OPEN PROTEOMICS 2016; 10:9-18. [PMID: 29900094 PMCID: PMC5988570 DOI: 10.1016/j.euprot.2015.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/19/2015] [Accepted: 10/25/2015] [Indexed: 01/14/2023]
Abstract
Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described. Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30 min. The protein content of the samples was characterized by high throughput quantitative proteomics. We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.
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Key Words
- CAN, acetonitrile
- DF, directly-frozen
- FA, formic acid
- FASP, filter-aided sample preparation
- FDR, false discovery rate
- FFPE, formalin-fixed
- Formalin-fixed
- HLA-A class I, histocompatibility antigen A-23 alpha chain
- HLA-DRB1 class II, histocompatibility antigen DRB1-4 beta chain
- Human colon mucosa
- LFQ, label-free quantification
- Mass spectrometry
- PCA, principle component analysis
- PSM, peptide spectral match
- PTM, post-translational modification
- Paraffin-embedded
- Preservation
- Proteomics
- RNAlater
- SDC, sodium deoxycholate
- SDS, sodium dodecyl sulfate
- TEAB, triethylammonium bicarbonate
- iFFPE, immediately formalin-fixed
- s, standard deviation
- sFFPE, stored for 30 min prior to formalin-fixed
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Affiliation(s)
- Tue Bjerg Bennike
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Simona Padurariu
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Gaihede
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Vibeke Andersen
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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Rapid alteration of protein phosphorylation during postmortem: implication in the study of protein phosphorylation. Sci Rep 2015; 5:15709. [PMID: 26511732 PMCID: PMC4625177 DOI: 10.1038/srep15709] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/29/2015] [Indexed: 11/26/2022] Open
Abstract
Protein phosphorylation is an important post-translational modification of proteins. Postmortem tissues are widely being utilized in the biomedical studies, but the effects of postmortem on protein phosphorylation have not been received enough attention. In the present study, we found here that most proteins in mouse brain, heart, liver, and kidney were rapidly dephosphorylated to various degrees during 20 sec to 10 min postmortem. Phosphorylation of tau at Thr212 and glycogen synthase kinase 3β (GSK-3β) at Ser9 was reduced by 50% in the brain with 40 sec postmortem, a regular time for tissue processing. During postmortem, phosphorylation of cAMP-dependent protein kinase (PKA) and AMP activated kinase (AMPK) was increased in the brain, but not in other organs. Perfusion of the brain with cold or room temperature phosphate-buffered saline (PBS) also caused significant alteration of protein phosphorylation. Cooling down and maintaining mouse brains in the ice-cold buffer prevented the alteration effectively. This study suggests that phosphorylation of proteins is rapidly changed during postmortem. Thus, immediate processing of tissues followed by cooling down in ice-cold buffer is vitally important and perfusion has to be avoided when protein phosphorylation is to be studied.
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Michalski B, Corrada MM, Kawas CH, Fahnestock M. Brain-derived neurotrophic factor and TrkB expression in the "oldest-old," the 90+ Study: correlation with cognitive status and levels of soluble amyloid-beta. Neurobiol Aging 2015; 36:3130-3139. [PMID: 26410307 DOI: 10.1016/j.neurobiolaging.2015.08.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 12/20/2022]
Abstract
Factors associated with maintaining good cognition into old age are unclear. Decreased brain-derived neurotrophic factor (BDNF) contributes to memory loss in Alzheimer's disease (AD), and soluble assemblies of amyloid-beta (Aβ) and tau contribute to neurodegeneration. However, it is unknown whether AD-type neuropathology, soluble Aβ and tau, or levels of BDNF and its receptor tropomyosin-related kinase B (TrkB) correlate with dementia in the oldest-old. We examined these targets in postmortem Brodmann's areas 7 and 9 (BA7 and BA9) in 4 groups of subjects >90 years old: (1) no dementia/no AD pathology, (2) no dementia/AD pathology, (3) dementia/no AD pathology, (4) dementia/AD pathology. In BA7, BDNF messenger RNA correlated with Mini-Mental State Examination scores and was decreased in demented versus nondemented subjects, regardless of pathology. Soluble Aβ42 was increased in both groups with AD pathology, demented or not, compared to no dementia/no AD pathology subjects. Groups did not differ in TrkB isoform levels or in levels of total soluble tau, individual tau isoforms, threonine-181 tau phosphorylation, or ratio of phosphorylated 3R-4R isoforms. In BA9, soluble Aβ42 correlated with Mini-Mental State Examination scores and with BDNF messenger RNA expression. Thus, soluble Aβ42 and BDNF, but not TrkB or soluble tau, correlate with dementia in the oldest-old.
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Affiliation(s)
- Bernadeta Michalski
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - Maria M Corrada
- Department of Epidemiology, University of California, Irvine, CA, USA; Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Claudia H Kawas
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Margaret Fahnestock
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada.
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Vitamin D and Alzheimer's Disease: Neurocognition to Therapeutics. Int J Alzheimers Dis 2015; 2015:192747. [PMID: 26351614 PMCID: PMC4553343 DOI: 10.1155/2015/192747] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/16/2015] [Indexed: 12/21/2022] Open
Abstract
Alzheimer's disease (AD), the major cause of dementia worldwide, is characterized by progressive loss of memory and cognition. The sporadic form of AD accounts for nearly 90% of the patients developing this disease. The last century has witnessed significant research to identify various mechanisms and risk factors contributing to the complex etiopathogenesis of AD by analyzing postmortem AD brains and experimenting with animal and cell culture based models. However, the treatment strategies, as of now, are only symptomatic. Accumulating evidences suggested a significant association between vitamin D deficiency, dementia, and AD. This review encompasses the beneficial role of vitamin D in neurocognition and optimal brain health along with epidemiological evidence of the high prevalence of hypovitaminosis D among aged and AD population. Moreover, disrupted signaling, altered utilization of vitamin D, and polymorphisms of several related genes including vitamin D receptor (VDR) also predispose to AD or AD-like neurodegeneration. This review explores the relationship between this gene-environmental influence and long term vitamin D deficiency as a risk factor for development of sporadic AD along with the role and rationale of therapeutic trials with vitamin D. It is, therefore, urgently warranted to further establish the role of this potentially neuroprotective vitamin in preventing and halting progressive neurodegeneration in AD patients.
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Abstract
Reverse phase protein array (RPPA) technology evolved from the advent of miniaturized immunoassays and gene microarray technology. Reverse phase protein arrays provide either a low throughput or high throughput methodology for quantifying proteins and their post-translationally modified forms in both cellular and non-cellular samples. As the demand for patient tailored therapies increases so does the need for precise and sensitive technology to accurately profile the molecular circuitry driving an individual patient's disease. RPPAs are currently utilized in clinical trials for profiling and comparing the functional state of protein signaling pathways, either temporally within tumors, between patients, or within the same patients before/after treatment. RPPAs are generally employed for quantifying large numbers of samples on one array, under identical experimental conditions. However, the goal of personalized cancer medicine is to design therapies based on the molecular portrait of a patient's tumor, which in turn result in more efficacious treatments with less toxicity. Therefore, RPPAs are also being validated for low throughput assays of individual patient samples. This review explores RPPA technology in the cancer research field, concentrating on its role as a fundamental tool for deciphering protein signaling networks and its emerging role in personalized medicine.
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Ozcan S, Kim BJ, Ro G, Kim JH, Bereuter TL, Reiter C, Dimapasoc L, Garrido D, Mills DA, Grimm R, Lebrilla CB, An HJ. Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior. Sci Rep 2014; 4:4963. [PMID: 24831691 PMCID: PMC4894394 DOI: 10.1038/srep04963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/24/2014] [Indexed: 12/02/2022] Open
Abstract
An improved understanding of glycosylation will provide new insights into many biological processes. In the analysis of oligosaccharides from biological samples, a strict regime is typically followed to ensure sample integrity. However, the fate of glycans that have been exposed to environmental conditions over millennia has not yet been investigated. This is also true for understanding the evolution of the glycosylation machinery in humans as well as in any other biological systems. In this study, we examined the glycosylation of tissue samples derived from four mummies which have been naturally preserved: – the 5,300 year old “Iceman called Oetzi”, found in the Tyrolean Alps; the 2,400 year old “Scythian warrior” and “Scythian Princess”, found in the Altai Mountains; and a 4 year old apartment mummy, found in Vienna/Austria. The number of N-glycans that were identified varied both with the age and the preservation status of the mummies. More glycan structures were discovered in the contemporary sample, as expected, however it is significant that glycan still exists in the ancient tissue samples. This discovery clearly shows that glycans persist for thousands of years, and these samples provide a vital insight into ancient glycosylation, offering us a window into the distant past.
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Affiliation(s)
- Sureyya Ozcan
- 1] Department of Chemistry, University of California, Davis, California 95616, USA [2] Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea [3]
| | - Bum Jin Kim
- 1] Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea [2]
| | - Grace Ro
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jae-Han Kim
- Department of Food Nutrition, Chungnam National University, Daejeon, Korea
| | - Thomas L Bereuter
- Institute of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Christian Reiter
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Lauren Dimapasoc
- Department of Chemistry, University of California, Davis, California 95616, USA
| | | | - David A Mills
- University of California, Davis, California 95616, USA
| | - Rudolf Grimm
- 1] Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea [2] Agilent Technologies Inc., Santa Clara, California 95051, USA [3] Robert Mondavi Institute for Food Science, University of California, Davis, California 95616, USA [4]
| | - Carlito B Lebrilla
- 1] Department of Chemistry, University of California, Davis, California 95616, USA [2] Department of Biochemistry and Molecular Medicine, University of California, Davis, California 95616, USA [3]
| | - Hyun Joo An
- 1] Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea [2]
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McGuire JL, Hammond JH, Yates SD, Chen D, Haroutunian V, Meador-Woodruff JH, McCullumsmith RE. Altered serine/threonine kinase activity in schizophrenia. Brain Res 2014; 1568:42-54. [PMID: 24780530 DOI: 10.1016/j.brainres.2014.04.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 04/19/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
Abstract
Converging evidence implicates alterations in multiple signaling pathways in the etiology of schizophrenia. Previously, these studies were limited to the analysis of one or a few phosphoproteins at a time. Here, we use a novel kinase array platform to simultaneously investigate the convergence of multiple signaling cascades implicated in schizophrenia. This technology uses consensus peptide substrates to assess activity levels of a large number (>100) of serine/threonine protein kinases. 19 peptide substrates were differentially phosphorylated (>15% change) in the frontal cortex in schizophrenia. These peptide substrates were examined using Ingenuity Pathway Analysis to group them according to the functions and to identify processes most likely affected in schizophrenia. Pathway analysis placed 14 of the 19 peptides into cellular homeostatic pathways, 10 into pathways governing cytoskeletal organization, and 8 into pathways governing ion homeostasis. These data are the first to simultaneously investigate comprehensive changes in signaling cascades in a severe psychiatric disorder. The examination of kinase activity in signaling pathways may facilitate the identification of novel substrates for drug discovery and the development of safer and more effective pharmacological treatment for schizophrenia.
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Affiliation(s)
- Jennifer L McGuire
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, USA.
| | - John H Hammond
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Stefani D Yates
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Dongquan Chen
- Division of Preventative Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Vahram Haroutunian
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA.
| | - James H Meador-Woodruff
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Robert E McCullumsmith
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati, Cincinnati, OH, 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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Sköld K, Alm H, Scholz B. The impact of biosampling procedures on molecular data interpretation. Mol Cell Proteomics 2013; 12:1489-501. [PMID: 23382104 PMCID: PMC3675808 DOI: 10.1074/mcp.r112.024869] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 01/17/2013] [Indexed: 01/06/2023] Open
Abstract
The separation between biological and technical variation without extensive use of technical replicates is often challenging, particularly in the context of different forms of protein and peptide modifications. Biosampling procedures in the research laboratory are easier to conduct within a shorter time frame and under controlled conditions as compared with clinical sampling, with the latter often having issues of reproducibility. But is the research laboratory biosampling really less variable? Biosampling introduces within minutes rapid tissue-specific changes in the cellular microenvironment, thus inducing a range of different pathways associated with cell survival. Biosampling involves hypoxia and, depending on the circumstances, hypothermia, circumstances for which there are evolutionarily conserved defense strategies in the range of species and also are relevant for the range of biomedical conditions. It remains unclear to what extent such adaptive processes are reflected in different biosampling procedures or how important they are for the definition of sample quality. Lately, an increasing number of comparative studies on different biosampling approaches, post-mortem effects and pre-sampling biological state, have investigated such immediate early biosampling effects. Commonalities between biosampling effects and a range of ischemia/reperfusion- and hypometabolism/anoxia-associated biological phenomena indicate that even small variations in post-sampling time intervals are likely to introduce a set of nonrandom and tissue-specific effects of experimental importance (both in vivo and in vitro). This review integrates the information provided by these comparative studies and discusses how an adaptive biological perspective in biosampling procedures may be relevant for sample quality issues.
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Affiliation(s)
- Karl Sköld
- From ‡Denator AB, Uppsala Science Park, SE-75183 Uppsala and
| | - Henrik Alm
- the §Department of Pharmaceutical Biosciences, Division of Drug Safety and Toxicology, Uppsala University, SE-75124 Uppsala, Sweden
| | - Birger Scholz
- the §Department of Pharmaceutical Biosciences, Division of Drug Safety and Toxicology, Uppsala University, SE-75124 Uppsala, Sweden
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Thompson SM, Craven RA, Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue. Proteomics Clin Appl 2013; 7:241-51. [PMID: 23027712 DOI: 10.1002/prca.201200086] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 12/14/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue.
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Affiliation(s)
- Seonaid M Thompson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Molecular Medicine, St. James's University Hospital, United Kingdom
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Kazuno AA, Ohtawa K, Otsuki K, Usui M, Sugawara H, Okazaki Y, Kato T. Proteomic analysis of lymphoblastoid cells derived from monozygotic twins discordant for bipolar disorder: a preliminary study. PLoS One 2013; 8:e53855. [PMID: 23408933 PMCID: PMC3567087 DOI: 10.1371/journal.pone.0053855] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 12/05/2012] [Indexed: 01/22/2023] Open
Abstract
Bipolar disorder is a severe mental illness characterized by recurrent manic and depressive episodes. In bipolar disorder, family and twin studies suggest contributions from genetic and environmental factors; however, the detailed molecular pathogenesis is yet unknown. Thus, identification of biomarkers may contribute to the clinical diagnosis of bipolar disorder. Monozygotic twins discordant for bipolar disorder are relatively rare but have been reported. Here we performed a comparative proteomic analysis of whole cell lysate derived from lymphoblastoid cells of monozygotic twins discordant for bipolar disorder by using two-dimensional differential in-gel electrophoresis (2D-DIGE). We found approximately 200 protein spots to be significantly differentially expressed between the patient and the co-twin (t test, p<0.05). Some of the proteins were subsequently identified by liquid chromatography tandem mass spectrometry and included proteins involved in cell death and glycolysis. To examine whether these proteins could serve as biomarkers of bipolar disorder, we performed Western blot analysis using case–control samples. Expression of phosphoglycerate mutase 1 (PGAM1), which is involved in glycolysis, was significantly up-regulated in patients with bipolar disorder (t test, p<0.05). Although PGAM1 cannot be regarded as a qualified biomarker of bipolar disorder from this preliminary finding, it could be one of the candidates for further study to identify biomarkers of bipolar disorder.
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Affiliation(s)
- An-a Kazuno
- Laboratory for Molecular Dynamics of Mental Disorders, Brain Science Institute, RIKEN, Saitama, Japan
| | - Kenji Ohtawa
- Research Resources Center, Brain Science Institute, RIKEN, Saitama, Japan
| | - Kaori Otsuki
- Research Resources Center, Brain Science Institute, RIKEN, Saitama, Japan
| | - Masaya Usui
- Research Resources Center, Brain Science Institute, RIKEN, Saitama, Japan
| | - Hiroko Sugawara
- Laboratory for Molecular Dynamics of Mental Disorders, Brain Science Institute, RIKEN, Saitama, Japan
| | - Yuji Okazaki
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, Brain Science Institute, RIKEN, Saitama, Japan
- * E-mail:
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Betsou F, Gunter E, Clements J, DeSouza Y, Goddard KAB, Guadagni F, Yan W, Skubitz A, Somiari S, Yeadon T, Chuaqui R. Identification of evidence-based biospecimen quality-control tools: a report of the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group. J Mol Diagn 2013; 15:3-16. [PMID: 23195791 PMCID: PMC5707193 DOI: 10.1016/j.jmoldx.2012.06.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/11/2012] [Accepted: 06/20/2012] [Indexed: 01/20/2023] Open
Abstract
Control of biospecimen quality that is linked to processing is one of the goals of biospecimen science. Consensus is lacking, however, regarding optimal sample quality-control (QC) tools (ie, markers and assays). The aim of this review was to identify QC tools, both for fluid and solid-tissue samples, based on a comprehensive and critical literature review. The most readily applicable tools are those with a known threshold for the preanalytical variation and a known reference range for the QC analyte. Only a few meaningful markers were identified that meet these criteria, such as CD40L for assessing serum exposure at high temperatures and VEGF for assessing serum freeze-thawing. To fully assess biospecimen quality, multiple QC markers are needed. Here we present the most promising biospecimen QC tools that were identified.
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Hippocampal angiogenesis and progenitor cell proliferation are increased with antidepressant use in major depression. Biol Psychiatry 2012; 72:562-71. [PMID: 22652019 PMCID: PMC3438317 DOI: 10.1016/j.biopsych.2012.04.024] [Citation(s) in RCA: 239] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 03/29/2012] [Accepted: 04/20/2012] [Indexed: 01/19/2023]
Abstract
BACKGROUND Adult neurogenesis is coupled to angiogenesis in neurogenic niches in the dentate gyrus (DG) and increased by antidepressants in rodents. We hypothesized that, in major depressive disorder (MDD), antidepressants increase neural progenitor cells (NPCs) and capillaries in the human DG. METHODS Neural progenitor cells and capillaries, detected on hippocampal sections by immunohistochemistry for neural stem cell protein, were quantified by stereology in matched MDDs (untreated, n = 12), MDD treated with selective serotonin reuptake inhibitors (MDD*SSRI, n = 6) or tricyclic antidepressants (MDD*TCA, n = 6), and nonpsychiatric control subjects (n = 12), all confirmed by psychological autopsy. RESULTS The MDD*SSRI had a larger capillary area and more NPCs versus MDDs (p = .034 and p = .008, respectively) and control subjects (p = .010 and p = .002, respectively) in the whole DG, more NPCs in the anterior (pes, p = .042) and central (midbody, p = .004) DG, and greater capillary area in the pes (p = .002) and midbody (p = .021). The NPC number and capillary area correlated positively in the whole sample (R2 = .454, p < .001) and in treated subjects (R2 = .749, p = .001). We found no NPCs or antidepressant-related angiogenesis in CA1 and parahippocampal gyrus. The DG volume correlated positively with NPC number (p = .004) and capillary area (p < .001) and differed between groups in whole hippocampus (p = .013) and midbody (p = .036). Age negatively correlated with NPC number (p = .042), capillary area (p = .037), and bifurcations (p = .030). No gender effect was detected. CONCLUSIONS Antidepressants increase human hippocampal NPCs and angiogenesis selectively in the anterior and mid DG. These results raise the possibility of a causal relationship between angiogenesis and neurogenesis, as seen in other proliferating tissues, and support their possible role in the mechanism of action of antidepressants.
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Insulin receptor expression and activity in the brains of nondiabetic sporadic Alzheimer's disease cases. Int J Alzheimers Dis 2012; 2012:321280. [PMID: 22666619 PMCID: PMC3362009 DOI: 10.1155/2012/321280] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 02/10/2012] [Accepted: 02/13/2012] [Indexed: 11/18/2022] Open
Abstract
We investigated the contents of the insulin receptor-beta subunit (IRβ) and [Tyr1162/1163]-phosphorylated IRβ as surrogate indices of total IR content and IR activation in postmortem hippocampal formation brain specimens from nondiabetic sporadic Alzheimer's disease (AD) cases. We found no significant changes in the brain contents of total IRβ or [Tyr1162/1163]-phosphorylated IRβ, suggesting normal IR content and activation in the brains of nondiabetic sporadic AD cases. Moreover, total IRβ and [Tyr1162/1163]-phosphorylated IRβ levels in the hippocampal formation are not correlated with the severity of amyloid or tau-neuropathology. Exploring the regulation of glycogen synthase kinase 3 (GSK3) α/β, key IR-signaling components, we observed significantly lower levels of total GSK3 α/β in brain specimens from nondiabetic AD cases, suggesting that impaired IR signaling mechanisms might contribute to the onset and/or progression of AD dementia. Outcomes from our study support the development of insulin-sensitizing therapeutic strategies to stimulate downstream IR signaling in nondiabetic AD cases.
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Methodology and technology for stabilization of specific states of signal transduction proteins. Methods Mol Biol 2011; 717:91-100. [PMID: 21370026 DOI: 10.1007/978-1-61779-024-9_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The ability to adequately measure the phosphorylation state of a protein has major biological as well as clinical relevance. Due to its variable nature, reversible protein phosphorylations are sensitive to changes in the tissue environment. Stabilizor T1 is a system for rapid inactivation of enzymatic activity in biological samples. Enzyme inactivation is accomplished using thermal denaturation in a rapid, homogeneous, and reproducible fashion without the need for added inhibitors. Using pCREB(Ser133) as a model system, the applicability of the Stabilizor system to preserve a rapidly lost phosphorylation is shown.
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Espina V, Mueller C, Liotta LA. Phosphoprotein stability in clinical tissue and its relevance for reverse phase protein microarray technology. Methods Mol Biol 2011; 785:23-43. [PMID: 21901591 DOI: 10.1007/978-1-61779-286-1_3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phosphorylated proteins reflect the activity of specific cell signaling nodes in biological kinase protein networks. Cell signaling pathways can be either activated or deactivated depending on the phosphorylation state of the constituent proteins. The state of these kinase pathways reflects the in vivo activity of the cells and tissue at any given point in time. As such, cell signaling pathway information can be extrapolated to infer which phosphorylated proteins/pathways are driving an individual tumor's growth. Reverse phase protein microarrays (RPMAs) are a sensitive and precise platform that can be applied to the quantitative measurement of hundreds of phosphorylated signal proteins from a small sample of tissue. Pre-analytical variability originating from tissue procurement and preservation may cause significant variability and bias in downstream molecular analysis. Depending on the ex vivo delay time in tissue processing, and the manner of tissue handling, protein biomarkers such as signal pathway phosphoproteins will be elevated or suppressed in a manner that does not represent the biomarker levels at the time of excision. Consequently, assessment of the state of these kinase networks requires stabilization, or preservation, of the phosphoproteins immediately post-tissue procurement. We have employed RPMA analysis of phosphoproteins to study the factors influencing stability of phosphoproteins in tissue following procurement. Based on this analysis we have established tissue procurement guidelines for clinical research with an emphasis on quantifying phosphoproteins by RPMA.
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Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
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Mueller C, Liotta LA, Espina V. Reverse phase protein microarrays advance to use in clinical trials. Mol Oncol 2010; 4:461-81. [PMID: 20974554 PMCID: PMC2981612 DOI: 10.1016/j.molonc.2010.09.003] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 12/18/2022] Open
Abstract
Individualizing cancer therapy for molecular targeted inhibitors requires a new class of molecular profiling technology that can map the functional state of the cancer cell signal pathways containing the drug targets. Reverse phase protein microarrays (RPMA) are a technology platform designed for quantitative, multiplexed analysis of specific phosphorylated, cleaved, or total (phosphorylated and non-phosphorylated) forms of cellular proteins from a limited amount of sample. This class of microarray can be used to interrogate tissue samples, cells, serum, or body fluids. RPMA were previously a research tool; now this technology has graduated to use in research clinical trials with clinical grade sensitivity and precision. In this review we describe the application of RPMA for multiplexed signal pathway analysis in therapeutic monitoring, biomarker discovery, and evaluation of pharmaceutical targets, and conclude with a summary of the technical aspects of RPMA construction and analysis.
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Affiliation(s)
- Claudius Mueller
- George Mason University, Center for Applied Proteomics and Molecular Medicine, Manassas, VA 20110, USA
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Herskowitz JH, Seyfried NT, Duong DM, Xia Q, Rees HD, Gearing M, Peng J, Lah JJ, Levey AI. Phosphoproteomic analysis reveals site-specific changes in GFAP and NDRG2 phosphorylation in frontotemporal lobar degeneration. J Proteome Res 2010; 9:6368-79. [PMID: 20886841 DOI: 10.1021/pr100666c] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Frontotemporal lobar degeneration (FTLD) is a progressive neurodegenerative disease characterized by behavioral abnormalities, personality changes, language dysfunction, and can co-occur with the development of motor neuron disease. One major pathological form of FTLD is characterized by intracellular deposition of ubiquitinated and phosphorylated TAR DNA binding protein-43 (TDP-43), suggesting that dysregulation in phosphorylation events may contribute to disease progression. However, to date systematic analysis of the phosphoproteome in FTLD brains has not been reported. In this study, we employed immobilized metal affinity chromatography (IMAC) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify phosphopeptides from FTLD and age-matched control post-mortem human brain tissue. Using this approach, we identified 786 phosphopeptides in frontal cortex (control and FTLD), in which the population of phosphopeptides represented approximately 50% of the total peptides analyzed. Label-free quantification using spectral counts revealed six proteins with significant changes in the FTLD phosphoproteome. N-myc-Downstream regulated gene 2 (NDRG2) and glial fibrillary acidic protein (GFAP) had an increased number of phosphospectra in FTLD, whereas microtubule associated protein 1A (MAP1A), reticulon 4 (RTN4; also referred to as neurite outgrowth inhibitor (Nogo)), protein kinase C gamma (PRKCG), and heat shock protein 90 kDa alpha, class A member 1(HSP90AA1) had significantly fewer phosphospectra compared to control brain. To validate these differences, we examined NDRG2 phosphorylation in FTLD brain by immunoblot analyses, and using a phosphoserine-13 (pSer13) GFAP monoclonal antibody we show an increase in pSer13 GFAP levels by immunoblot concomitant with increased overall GFAP levels in FTLD cases. These data highlight the utility of combining proteomic and phosphoproteomic strategies to characterize post-mortem human brain tissue.
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Affiliation(s)
- Jeremy H Herskowitz
- Department of Neurology, the Center for Neurodegenerative Diseases, Laboratory Medicine, and Proteomics Service Center, Emory University School of Medicine, Atlanta, Georgia 30322, United States
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Altered levels of extracellular signal-regulated kinase signaling proteins in postmortem frontal cortex of individuals with mood disorders and schizophrenia. J Affect Disord 2010; 124:164-9. [PMID: 19913919 PMCID: PMC2875351 DOI: 10.1016/j.jad.2009.10.017] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 10/15/2009] [Accepted: 10/15/2009] [Indexed: 12/11/2022]
Abstract
BACKGROUND The extracellular-regulated protein kinase (ERK) pathway has been implicated in processes such as neuronal plasticity and resilience in psychiatric disorders including major depressive disorder (MDD), bipolar disorder (BPD), and schizophrenia. The extent of the possible involvement of this pathway in psychiatric disorders remains unknown, as does its potential utility as a pharmacological target for the future development of novel therapeutics. METHODS Western blot analyses were used to measure levels of different proteins-Rap1, B-Raf, MEK1, MEK2, ERK1/2, RSK1, CREB, NSE, and beta-actin-in the postmortem frontal cortex of individuals with schizophrenia, MDD, and BPD, as well as healthy non-psychiatric controls. RESULTS Levels of most studied protein members of the ERK cascade were lower in individuals with psychiatric disorders than controls; differences between psychiatric groups were not statistically significant. In general, protein levels were lower in individuals with schizophrenia than in those with BPD or MDD, but protein levels varied across groups. LIMITATIONS The small number of individuals in each diagnostic group may limit our interpretation of the results. Factors such as postmortem interval, medication status at time of death, and mood state at time of death may also have influenced the findings. DISCUSSION The results are consistent with the hypothesis that the ERK pathway is implicated in reduced neuronal plasticity associated with the course of these psychiatric illnesses. The results warrant an expanded investigation into the activity of other members of this pathway as well as other brain areas of interest.
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Scholz B, Sköld K, Kultima K, Fernandez C, Waldemarson S, Savitski MM, Söderquist M, Borén M, Stella R, Andrén P, Zubarev R, James P. Impact of temperature dependent sampling procedures in proteomics and peptidomics--a characterization of the liver and pancreas post mortem degradome. Mol Cell Proteomics 2010; 10:M900229MCP200. [PMID: 20110281 DOI: 10.1074/mcp.m900229-mcp200] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Little is known about the nature of post mortem degradation of proteins and peptides on a global level, the so-called degradome. This is especially true for nonneural tissues. Degradome properties in relation to sampling procedures on different tissues are of great importance for the studies of, for instance, post translational modifications and/or the establishment of clinical biobanks. Here, snap freezing of fresh (<2 min post mortem time) mouse liver and pancreas tissue is compared with rapid heat stabilization with regard to effects on the proteome (using two-dimensional differential in-gel electrophoresis) and peptidome (using label free liquid chromatography). We report several proteins and peptides that exhibit heightened degradation sensitivity, for instance superoxide dismutase in liver, and peptidyl-prolyl cis-trans isomerase and insulin C-peptides in pancreas. Tissue sampling based on snap freezing produces a greater amount of degradation products and lower levels of endogenous peptides than rapid heat stabilization. We also demonstrate that solely snap freezing related degradation can be attenuated by subsequent heat stabilization. We conclude that tissue sampling involving a rapid heat stabilization step is preferable to freezing with regard to proteomic and peptidomic sample quality.
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Affiliation(s)
- Birger Scholz
- Department of Pharmaceutical Biosciences, Division of Toxicology, BMC, Box 594, SE-75124 Uppsala University, and Department of Medical Sciences, Clinical Pharmacology, Uppsala University Hospital, Uppsala, Sweden
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Boldrini M, Underwood MD, Hen R, Rosoklija GB, Dwork AJ, Mann JJ, Arango V. Antidepressants increase neural progenitor cells in the human hippocampus. Neuropsychopharmacology 2009; 34:2376-89. [PMID: 19606083 PMCID: PMC2743790 DOI: 10.1038/npp.2009.75] [Citation(s) in RCA: 501] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Selective serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs) increase neurogenesis in the dentate gyrus (DG) of rodents and nonhuman primates. We determined whether SSRIs or TCAs increase neural progenitor (NPCs) and dividing cells in the human DG in major depressive disorder (MDD). Whole frozen hippocampi from untreated subjects with MDD (N=5), antidepressant-treated MDD (MDDT, N=7), and controls (C, N=7) were fixed, sectioned, and immunostained for NPCs and dividing cell markers (nestin and Ki-67, respectively), NeuN and GFAP, in single and double labeling. NPC and dividing cell numbers in the DG were estimated by stereology. Clinical data were obtained by psychological autopsy, and by toxicological and neuropathological examination performed on all subjects. NPCs decreased with age (p = 0.034). Females had more NPCs than males (p = 0.023). Correcting for age and sex, MDDT receiving SSRIs had more NPCs than untreated MDD (p < or = 0.001) and controls (p < or = 0.001), NPCs were not different in SSRI- and TCA-treated MDDT (p = 0.169). Dividing cell number, unaffected by age or sex, was greater in MDDT receiving TCAs than in untreated MDD (p < or = 0.001), SSRI-treated MDD (p = 0.001), and controls (p < or = 0.001). The increase of NPCs and dividing cells in MDDT was localized to the rostral DG. MDDT had a larger DG volume compared with untreated MDD or controls (p = 0.009). Antidepressants increase NPC number in the anterior human DG. Whether this finding is critical or necessary for the antidepressants effect remains to be determined.
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Affiliation(s)
- Maura Boldrini
- Department of Psychiatry, Columbia University College of Physicians & Surgeons, New York State Psychiatric Institute, 1051 Riverside Drive, Box 42, New York, NY 10032, USA.
| | - Mark D. Underwood
- Department of Psychiatry, Columbia University,Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute
| | - René Hen
- Department of Psychiatry, Columbia University,Department of Neuroscience, Columbia University,Department of Pharmacology, Columbia University,Division of Integrative Neuroscience, New York State Psychiatric Institute
| | - Gorazd B. Rosoklija
- Department of Psychiatry, Columbia University,Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute,Macedonian Academy of Sciences & Arts
| | - Andrew J. Dwork
- Department of Psychiatry, Columbia University,Department of Pathology and Cell Biology, Columbia University,Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute
| | - J. John Mann
- Department of Psychiatry, Columbia University,Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute
| | - Victoria Arango
- Department of Psychiatry, Columbia University,Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute
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Espina V, Mueller C, Edmiston K, Sciro M, Petricoin EF, Liotta LA. Tissue is alive: New technologies are needed to address the problems of protein biomarker pre-analytical variability. Proteomics Clin Appl 2009; 3:874-882. [PMID: 20871745 DOI: 10.1002/prca.200800001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Instability of tissue protein biomarkers is a critical issue for molecular profiling. Pre-analytical variables during tissue procurement, such as time delays during which the tissue remains stored at room temperature, can cause significant variability and bias in downstream molecular analysis. Living tissue, ex vivo, goes through a defined stage of reactive changes that begin with oxidative, hypoxic and metabolic stress, and culminate in apoptosis. Depending on the delay time ex vivo, and reactive stage, protein biomarkers, such as signal pathway phosphoproteins will be elevated or suppressed in a manner which does not represent the biomarker levels at the time of excision. Proteomic data documenting reactive tissue protein changes post collection indicate the need to recognize and address tissue stability, preservation of post-translational modifications, and preservation of morphologic features for molecular analysis. Based on the analysis of phosphoproteins, one of the most labile tissue protein biomarkers, we set forth tissue procurement guidelines for clinical research. We propose technical solutions for (i) assessing the state of protein analyte preservation and specimen quality via identification of a panel of natural proteins (surrogate stability markers), and (ii) using multi-purpose fixative solution designed to stabilize, preserve and maintain proteins, nucleic acids, and tissue architecture.
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Affiliation(s)
- Virginia Espina
- George Mason University, Center for Applied Proteomics and Molecular Medicine, Manassas, VA, USA
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