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Dias C, Mo A, Cai C, Sun L, Cabral K, Brownstein CA, Rockowitz S, Walsh CA. Cell-type-specific effects of autism-associated 15q duplication syndrome in the human brain. Am J Hum Genet 2024; 111:1544-1558. [PMID: 39079538 DOI: 10.1016/j.ajhg.2024.07.002] [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: 04/02/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 08/11/2024] Open
Abstract
Recurrent copy-number variation represents one of the most well-established genetic drivers in neurodevelopmental disorders, including autism spectrum disorder. Duplication of 15q11-q13 (dup15q) is a well-described neurodevelopmental syndrome that increases the risk of autism more than 40-fold. However, the effects of this duplication on gene expression and chromatin accessibility in specific cell types in the human brain remain unknown. To identify the cell-type-specific transcriptional and epigenetic effects of dup15q in the human frontal cortex, we conducted single-nucleus RNA sequencing and multi-omic sequencing on dup15q-affected individuals (n = 6) as well as individuals with non-dup15q autism (n = 7) and neurotypical control individuals (n = 7). Cell-type-specific differential expression analysis identified significantly regulated genes, critical biological pathways, and differentially accessible genomic regions. Although there was overall increased gene expression across the duplicated genomic region, cellular identity represented an important factor mediating gene-expression changes. As compared to other cell types, neuronal subtypes showed greater upregulation of gene expression across a critical region within the duplication. Genes that fell within the duplicated region and had high baseline expression in control individuals showed only modest changes in dup15q, regardless of cell type. Of note, dup15q and autism had largely distinct signatures of chromatin accessibility but shared the majority of transcriptional regulatory motifs, suggesting convergent biological pathways. However, the transcriptional binding-factor motifs implicated in each condition implicated distinct biological mechanisms: neuronal JUN and FOS networks in autism vs. an inflammatory transcriptional network in dup15q microglia. This work provides a cell-type-specific analysis of how dup15q changes gene expression and chromatin accessibility in the human brain, and it finds evidence of marked cell-type-specific effects of this genetic driver. These findings have implications for guiding therapeutic development in dup15q syndrome, as well as understanding the functional effects of copy-number variants more broadly in neurodevelopmental disorders.
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Affiliation(s)
- Caroline Dias
- Division of Developmental Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Alisa Mo
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chunhui Cai
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kristen Cabral
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Shira Rockowitz
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
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2
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Sun S, Liu Q, Wang Z, Huang YY, Sublette ME, Dwork AJ, Rosoklija G, Ge Y, Galfalvy H, Mann JJ, Haghighi F. Brain and blood transcriptome profiles delineate common genetic pathways across suicidal ideation and suicide. Mol Psychiatry 2024; 29:1417-1426. [PMID: 38278992 PMCID: PMC11189724 DOI: 10.1038/s41380-024-02420-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
Human genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to the severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with the presence of suicidal ideation were found within 18 co-expressed modules (p < 0.05), as well as in 3 co-expressed modules associated with suicidal ideation severity (p < 0.05, not explained by severity of depression). Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified and investigated using RNA-seq data from postmortem brain that revealed gene expression differences with moderate effect sizes in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity are associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.
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Affiliation(s)
- Shengnan Sun
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Qingkun Liu
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Zhaoyu Wang
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Yung-Yu Huang
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - M Elizabeth Sublette
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Gorazd Rosoklija
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hanga Galfalvy
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Fatemeh Haghighi
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- James J. Peters VA Medical Center, Bronx, NY, 10468, USA.
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3
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Tayler HM, MacLachlan R, Güzel Ö, Fisher RA, Skrobot OA, Abulfadl MA, Kehoe PG, Miners JS. Altered Gene Expression Within the Renin-Angiotensin System in Normal Aging and Dementia. J Gerontol A Biol Sci Med Sci 2024; 79:glad241. [PMID: 37813091 PMCID: PMC10733177 DOI: 10.1093/gerona/glad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Indexed: 10/11/2023] Open
Abstract
The renin-angiotensin system (RAS) is dysregulated in Alzheimer's disease (AD). In this study, we have explored the hypothesis that an -age--related imbalance in brain RAS is a trigger for RAS dysregulation in AD. We characterized RAS gene expression in the frontal cortex from (i) a cohort of normal aging (n = 99, age range = 19-96 years) and (ii) a case-control cohort (n = 209) including AD (n = 66), mixed dementia (VaD + AD; n = 50), pure vascular dementia (VaD; n = 42), and age-matched controls (n = 51). The AD, mixed dementia, and age-matched controls were further stratified by Braak tangle stage (BS): BS0-II (n = 48), BSIII-IV (n = 44), and BSV-VI (n = 85). Gene expression was calculated by quantitative PCR (qPCR) for ACE1, AGTR1, AGTR2, ACE2, LNPEP, and MAS1 using the 2-∆∆Cq method, after adjustment for reference genes (RPL13 and UBE2D2) and cell-specific calibrator genes (NEUN, GFAP, PECAM). ACE1 and AGTR1, markers of classical RAS signaling, and AGTR2 gene expression were elevated in normal aging and gene expression in markers of protective downstream regulatory RAS signaling, including ACE2, MAS1, and LNPEP, were unchanged. In AD and mixed dementia, AGTR1 and AGTR2 gene expression were elevated in BSIII-IV and BSV-VI, respectively. MAS1 gene expression was reduced at BSV-VI and was inversely related to parenchymal Aβ and tau load. LNPEP gene expression was specifically elevated in VaD. These data provide novel insights into RAS signaling in normal aging and dementia.
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Affiliation(s)
- Hannah M Tayler
- Dementia Research Group, Clinical Neurosciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Robert MacLachlan
- Dementia Research Group, Clinical Neurosciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Özge Güzel
- Dementia Research Group, Clinical Neurosciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Robert A Fisher
- Dementia Research Group, Clinical Neurosciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Olivia A Skrobot
- Dementia Research Group, Clinical Neurosciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Mohamed A Abulfadl
- Dementia Research Group, Clinical Neurosciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Patrick G Kehoe
- Dementia Research Group, Clinical Neurosciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - J Scott Miners
- Dementia Research Group, Clinical Neurosciences, Bristol Medical School, University of Bristol, Bristol, UK
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4
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Sun S, Liu Q, Wang Z, Huang YY, Sublette M, Dwork A, Rosoklija G, Ge Y, Galfalvy H, Mann JJ, Haghighi F. Functional Architecture of Brain and Blood Transcriptome Delineate Biological Continuity Between Suicidal Ideation and Suicide. RESEARCH SQUARE 2023:rs.3.rs-2958575. [PMID: 37398042 PMCID: PMC10312911 DOI: 10.21203/rs.3.rs-2958575/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Human genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with presence and severity of suicidal ideation were found within 18 and 3 co-expressed modules respectively (p < 0.05), not explained by severity of depression. Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified, and tested using RNA-seq data from postmortem brain that revealed gene expression differences in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity is associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.
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5
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Tauber CV, Schwarz SC, Rösler TW, Arzberger T, Gentleman S, Windl O, Krumbiegel M, Reis A, Ruf VC, Herms J, Höglinger GU. Different MAPT haplotypes influence expression of total MAPT in postmortem brain tissue. Acta Neuropathol Commun 2023; 11:40. [PMID: 36906636 PMCID: PMC10008602 DOI: 10.1186/s40478-023-01534-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
The MAPT gene, encoding the microtubule-associated protein tau on chromosome 17q21.31, is result of an inversion polymorphism, leading to two allelic variants (H1 and H2). Homozygosity for the more common haplotype H1 is associated with an increased risk for several tauopathies, but also for the synucleinopathy Parkinson's disease (PD). In the present study, we aimed to clarify whether the MAPT haplotype influences expression of MAPT and SNCA, encoding the protein α-synuclein (α-syn), on mRNA and protein levels in postmortem brains of PD patients and controls. We also investigated mRNA expression of several other MAPT haplotype-encoded genes. Postmortem tissues from cortex of fusiform gyrus (ctx-fg) and of the cerebellar hemisphere (ctx-cbl) of neuropathologically confirmed PD patients (n = 95) and age- and sex-matched controls (n = 81) were MAPT haplotype genotyped to identify cases homozygous for either H1 or H2. Relative expression of genes was quantified using real-time qPCR; soluble and insoluble protein levels of tau and α-syn were determined by Western blotting. Homozygosity for H1 versus H2 was associated with increased total MAPT mRNA expression in ctx-fg regardless of disease state. Inversely, H2 homozygosity was associated with markedly increased expression of the corresponding antisense MAPT-AS1 in ctx-cbl. PD patients had higher levels of insoluble 0N3R and 1N4R tau isoforms regardless of the MAPT genotype. The increased presence of insoluble α-syn in PD patients in ctx-fg validated the selected postmortem brain tissue. Our findings in this small, but well controlled cohort of PD and controls support a putative biological relevance of tau in PD. However, we did not identify any link between the disease-predisposing H1/H1 associated overexpression of MAPT with PD status. Further studies are required to gain a deeper understanding of the potential regulatory role of MAPT-AS1 and its association to the disease-protective H2/H2 condition in the context of PD.
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Affiliation(s)
- Christina V Tauber
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Department of Neurology, School of Medicine, Technical University Munich, Munich, Germany.,Department of Obstetrics and Gynecology, Ludiwgs-Maximilians University of Munich, Munich, Germany
| | - Sigrid C Schwarz
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Thomas W Rösler
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Department of Neurology, School of Medicine, Technical University Munich, Munich, Germany
| | - Thomas Arzberger
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University of Munich, Munich, Germany.,Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Steve Gentleman
- Parkinson's UK Brain Bank, Department of Brain Sciences, Imperial College London, London, UK.,Neuropathology Unit, Department of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - Otto Windl
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Mandy Krumbiegel
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Viktoria C Ruf
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Jochen Herms
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University of Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Günter U Höglinger
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. .,Department of Neurology, Ludwig-Maximilians University of Munich, Munich, Germany.
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6
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Isolating mineralized bone and bone marrow mRNA from transiliac bone biopsies stored in a stabilizing solution: A comparative study. Bone Rep 2022; 17:101624. [PMID: 36238088 PMCID: PMC9551114 DOI: 10.1016/j.bonr.2022.101624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
The molecular mechanisms underlying metabolic bone diseases, including renal osteodystrophy, are poorly understood. Transcriptomics are increasingly used to characterize biological molecular networks and prove promising in identifying therapeutic targets and biomarkers. A reliable method for obtaining sufficient amounts of high quality RNA from human bone biopsies is a prerequisite for the implementation of molecular diagnostics in clinical research and practice. The present study aimed to develop a simple and adequate method for isolating bone and bone marrow mRNA from transiliac bone biopsies. Several storage, separation, and extraction procedures were compared. The procedure was optimized in pig samples and subsequently validated in human samples. Appropriate amounts of mineralized bone and bone marrow mRNA of moderate to high quality were obtained from transiliac bone biopsies that were immersed in the stabilizing solution Allprotect Tissue Reagent at room temperature for up to 3 days prior to freezing. After thawing, bone marrow and mineralized bone were separated by a multistep centrifugation procedure and subsequently disrupted and homogenized by a bead crusher. Appropriate separation of mineralized bone and bone marrow was confirmed by discriminatory gene expression profiles. Molecular diagnostics increasingly gain interest in clinical practice. A bone biopsy immersed in a stabilization reagent yields moderate mRNA quality. Use of a stabilization reagent allows for easy separation of bone and bone marrow.
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Understanding quantitative polymerase chain reaction bioanalysis issues before validation planning: Japan Bioanalysis Forum discussion group. Bioanalysis 2022; 14:1391-1405. [PMID: 36621859 DOI: 10.4155/bio-2022-0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Investigating the biodistribution of cell and gene therapy products may play an important role in evaluating their safety and pharmacology. As quantitative polymerase chain reaction (qPCR) is often used for these analyses, it is essential to improve the reliability of bioanalysis performed using qPCR. In this report, the authors discuss the use of qPCR in nonclinical studies, as it can be used to detect target DNA/RNA and it is quantitative and applicable for long-term analysis. The authors also discuss points to consider during bioanalysis using qPCR and present appropriate validation items and their criteria. The authors anticipate the discussion provided herein to contribute to the development of validation and sample analysis for pharmaceuticals analyzed using qPCR.
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Santana DA, Bedrat A, Puga RD, Turecki G, Mechawar N, Faria TC, Gigek CO, Payão SL, Smith MA, Lemos B, Chen ES. The role of H3K9 acetylation and gene expression in different brain regions of Alzheimer's disease patients. Epigenomics 2022; 14:651-670. [PMID: 35588246 DOI: 10.2217/epi-2022-0096] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To evaluate H3K9 acetylation and gene expression profiles in three brain regions of Alzheimer's disease (AD) patients and elderly controls, and to identify AD region-specific abnormalities. Methods: Brain samples of auditory cortex, hippocampus and cerebellum from AD patients and controls underwent chromatin immunoprecipitation sequencing, RNA sequencing and network analyses. Results: We found a hyperacetylation of AD cerebellum and a slight hypoacetylation of AD hippocampus. The transcriptome revealed differentially expressed genes in the hippocampus and auditory cortex. Network analysis revealed Rho GTPase-mediated mechanisms. Conclusions: These findings suggest that some crucial mechanisms, such as Rho GTPase activity and cytoskeletal organization, are differentially dysregulated in brain regions of AD patients at the epigenetic and transcriptomic levels, and might contribute toward future research on AD pathogenesis.
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Affiliation(s)
- Daliléia A Santana
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Amina Bedrat
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Renato D Puga
- Hermes Pardini Institute, São Paulo, SP, 04038-030, Brazil
| | - Gustavo Turecki
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Naguib Mechawar
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Tathyane C Faria
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Carolina O Gigek
- Department of Pathology, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, 04023-062, Brazil
| | - Spencer Lm Payão
- Department of Genetics, Blood Center, Faculdade de Medicina de Marília (FAMEMA), Marília, SP, 17519-050, Brazil
| | - Marília Ac Smith
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Bernardo Lemos
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Elizabeth S Chen
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil.,Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
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9
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Zhang X, McFarland TJ, Vartanian K, Zhu Y, Harrington CA, Chu CQ. RNA isolation from micro-quantity of articular cartilage for quantitative gene expression by microarray analysis. Int J Med Sci 2022; 19:98-104. [PMID: 34975303 PMCID: PMC8692110 DOI: 10.7150/ijms.65343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Isolation of quality RNA from articular cartilage has been challenging due to low cellularity and the high abundance of extracellular matrix and proteoglycan proteins. Recently developed methods for isolation of high quality RNA from cartilage are more applicable to larger cartilage specimens typically weighing at least 25 mg. While these methods generate RNA suitable for analysis, they are less successful with smaller tissue inputs. For the study of small focal defect cartilage specimens an improved RNA extraction method is needed. Here we report a protocol for direct RNA isolation from less than 3 mg of wet weight rabbit articular cartilage for quantitative microarray gene profiling. This protocol is useful for identifying differentially expressed genes in chondrocytes following focal cartilage repair and can potentially be adopted for gene expression analysis of cartilage biopsy specimens from human joints.
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Affiliation(s)
- Xiaowei Zhang
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, Oregon 97239
- Section of Rheumatology, VA Portland Health Care System, Portland, Oregon 97239
| | - Trevor J. McFarland
- Gene Profiling Shared Resource, Oregon Health & Science University; Portland, Oregon 97239
| | - Kristina Vartanian
- Gene Profiling Shared Resource, Oregon Health & Science University; Portland, Oregon 97239
| | - Yong Zhu
- Vivoscript, Inc, P. O. Box 63025, Irvine, CA 92602
| | - Christina A. Harrington
- Gene Profiling Shared Resource, Oregon Health & Science University; Portland, Oregon 97239
- Department of Molecular and Medical Genetics, Oregon Health & Science University; Portland, Oregon 97239
| | - Cong-Qiu Chu
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, Oregon 97239
- Section of Rheumatology, VA Portland Health Care System, Portland, Oregon 97239
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10
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Grima N, Henden L, Watson O, Blair IP, Williams KL. Simultaneous Isolation of High-Quality RNA and DNA From Postmortem Human Central Nervous System Tissues for Omics Studies. J Neuropathol Exp Neurol 2021; 81:135-145. [PMID: 34939123 DOI: 10.1093/jnen/nlab129] [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
Multi-omics approaches are increasingly being adopted to understand the complex networks underlying disease. The coisolation of high-quality nucleotides from affected tissues is paramount for the parallel analysis of transcriptomic, genomic, and epigenomic data sets. Although nucleotides extracted from postmortem central nervous system (CNS) tissue are widely used in the study of neurodegenerative disease, assessment of methods for the simultaneous isolation of DNA and RNA is limited. Herein, we describe a strategy for the isolation of high-quality DNA and RNA from postmortem human tissue from 7 CNS regions. Motor cortex, frontal cortex, hippocampus, occipital cortex, anterior cingulate cortex, cerebellum, and spinal cord tissues were obtained from 22 individuals diagnosed with motor neuron disease (MND) and 13 neurologically normal controls (n = 245 tissues). We demonstrated that the Qiagen AllPrep DNA/RNA kit consistently isolated DNA and RNA of high yield and quality from all 6 brain regions. Importantly, phenol-chloroform-based extraction was required to isolate high-yield RNA from spinal cord. RNA sequencing using RNA extracted from 6 CNS regions (n = 60) generated high-quality transcriptomes. Hierarchical clustering of data from motor cortex, using an MND susceptibility gene panel and marker genes of disease-associated microglia, demonstrated that MND-specific gene expression signatures could be detected in the transcriptome data.
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Affiliation(s)
- Natalie Grima
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Lyndal Henden
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Owen Watson
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P Blair
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
| | - Kelly L Williams
- From the Faculty of Medicine, Health and Human Sciences, Macquarie University Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, New South Wales, Australia
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11
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Chaudhary S, Ashok A, Wise AS, Rana NA, McDonald D, Kritikos AE, Kong Q, Singh N. Upregulation of brain hepcidin in prion diseases. Prion 2021; 15:126-137. [PMID: 34224321 PMCID: PMC8259718 DOI: 10.1080/19336896.2021.1946377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/04/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
Accumulation of redox-active iron in human sporadic Creutzfeldt-Jakob disease (sCJD) brain tissue and scrapie-infected mouse brains has been demonstrated previously. Here, we explored whether upregulation of local hepcidin secreted within the brain is the underlying cause of iron accumulation and associated toxicity. Using scrapie-infected mouse brains, we demonstrate transcriptional upregulation of hepcidin relative to controls. As a result, ferroportin (Fpn), the downstream effector of hepcidin and the only known iron export protein was downregulated, and ferritin, an iron storage protein was upregulated, suggesting increased intracellular iron. A similar transcriptional and translational upregulation of hepcidin, and decreased expression of Fpn and an increase in ferritin expression was observed in sCJD brain tissue. Further evaluation in human neuroblastoma cells (M17) exposed to synthetic mini-hepcidin showed downregulation of Fpn, upregulation of ferritin, and an increase in reactive oxygen species (ROS), resulting in cytotoxicity in a dose-dependent manner. Similar effects were noted in primary neurons isolated from mouse brain. As in M17 cells, primary neurons accumulated ferritin and ROS, and showed toxicity at five times lower concentration of mini-hepcidin. These observations suggest that upregulation of brain hepcidin plays a significant role in iron accumulation and associated neurotoxicity in human and animal prion disorders.
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Affiliation(s)
- Suman Chaudhary
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ajay Ashok
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Aaron S. Wise
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Neil A. Rana
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dallas McDonald
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alexander E. Kritikos
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Qingzhong Kong
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Neena Singh
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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12
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Chaudhary S, Ashok A, McDonald D, Wise AS, Kritikos AE, Rana NA, Harding CV, Singh N. Upregulation of Local Hepcidin Contributes to Iron Accumulation in Alzheimer's Disease Brains. J Alzheimers Dis 2021; 82:1487-1497. [PMID: 34180415 DOI: 10.3233/jad-210221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Accumulation of iron is a consistent feature of Alzheimer's disease (AD) brains. The underlying cause, however, remains debatable. OBJECTIVE To explore whether local hepcidin synthesized by brain cells contributes to iron accumulation in AD brains. METHODS Brain tissue from the cingulate cortex of 33 cases of AD pre-assigned to Braak stage I-VI, 6 cases of non-dementia, and 15 cases of non-AD dementia were analyzed for transcriptional upregulation of hepcidin by RT-qPCR and RT-PCR. Change in the expression of ferritin, ferroportin (Fpn), microglial activation marker Iba1, IL-6, and TGFβ2 was determined by western blotting. Total tissue iron was determined by colorimetry. RESULTS Significant transcriptional upregulation of hepcidin was observed in Braak stage III-VI relative to Braak stage I and II, non-AD dementia, and non-dementia samples. Ferritin was increased in Braak stage V, and a significant increase in tissue iron was evident in Braak stage III-VI. The expression of Iba1 and IL-6 was also increased in Braak stage III-VI relative to Braak stage I and II and non-AD dementia samples. Amyloid-β plaques were absent in most Braak stage I and II samples, and present in Braak stage III-VI samples with few exceptions. CONCLUSION These observations suggest that upregulation of brain hepcidin is mediated by IL-6, a known transcriptional activator of hepcidin. The consequent downregulation of Fpn on neuronal and other cells results in accumulation of iron in AD brains. The increase in hepcidin is disease-specific, and increases with disease progression, implicating AD-specific pathology in the accumulation of iron.
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Affiliation(s)
- Suman Chaudhary
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ajay Ashok
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Dallas McDonald
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Aaron S Wise
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alexander E Kritikos
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Neil A Rana
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Clifford V Harding
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Neena Singh
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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13
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Purves-Tyson TD, Brown AM, Weissleder C, Rothmond DA, Shannon Weickert C. Reductions in midbrain GABAergic and dopamine neuron markers are linked in schizophrenia. Mol Brain 2021; 14:96. [PMID: 34174930 PMCID: PMC8235806 DOI: 10.1186/s13041-021-00805-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/07/2021] [Indexed: 01/16/2023] Open
Abstract
Reductions in the GABAergic neurotransmitter system exist across multiple brain regions in schizophrenia and encompass both pre- and postsynaptic components. While reduced midbrain GABAergic inhibitory neurotransmission may contribute to the hyperdopaminergia thought to underpin psychosis in schizophrenia, molecular changes consistent with this have not been reported. We hypothesised that reduced GABA-related molecular markers would be found in the midbrain of people with schizophrenia and that these would correlate with dopaminergic molecular changes. We hypothesised that downregulation of inhibitory neuron markers would be exacerbated in schizophrenia cases with high levels of neuroinflammation. Eight GABAergic-related transcripts were measured with quantitative PCR, and glutamate decarboxylase (GAD) 65/67 and GABAA alpha 3 (α3) (GABRA3) protein were measured with immunoblotting, in post-mortem midbrain (28/28 and 28/26 control/schizophrenia cases for mRNA and protein, respectively), and analysed by both diagnosis and inflammatory subgroups (as previously defined by higher levels of four pro-inflammatory cytokine transcripts). We found reductions (21 – 44%) in mRNA encoding both presynaptic and postsynaptic proteins, vesicular GABA transporter (VGAT), GAD1, and parvalbumin (PV) mRNAs and four alpha subunits (α1, α2, α3, α5) of the GABAA receptor in people with schizophrenia compared to controls (p < 0.05). Gene expression of somatostatin (SST) was unchanged (p = 0.485). We confirmed the reduction in GAD at the protein level (34%, p < 0.05). When stratifying by inflammation, only GABRA3 mRNA exhibited more pronounced changes in high compared to low inflammatory subgroups in schizophrenia. GABRA3 protein was expressed by 98% of tyrosine hydroxylase-positive neurons and was 23% lower in schizophrenia, though this did not reach statistical significance (p > 0.05). Expression of transcripts for GABAA receptor alpha subunits 2 and 3 (GABRA2, GABRA3) were positively correlated with tyrosine hydroxylase (TH) and dopamine transporter (DAT) transcripts in schizophrenia cases (GABRA2; r > 0.630, GABRA3; r > 0.762, all p < 0.001) but not controls (GABRA2; r < − 0.200, GABRA3; r < 0.310, all p > 0.05). Taken together, our results support a profound disruption to inhibitory neurotransmission in the substantia nigra regardless of inflammatory status, which provides a potential mechanism for disinhibition of nigrostriatal dopamine neurotransmission.
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Affiliation(s)
- Tertia D Purves-Tyson
- Schizophrenia Research Laboratory, Neuroscience Research Australia, 139 Barker Street, Margarete Ainsworth Building, Level 5, Randwick, NSW, 2031, Australia. .,School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Amelia M Brown
- Schizophrenia Research Laboratory, Neuroscience Research Australia, 139 Barker Street, Margarete Ainsworth Building, Level 5, Randwick, NSW, 2031, Australia
| | - Christin Weissleder
- Schizophrenia Research Laboratory, Neuroscience Research Australia, 139 Barker Street, Margarete Ainsworth Building, Level 5, Randwick, NSW, 2031, Australia
| | - Debora A Rothmond
- Schizophrenia Research Laboratory, Neuroscience Research Australia, 139 Barker Street, Margarete Ainsworth Building, Level 5, Randwick, NSW, 2031, Australia
| | - Cynthia Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia, 139 Barker Street, Margarete Ainsworth Building, Level 5, Randwick, NSW, 2031, Australia. .,School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia. .,Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY, 13210, USA.
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14
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Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing. BMC Genomics 2021; 22:69. [PMID: 33478392 PMCID: PMC7818915 DOI: 10.1186/s12864-021-07381-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Both RNA-Seq and sample freeze-thaw are ubiquitous. However, knowledge about the impact of freeze-thaw on downstream analyses is limited. The lack of common quality metrics that are sufficiently sensitive to freeze-thaw and RNA degradation, e.g. the RNA Integrity Score, makes such assessments challenging. Results Here we quantify the impact of repeated freeze-thaw cycles on the reliability of RNA-Seq by examining poly(A)-enriched and ribosomal RNA depleted RNA-seq from frozen leukocytes drawn from a toddler Autism cohort. To do so, we estimate the relative noise, or percentage of random counts, separating technical replicates. Using this approach we measured noise associated with RIN and freeze-thaw cycles. As expected, RIN does not fully capture sample degradation due to freeze-thaw. We further examined differential expression results and found that three freeze-thaws should extinguish the differential expression reproducibility of similar experiments. Freeze-thaw also resulted in a 3′ shift in the read coverage distribution along the gene body of poly(A)-enriched samples compared to ribosomal RNA depleted samples, suggesting that library preparation may exacerbate freeze-thaw-induced sample degradation. Conclusion The use of poly(A)-enrichment for RNA sequencing is pervasive in library preparation of frozen tissue, and thus, it is important during experimental design and data analysis to consider the impact of repeated freeze-thaw cycles on reproducibility. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07381-z.
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Affiliation(s)
- Benjamin P Kellman
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Hratch M Baghdassarian
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Tiziano Pramparo
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Isaac Shamie
- Department of Pediatrics, University of California, San Diego, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, San Diego, USA
| | - Vahid Gazestani
- Department of Pediatrics, University of California, San Diego, USA.,Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Arjana Begzati
- Department of Medicine, University of California San Diego, San Diego, USA
| | - Shangzhong Li
- Department of Pediatrics, University of California, San Diego, USA.,Department of Bioengineering, University of California San Diego, San Diego, USA
| | - Srinivasa Nalabolu
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Sarah Murray
- Department of Pathology, University of California San Diego, San Diego, USA
| | - Linda Lopez
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, San Diego, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, USA. .,Department of Bioengineering, University of California San Diego, San Diego, USA. .,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, USA.
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15
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Kumar V, Krolewski DM, Hebda-Bauer EK, Parsegian A, Martin B, Foltz M, Akil H, Watson SJ. Optimization and evaluation of fluorescence in situ hybridization chain reaction in cleared fresh-frozen brain tissues. Brain Struct Funct 2021; 226:481-499. [PMID: 33386994 DOI: 10.1007/s00429-020-02194-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/27/2020] [Indexed: 11/27/2022]
Abstract
Transcript labeling in intact tissues using in situ hybridization chain reaction has potential to provide vital spatiotemporal information for molecular characterization of heterogeneous neuronal populations. However, large tissue labeling in non-perfused or fresh-frozen rodent and postmortem human samples, which provide more flexible utilization than perfused tissues, is largely unexplored. In the present study, we optimized the combination of in situ hybridization chain reaction in fresh-frozen rodent brains and then evaluated the uniformity of neuronal labeling between two clearing methods, CLARITY and iDISCO+. We found that CLARITY yielded higher signal-to-noise ratios but more limited imaging depth and required longer clearing times, whereas, iDISCO+ resulted in better tissue clearing, greater imaging depth and a more uniform labeling of larger samples. Based on these results, we used iDISCO+-cleared fresh-frozen rodent brains to further validate this combination and map the expression of a few genes of interest pertaining to mood disorders. We then examined the potential of in situ hybridization chain reaction to label transcripts in cleared postmortem human brain tissues. The combination failed to produce adequate mRNA labeling in postmortem human cortical slices but produced visually adequate labeling in the cerebellum tissues. We next, investigated the multiplexing ability of in situ hybridization chain reaction in cleared tissues which revealed inconsistent fluorescence output depending upon the fluorophore conjugated to the hairpins. Finally, we applied our optimized protocol to assess the effect of glucocorticoid receptor overexpression on basal somatostatin expression in the mouse cortex. The constitutive glucocorticoid receptor overexpression resulted in lower number density of somatostatin-expressing neurons compared to wild type. Overall, the combination of in situ hybridization chain reaction with clearing methods, especially iDISCO+, may find broad application in the transcript analysis in rodent studies, but its limited use in postmortem human tissues can be improved by further optimizations.
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Affiliation(s)
- Vivek Kumar
- Michigan Neuroscience Institute, University of Michigan, 205 Zina Pitcher pl, Ann Arbor, MI, 48109, USA.
| | - David M Krolewski
- Michigan Neuroscience Institute, University of Michigan, 205 Zina Pitcher pl, Ann Arbor, MI, 48109, USA
| | - Elaine K Hebda-Bauer
- Michigan Neuroscience Institute, University of Michigan, 205 Zina Pitcher pl, Ann Arbor, MI, 48109, USA
| | - Aram Parsegian
- Michigan Neuroscience Institute, University of Michigan, 205 Zina Pitcher pl, Ann Arbor, MI, 48109, USA
| | - Brian Martin
- Michigan Neuroscience Institute, University of Michigan, 205 Zina Pitcher pl, Ann Arbor, MI, 48109, USA
| | - Matthew Foltz
- Michigan Neuroscience Institute, University of Michigan, 205 Zina Pitcher pl, Ann Arbor, MI, 48109, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, 205 Zina Pitcher pl, Ann Arbor, MI, 48109, USA
| | - Stanley J Watson
- Michigan Neuroscience Institute, University of Michigan, 205 Zina Pitcher pl, Ann Arbor, MI, 48109, USA
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16
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Swaab DF, Bao AM. Matching of the postmortem hypothalamus from patients and controls. HANDBOOK OF CLINICAL NEUROLOGY 2021; 179:141-156. [PMID: 34225959 DOI: 10.1016/b978-0-12-819975-6.00007-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The quality of postmortem hypothalamus research depends strongly on a thorough clinical investigation and documentation of the patient's disorder and therapies. In addition, a systematic and professional neuropathological investigation of the entire brain of both the cases and the controls is absolutely crucial. In the experience of the Netherlands Brain Bank (NBB), about 20% of the clinical neurological diagnoses, despite being made in first rate clinics, have to be revised or require extra diagnoses after a complete and thorough neuropathologic review by the NBB. The neuropathology examination may reveal for instance that the elderly "controls" already have preclinical neurodegenerative alterations. In postmortem studies, the patient and control groups must be matched for as many as possible of the known confounding factors. This is necessary to make the groups as similar as possible, except for the topic being investigated. Confounding factors are present (i) before, (ii) during, and (iii) after death. They are, respectively: (i) genetic background, systemic diseases, duration and gravity of illness, medicines and addictive compounds used, age, sex, gender identity, sexual orientation, clock- and seasonal time of death, and lateralization; (ii) agonal state, stress of dying; and (iii) postmortem delay, freezing procedures, fixation, and storage time. Agonal state is generally estimated by measuring the pH of the brain. However, there are disorders in which pH is lower as a part of the disease process. Because of the large number of potentially confounding factors that differ according to, for instance, brain area and disease, a brain bank should have a large number of controls at its disposal for appropriate matching. If matching fails for some confounders, the influence of the confounders may be determined by statistical methods, such as analysis of variance or the regression models.
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Affiliation(s)
- Dick F Swaab
- Department Neuropsychiatric Disorders, Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.
| | - Ai-Min Bao
- Department of Neurobiology and Department of Neurology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, China
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17
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Regulation of cannabinoid CB 1 and CB 2 receptors, neuroprotective mTOR and pro-apoptotic JNK1/2 kinases in postmortem prefrontal cortex of subjects with major depressive disorder. J Affect Disord 2020; 276:626-635. [PMID: 32871695 DOI: 10.1016/j.jad.2020.07.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/26/2020] [Accepted: 07/05/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Dysregulations of endocannabinoids and/or cannabinoid (CB) receptors have been implicated in the pathophysiology and treatment of major depressive disorder (MDD). METHODS CB1 and CB2 receptors, neuroprotective mTOR (mechanistic target of rapamycin) and pro-apoptotic JNK1/2 (c-Jun-N-terminal kinases) were quantified by immunoblotting in postmortem prefrontal cortex of MDD and controls, and further compared in antidepressant (AD)-free and AD-treated subjects. Neuroplastic proteins (PSD-95, Arc, spinophilin) were quantified in MDD brains. RESULTS Total cortical CB1 glycosylated (≈54/64 kDa) receptor was increased in MDD (+20%, n=23, p=0.02) when compared with controls (100%, n=19). This CB1 receptor upregulation was quantified in AD-treated (+23%, n=14, p=0.02) but not in AD-free (+14%, n=9, p=0.34) MDD subjects. In the same MDD cortical samples, CB2 glycosylated (≈45 kDa) receptor was unaltered (all MDD: +11%, n=23, p=0.10; AD-free: +12%, n=9, p=0.31; AD-treated: +10%, n=14, p=0.23). In MDD, mTOR activity (p-Ser2448 TOR/t-TOR) was increased (all MDD: +29%, n=18, p=0.002; AD-free: +33%, n=8, p=0.03; AD-treated: +25%, n=10, p=0.04). In contrast, JNK1/2 activity (p-Thr183/Tyr185/t-JNK) was unaltered in MDD subjects. Cortical PSD-95, Arc, and spinophilin contents were unchanged in MDD. LIMITATIONS A relative limited sample size. Some MDD subjects had been treated with a variety of ADs. The results must be understood in the context of suicide victims with MDD. CONCLUSIONS The upregulation of CB1 receptor density, but not that of CB2 receptor, as well as the increased mTOR activity in PFC/BA9 of subjects with MDD (AD-free/treated) support their contributions in the complex pathophysiology of MDD and in the molecular mechanisms of antidepressant drugs.
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18
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Raghunathan R, Hogan JD, Labadorf A, Myers RH, Zaia J. A glycomics and proteomics study of aging and Parkinson's disease in human brain. Sci Rep 2020; 10:12804. [PMID: 32733076 PMCID: PMC7393382 DOI: 10.1038/s41598-020-69480-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 05/04/2020] [Indexed: 01/08/2023] Open
Abstract
Previous studies on Parkinson’s disease mechanisms have shown dysregulated extracellular transport of α-synuclein and growth factors in the extracellular space. In the human brain these consist of perineuronal nets, interstitial matrices, and basement membranes, each composed of a set of collagens, non-collagenous glycoproteins, proteoglycans, and hyaluronan. The manner by which amyloidogenic proteins spread extracellularly, become seeded, oligomerize, and are taken up by cells, depends on intricate interactions with extracellular matrix molecules. We sought to assess the alterations to structure of glycosaminoglycans and proteins that occur in PD brain relative to controls of similar age. We found that PD differs markedly from normal brain in upregulation of extracellular matrix structural components including collagens, proteoglycans and glycosaminoglycan binding molecules. We also observed that levels of hemoglobin chains, possibly related to defects in iron metabolism, were enriched in PD brains. These findings shed important new light on disease processes that occur in association with PD.
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Affiliation(s)
- Rekha Raghunathan
- Graduate Program in Molecular and Translational Medicine, Boston University School of Medicine, Boston, 02118, USA
| | - John D Hogan
- Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, 02118, USA
| | - Adam Labadorf
- Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, 02118, USA.,Department of Neurology, Boston University School of Medicine, Boston, 02118, USA
| | - Richard H Myers
- Graduate Program in Molecular and Translational Medicine, Boston University School of Medicine, Boston, 02118, USA.,Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, 02118, USA.,Department of Neurology, Boston University School of Medicine, Boston, 02118, USA
| | - Joseph Zaia
- Graduate Program in Molecular and Translational Medicine, Boston University School of Medicine, Boston, 02118, USA. .,Department of Biochemistry, Boston University School of Medicine, 670 Albany St., Rm. 509, Boston, 02118, USA. .,Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, 02118, USA.
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19
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IL-38 inhibits microglial inflammatory mediators and is decreased in amygdala of children with autism spectrum disorder. Proc Natl Acad Sci U S A 2020; 117:16475-16480. [PMID: 32601180 DOI: 10.1073/pnas.2004666117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Autism spectrum disorder (ASD) is characterized by impaired social interactions and communication. The pathogenesis of ASD is not known, but it involves activation of microglia. We had shown that the peptide neurotensin (NT) is increased in the serum of children with ASD and stimulates cultured adult human microglia to secrete the proinflammatory molecules IL-1β and CXCL8. This process is inhibited by the cytokine IL-37. Another cytokine, IL-38, has been reported to have antiinflammatory actions. In this report, we show that pretreatment of cultured adult human microglia with recombinant IL-38 (aa3-152, 1-100 ng/mL) inhibits (P < 0.0001) NT-stimulated (10 nM) secretion of IL-1β (at 1 ng/mL) and CXCL8 (at 100 ng/mL). In fact, IL-38 (aa3-152, 1 ng/mL) is more potent than IL-37 (100 ng/mL). Here, we report that pretreatment with IL-38 (100 ng/mL) of embryonic microglia (HMC3), in which secretion of IL-1β was undetectable, inhibits secretion of CXCL8 (P = 0.004). Gene expression of IL-38 and its receptor IL-36R are decreased (P = 0.001 and P = 0.04, respectively) in amygdala from patients with ASD (n = 8) compared to non-ASD controls (n = 8), obtained from the University of Maryland NeuroBioBank. IL-38 is increased (P = 0.03) in the serum of children with ASD. These findings indicate an important role for IL-38 in the inhibition of activation of human microglia, thus supporting its development as a treatment approach for ASD.
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20
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IL-37 is increased in brains of children with autism spectrum disorder and inhibits human microglia stimulated by neurotensin. Proc Natl Acad Sci U S A 2019; 116:21659-21665. [PMID: 31591201 DOI: 10.1073/pnas.1906817116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) does not have a distinct pathogenesis or effective treatment. Increasing evidence supports the presence of immune dysfunction and inflammation in the brains of children with ASD. In this report, we present data that gene expression of the antiinflammatory cytokine IL-37, as well as of the proinflammatory cytokines IL-18 and TNF, is increased in the amygdala and dorsolateral prefrontal cortex of children with ASD as compared to non-ASD controls. Gene expression of IL-18R, which is a receptor for both IL-18 and IL-37, is also increased in the same brain areas of children with ASD. Interestingly, gene expression of the NTR3/sortilin receptor is reduced in the amygdala and dorsolateral prefrontal cortex. Pretreatment of cultured human microglia from normal adult brains with human recombinant IL-37 (1 to 100 ng/mL) inhibits neurotensin (NT)-stimulated secretion and gene expression of IL-1β and CXCL8. Another key finding is that NT, as well as the proinflammatory cytokines IL-1β and TNF increase IL-37 gene expression in cultured human microglia. The data presented here highlight the connection between inflammation and ASD, supporting the development of IL-37 as a potential therapeutic agent of ASD.
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21
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Meda S, Freund N, Norman KJ, Thompson BS, Sonntag KC, Andersen SL. The use of laser capture microdissection to identify specific pathways and mechanisms involved in impulsive choice in rats. Heliyon 2019; 5:e02254. [PMID: 31485508 PMCID: PMC6716106 DOI: 10.1016/j.heliyon.2019.e02254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/29/2019] [Accepted: 08/05/2019] [Indexed: 01/08/2023] Open
Abstract
Background Microinjections, lesions, viral-mediated gene transfer, or designer receptors exclusively activated by designer drugs (DREADDs) can identify brain signaling pathways and their pharmacology in research animals. Genetically modified animals are used for more precise assessment of neural circuits. However, only a few of the gene-based pathway modifications are available for use in outbred rat strains. New method Behaviorally characterized Sprague-Dawley rats undergo tract tracing through microinjection of fluorospheres, followed by laser capture microdissection (LCM) and qPCR for detecting mRNA of pathway-associated gene products. Correlations between mRNA expression and behavior identify specific involvement of pharmacologically relevant molecules within cells of interest. Here, we examined this methodology in an impulsive choice paradigm and targeted projections from the orbital and medial prefrontal cortex. Results In this proof of concept study, we demonstrate relationships between measures of impulsive choice with distinct neurotransmitter receptor expression in cell populations from four different signaling pathways. Comparisons with existing methods Combining behavior, tract tracing, LCM, and gene expression profiling provides more cellular selectivity than localized lesions and DREADDs, and greater pharmacological specificity than microinjections and viral-mediated gene transfer due to targeting identified neurons. Furthermore, the assessment of inter-individual pathways provides insight into the complex nature of underlying mechanisms involved in typical and atypical behavior. Conclusions The novel combination of behavior, tract tracing, LCM, and single gene or potential whole genome transcriptome analysis allows for a more targeted understanding of the interconnection of neural circuitry with behavior, and holds promise to identify more specific drug targets that are relevant to behavioral phenotypes.
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Affiliation(s)
- Shirisha Meda
- Laboratory of Developmental Neuropharmacology, McLean Hospital, Harvard Medical School, USA
| | - Nadja Freund
- Laboratory of Developmental Neuropharmacology, McLean Hospital, Harvard Medical School, USA.,Experimental and Molecular Psychiatry, Ruhr-University, Germany
| | - Kevin J Norman
- Laboratory of Developmental Neuropharmacology, McLean Hospital, Harvard Medical School, USA
| | - Britta S Thompson
- Laboratory of Developmental Neuropharmacology, McLean Hospital, Harvard Medical School, USA
| | - Kai-C Sonntag
- Laboratory for Translational Research on Neurodegeneration, Program for Neuropsychiatric Research, McLean Hospital, Harvard Medical School, USA.,Basic Neuroscience Division, McLean Hospital, Harvard Medical School, USA.,Department of Psychiatry, McLean Hospital, Harvard Medical School, USA
| | - Susan L Andersen
- Laboratory of Developmental Neuropharmacology, McLean Hospital, Harvard Medical School, USA.,Basic Neuroscience Division, McLean Hospital, Harvard Medical School, USA.,Department of Psychiatry, McLean Hospital, Harvard Medical School, USA
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22
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Hirata T, Otsuka I, Okazaki S, Mouri K, Horai T, Boku S, Takahashi M, Ueno Y, Sora I, Shirakawa O, Hishimoto A. Major depressive disorder-associated SIRT1 locus affects the risk for suicide in women after middle age. Psychiatry Res 2019; 278:141-145. [PMID: 31176830 DOI: 10.1016/j.psychres.2019.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/20/2019] [Accepted: 06/01/2019] [Indexed: 01/07/2023]
Abstract
A recent genome-wide association study (GWAS) for major depressive disorder (MDD) in Chinese women identified a single-nucleotide polymorphism (SNP), rs12415800, near the Sirtuin1 (SIRT1) gene as one of the top candidate loci. However, no study has shown a genetic association between SIRT1 and completed suicide, which is one of the most serious outcomes of MDD. In this study, 778 suicide completers and 760 controls in a Japanese population were genotyped for two SNPs in strong linkage disequilibrium (rs12415800 and rs4746720 in 3'UTR). We found significant associations between both SNPs and completed suicide among women aged ≥50 years. Additional analysis using postmortem brain tissues (10 suicide brains and 13 non-suicide brains) revealed the following: while SIRT1 gene expression in the prefrontal cortex did not differ between suicide and non-suicide brains, DNAJC12 gene expression, potentially implicated by the SNPs genotyped here, was significantly decreased in suicide brains (p = 0.003). In conclusion, regarding the genetic association of SIRT1 with MDD that was previously identified in women by the Chinese GWAS, we successfully validated our results using a female suicidal cohort in the same Asian population with the same direction of allelic effect.
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Affiliation(s)
- Takashi Hirata
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kentaro Mouri
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shuken Boku
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Motonori Takahashi
- Division of Legal Medicine, Department of Community Medicine and Social Health Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yasuhiro Ueno
- Division of Legal Medicine, Department of Community Medicine and Social Health Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ichiro Sora
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Osamu Shirakawa
- Department of Neuropsychiatry, Kindai University Faculty of Medicine, Osaka, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.
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Garson JA, Usher L, Al-Chalabi A, Huggett J, Day EF, McCormick AL. Response to the Letter from Garcia-Montojo and colleagues concerning our paper entitled, Quantitative analysis of human endogenous retrovirus-K transcripts in postmortem premotor cortex fails to confirm elevated expression of HERV-K RNA in amyotrophic lateral sclerosis. Acta Neuropathol Commun 2019; 7:102. [PMID: 31269988 PMCID: PMC6607588 DOI: 10.1186/s40478-019-0756-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 01/08/2023] Open
Affiliation(s)
- Jeremy A. Garson
- Division of Infection and Immunity, University College London, London, UK
- National Transfusion Microbiology Laboratories, NHS Blood and Transplant, Colindale, London, UK
| | - Louise Usher
- School of Life Sciences, University of Westminster, London, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Jim Huggett
- Molecular and Cell Biology Team, LGC, Teddington, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, UK
| | - Edmund F. Day
- School of Life Sciences, University of Westminster, London, UK
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Hay A, Lapointe JM, Lewis A, Moreno Quinn C, Miranda E. Optimization of RNA extraction from laser captured microdissected glomeruli from formalin-fixed paraffin-embedded mouse kidney samples for Nanostring analysis. Histol Histopathol 2019; 35:57-68. [PMID: 31184368 DOI: 10.14670/hh-18-135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Optimized protocols for the microdissection of specific areas from archival tissues and the subsequent RNA analysis are needed but challenging due to RNA degradation and chemical modifications. The aim of this study was to present the most appropriate protocol for utilizing mouse FFPE kidney for laser capture microdissection and Nanostring gene expression analysis. We evaluated different section thicknesses (3, 5, 10 μm), 2 RNA extraction kits (Qiagen and Roche) and different H&E staining methods to optimize microdissection and RNA extraction from glomeruli and cortical tubules samples from FFPE mouse kidney. RNA quality and quantity were assessed via Nanodrop and Qubit. The protocol providing the best results consisted of 5 μm sections, a shorter protocol for H&E staining, and RNA extracted with the Roche kit. Higher Nanostring gene counts and lower qPCR cT significantly correlated with RNA concentrations measured with the Qubit, but not with measures obtained with the Nanodrop. The Nanostring data showed that none of the genes included in the panel was differentially expressed in the cortical tubule compartment compared to the whole kidney. However, 25 genes were differentially expressed in the glomerular compartment compared to the whole kidney. Our data showed that sufficient RNA can be extracted from small compartments like mouse renal glomeruli from archival FFPE tissue, and that whole kidney analysis does not accurately represent the transcriptome state of the glomeruli, which comprise only a small proportion of the overall kidney volume.
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Affiliation(s)
- Abigail Hay
- Pathology, MedImmune, Cambridge, United Kingdom
| | | | | | - Carol Moreno Quinn
- Cardiovascular and Metabolic Diseases, MedImmune, Cambridge, United Kingdom
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Zhang Q, Zhang H, Liu F, Yang Q, Chen K, Liu P, Sun T, Ma C, Qiu W, Qian X. Comparison of Reference Genes for Transcriptional Studies in Postmortem Human Brain Tissue Under Different Conditions. Neurosci Bull 2019; 35:225-228. [PMID: 30406345 PMCID: PMC6426908 DOI: 10.1007/s12264-018-0309-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/28/2018] [Indexed: 11/30/2022] Open
Affiliation(s)
- Qing Zhang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China
- Joint Laboratory of Anesthesia and Pain, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Hanlin Zhang
- Joint Laboratory of Anesthesia and Pain, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
- Eight-Year MD Program, Peking Union Medical College, Beijing, 100730, China
| | - Fan Liu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China
- Joint Laboratory of Anesthesia and Pain, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Qian Yang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China
- Joint Laboratory of Anesthesia and Pain, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Kang Chen
- Joint Laboratory of Anesthesia and Pain, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
- Eight-Year MD Program, Peking Union Medical College, Beijing, 100730, China
| | - Pan Liu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China
- Joint Laboratory of Anesthesia and Pain, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Tianyi Sun
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China
- Joint Laboratory of Anesthesia and Pain, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China
- Joint Laboratory of Anesthesia and Pain, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Wenying Qiu
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Xiaojing Qian
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China.
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Cell Type-Specific Laser Capture Microdissection for Gene Expression Profiling in the Human Brain. Methods Mol Biol 2019; 1723:203-221. [PMID: 29344862 DOI: 10.1007/978-1-4939-7558-7_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Cell type-specific laser microdissection technologies in combination with molecular techniques to determine gene expression profiles have become powerful tools to gain insight into the neurobiological basis of neural circuit disturbances in various neurologic or psychiatric diseases. To identify specific cell populations in human postmortem brain tissue, one can use the inherent properties of the cells, such as pigmentation and morphology or their structural composition through immunohistochemistry (IHC). Here, we describe the isolation of homogeneous neurons and oligodendrocytes and the extraction of high-quality RNA from these cells in human postmortem brain using a combination of rapid IHC, Nissl staining, or simple morphology with Laser Capture Microdissection (LCM), or Laser Microdissection (LMD).
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Canivet C, Gourgou-Bourgade S, Napoléon B, Palazzo L, Flori N, Guibert P, Piessen G, Farges-Bancel D, Seitz JF, Assenat E, Vendrely V, Truant S, Vanbiervliet G, Berthelémy P, Garcia S, Gomez-Brouchet A, Buscail L, Bournet B. A prospective clinical and biological database for pancreatic adenocarcinoma: the BACAP cohort. BMC Cancer 2018; 18:986. [PMID: 30326968 PMCID: PMC6191891 DOI: 10.1186/s12885-018-4906-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The prognosis for pancreatic cancer remains poor despite diagnostic advances and treatments with new chemotherapeutic regimens. The five year survival rate remains below 3%. Consequently, there is an urgent need for new treatments to significantly improve the prognosis. In addition, there is a big gap in terms of the screening, early diagnosis and prevention of pancreatic cancer the incidence of which is increasing dramatically. METHODS Design: the BACAP cohort is a prospective multicenter pancreatic cancer cohort (pancreatic ductal carcinoma) with clinical and multiple biological samples; Participating centers: 15 French academic and private hospitals; Study Population: any cytologically and/or histologically proven pancreatic carcinoma regardless of the stage (resectable, borderline, locally advanced or metastatic) or treatment (surgery, palliative chemotherapy, best supportive care). At least 1500 patients will be included. Clinical data collected include: disease presentation, epidemiological and social factors, baseline biology, radiology, endoscopic ultrasound, staging, pathology, treatments, follow-up (including biological and radiological), and survival. All these data are collected and stored through an e-observation system at a centralized data center. Biological samples and derived products (i.e. before any treatment): blood, saliva, endoscopic ultrasound-guided fine needle aspiration materials from the primary tumor, fine needle biopsy of metastases and surgically resected tissue. DNA and RNA are extracted from fine needle aspiration materials and are quantified and characterized for quality. Whole blood, plasma and serum are isolated from blood samples. Frozen tissues were specifically allocated to the cohort. All derived products and saliva are stored at - 80 °C. Main end-points: i) to centralize clinical data together with multiple biological samples that are harmonized in terms of sampling, the post sampling process and storage; ii) to identify new molecular markers for the diagnosis, prognosis and possibly the predictive response to pancreatic cancer surgery and or chemotherapy. DISCUSSION The BACAP cohort is a unique prospective biological clinical database that provides the opportunity to identify correlations between the presence/expression of a broad panel of biomarkers (DNA, RNA, miRNA, proteins, etc.), epidemiological and social data, various clinical situations, various stages and the differentiation of the tumor, treatments and survival. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02818829 . Registration date: June 30, 2016.
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Affiliation(s)
- Cindy Canivet
- The Department of Gastroenterology and Pancreatology, CHU - Rangueil and the University of Toulouse, 1 avenue Jean Poulhès, TSA 50032, 31059, Toulouse Cedex 9, France
| | - Sophie Gourgou-Bourgade
- The Biometrics Unit - CTD Inca, the Cancer Institute and the University of Montpellier, Montpellier, France
| | - Bertrand Napoléon
- The Department of Gastroenterology, Jean Mermoz Hospital, Ramsay Générale de Santé, Lyon, France
| | - Laurent Palazzo
- The Department of Endoscopy, Trocadéro Clinic, Paris, France
| | - Nicolas Flori
- The Department of Oncology, the Cancer Institute and the University of Montpellier, Montpellier, France
| | - Pierre Guibert
- The Department of Oncology, Leon Bérard Institute, Lyon, France
| | - Guillaume Piessen
- Univ. Lille, Department of Digestive and Oncological Surgery, Claude Huriez University Hospital, F-59000, Lille, France
| | - Dominique Farges-Bancel
- The Department of Internal Medicine, Saint-Louis Hospital and Paris 7 Diderot University, Paris, France
| | - Jean-François Seitz
- The Department of Oncology, CHU - La Timone and the University of Marseille, Marseille, France
| | - Eric Assenat
- The Department of Oncology, CHU - ST-Eloi and the University of Montpellier, Montpellier, France
| | - Véronique Vendrely
- The Department of Oncology and Radiotherapy, CHU - Haut-Levêque and the University of Bordeaux, Bordeaux, France
| | - Stéphanie Truant
- The Department of Digestive Surgery and Transplantation, the CHU and the University of Lille, Lille, France
| | - Geoffroy Vanbiervliet
- The Department of Gastroenterology, CHU - L'Archet and the University of Nice, Nice, France
| | | | - Stéphane Garcia
- The Department of Pathology, CHU - Nord and the University of Marseille, Marseille, France
| | - Anne Gomez-Brouchet
- The Biobank, the Cancer Institute and the University of Toulouse, Toulouse, France
| | - Louis Buscail
- The Department of Gastroenterology and Pancreatology, CHU - Rangueil and the University of Toulouse, 1 avenue Jean Poulhès, TSA 50032, 31059, Toulouse Cedex 9, France
| | - Barbara Bournet
- The Department of Gastroenterology and Pancreatology, CHU - Rangueil and the University of Toulouse, 1 avenue Jean Poulhès, TSA 50032, 31059, Toulouse Cedex 9, France.
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Investigating the neuroimmunogenic architecture of schizophrenia. Mol Psychiatry 2018; 23:1251-1260. [PMID: 28485405 DOI: 10.1038/mp.2017.89] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/29/2017] [Accepted: 03/08/2017] [Indexed: 12/13/2022]
Abstract
The role of the immune system in schizophrenia remains controversial despite numerous studies to date. Most studies have profiled expression of select genes or proteins in peripheral blood, but none have focused on the expression of canonical pathways that mediate overall immune response. The current study used a systematic genetic approach to investigate the role of the immune system in a large sample of post-mortem brain of patients with schizophrenia: RNA sequencing was performed to assess the differential expression of 561 immune genes and 20 immune pathways in dorsolateral prefrontal cortex (DLPFC) (144 schizophrenia and 196 control subjects) and hippocampus (83 schizophrenia and 187 control subjects). The effect of RNA quality on gene expression was found to be highly correlated with the effect of diagnosis even after adjustment for observable RNA quality parameters (i.e. RNA integrity), thus this confounding relationship was statistically controlled using principal components derived from the gene expression matrix. In DLPFC, 23 immune genes were found to be differentially expressed (false discovery rate <0.05), of which seven genes replicated in both directionality and at nominal significance (P<0.05) in an independent post-mortem DLPFC data set (182 schizophrenia and 212 control subjects), although notably at least five of these genes have prominent roles in pathways other than immune function and overall the effect sizes were minimal (fold change <1.1). In the hippocampus, no individual immune genes were identified to be differentially expressed, and in both DLPFC and hippocampus none of the individual immune pathways were relatively differentially expressed. Further, genomic schizophrenia risk profiles scores were not correlated with the expression of individual immune pathways or differentially expressed genes. Overall, past reports claiming a primary pathogenic role of the immune system intrinsic to the brain in schizophrenia could not be confirmed.
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White K, Yang P, Li L, Farshori A, Medina AE, Zielke HR. Effect of Postmortem Interval and Years in Storage on RNA Quality of Tissue at a Repository of the NIH NeuroBioBank. Biopreserv Biobank 2018; 16:148-157. [PMID: 29498539 PMCID: PMC5906728 DOI: 10.1089/bio.2017.0099] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Brain tissue from 1068 donors was analyzed for RNA quality as a function of postmortem interval (PMI) and years in storage. Approximately 83% of the cortical and cerebellar samples had an RNA integrity number (RIN) of 6 or greater, indicating their likely suitability for real-time quantitative polymerase chain reaction research. The average RIN value was independent of the PMI, up to at least 36 hours. The RNA quality for specific donated brains could not be predicted based on the PMI. Individual samples with a low PMI could have a poor RIN value, while a sample with a PMI over 36 hours may have a high RIN value. The RIN values for control brain donors, all of whom died suddenly and unexpectedly, were marginally higher than for individuals with clinical brain disorders. Polymerase chain reaction (PCR) analysis of samples confirmed that RIN values were more critical than PMI for determining suitability of tissue for molecular biological studies and samples should be matched by their RIN values rather than PMI. Importantly, PCR analysis established that tissue stored up to 23 years at −80°C yielded high-quality RNA. These results confirm that postmortem human brain tissue collected by brain and tissue banks over decades can serve as high quality material for the study of human disorders.
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Affiliation(s)
- Kimberly White
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
| | - Peixin Yang
- 2 Department of Obstetrics and Gynecology, University of Maryland School of Medicine , Baltimore, Maryland
| | - Ling Li
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland.,3 Office of the Chief Medical Examiner, Baltimore, Maryland
| | - Amna Farshori
- 4 Degree Program in Osteopathic Medicine, Edward Via College of Osteopathic Medicine , Blacksburg, Virginia
| | - Alexandre E Medina
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
| | - Horst Ronald Zielke
- 1 Department of Pediatrics, University of Maryland School of Medicine , Baltimore, Maryland
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Weickert CS, Rothmond DA, Purves-Tyson TD. Considerations for optimal use of postmortem human brains for molecular psychiatry: lessons from schizophrenia. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:221-235. [PMID: 29496143 DOI: 10.1016/b978-0-444-63639-3.00016-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Schizophrenia is a disabling disease impacting millions of people around the world, for which there is no known cure. Current antipsychotic treatments for schizophrenia mainly target psychotic symptoms, do little to ameliorate social or cognitive deficits, have side-effects that cause weight gain, and diabetes and 30% of people do not respond. Thus, better therapeutics for schizophrenia aimed at the route biologic changes are needed and discovering the underlying neurobiology is key to this quest. Postmortem brain studies provide the most direct and detailed way to determine the pathophysiology of schizophrenia. This chapter outlines steps that can be taken to ensure the best-quality molecular data from postmortem brain tissue are obtained. In this chapter, we also discuss targeted and high-throughput methods for examining gene and protein expression and some of the strengths and limitations of each method. We briefly consider why gene and protein expression changes may not always concur within brain tissue. We conclude that postmortem brain research that investigates gene and protein expression in well-characterized and matched brain cohorts provides an important foundation to be considered when interpreting data obtained from studies of living schizophrenia patients.
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Affiliation(s)
- Cynthia Shannon Weickert
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia; Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, Australia.
| | - Debora A Rothmond
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, Australia
| | - Tertia D Purves-Tyson
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, Australia; Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, Australia
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Sonntag KC, Woo TUW. Laser microdissection and gene expression profiling in the human postmortem brain. HANDBOOK OF CLINICAL NEUROLOGY 2018; 150:263-272. [PMID: 29496145 DOI: 10.1016/b978-0-444-63639-3.00018-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Laser microdissection in combination with gene expression profiling using postmortem human brain tissue provides a powerful approach to interrogating cell type-specific pathologies within neural circuits that are known to be dysfunctional in neuropsychiatric disorders. The success of these experiments critically depends on a number of factors, such as the cellular purity of the sample, the quality of the RNA, the methodologies of data normalization and computational data analysis, and how data are interpreted. Data obtained from these experiments should be validated at the protein level. Furthermore, from the perspective of disease mechanism discovery, it would be ideal to investigate whether manipulation of the expression of genes identified as differentially expressed can rescue or ameliorate the neurobiologic or behavioral phenotypes associated with the specific disease. Thus, the ultimate value of this approach rests upon the fact that the generation of novel disease-related pathophysiologic hypotheses may lead to deeper understanding of disease mechanisms and possible development of effective targeted treatments.
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Affiliation(s)
- Kai-Christian Sonntag
- Laboratory for Translational Research on Neurodegeneration, Belmont, MA, United States; Department of Psychiatry, Harvard Medical School, Boston, MA, United States
| | - Tsung-Ung W Woo
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, MA, United States; Department of Psychiatry, Harvard Medical School, Boston, MA, United States.
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Keller B, García-Sevilla JA. Dysregulation of IRAS/nischarin and other potential I 1-imidazoline receptors in major depression postmortem brain: Downregulation of basal contents by antidepressant drug treatments. J Affect Disord 2017; 208:646-652. [PMID: 27836117 DOI: 10.1016/j.jad.2016.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/28/2016] [Accepted: 10/16/2016] [Indexed: 11/16/2022]
Abstract
BACKGROUND Major depressive disorder (MDD) has been associated with altered brain densities of imidazoline receptors (I1-IR and I2-IR types). METHODS The contents of potential I1-IR IRAS/nischarin (167kDa) and, for comparison, those of I1- (85kDa) and I2- (45kDa and 30kDa) IR proteins were quantified by western blotting in postmortem prefrontal cortex (PFC/BA9) of antidepressant-free ([MDD(-)], n=9) and antidepressant-treated ([MDD(+)], n=12) subjects and matched controls (n=19). RESULTS In MDD, regardless of antidepressant treatment (n=21), IRAS/nischarin was not altered in PFC/BA9. However, the content of IRAS/nischarin was found modestly and not significantly increased (+19%, p=0.075) in MDD(-) and significantly decreased (-24%, p=0.001) in MDD(+), revealing that basal I1-IR content was downregulated by antidepressants. Putative 85kDa I1-IR was upregulated (+35%, p=0.035) in MDD(-) but it was not reduced (-14%, p=0.37) in MDD(+). There was a positive correlation (r=0.33, p=0.037, n=40) between the contents of IRAS/nischarin and 85kDa IR proteins in PFC/BA9 (control and MDD subjects). In MDD and regardless of antidepressants, the content of cortical 45kDa I2-IR was increased (+31%, p=0.006) and that of 30kDa I2-IR decreased (-14%, p=0.002), indicating basal dysregulations of these potential IRs. LIMITATIONS MDD(+) subjects had been treated with a variety of antidepressant drugs. The results must be understood in the context of suicide victims with MDD. CONCLUSIONS The dysregulation of IRAS/nischarin in depressed brains is a major novel finding that supports a role of this potential I1-IR in the neurobiology of MDD and in the molecular mechanisms of antidepressant drugs.
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Affiliation(s)
- Benjamin Keller
- Laboratori de Neurofarmacologia, IUNICS/IdISPa, Universitat de les Illes Balears (UIB), Palma de Mallorca, Spain; Redes Temáticas de Investigación Cooperativa en Salud-Red de Trastornos Adictivos (RETICS-RTA), ISCIII, Madrid, Spain
| | - Jesús A García-Sevilla
- Laboratori de Neurofarmacologia, IUNICS/IdISPa, Universitat de les Illes Balears (UIB), Palma de Mallorca, Spain; Redes Temáticas de Investigación Cooperativa en Salud-Red de Trastornos Adictivos (RETICS-RTA), ISCIII, Madrid, Spain.
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Wei J, Damania A, Gao X, Liu Z, Mejia R, Mitreva M, Strych U, Bottazzi ME, Hotez PJ, Zhan B. The hookworm Ancylostoma ceylanicum intestinal transcriptome provides a platform for selecting drug and vaccine candidates. Parasit Vectors 2016; 9:518. [PMID: 27677574 PMCID: PMC5039805 DOI: 10.1186/s13071-016-1795-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/12/2016] [Indexed: 12/02/2022] Open
Abstract
Background The intestine of hookworms contains enzymes and proteins involved in the blood-feeding process of the parasite and is therefore a promising source of possible vaccine antigens. One such antigen, the hemoglobin-digesting intestinal aspartic protease known as Na-APR-1 from the human hookworm Necator americanus, is currently a lead candidate antigen in clinical trials, as is Na-GST-1 a heme-detoxifying glutathione S-transferase. Methods In order to discover additional hookworm vaccine antigens, messenger RNA was obtained from the intestine of male hookworms, Ancylostoma ceylanicum, maintained in hamsters. RNA-seq was performed using Illumina high-throughput sequencing technology. The genes expressed in the hookworm intestine were compared with those expressed in the whole worm and those genes overexpressed in the parasite intestine transcriptome were further analyzed. Results Among the lead transcripts identified were genes encoding for proteolytic enzymes including an A. ceylanicum APR-1, but the most common proteases were cysteine-, serine-, and metallo-proteases. Also in abundance were specific transporters of key breakdown metabolites, including amino acids, glucose, lipids, ions and water; detoxifying and heme-binding glutathione S-transferases; a family of cysteine-rich/antigen 5/pathogenesis-related 1 proteins (CAP) previously found in high abundance in parasitic nematodes; C-type lectins; and heat shock proteins. These candidates will be ranked for downstream antigen target selection based on key criteria including abundance, uniqueness in the parasite versus the vertebrate host, as well as solubility and yield of expression. Conclusion The intestinal transcriptome of A. ceylanicum provides useful information for the identification of proteins involved in the blood-feeding process, representing a first step towards a reverse vaccinology approach to a human hookworm vaccine. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1795-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junfei Wei
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ashish Damania
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xin Gao
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Zhuyun Liu
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rojelio Mejia
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Makedonka Mitreva
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.,Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Ulrich Strych
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Elena Bottazzi
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Biology, Baylor University, Waco, TX, 76706, USA
| | - Peter J Hotez
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Biology, Baylor University, Waco, TX, 76706, USA
| | - Bin Zhan
- Sabin Vaccine Institute and Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
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