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Yalcinbas EA, Ajanaku B, Nelson ED, Garcia-Flores R, Montgomery KD, Stolz JM, Wu J, Divecha HR, Chandra A, Bharadwaj RA, Bach S, Rajpurohit A, Tao R, Shin JH, Kleinman JE, Hyde TM, Weinberger DR, Huuki-Myers LA, Collado-Torres L, Maynard KR. Transcriptomic analysis of the human habenula in schizophrenia. bioRxiv 2024:2024.02.26.582081. [PMID: 38463979 PMCID: PMC10925152 DOI: 10.1101/2024.02.26.582081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Importance Habenula (Hb) pathophysiology is involved in many neuropsychiatric disorders, including schizophrenia. Deep brain stimulation and pharmacological targeting of the Hb are emerging as promising therapeutic treatments. However, little is known about the cell type-specific transcriptomic organization of the human Hb or how it is altered in schizophrenia. Objective To define the molecular neuroanatomy of the human habenula and identify transcriptomic changes in individuals with schizophrenia compared to neurotypical controls. Design Setting and Participants This study utilized Hb-enriched postmortem human brain tissue. Single nucleus RNA-sequencing (snRNA-seq) and single molecule fluorescent in situ hybridization (smFISH) experiments were conducted to identify molecularly defined Hb cell types and map their spatial location (n=3-7 donors). Bulk RNA-sequencing and cell type deconvolution were used to investigate transcriptomic changes in Hb-enriched tissue from 35 individuals with schizophrenia and 33 neurotypical controls. Gene expression changes associated with schizophrenia in the Hb were compared to those previously identified in the dorsolateral prefrontal cortex (DLPFC), hippocampus, and caudate. Main Outcomes and Measures Semi-supervised snRNA-seq cell type clustering. Transcript visualization and quantification of smFISH probes. Bulk RNA-seq cell type deconvolution using reference snRNA-seq data. Schizophrenia-associated gene differential expression analysis adjusting for Hb and thalamus fractions, RNA degradation-associated quality surrogate variables, and other covariates. Cross-brain region schizophrenia-associated gene expression comparison. Results snRNA-seq identified 17 cell type clusters across 16,437 nuclei, including 3 medial and 7 lateral Hb populations. Cell types were conserved with those identified in a rodent model. smFISH for cell type marker genes validated snRNA-seq Hb cell types and depicted the spatial organization of subpopulations. Bulk RNA-seq analyses yielded 45 schizophrenia-associated differentially expressed genes (FDR < 0.05), with 32 (71%) unique to Hb-enriched tissue. Conclusions These results identify topographically organized cell types with distinct molecular signatures in the human Hb. They further demonstrate unique transcriptomic changes in the epithalamus associated with schizophrenia, thereby providing molecular insights into the role of Hb in neuropsychiatric disorders.
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Affiliation(s)
- Ege A Yalcinbas
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Bukola Ajanaku
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Erik D Nelson
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Renee Garcia-Flores
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Kelsey D Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Joshua M Stolz
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Joshua Wu
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Heena R Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Atharv Chandra
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Rahul A Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Svitlana Bach
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Anandita Rajpurohit
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Joo-Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Louise A Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
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2
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Huuki-Myers LA, Montgomery KD, Kwon SH, Cinquemani S, Maden SK, Eagles NJ, Kleinman JE, Hyde TM, Hicks SC, Maynard KR, Collado-Torres L. Benchmark of cellular deconvolution methods using a multi-assay reference dataset from postmortem human prefrontal cortex. bioRxiv 2024:2024.02.09.579665. [PMID: 38405805 PMCID: PMC10888823 DOI: 10.1101/2024.02.09.579665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background Cellular deconvolution of bulk RNA-sequencing (RNA-seq) data using single cell or nuclei RNA-seq (sc/snRNA-seq) reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as human brain. Several deconvolution methods have been developed and they have been previously benchmarked against simulated data, pseudobulked sc/snRNA-seq data, or cell type proportions derived from immunohistochemistry reference data. A major limitation preventing the improvement of deconvolution algorithms has been the lack of highly integrated datasets with orthogonal measurements of gene expression and estimates of cell type proportions on the same tissue block. The performance of existing deconvolution algorithms has not yet been explored across different RNA extraction methods (e.g. cytosolic, nuclear, or whole cell RNA), different library preparation types (e.g. mRNA enrichment vs. ribosomal RNA depletion), or with matched single cell reference datasets. Results A rich multi-assay dataset was generated in postmortem human dorsolateral prefrontal cortex (DLPFC) from 22 tissue blocks. Assays included spatially-resolved transcriptomics, snRNA-seq, bulk RNA-seq across six RNA extraction and RNA-seq library combinations, and orthogonal cell type measurements via RNAScope/Immunofluorescence (RNAScope/IF). The Mean Ratio method was developed for selecting cell type marker genes for deconvolution and is implemented in the DeconvoBuddies R package. Five extensively benchmarked computational deconvolution algorithms were evaluated in DLPFC across six RNA-seq combinations and predicted cell type proportions were compared to those measured by RNAScope/IF. Conclusions We show that Bisque and hspe are the top performing methods with performance dependent on the RNA-seq library preparation conditions. We provide a multi-assay resource for the development and evaluation of deconvolution algorithms.
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Affiliation(s)
- Louise A. Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Kelsey D. Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Sophia Cinquemani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Sean K. Maden
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Nicholas J. Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kristen R. Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA
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3
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Tietze E, Barbosa AR, Araujo B, Euclydes V, Spiegelberg B, Cho HJ, Lee YK, Wang Y, McCord A, Lorenzetti A, Feltrin A, van de Leemput J, Di Carlo P, Ursini G, Benjamin KJ, Brentani H, Kleinman JE, Hyde TM, Weinberger DR, McKay R, Shin JH, Sawada T, Paquola ACM, Erwin JA. Human archetypal pluripotent stem cells differentiate into trophoblast stem cells via endogenous BMP5/7 induction without transitioning through naive state. Sci Rep 2024; 14:3291. [PMID: 38332235 PMCID: PMC10853519 DOI: 10.1038/s41598-024-53381-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Primary human trophoblast stem cells (TSCs) and TSCs derived from human pluripotent stem cells (hPSCs) can potentially model placental processes in vitro. Yet, the pluripotent states and factors involved in the differentiation of hPSCs to TSCs remain poorly understood. In this study, we demonstrate that the primed pluripotent state can generate TSCs by activating pathways such as Epidermal Growth Factor (EGF) and Wingless-related integration site (WNT), and by suppressing tumor growth factor beta (TGFβ), histone deacetylases (HDAC), and Rho-associated protein kinase (ROCK) signaling pathways, all without the addition of exogenous Bone morphogenetic protein 4 (BMP4)-a condition we refer to as the TS condition. We characterized this process using temporal single-cell RNA sequencing to compare TS conditions with differentiation protocols involving BMP4 activation alone or BMP4 activation in conjunction with WNT inhibition. The TS condition consistently produced a stable, proliferative cell type that closely mimics first-trimester placental cytotrophoblasts, marked by the activation of endogenous retroviral genes and the absence of amnion expression. This was observed across multiple cell lines, including various primed induced pluripotent stem cell (iPSC) and embryonic stem cell (ESC) lines. Primed-derived TSCs can proliferate for over 30 passages and further specify into multinucleated syncytiotrophoblasts and extravillous trophoblast cells. Our research establishes that the differentiation of primed hPSCs to TSC under TS conditions triggers the induction of TMSB4X, BMP5/7, GATA3, and TFAP2A without progressing through a naive state. These findings propose that the primed hPSC state is part of a continuum of potency with the capacity to differentiate into TSCs through multiple routes.
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Affiliation(s)
- Ethan Tietze
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Andre Rocha Barbosa
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Inter-Institutional Graduate Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil
| | - Bruno Araujo
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Veronica Euclydes
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, University of Sao Paulo, Medical School, São Paulo, Brazil
| | - Bailey Spiegelberg
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hyeon Jin Cho
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Yong Kyu Lee
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Yanhong Wang
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | | | | | - Arthur Feltrin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Mathematics, Computation and Cognition, Federal University of ABC, Santo André, SP, Brazil
| | - Joyce van de Leemput
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Precision Disease Modeling and Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Pasquale Di Carlo
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Basic Medical Science, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kynon J Benjamin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Helena Brentani
- Inter-Institutional Graduate Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil
- Department of Psychiatry, University of Sao Paulo, Medical School, São Paulo, Brazil
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ronald McKay
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Tomoyo Sawada
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Apua C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer A Erwin
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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4
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Zhou J, Luo C, Liu H, Heffel MG, Straub RE, Kleinman JE, Hyde TM, Ecker JR, Weinberger DR, Han S. scMeFormer: a transformer-based deep learning model for imputing DNA methylation states in single cells enhances the detection of epigenetic alterations in schizophrenia. bioRxiv 2024:2024.01.25.577200. [PMID: 38328094 PMCID: PMC10849713 DOI: 10.1101/2024.01.25.577200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
DNA methylation (DNAm), a crucial epigenetic mark, plays a key role in gene regulation, mammalian development, and various human diseases. Single-cell technologies enable the profiling of DNAm states at cytosines within the DNA sequence of individual cells, but they often suffer from limited coverage of CpG sites. In this study, we introduce scMeFormer, a transformer-based deep learning model designed to impute DNAm states for each CpG site in single cells. Through comprehensive evaluations, we demonstrate the superior performance of scMeFormer compared to alternative models across four single-nucleus DNAm datasets generated by distinct technologies. Remarkably, scMeFormer exhibits high-fidelity imputation, even when dealing with significantly reduced coverage, as low as 10% of the original CpG sites. Furthermore, we applied scMeFormer to a single-nucleus DNAm dataset generated from the prefrontal cortex of four schizophrenia patients and four neurotypical controls. This enabled the identification of thousands of differentially methylated regions associated with schizophrenia that would have remained undetectable without imputation and added granularity to our understanding of epigenetic alterations in schizophrenia within specific cell types. Our study highlights the power of deep learning in imputing DNAm states in single cells, and we expect scMeFormer to be a valuable tool for single-cell DNAm studies.
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Affiliation(s)
- Jiyun Zhou
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Hanqing Liu
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Matthew G. Heffel
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Richard E. Straub
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Joseph R. Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shizhong Han
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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5
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Weber LM, Divecha HR, Tran MN, Kwon SH, Spangler A, Montgomery KD, Tippani M, Bharadwaj R, Kleinman JE, Page SC, Hyde TM, Collado-Torres L, Maynard KR, Martinowich K, Hicks SC. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife 2024; 12:RP84628. [PMID: 38266073 PMCID: PMC10945708 DOI: 10.7554/elife.84628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
Norepinephrine (NE) neurons in the locus coeruleus (LC) make long-range projections throughout the central nervous system, playing critical roles in arousal and mood, as well as various components of cognition including attention, learning, and memory. The LC-NE system is also implicated in multiple neurological and neuropsychiatric disorders. Importantly, LC-NE neurons are highly sensitive to degeneration in both Alzheimer's and Parkinson's disease. Despite the clinical importance of the brain region and the prominent role of LC-NE neurons in a variety of brain and behavioral functions, a detailed molecular characterization of the LC is lacking. Here, we used a combination of spatially-resolved transcriptomics and single-nucleus RNA-sequencing to characterize the molecular landscape of the LC region and the transcriptomic profile of LC-NE neurons in the human brain. We provide a freely accessible resource of these data in web-accessible and downloadable formats.
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Affiliation(s)
- Lukas M Weber
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Heena R Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Matthew N Tran
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Neuroscience, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Abby Spangler
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Kelsey D Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Rahul Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
- Department of Neurology, Johns Hopkins School of MedicineBaltimoreUnited States
| | | | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical CampusBaltimoreUnited States
- Department of Neuroscience, Johns Hopkins School of MedicineBaltimoreUnited States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of MedicineBaltimoreUnited States
- The Kavli Neuroscience Discovery Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
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6
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White JD, Minto MS, Willis C, Quach BC, Han S, Tao R, Deep-Soboslay A, Zillich L, Clark SL, van den Oord EJCG, Hyde TM, Mayfield RD, Webb BT, Johnson EO, Kleinman JE, Bierut LJ, Hancock DB. Alcohol Use Disorder-Associated DNA Methylation in the Nucleus Accumbens and Dorsolateral Prefrontal Cortex. medRxiv 2024:2024.01.17.23300238. [PMID: 38293028 PMCID: PMC10827272 DOI: 10.1101/2024.01.17.23300238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Alcohol use disorder (AUD) has a profound public health impact. However, understanding of the molecular mechanisms underlying the development and progression of AUD remain limited. Here, we interrogate AUD-associated DNA methylation (DNAm) changes within and across addiction-relevant brain regions: the nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC). Methods Illumina HumanMethylation EPIC array data from 119 decedents of European ancestry (61 cases, 58 controls) were analyzed using robust linear regression, with adjustment for technical and biological variables. Associations were characterized using integrative analyses of public gene regulatory data and published genetic and epigenetic studies. We additionally tested for brain region-shared and -specific associations using mixed effects modeling and assessed implications of these results using public gene expression data. Results At a false discovery rate ≤ 0.05, we identified 53 CpGs significantly associated with AUD status for NAc and 31 CpGs for DLPFC. In a meta-analysis across the regions, we identified an additional 21 CpGs associated with AUD, for a total of 105 unique AUD-associated CpGs (120 genes). AUD-associated CpGs were enriched in histone marks that tag active promoters and our strongest signals were specific to a single brain region. Of the 120 genes, 23 overlapped with previous genetic associations for substance use behaviors; all others represent novel associations. Conclusions Our findings identify AUD-associated methylation signals, the majority of which are specific within NAc or DLPFC. Some signals may constitute predisposing genetic and epigenetic variation, though more work is needed to further disentangle the neurobiological gene regulatory differences associated with AUD.
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Affiliation(s)
- Julie D. White
- GenOmics and Translational Research Center, RTI International
| | | | - Caryn Willis
- GenOmics and Translational Research Center, RTI International
| | - Bryan C. Quach
- GenOmics and Translational Research Center, RTI International
| | | | - Ran Tao
- Lieber Institute for Brain Development (LIBD)
| | | | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shaunna L. Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University
| | | | | | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin
| | - Bradley T. Webb
- GenOmics and Translational Research Center, RTI International
| | - Eric O. Johnson
- GenOmics and Translational Research Center, RTI International
- Fellow Program, RTI International
| | | | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine
| | - Dana B. Hancock
- GenOmics and Translational Research Center, RTI International
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7
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Ramnauth AD, Tippani M, Divecha HR, Papariello AR, Miller RA, Pattie EA, Kleinman JE, Maynard KR, Collado-Torres L, Hyde TM, Martinowich K, Hicks SC, Page SC. Spatially-resolved transcriptomics of human dentate gyrus across postnatal lifespan reveals heterogeneity in markers for proliferation, extracellular matrix, and neuroinflammation. bioRxiv 2023:2023.11.20.567883. [PMID: 38045413 PMCID: PMC10690172 DOI: 10.1101/2023.11.20.567883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The dentate gyrus of the anterior hippocampus is important for many human cognitive functions, including regulation of learning, memory, and mood. However, the postnatal development and aging of the dentate gyrus throughout the human lifespan has yet to be fully characterized in the same molecular and spatial detail as other species. Here, we generated a spatially-resolved molecular atlas of the dentate gyrus in postmortem human tissue using the 10x Genomics Visium platform to retain extranuclear transcripts and identify changes in molecular topography across the postnatal lifespan. We found enriched expression of extracellular matrix markers during infancy and increased expression of GABAergic cell-type markers GAD1, LAMP5, and CCK after infancy. While we identified a conserved gene signature for mouse neuroblasts in the granule cell layer (GCL), many of those genes are not specific to the GCL, and we found no evidence of signatures for other granule cell lineage stages at the GCL post-infancy. We identified a wide-spread hippocampal aging signature and an age-dependent increase in neuroinflammation associated genes. Our findings suggest major changes to the putative neurogenic niche after infancy and identify molecular foci of brain aging in glial and neuropil enriched tissue.
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Affiliation(s)
- Anthony D Ramnauth
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Heena R Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Alexis R Papariello
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Ryan A Miller
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Elizabeth A Pattie
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Johns Hopkins Kavli Neuroscience Discovery Institute, Baltimore, MD, USA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
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Tippani M, Divecha HR, Catallini JL, Kwon SH, Weber LM, Spangler A, Jaffe AE, Hyde TM, Kleinman JE, Hicks SC, Martinowich K, Collado-Torres L, Page SC, Maynard KR. VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data. Biol Imaging 2023; 3:e23. [PMID: 38510173 PMCID: PMC10951916 DOI: 10.1017/s2633903x23000235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/14/2023] [Accepted: 09/19/2023] [Indexed: 03/22/2024]
Abstract
Spatially resolved transcriptomics (SRT) is a growing field that links gene expression to anatomical context. SRT approaches that use next-generation sequencing (NGS) combine RNA sequencing with histological or fluorescent imaging to generate spatial maps of gene expression in intact tissue sections. These technologies directly couple gene expression measurements with high-resolution histological or immunofluorescent images that contain rich morphological information about the tissue under study. While broad access to NGS-based spatial transcriptomic technology is now commercially available through the Visium platform from the vendor 10× Genomics, computational tools for extracting image-derived metrics for integration with gene expression data remain limited. We developed VistoSeg as a MATLAB pipeline to process, analyze and interactively visualize the high-resolution images generated in the Visium platform. VistoSeg outputs can be easily integrated with accompanying transcriptomic data to facilitate downstream analyses in common programing languages including R and Python. VistoSeg provides user-friendly tools for integrating image-derived metrics from histological and immunofluorescent images with spatially resolved gene expression data. Integration of this data enhances the ability to understand the transcriptional landscape within tissue architecture. VistoSeg is freely available at http://research.libd.org/VistoSeg/.
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Affiliation(s)
- Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Heena R. Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Joseph L. Catallini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sang H. Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Lukas M. Weber
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abby Spangler
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stephanie C. Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Kristen R. Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Collado-Torres L, Klei L, Liu C, Kleinman JE, Hyde TM, Geschwind DH, Gandal MJ, Devlin B, Weinberger DR. Comparison of gene expression in living and postmortem human brain. medRxiv 2023:2023.11.08.23298172. [PMID: 37986747 PMCID: PMC10659492 DOI: 10.1101/2023.11.08.23298172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Molecular mechanisms of neuropsychiatric disorders are challenging to study in human brain. For decades, the preferred model has been to study postmortem human brain samples despite the limitations they entail. A recent study generated RNA sequencing data from biopsies of prefrontal cortex from living patients with Parkinson's Disease and compared gene expression to postmortem tissue samples, from which they found vast differences between the two. This led the authors to question the utility of postmortem human brain studies. Through re-analysis of the same data, we unexpectedly found that the living brain tissue samples were of much lower quality than the postmortem samples across multiple standard metrics. We also performed simulations that illustrate the effects of ignoring RNA degradation in differential gene expression analyses, showing the effects can be substantial and of similar magnitude to what the authors find. For these reasons, we believe the authors' conclusions are unjustified. To the contrary, while opportunities to study gene expression in the living brain are welcome, evidence that this eclipses the value of postmortem analyses is not apparent.
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Affiliation(s)
- Leonardo Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Daniel H Geschwind
- Intellectual and Developmental Disabilities Research Center, Department of Psychiatry, Department of Human Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, Center for Autism Research and Treatment, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
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10
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Sawada T, Barbosa AR, Araujo B, McCord AE, D'Ignazio L, Benjamin KJM, Sheehan B, Zabolocki M, Feltrin A, Arora R, Brandtjen AC, Kleinman JE, Hyde TM, Bardy C, Weinberger DR, Paquola ACM, Erwin JA. Recapitulation of Perturbed Striatal Gene Expression Dynamics of Donor's Brains With Ventral Forebrain Organoids Derived From the Same Individuals With Schizophrenia. Am J Psychiatry 2023:appiajp20220723. [PMID: 37915216 DOI: 10.1176/appi.ajp.20220723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
OBJECTIVE Schizophrenia is a brain disorder that originates during neurodevelopment and has complex genetic and environmental etiologies. Despite decades of clinical evidence of altered striatal function in affected patients, studies examining its cellular and molecular mechanisms in humans are limited. To explore neurodevelopmental alterations in the striatum associated with schizophrenia, the authors established a method for the differentiation of induced pluripotent stem cells (iPSCs) into ventral forebrain organoids (VFOs). METHODS VFOs were generated from postmortem dural fibroblast-derived iPSCs of four individuals with schizophrenia and four neurotypical control individuals for whom postmortem caudate genotypes and transcriptomic data were profiled in the BrainSeq neurogenomics consortium. Individuals were selected such that the two groups had nonoverlapping schizophrenia polygenic risk scores (PRSs). RESULTS Single-cell RNA sequencing analyses of VFOs revealed differences in developmental trajectory between schizophrenia and control individuals in which inhibitory neuronal cells from the patients exhibited accelerated maturation. Furthermore, upregulated genes in inhibitory neurons in schizophrenia VFOs showed a significant overlap with upregulated genes in postmortem caudate tissue of individuals with schizophrenia compared with control individuals, including the donors of the iPSC cohort. CONCLUSIONS The findings suggest that striatal neurons derived from high-PRS individuals with schizophrenia carry abnormalities that originated during early brain development and that the VFO model can recapitulate disease-relevant cell type-specific neurodevelopmental phenotypes in a dish.
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Affiliation(s)
- Tomoyo Sawada
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - André R Barbosa
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Bruno Araujo
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Alejandra E McCord
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Laura D'Ignazio
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Bonna Sheehan
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Michael Zabolocki
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Arthur Feltrin
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Ria Arora
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Anna C Brandtjen
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Cedric Bardy
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Apuã C M Paquola
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
| | - Jennifer A Erwin
- Lieber Institute for Brain Development, Baltimore (Sawada, Barbosa, Araujo, McCord, D'Ignazio, Benjamin, Sheehan, Feltrin, Arora, Brandtjen, Kleinman, Hyde, Weinberger, Paquola, Erwin); Department of Neurology (D'Ignazio, Benjamin, Kleinman, Hyde, Weinberger, Paquola, Erwin), Department of Psychiatry and Behavioral Sciences (Benjamin, Kleinman, Hyde, Weinberger), and Department of Neuroscience (Weinberger, Erwin), Johns Hopkins School of Medicine, Baltimore; South Australian Health and Medical Research Institute, Laboratory for Human Neurophysiology and Genetics, Adelaide (Zabolocki, Bardy); Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide (Zabolocki, Bardy)
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Chen Q, Aguirre L, Zhao H, Borrego F, de Rojas I, Su L, Li PP, Zhang B, Kokovay E, Lechleiter JD, Göring HH, De Jager PL, Kleinman JE, Hyde TM, Ruiz A, Weinberger DR, Seshadri S, Ma L. Identification of a specific APOE transcript and functional elements associated with Alzheimer's disease. medRxiv 2023:2023.10.30.23297431. [PMID: 37961425 PMCID: PMC10635228 DOI: 10.1101/2023.10.30.23297431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
INTRODUCTION The APOE gene is the strongest genetic risk factor for late-onset Alzheimer's Disease (LOAD). However, the gene regulatory mechanisms at this locus have not been fully characterized. METHODS To identify novel AD-linked functional elements within the APOE locus, we integrated SNP variants with RNA-seq, DNA methylation, and ChIP-seq data from human postmortem brains. RESULTS We identified an AD-linked APOE transcript (jxn1.2.2) observed in the dorsolateral prefrontal cortex (DLPFC). The APOE jxn1.2.2 transcript is associated with brain neuropathological features in DLPFC. We prioritized an independent functional SNP, rs157580, significantly associated with jxn1.2.2 transcript abundance and DNA methylation levels. rs157580 is located within active chromatin regions and predicted to affect brain-related transcriptional factors binding affinity. rs157580 shared the effects on the jxn1.2.2 transcript between European and African ethnic groups. DISCUSSION The novel APOE functional elements provide potential therapeutic targets with mechanistic insight into the disease's etiology.
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12
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Benjamin KJM, Chen Q, Eagles NJ, Huuki-Myers LA, Collado-Torres L, Stolz JM, Pertea G, Shin JH, Paquola ACM, Hyde TM, Kleinman JE, Jaffe AE, Han S, Weinberger DR. Genetic and environmental contributions to ancestry differences in gene expression in the human brain. bioRxiv 2023:2023.03.28.534458. [PMID: 37034760 PMCID: PMC10081196 DOI: 10.1101/2023.03.28.534458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Ancestral differences in genomic variation are determining factors in gene regulation; however, most gene expression studies have been limited to European ancestry samples or adjusted for ancestry to identify ancestry-independent associations. We instead examined the impact of genetic ancestry on gene expression and DNA methylation (DNAm) in admixed African/Black American neurotypical individuals to untangle effects of genetic and environmental factors. Ancestry-associated differentially expressed genes (DEGs), transcripts, and gene networks, while notably not implicating neurons, are enriched for genes related to immune response and vascular tissue and explain up to 26% of heritability for ischemic stroke, 27% of heritability for Parkinson's disease, and 30% of heritability for Alzhemier's disease. Ancestry-associated DEGs also show general enrichment for heritability of diverse immune-related traits but depletion for psychiatric-related traits. The cell-type enrichments and direction of effects vary by brain region. These DEGs are less evolutionarily constrained and are largely explained by genetic variations; roughly 15% are predicted by DNAm variation implicating environmental exposures. We also compared Black and White Americans, confirming most of these ancestry-associated DEGs. Our results highlight how environment and genetic background affect genetic ancestry differences in gene expression in the human brain and affect risk for brain illness.
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Affiliation(s)
- Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qiang Chen
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | | | | | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Joshua M Stolz
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Geo Pertea
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Apuã C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Jaffe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Neumora Therapeutics, Watertown, MA, USA
| | - Shizhong Han
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Radulescu E, Chen Q, Pergola G, Di Carlo P, Han S, Shin JH, Hyde TM, Kleinman JE, Weinberger DR. Investigating trait variability of gene co-expression network architecture in brain by controlling for genomic risk of schizophrenia. PLoS Genet 2023; 19:e1010989. [PMID: 37831723 PMCID: PMC10599557 DOI: 10.1371/journal.pgen.1010989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 10/25/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The effect of schizophrenia (SCZ) genetic risk on gene expression in brain remains elusive. A popular approach to this problem has been the application of gene co-expression network algorithms (e.g., WGCNA). To improve reliability with this method it is critical to remove unwanted sources of variance while also preserving biological signals of interest. In this WCGNA study of RNA-Seq data from postmortem prefrontal cortex (78 neurotypical donors, EUR ancestry), we tested the effects of SCZ genetic risk on co-expression networks. Specifically, we implemented a novel design in which gene expression was adjusted by linear regression models to preserve or remove variance explained by biological signal of interest (GWAS genomic scores for SCZ risk-(GS-SCZ), and genomic scores- GS of height (GS-Ht) as a negative control), while removing variance explained by covariates of non-interest. We calculated co-expression networks from adjusted expression (GS-SCZ and GS-Ht preserved or removed), and consensus between them (representative of a "background" network free of genomic scores effects). We then tested the overlap between GS-SCZ preserved modules and background networks reasoning that modules with reduced overlap would be most affected by GS-SCZ biology. Additionally, we tested these modules for convergence of SCZ risk (i.e., enrichment in PGC3 SCZ GWAS priority genes, enrichment in SCZ risk heritability and relevant biological ontologies. Our results highlight key aspects of GS-SCZ effects on brain co-expression networks, specifically: 1) preserving/removing SCZ genetic risk alters the co-expression modules; 2) biological pathways enriched in modules affected by GS-SCZ implicate processes of transcription, translation and metabolism that converge to influence synaptic transmission; 3) priority PGC3 SCZ GWAS genes and SCZ risk heritability are enriched in modules associated with GS-SCZ effects. Overall, our results indicate that gene co-expression networks that selectively integrate information about genetic risk can reveal novel combinations of biological pathways involved in schizophrenia.
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Affiliation(s)
- Eugenia Radulescu
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
| | - Giulio Pergola
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Pasquale Di Carlo
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
| | - Shizhong Han
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland United States of America
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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14
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Sportelli L, Eisenberg DP, Passiatore R, D'Ambrosio E, Antonucci LA, Chen Q, Czarapata J, Goldman AL, Gregory M, Griffiths K, Hyde TM, Kleinman JE, Pardiñas AF, Parihar M, Popolizio T, Rampino A, Shin JH, Veronese M, Ulrich WS, Zink CF, Bertolino A, Howes OD, Berman KF, Weinberger DR, Pergola G. Dopamine and schizophrenia from bench to bedside: Discovery of a striatal co-expression risk gene set that predicts in vivo measures of striatal function. bioRxiv 2023:2023.09.20.558594. [PMID: 37786720 PMCID: PMC10541621 DOI: 10.1101/2023.09.20.558594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Schizophrenia (SCZ) is characterized by a polygenic risk architecture implicating diverse molecular pathways important for synaptic function. However, how polygenic risk funnels through these pathways to translate into syndromic illness is unanswered. To evaluate biologically meaningful pathways of risk, we used tensor decomposition to characterize gene co-expression in post-mortem brain (of neurotypicals: N=154; patients with SCZ: N=84; and GTEX samples N=120) from caudate nucleus (CN), hippocampus (HP), and dorsolateral prefrontal cortex (DLPFC). We identified a CN-predominant gene set showing dopaminergic selectivity that was enriched for genes associated with clinical state and for genes associated with SCZ risk. Parsing polygenic risk score for SCZ based on this specific gene set (parsed-PRS), we found that greater pathway-specific SCZ risk predicted greater in vivo striatal dopamine synthesis capacity measured by [ 18 F]-FDOPA PET in three independent cohorts of neurotypicals and patients (total N=235) and greater fMRI striatal activation during reward anticipation in two additional independent neurotypical cohorts (total N=141). These results reveal a 'bench to bedside' translation of dopamine-linked genetic risk variation in driving in vivo striatal neurochemical and hemodynamic phenotypes that have long been implicated in the pathophysiology of SCZ.
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Carnes MU, Quach BC, Zhou L, Han S, Tao R, Mandal M, Deep-Soboslay A, Marks JA, Page GP, Maher BS, Jaffe AE, Won H, Bierut LJ, Hyde TM, Kleinman JE, Johnson EO, Hancock DB. Smoking-informed methylation and expression QTLs in human brain and colocalization with smoking-associated genetic loci. medRxiv 2023:2023.09.18.23295431. [PMID: 37790540 PMCID: PMC10543041 DOI: 10.1101/2023.09.18.23295431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Smoking is a leading cause of preventable morbidity and mortality. Smoking is heritable, and genome-wide association studies (GWAS) of smoking behaviors have identified hundreds of significant loci. Most GWAS-identified variants are noncoding with unknown neurobiological effects. We used genome-wide genotype, DNA methylation, and RNA sequencing data in postmortem human nucleus accumbens (NAc) to identify cis-methylation/expression quantitative trait loci (meQTLs/eQTLs), investigate variant-by-cigarette smoking interactions across the genome, and overlay QTL evidence at smoking GWAS-identified loci to evaluate their regulatory potential. Active smokers (N=52) and nonsmokers (N=171) were defined based on cotinine biomarker levels and next-of-kin reporting. We simultaneously tested variant and variant-by-smoking interaction effects on methylation and expression, separately, adjusting for biological and technical covariates and using a two-stage multiple testing approach with eigenMT and Bonferroni corrections. We found >2 million significant meQTL variants (padj<0.05) corresponding to 41,695 unique CpGs. Results were largely driven by main effects; five meQTLs, mapping to NUDT12, FAM53B, RNF39, and ADRA1B, showed a significant interaction with smoking. We found 57,683 significant eQTLs for 958 unique eGenes (padj<0.05) and no smoking interactions. Colocalization analyses identified loci with smoking-associated GWAS variants that overlapped meQTLs/eQTLs, suggesting that these heritable factors may influence smoking behaviors through functional effects on methylation/expression. One locus containing MUSTIN1 and ITIH4 colocalized across all data types (GWAS + meQTL + eQTL). In this first genome-wide meQTL map in the human NAc, the enriched overlap with smoking GWAS-identified genetic loci provides evidence that gene regulation in the brain helps explain the neurobiology of smoking behaviors.
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Affiliation(s)
- Megan Ulmer Carnes
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Bryan C. Quach
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Linran Zhou
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Shizhong Han
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Ran Tao
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Meisha Mandal
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | | | - Jesse A. Marks
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Grier P. Page
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
- Fellow Program, RTI International, Research Triangle Park, North Carolina
| | - Brion S. Maher
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, Maryland
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Laura J. Bierut
- Department of Psychiatry, Washington University in St. Louis, Missouri
| | - Thomas M. Hyde
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland
| | - Joel E. Kleinman
- Lieber Institute for Brain Development (LIBD), Baltimore, Maryland
| | - Eric O. Johnson
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
- Fellow Program, RTI International, Research Triangle Park, North Carolina
| | - Dana B. Hancock
- Genomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
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16
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Affiliation(s)
- Joel E Kleinman
- Lieber Institute for Brain Development Maltz Research Laboratories, Johns Hopkins Medical Campus, Baltimore (Kleinman, Hyde); Department of Psychiatry and Behavioral Sciences (Kleinman and Hyde) and Department of Neurology (Dr. Hyde), Johns Hopkins University School of Medicine, Baltimore
| | - Thomas M Hyde
- Lieber Institute for Brain Development Maltz Research Laboratories, Johns Hopkins Medical Campus, Baltimore (Kleinman, Hyde); Department of Psychiatry and Behavioral Sciences (Kleinman and Hyde) and Department of Neurology (Dr. Hyde), Johns Hopkins University School of Medicine, Baltimore
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17
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Iverson GL, Jamshidi P, Fisher-Hubbard AO, Deep-Soboslay A, Hyde TM, Kleinman JE, deJong JL, Shepherd CE, Hazrati LN, Castellani RJ. Chronic traumatic encephalopathy neuropathologic change is uncommon in men who played amateur American football. Front Neurol 2023; 14:1143882. [PMID: 37404944 PMCID: PMC10315537 DOI: 10.3389/fneur.2023.1143882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/02/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction We examined postmortem brain tissue from men, over the age of 50, for chronic traumatic encephalopathy neuropathologic change (CTE-NC). We hypothesized that (i) a small percentage would have CTE-NC, (ii) those who played American football during their youth would be more likely to have CTE-NC than those who did not play contact or collision sports, and (iii) there would be no association between CTE-NC and suicide as a manner of death. Methods Brain tissue from 186 men and accompanying clinical information were obtained from the Lieber Institute for Brain Development. Manner of death was determined by a board-certified forensic pathologist. Information was obtained from next of kin telephone interviews, including medical, social, demographic, family, and psychiatric history. The 2016 and 2021 consensus definitions were used for CTE-NC. Two authors screened all cases, using liberal criteria for identifying "possible" CTE-NC, and five authors examined the 15 selected cases. Results The median age at the time of death was 65 years (interquartile range = 57-75; range = 50-96). There were 25.8% with a history of playing American football and 36.0% who had suicide as their manner of death. No case was rated as definitively having "features" of CTE-NC by all five authors. Ten cases were rated as having features of CTE-NC by three or more authors (5.4% of the sample), including 8.3% of those with a personal history of playing American football and 3.9% of those who did not play contact or collision sports. Of those with mood disorders during life, 5.5% had features of CTE-NC compared to 6.0% of those who did not have a reported mood disorder. Of those with suicide as a manner of death, 6.0% had features of CTE-NC compared to 5.0% of those who did not have suicide as a manner of death. Discussion We did not identify a single definitive case of CTE-NC, from the perspective of all raters, and only 5.4% of cases were identified as having possible features of CTE-NC by some raters. CTE-NC was very uncommon in men who played amateur American football, those with mood disorders during life, and those with suicide as a manner of death.
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Affiliation(s)
- Grant L. Iverson
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Boston, MA, United States
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Charlestown, MA, United States
- Department of Physical Medicine and Rehabilitation, Schoen Adams Research Institute at Spaulding Rehabilitation, Charlestown, MA, United States
- MassGeneral Hospital for Children Sports Concussion Program, Boston, MA, United States
- Home Base, A Red Sox Foundation and Massachusetts General Hospital Program, Charlestown, MA, United States
| | - Pouya Jamshidi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Amanda O. Fisher-Hubbard
- Department of Pathology, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Amy Deep-Soboslay
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Joyce L. deJong
- Department of Pathology, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Claire E. Shepherd
- Neuroscience Research Australia, Randwick, NSW, Australia
- School of Medical Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Lili-Naz Hazrati
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rudolph J. Castellani
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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18
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Türker F, Bharadwaj RA, Kleinman JE, Weinberger DR, Hyde TM, White CJ, Williams DW, Margolis SS. Orthogonal approaches required to measure proteasome composition and activity in mammalian brain tissue. J Biol Chem 2023:104811. [PMID: 37172721 DOI: 10.1016/j.jbc.2023.104811] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Proteasomes are large macromolecular complexes with multiple distinct catalytic activities that are each vital to human brain health and disease. Despite their importance, standardized approaches to investigate proteasomes have not been universally adapted. Here, we describe pitfalls and define straightforward orthogonal biochemical approaches essential to measure and understand changes in proteasome composition and activity in the mammalian central nervous system. Through our experimentation in the mammalian brain, we determined an abundance of catalytically active proteasomes exist with and without a 19S cap(s), the regulatory particle essential for ubiquitin-dependent degradation. Moreover, we learned that in-cell measurements using activity-based probes (ABPs) are more sensitive in determining the available activity of the 20S proteasome without the 19S cap and in measuring individual catalytic subunit activities of each β subunit within all neuronal proteasomes. Subsequently, applying these tools to human brain samples, we were surprised to find that post-mortem tissue retained little to no 19S-capped proteasome, regardless of age, sex, or disease state. Comparing brain tissues (parahippocampal gyrus) from human Alzheimer's disease (AD) patients and unaffected subjects, available 20S proteasome activity was significantly elevated in severe cases of AD, an observation not previously noted. Taken together, our study establishes standardized approaches for comprehensive investigation of proteasomes in mammalian brain tissue, and we reveal new insight into brain proteasome biology.
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Affiliation(s)
- Fulya Türker
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rahul A Bharadwaj
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas M Hyde
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cory J White
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dionna W Williams
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA; Department of Molecular Microbiology & Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA; Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Seth S Margolis
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Ofek P, Yeini E, Arad G, Danilevsky A, Pozzi S, Luna CB, Dangoor SI, Grossman R, Ram Z, Shomron N, Brem H, Hyde TM, Geiger T, Satchi-Fainaro R. Deoxyhypusine hydroxylase: A novel therapeutic target differentially expressed in short-term vs long-term survivors of glioblastoma. Int J Cancer 2023. [PMID: 37141410 DOI: 10.1002/ijc.34545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/13/2023] [Accepted: 03/10/2023] [Indexed: 05/06/2023]
Abstract
Glioblastoma (GB) is the most aggressive neoplasm of the brain. Poor prognosis is mainly attributed to tumor heterogeneity, invasiveness and drug resistance. Only a small fraction of GB patients survives longer than 24 months from the time of diagnosis (ie, long-term survivors [LTS]). In our study, we aimed to identify molecular markers associated with favorable GB prognosis as a basis to develop therapeutic applications to improve patients' outcome. We have recently assembled a proteogenomic dataset of 87 GB clinical samples of varying survival rates. Following RNA-seq and mass spectrometry (MS)-based proteomics analysis, we identified several differentially expressed genes and proteins, including some known cancer-related pathways and some less established that showed higher expression in short-term (<6 months) survivors (STS) compared to LTS. One such target found was deoxyhypusine hydroxylase (DOHH), which is known to be involved in the biosynthesis of hypusine, an unusual amino acid essential for the function of the eukaryotic translation initiation factor 5A (eIF5A), which promotes tumor growth. We consequently validated DOHH overexpression in STS samples by quantitative polymerase chain reaction (qPCR) and immunohistochemistry. We further showed robust inhibition of proliferation, migration and invasion of GB cells following silencing of DOHH with short hairpin RNA (shRNA) or inhibition of its activity with small molecules, ciclopirox and deferiprone. Moreover, DOHH silencing led to significant inhibition of tumor progression and prolonged survival in GB mouse models. Searching for a potential mechanism by which DOHH promotes tumor aggressiveness, we found that it supports the transition of GB cells to a more invasive phenotype via epithelial-mesenchymal transition (EMT)-related pathways.
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Affiliation(s)
- Paula Ofek
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eilam Yeini
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gali Arad
- Department of Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Artem Danilevsky
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Sabina Pozzi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Christian Burgos Luna
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sahar Israeli Dangoor
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Grossman
- Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Zvi Ram
- Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Noam Shomron
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Henry Brem
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, USA
- Department of Psychiatry & Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tamar Geiger
- Department of Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Satchi-Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
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20
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Pergola G, Parihar M, Sportelli L, Bharadwaj R, Borcuk C, Radulescu E, Bellantuono L, Blasi G, Chen Q, Kleinman JE, Wang Y, Sripathy SR, Maher BJ, Monaco A, Rossi F, Shin JH, Hyde TM, Bertolino A, Weinberger DR. Consensus molecular environment of schizophrenia risk genes in coexpression networks shifting across age and brain regions. Sci Adv 2023; 9:eade2812. [PMID: 37058565 PMCID: PMC10104472 DOI: 10.1126/sciadv.ade2812] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Schizophrenia is a neurodevelopmental brain disorder whose genetic risk is associated with shifting clinical phenomena across the life span. We investigated the convergence of putative schizophrenia risk genes in brain coexpression networks in postmortem human prefrontal cortex (DLPFC), hippocampus, caudate nucleus, and dentate gyrus granule cells, parsed by specific age periods (total N = 833). The results support an early prefrontal involvement in the biology underlying schizophrenia and reveal a dynamic interplay of regions in which age parsing explains more variance in schizophrenia risk compared to lumping all age periods together. Across multiple data sources and publications, we identify 28 genes that are the most consistently found partners in modules enriched for schizophrenia risk genes in DLPFC; twenty-three are previously unidentified associations with schizophrenia. In iPSC-derived neurons, the relationship of these genes with schizophrenia risk genes is maintained. The genetic architecture of schizophrenia is embedded in shifting coexpression patterns across brain regions and time, potentially underwriting its shifting clinical presentation.
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Affiliation(s)
- Giulio Pergola
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madhur Parihar
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Leonardo Sportelli
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Rahul Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Christopher Borcuk
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Eugenia Radulescu
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Loredana Bellantuono
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Istituto Nazionale di Fisica Nucleare, Bari, Italy
| | - Giuseppe Blasi
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, Italy
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yanhong Wang
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Srinidhi Rao Sripathy
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Brady J. Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare, Bari, Italy
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Fabiana Rossi
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alessandro Bertolino
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, Italy
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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21
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Matosin N, Arloth J, Czamara D, Edmond KZ, Maitra M, Fröhlich AS, Martinelli S, Kaul D, Bartlett R, Curry AR, Gassen NC, Hafner K, Müller NS, Worf K, Rehawi G, Nagy C, Halldorsdottir T, Cruceanu C, Gagliardi M, Gerstner N, Ködel M, Murek V, Ziller MJ, Scarr E, Tao R, Jaffe AE, Arzberger T, Falkai P, Kleinmann JE, Weinberger DR, Mechawar N, Schmitt A, Dean B, Turecki G, Hyde TM, Binder EB. Associations of psychiatric disease and ageing with FKBP5 expression converge on superficial layer neurons of the neocortex. Acta Neuropathol 2023; 145:439-459. [PMID: 36729133 PMCID: PMC10020280 DOI: 10.1007/s00401-023-02541-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023]
Abstract
Identification and characterisation of novel targets for treatment is a priority in the field of psychiatry. FKBP5 is a gene with decades of evidence suggesting its pathogenic role in a subset of psychiatric patients, with potential to be leveraged as a therapeutic target for these individuals. While it is widely reported that FKBP5/FKBP51 mRNA/protein (FKBP5/1) expression is impacted by psychiatric disease state, risk genotype and age, it is not known in which cell types and sub-anatomical areas of the human brain this occurs. This knowledge is critical to propel FKBP5/1-targeted treatment development. Here, we performed an extensive, large-scale postmortem study (n = 1024) of FKBP5/1, examining neocortical areas (BA9, BA11 and ventral BA24/BA24a) derived from subjects that lived with schizophrenia, major depression or bipolar disorder. With an extensive battery of RNA (bulk RNA sequencing, single-nucleus RNA sequencing, microarray, qPCR, RNAscope) and protein (immunoblot, immunohistochemistry) analysis approaches, we thoroughly investigated the effects of disease state, ageing and genotype on cortical FKBP5/1 expression including in a cell type-specific manner. We identified consistently heightened FKBP5/1 levels in psychopathology and with age, but not genotype, with these effects strongest in schizophrenia. Using single-nucleus RNA sequencing (snRNAseq; BA9 and BA11) and targeted histology (BA9, BA24a), we established that these disease and ageing effects on FKBP5/1 expression were most pronounced in excitatory superficial layer neurons of the neocortex, and this effect appeared to be consistent in both the granular and agranular areas examined. We then found that this increase in FKBP5 levels may impact on synaptic plasticity, as FKBP5 gex levels strongly and inversely correlated with dendritic mushroom spine density and brain-derived neurotrophic factor (BDNF) levels in superficial layer neurons in BA11. These findings pinpoint a novel cellular and molecular mechanism that has potential to open a new avenue of FKBP51 drug development to treat cognitive symptoms in psychiatric disorders.
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Affiliation(s)
- Natalie Matosin
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany.
- Molecular Horizons, School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Northfields Ave, Wollongong, 2522, Australia.
- Illawarra Health and Medical Research Institute, Northfields Ave, Wollongong, 2522, Australia.
| | - Janine Arloth
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Katrina Z Edmond
- Molecular Horizons, School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Northfields Ave, Wollongong, 2522, Australia
- Illawarra Health and Medical Research Institute, Northfields Ave, Wollongong, 2522, Australia
| | - Malosree Maitra
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - Anna S Fröhlich
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Silvia Martinelli
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Dominic Kaul
- Molecular Horizons, School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Northfields Ave, Wollongong, 2522, Australia
- Illawarra Health and Medical Research Institute, Northfields Ave, Wollongong, 2522, Australia
| | - Rachael Bartlett
- Molecular Horizons, School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Northfields Ave, Wollongong, 2522, Australia
- Illawarra Health and Medical Research Institute, Northfields Ave, Wollongong, 2522, Australia
| | - Amber R Curry
- Molecular Horizons, School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Northfields Ave, Wollongong, 2522, Australia
- Illawarra Health and Medical Research Institute, Northfields Ave, Wollongong, 2522, Australia
| | - Nils C Gassen
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- Neurohomeostasis Research Group, Institute of Psychiatry, Clinical Centre, University of Bonn, Bonn, Germany
| | - Kathrin Hafner
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Nikola S Müller
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Karolina Worf
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Ghalia Rehawi
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Corina Nagy
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | | | - Cristiana Cruceanu
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Gagliardi
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Nathalie Gerstner
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Maik Ködel
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
| | - Vanessa Murek
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Michael J Ziller
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Elizabeth Scarr
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
- Synaptic Neurobiology and Cognition Laboratory, Florey Institute for Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Ran Tao
- The Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Andrew E Jaffe
- The Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Thomas Arzberger
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians University Munich, Nussbaumstrasse 7, 80336, Munich, Germany
- Centre for Neuropathology and Prion Research, Ludwig-Maximilians University Munich, Nussbaumstrasse 7, 80336, Munich, Germany
| | - Peter Falkai
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians University Munich, Nussbaumstrasse 7, 80336, Munich, Germany
| | - Joel E Kleinmann
- The Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Daniel R Weinberger
- The Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Naguib Mechawar
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Andrea Schmitt
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians University Munich, Nussbaumstrasse 7, 80336, Munich, Germany
- Laboratory of Neuroscience (LIM27), Institute of Psychiatry, University of Sao Paulo, Rua Dr. Ovidio Pires de Campos 785, São Paulo, 05453-010, Brazil
| | - Brian Dean
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
- Synaptic Neurobiology and Cognition Laboratory, Florey Institute for Neuroscience and Mental Health, Parkville, VIC, Australia
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Thomas M Hyde
- The Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, Munich, Germany.
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA.
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22
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Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, Consortium P, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ. Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain. medRxiv 2023:2023.03.03.23286706. [PMID: 36945630 PMCID: PMC10029021 DOI: 10.1101/2023.03.03.23286706] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Genomic regulatory elements active in the developing human brain are notably enriched in genetic risk for neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia, and bipolar disorder. However, prioritizing the specific risk genes and candidate molecular mechanisms underlying these genetic enrichments has been hindered by the lack of a single unified large-scale gene regulatory atlas of human brain development. Here, we uniformly process and systematically characterize gene, isoform, and splicing quantitative trait loci (xQTLs) in 672 fetal brain samples from unique subjects across multiple ancestral populations. We identify 15,752 genes harboring a significant xQTL and map 3,739 eQTLs to a specific cellular context. We observe a striking drop in gene expression and splicing heritability as the human brain develops. Isoform-level regulation, particularly in the second trimester, mediates the greatest proportion of heritability across multiple psychiatric GWAS, compared with eQTLs. Via colocalization and TWAS, we prioritize biological mechanisms for ~60% of GWAS loci across five neuropsychiatric disorders, nearly two-fold that observed in the adult brain. Finally, we build a comprehensive set of developmentally regulated gene and isoform co-expression networks capturing unique genetic enrichments across disorders. Together, this work provides a comprehensive view of genetic regulation across human brain development as well as the stage-and cell type-informed mechanistic underpinnings of neuropsychiatric disorders.
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Affiliation(s)
- Cindy Wen
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Michael Margolis
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse, NY, 13210, USA
| | - Pan Zhang
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology; San Francisco, CA, 94158, USA
| | - Daniel D Vo
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia; Philadelphia, PA, 19104, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
| | - Chuan Jiao
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse, NY, 13210, USA
| | - Minsoo Kim
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Ellen Tsai
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Celine Hoh
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
| | - Rebecca L Walker
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Christos Chatzinakos
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02215, USA
- McLean Hospital; Belmont, MA, 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Declan Clarke
- Department of Molecular Biophysics and Biochemistry, Yale University; New Haven, CT, 06520, USA
| | - Henry Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Worcester, MA, 01605, USA
| | - PsychENCODE Consortium
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse, NY, 13210, USA
- Gladstone Institute of Data Science and Biotechnology; San Francisco, CA, 94158, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia; Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02215, USA
- McLean Hospital; Belmont, MA, 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Department of Molecular Biophysics and Biochemistry, Yale University; New Haven, CT, 06520, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Worcester, MA, 01605, USA
- CNS Data Coordination Group, Sage Bionetworks; Seattle, WA, 98109, USA
- Program in Computational Biology and Bioinformatics, Yale University; New Haven, CT, 06520, USA
- Department of Computer Science, Yale University; New Haven, CT, 06520, USA
- Department of Statistics and Data Science, Yale University; New Haven, CT, 06520, USA
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health; Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health; Baltimore, MD, 21205, USA
- Neumora Therapeutics; Watertown, MA, 02472, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University School of Medicine; Cardiff, CF24 4HQ, UK
- Department of Comparative Medicine, Yale University School of Medicine; New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University School of Medicine; New Haven, CT, 06520, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Precision Health, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Statistics & Data Science, Carnegie Mellon University; Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University; Pittsburgh, PA, 15213, USA
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute; Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Harvard Medical School; Boston, MA, 02215, USA
- Division of Genetics, Brigham and Women's Hospital; Boston, MA, 02215, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco; San Francisco, CA, 94158, USA
- Chan Zuckerberg Biohub; San Francisco, CA, 94158, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan, 410008, China
| | - Mette A Peters
- CNS Data Coordination Group, Sage Bionetworks; Seattle, WA, 98109, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University; New Haven, CT, 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University; New Haven, CT, 06520, USA
- Department of Computer Science, Yale University; New Haven, CT, 06520, USA
- Department of Statistics and Data Science, Yale University; New Haven, CT, 06520, USA
| | - Nikolaos P Daskalakis
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02215, USA
- McLean Hospital; Belmont, MA, 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Worcester, MA, 01605, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health; Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health; Baltimore, MD, 21205, USA
- Neumora Therapeutics; Watertown, MA, 02472, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University School of Medicine; Cardiff, CF24 4HQ, UK
| | - Nenad Sestan
- Department of Comparative Medicine, Yale University School of Medicine; New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University School of Medicine; New Haven, CT, 06520, USA
| | - Daniel H Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Precision Health, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Kathryn Roeder
- Department of Statistics & Data Science, Carnegie Mellon University; Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University; Pittsburgh, PA, 15213, USA
| | - Alexander Gusev
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute; Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Harvard Medical School; Boston, MA, 02215, USA
- Division of Genetics, Brigham and Women's Hospital; Boston, MA, 02215, USA
| | - Bogdan Pasaniuc
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Precision Health, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology; San Francisco, CA, 94158, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco; San Francisco, CA, 94158, USA
- Chan Zuckerberg Biohub; San Francisco, CA, 94158, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse, NY, 13210, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan, 410008, China
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia; Philadelphia, PA, 19104, USA
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23
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Huuki-Myers L, Spangler A, Eagles N, Montgomery KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, Hyde TM, Kleinman JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, Collado-Torres L, Maynard KR. Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex. bioRxiv 2023:2023.02.15.528722. [PMID: 36824961 PMCID: PMC9949126 DOI: 10.1101/2023.02.15.528722] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Generation of a molecular neuroanatomical map of the human prefrontal cortex reveals novel spatial domains and cell-cell interactions relevant for psychiatric disease. The molecular organization of the human neocortex has been historically studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally-defined spatial domains that move beyond classic cytoarchitecture. Here we used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex (DLPFC). Integration with paired single nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we map the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains. Finally, we provide resources for the scientific community to explore these integrated spatial and single cell datasets at research.libd.org/spatialDLPFC/.
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Affiliation(s)
- Louise Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Abby Spangler
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Nick Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Kelsey D Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Boyi Guo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Melissa Grant-Peters
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Heena R Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Chaichontat Sriworarat
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Annie B Nguyen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | | | - Matthew N Tran
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Arta Seyedian
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
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24
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Chen F, Wang X, Jang SK, Quach BC, Weissenkampen JD, Khunsriraksakul C, Yang L, Sauteraud R, Albert CM, Allred NDD, Arnett DK, Ashley-Koch AE, Barnes KC, Barr RG, Becker DM, Bielak LF, Bis JC, Blangero J, Boorgula MP, Chasman DI, Chavan S, Chen YDI, Chuang LM, Correa A, Curran JE, David SP, Fuentes LDL, Deka R, Duggirala R, Faul JD, Garrett ME, Gharib SA, Guo X, Hall ME, Hawley NL, He J, Hobbs BD, Hokanson JE, Hsiung CA, Hwang SJ, Hyde TM, Irvin MR, Jaffe AE, Johnson EO, Kaplan R, Kardia SLR, Kaufman JD, Kelly TN, Kleinman JE, Kooperberg C, Lee IT, Levy D, Lutz SM, Manichaikul AW, Martin LW, Marx O, McGarvey ST, Minster RL, Moll M, Moussa KA, Naseri T, North KE, Oelsner EC, Peralta JM, Peyser PA, Psaty BM, Rafaels N, Raffield LM, Reupena MS, Rich SS, Rotter JI, Schwartz DA, Shadyab AH, Sheu WHH, Sims M, Smith JA, Sun X, Taylor KD, Telen MJ, Watson H, Weeks DE, Weir DR, Yanek LR, Young KA, Young KL, Zhao W, Hancock DB, Jiang B, Vrieze S, Liu DJ. Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing. Nat Genet 2023; 55:291-300. [PMID: 36702996 PMCID: PMC9925385 DOI: 10.1038/s41588-022-01282-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/08/2022] [Indexed: 01/27/2023]
Abstract
Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with alternative TWAS methods. These hits and subsequent fine mapping using TESLA point to target genes with biological relevance. In silico drug-repurposing analyses highlight several drugs with known efficacy, including dextromethorphan and galantamine, and new drugs such as muscle relaxants that may be repurposed for treating nicotine addiction.
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Affiliation(s)
- Fang Chen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Xingyan Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Seon-Kyeong Jang
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | | | - J Dylan Weissenkampen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychology, Penn State College of Medicine, Hershey, PA, USA
| | | | - Lina Yang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Renan Sauteraud
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Christine M Albert
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
| | - Kathleen C Barnes
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Meher Preethi Boorgula
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sameer Chavan
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Yii-Der I Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lee-Ming Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Sean P David
- University of Chicago, Chicago, IL, USA
- NorthShore University Health System, Evanston, IL, USA
| | - Lisa de Las Fuentes
- Department of Medicine, Division of Biostatistics and Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Ranjan Deka
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Jessica D Faul
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Sina A Gharib
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael E Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Nicola L Hawley
- Department of Epidemiology (Chronic Disease), School of Public Health, Yale University, New Haven, CT, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Brian D Hobbs
- Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Jen Hwang
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Human Genetics and Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, The Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joel D Kaufman
- Departments of Environmental & Occupational Health Sciences, Medicine, and Epidemiology, University of Washington Seattle, Seattle, WA, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - I-Te Lee
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Daniel Levy
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon M Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care, Boston, MA, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lisa W Martin
- Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Olivia Marx
- Department of Biomedical Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Stephen T McGarvey
- Department of Epidemiology, International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Ryan L Minster
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Karine A Moussa
- Penn State Huck Institutes of Life Sciences, Penn State College of Medicine, University Park, PA, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Juan M Peralta
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Mario Sims
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Harold Watson
- Faculty of Medical Sciences, University of the West Indies, Cave Hill Campus, Barbados
| | - Daniel E Weeks
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - David R Weir
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA.
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
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25
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Sadashivaiah V, Tippani M, Page SC, Kwon SH, Bach SV, Bharadwaj RA, Hyde TM, Kleinman JE, Jaffe AE, Maynard KR. SUFI: an automated approach to spectral unmixing of fluorescent multiplex images captured in mouse and post-mortem human brain tissues. BMC Neurosci 2023; 24:6. [PMID: 36698068 PMCID: PMC9878864 DOI: 10.1186/s12868-022-00765-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/06/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Multispectral fluorescence imaging coupled with linear unmixing is a form of image data collection and analysis that allows for measuring multiple molecular signals in a single biological sample. Multiple fluorescent dyes, each measuring a unique molecule, are simultaneously measured and subsequently "unmixed" to provide a read-out for each molecular signal. This strategy allows for measuring highly multiplexed signals in a single data capture session, such as multiple proteins or RNAs in tissue slices or cultured cells, but can often result in mixed signals and bleed-through problems across dyes. Existing spectral unmixing algorithms are not optimized for challenging biological specimens such as post-mortem human brain tissue, and often require manual intervention to extract spectral signatures. We therefore developed an intuitive, automated, and flexible package called SUFI: spectral unmixing of fluorescent images. RESULTS This package unmixes multispectral fluorescence images by automating the extraction of spectral signatures using vertex component analysis, and then performs one of three unmixing algorithms derived from remote sensing. We evaluate these remote sensing algorithms' performances on four unique biological datasets and compare the results to unmixing results obtained using ZEN Black software (Zeiss). We lastly integrate our unmixing pipeline into the computational tool dotdotdot, which is used to quantify individual RNA transcripts at single cell resolution in intact tissues and perform differential expression analysis, and thereby provide an end-to-end solution for multispectral fluorescence image analysis and quantification. CONCLUSIONS In summary, we provide a robust, automated pipeline to assist biologists with improved spectral unmixing of multispectral fluorescence images.
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Affiliation(s)
- Vijay Sadashivaiah
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Svitlana V Bach
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Rahul A Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Andrew E Jaffe
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.
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26
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Su Y, Zhou Y, Bennett ML, Li S, Carceles-Cordon M, Lu L, Huh S, Jimenez-Cyrus D, Kennedy BC, Kessler SK, Viaene AN, Helbig I, Gu X, Kleinman JE, Hyde TM, Weinberger DR, Nauen DW, Song H, Ming GL. A single-cell transcriptome atlas of glial diversity in the human hippocampus across the postnatal lifespan. Cell Stem Cell 2023; 30:113. [PMID: 36608676 PMCID: PMC9901278 DOI: 10.1016/j.stem.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yijing Su
- Correspondence:
(Y.S.),
(H.S.),
(G.-l.M.)
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27
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Su Y, Zhou Y, Bennett ML, Li S, Carceles-Cordon M, Lu L, Huh S, Jimenez-Cyrus D, Kennedy BC, Kessler SK, Viaene AN, Helbig I, Gu X, Kleinman JE, Hyde TM, Weinberger DR, Nauen DW, Song H, Ming GL. A single-cell transcriptome atlas of glial diversity in the human hippocampus across the postnatal lifespan. Cell Stem Cell 2022; 29:1594-1610.e8. [PMID: 36332572 PMCID: PMC9844262 DOI: 10.1016/j.stem.2022.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/26/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
The molecular diversity of glia in the human hippocampus and their temporal dynamics over the lifespan remain largely unknown. Here, we performed single-nucleus RNA sequencing to generate a transcriptome atlas of the human hippocampus across the postnatal lifespan. Detailed analyses of astrocytes, oligodendrocyte lineages, and microglia identified subpopulations with distinct molecular signatures and revealed their association with specific physiological functions, age-dependent changes in abundance, and disease relevance. We further characterized spatiotemporal heterogeneity of GFAP-enriched astrocyte subpopulations in the hippocampal formation using immunohistology. Leveraging glial subpopulation classifications as a reference map, we revealed the diversity of glia differentiated from human pluripotent stem cells and identified dysregulated genes and pathological processes in specific glial subpopulations in Alzheimer's disease (AD). Together, our study significantly extends our understanding of human glial diversity, population dynamics across the postnatal lifespan, and dysregulation in AD and provides a reference atlas for stem-cell-based glial differentiation.
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Affiliation(s)
- Yijing Su
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Yi Zhou
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariko L Bennett
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiying Li
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Marc Carceles-Cordon
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lu Lu
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sooyoung Huh
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dennisse Jimenez-Cyrus
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin C Kennedy
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sudha K Kessler
- Department of Pediatrics, Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- Department of Pediatrics, Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xiaosong Gu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | - Joel E Kleinman
- Lieber Institute for Brain Development, The Solomon H. Snyder Department of Neuroscience, Department of Neurology, and Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, The Solomon H. Snyder Department of Neuroscience, Department of Neurology, and Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, The Solomon H. Snyder Department of Neuroscience, Department of Neurology, and Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David W Nauen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Benjamin KJM, Chen Q, Jaffe AE, Stolz JM, Collado-Torres L, Huuki-Myers LA, Burke EE, Arora R, Feltrin AS, Barbosa AR, Radulescu E, Pergola G, Shin JH, Ulrich WS, Deep-Soboslay A, Tao R, Hyde TM, Kleinman JE, Erwin JA, Weinberger DR, Paquola ACM. Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes. Nat Neurosci 2022; 25:1559-1568. [PMID: 36319771 PMCID: PMC10599288 DOI: 10.1038/s41593-022-01182-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/13/2022] [Indexed: 11/06/2022]
Abstract
Most studies of gene expression in the brains of individuals with schizophrenia have focused on cortical regions, but subcortical nuclei such as the striatum are prominently implicated in the disease, and current antipsychotic drugs target the striatum's dense dopaminergic innervation. Here, we performed a comprehensive analysis of the genetic and transcriptional landscape of schizophrenia in the postmortem caudate nucleus of the striatum of 443 individuals (245 neurotypical individuals, 154 individuals with schizophrenia and 44 individuals with bipolar disorder), 210 from African and 233 from European ancestries. Integrating expression quantitative trait loci analysis, Mendelian randomization with the latest schizophrenia genome-wide association study, transcriptome-wide association study and differential expression analysis, we identified many genes associated with schizophrenia risk, including potentially the dopamine D2 receptor short isoform. We found that antipsychotic medication has an extensive influence on caudate gene expression. We constructed caudate nucleus gene expression networks that highlight interactions involving schizophrenia risk. These analyses provide a resource for the study of schizophrenia and insights into risk mechanisms and potential therapeutic targets.
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Affiliation(s)
- Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qiang Chen
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Neumora Therapeutics, Watertown, MA, USA
| | - Joshua M Stolz
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Emily E Burke
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Ria Arora
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Arthur S Feltrin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Center for Mathematics, Computation and Cognition, Federal University of ABC, Santo André, Brazil
| | - André Rocha Barbosa
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Inter-Institutional Graduate Program on Bioinformatics, University of São Paulo, São Paulo, Brazil
- Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil
| | | | - Giulio Pergola
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Ran Tao
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer A Erwin
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Apuã C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Zaharija B, Odorčić M, Hart A, Samardžija B, Marreiros R, Prikulis I, Juković M, Hyde TM, Kleinman JE, Korth C, Bradshaw NJ. TRIOBP-1 Protein Aggregation Exists in Both Major Depressive Disorder and Schizophrenia, and Can Occur through Two Distinct Regions of the Protein. Int J Mol Sci 2022; 23:ijms231911048. [PMID: 36232351 PMCID: PMC9569677 DOI: 10.3390/ijms231911048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
The presence of proteinopathy, the accumulation of specific proteins as aggregates in neurons, is an emerging aspect of the pathology of schizophrenia and other major mental illnesses. Among the initial proteins implicated in forming such aggregates in these conditions is Trio and F-actin Binding Protein isoform 1 (TRIOBP-1), a ubiquitously expressed protein involved in the stabilization of the actin cytoskeleton. Here we investigate the insolubility of TRIOBP-1, as an indicator of aggregation, in brain samples from 25 schizophrenia patients, 25 major depressive disorder patients and 50 control individuals (anterior cingulate cortex, BA23). Strikingly, insoluble TRIOBP-1 is considerably more prevalent in both of these conditions than in controls, further implicating TRIOBP-1 aggregation in schizophrenia and indicating a role in major depressive disorder. These results were only seen using a high stringency insolubility assay (previously used to study DISC1 and other proteins), but not a lower stringency assay that would be expected to also detect functional, actin-bound TRIOBP-1. Previously, we have also determined that a region of 25 amino acids in the center of this protein is critical for its ability to form aggregates. Here we attempt to refine this further, through the expression of various truncated mutant TRIOBP-1 vectors in neuroblastoma cells and examining their aggregation. In this way, it was possible to narrow down the aggregation-critical region of TRIOBP-1 to just 8 amino acids (333–340 of the 652 amino acid-long TRIOBP-1). Surprisingly our results suggested that a second section of TRIOBP-1 is also capable of independently inducing aggregation: the optionally expressed 59 amino acids at the extreme N-terminus of the protein. As a result, the 597 amino acid long version of TRIOBP-1 (also referred to as “Tara” or “TAP68”) has reduced potential to form aggregates. The presence of insoluble TRIOBP-1 in brain samples from patients, combined with insight into the mechanism of aggregation of TRIOBP-1 and generation of an aggregation-resistant mutant TRIOBP-1 that lacks both these regions, will be of significant use in further investigating the mechanism and consequences of TRIOBP-1 aggregation in major mental illness.
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Affiliation(s)
- Beti Zaharija
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Maja Odorčić
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Anja Hart
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Bobana Samardžija
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Rita Marreiros
- Department of Neuropathology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Ingrid Prikulis
- Department of Neuropathology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Maja Juković
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Baltimore, MD 21295, USA
- Department of Psychiatry and Behavioral Sciences, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, John Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Baltimore, MD 21295, USA
- Department of Psychiatry and Behavioral Sciences, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Carsten Korth
- Department of Neuropathology, Heinrich Heine University, 40225 Düsseldorf, Germany
- Correspondence: (C.K.); (N.J.B.)
| | - Nicholas J. Bradshaw
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
- Department of Neuropathology, Heinrich Heine University, 40225 Düsseldorf, Germany
- Correspondence: (C.K.); (N.J.B.)
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30
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Jaffe AE, Tao R, Page SC, Maynard KR, Pattie EA, Nguyen CV, Deep-Soboslay A, Bharadwaj R, Young KA, Friedman MJ, Williamson DE, Shin JH, Hyde TM, Martinowich K, Kleinman JE. Decoding Shared Versus Divergent Transcriptomic Signatures Across Cortico-Amygdala Circuitry in PTSD and Depressive Disorders. Am J Psychiatry 2022; 179:673-686. [PMID: 35791611 PMCID: PMC10697016 DOI: 10.1176/appi.ajp.21020162] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Posttraumatic stress disorder (PTSD) is a debilitating neuropsychiatric disease that is highly comorbid with major depressive disorder (MDD) and bipolar disorder. The overlap in symptoms is hypothesized to stem from partially shared genetics and underlying neurobiological mechanisms. To delineate conservation between transcriptional patterns across PTSD and MDD, the authors examined gene expression in the human cortex and amygdala in these disorders. METHODS RNA sequencing was performed in the postmortem brain of two prefrontal cortex regions and two amygdala regions from donors diagnosed with PTSD (N=107) or MDD (N=109) as well as from neurotypical donors (N=109). RESULTS The authors identified a limited number of differentially expressed genes (DEGs) specific to PTSD, with nearly all mapping to cortical versus amygdala regions. PTSD-specific DEGs were enriched in gene sets associated with downregulated immune-related pathways and microglia as well as with subpopulations of GABAergic inhibitory neurons. While a greater number of DEGs associated with MDD were identified, most overlapped with PTSD, and only a few were MDD specific. The authors used weighted gene coexpression network analysis as an orthogonal approach to confirm the observed cellular and molecular associations. CONCLUSIONS These findings provide supporting evidence for involvement of decreased immune signaling and neuroinflammation in MDD and PTSD pathophysiology, and extend evidence that GABAergic neurons have functional significance in PTSD.
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Affiliation(s)
- Andrew E. Jaffe
- Lieber Institute for Brain Development, Baltimore, MD
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Ran Tao
- Lieber Institute for Brain Development, Baltimore, MD
| | | | | | | | | | | | | | - Keith A. Young
- Department of Psychiatry and Behavioral Sciences, Texas A&M College of Medicine, Bryan TX
- Department of Veterans Affairs, VISN 17 Center of Excellence for Research on Returning War Veterans, Waco, TX
- Central Texas Veterans Health Care System, Temple, TX, 76504, USA
- Baylor Scott & White Psychiatry, Temple, TX
| | - Matthew J. Friedman
- Department of Psychiatry, Geisel School of Medicine at Dartmouth, Dartmouth Hanover, NH
- National Center for PTSD, U.S. Department of Veterans Affairs
| | - Douglas E. Williamson
- Duke Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, 300 North Duke St, Durham, North Carolina
- Durham VA Healthcare System, 508 Fulton St, Durham, North Carolina
| | | | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Keri Martinowich
- Lieber Institute for Brain Development, Baltimore, MD
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
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31
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Zhou J, Chen Q, Braun PR, Perzel Mandell KA, Jaffe AE, Tan HY, Hyde TM, Kleinman JE, Potash JB, Shinozaki G, Weinberger DR, Han S. Deep learning predicts DNA methylation regulatory variants in the human brain and elucidates the genetics of psychiatric disorders. Proc Natl Acad Sci U S A 2022; 119:e2206069119. [PMID: 35969790 PMCID: PMC9407663 DOI: 10.1073/pnas.2206069119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
There is growing evidence for the role of DNA methylation (DNAm) quantitative trait loci (mQTLs) in the genetics of complex traits, including psychiatric disorders. However, due to extensive linkage disequilibrium (LD) of the genome, it is challenging to identify causal genetic variations that drive DNAm levels by population-based genetic association studies. This limits the utility of mQTLs for fine-mapping risk loci underlying psychiatric disorders identified by genome-wide association studies (GWAS). Here we present INTERACT, a deep learning model that integrates convolutional neural networks with transformer, to predict effects of genetic variations on DNAm levels at CpG sites in the human brain. We show that INTERACT-derived DNAm regulatory variants are not confounded by LD, are concentrated in regulatory genomic regions in the human brain, and are convergent with mQTL evidence from genetic association analysis. We further demonstrate that predicted DNAm regulatory variants are enriched for heritability of brain-related traits and improve polygenic risk prediction for schizophrenia across diverse ancestry samples. Finally, we applied predicted DNAm regulatory variants for fine-mapping schizophrenia GWAS risk loci to identify potential novel risk genes. Our study shows the power of a deep learning approach to identify functional regulatory variants that may elucidate the genetic basis of complex traits.
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Affiliation(s)
- Jiyun Zhou
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Qiang Chen
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
| | - Patricia R. Braun
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kira A. Perzel Mandell
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Mental Health, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Hao Yang Tan
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - James B. Potash
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Gen Shinozaki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94305
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shizhong Han
- Lieber Institute for Brain Development, The Johns Hopkins Medical Campus, Baltimore, MD 21287
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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32
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Pozzi S, Scomparin A, Ben-Shushan D, Yeini E, Ofek P, Nahmad AD, Soffer S, Ionescu A, Ruggiero A, Barzel A, Brem H, Hyde TM, Barshack I, Sinha S, Ruppin E, Weiss T, Madi A, Perlson E, Slutsky I, Florindo HF, Satchi-Fainaro R. MCP-1/CCR2 axis inhibition sensitizes the brain microenvironment against melanoma brain metastasis progression. JCI Insight 2022; 7:154804. [PMID: 35980743 PMCID: PMC9536270 DOI: 10.1172/jci.insight.154804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Development of resistance to chemo- and immunotherapies often occurs following treatment of melanoma brain metastasis (MBM). The brain microenvironment (BME), particularly astrocytes, cooperate toward MBM progression by upregulating secreted factors, among which we found that monocyte chemoattractant protein-1 (MCP-1) and its receptors, CCR2 and CCR4, were overexpressed in MBM compared with primary lesions. Among other sources of MCP-1 in the brain, we show that melanoma cells altered astrocyte secretome and evoked MCP-1 expression and secretion, which in turn induced CCR2 expression in melanoma cells, enhancing in vitro tumorigenic properties, such as proliferation, migration, and invasion of melanoma cells. In vivo pharmacological blockade of MCP-1 or molecular knockout of CCR2/CCR4 increased the infiltration of cytotoxic CD8+ T cells and attenuated the immunosuppressive phenotype of the BME as shown by decreased infiltration of Tregs and tumor-associated macrophages/microglia in several models of intracranially injected MBM. These in vivo strategies led to decreased MBM outgrowth and prolonged the overall survival of the mice. Our findings highlight the therapeutic potential of inhibiting interactions between BME and melanoma cells for the treatment of this disease.
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Affiliation(s)
- Sabina Pozzi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna Scomparin
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Dikla Ben-Shushan
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eilam Yeini
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paula Ofek
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alessio D Nahmad
- The School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shelly Soffer
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ariel Ionescu
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Antonella Ruggiero
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Barzel
- The School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Henry Brem
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, United States of America
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - Sanju Sinha
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, United States of America
| | - Eytan Ruppin
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, United States of America
| | - Tomer Weiss
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Asaf Madi
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Inna Slutsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Ronit Satchi-Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban AE, Leckman JF, Weinberger DR, Vaccarino FM, Abyzov A. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022; 377:511-517. [PMID: 35901164 PMCID: PMC9420557 DOI: 10.1126/science.abm6222] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.
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Affiliation(s)
- Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT 06520
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Milovan Suvakov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520
| | - Caroline Dias
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | | | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT 06520
| | - Arijit Panda
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Yasmine Chahine
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Yeh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rosalinda C. Roberts
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham Al, 35294
| | - Anita Huttner
- Department of Pathology, Yale University, New Haven, CT 06520
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Richard E. Straub
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD
| | - Flora M. Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520
- Department of Neuroscience, Yale University, New Haven, CT 06520
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
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D'Ignazio L, Jacomini RS, Qamar B, Benjamin KJM, Arora R, Sawada T, Evans TA, Diffenderfer KE, Pankonin AR, Hendriks WT, Hyde TM, Kleinman JE, Weinberger DR, Bragg DC, Paquola ACM, Erwin JA. Variation in TAF1 expression in female carrier induced pluripotent stem cells and human brain ontogeny has implications for adult neostriatum vulnerability in X-linked Dystonia Parkinsonism. eNeuro 2022; 9:ENEURO.0129-22.2022. [PMID: 35868859 PMCID: PMC9428949 DOI: 10.1523/eneuro.0129-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/14/2022] [Accepted: 07/03/2022] [Indexed: 11/21/2022] Open
Abstract
X-linked Dystonia-Parkinsonism (XDP) is an inherited, X-linked, adult-onset movement disorder characterized by degeneration in the neostriatum. No therapeutics alter disease progression. The mechanisms underlying regional differences in degeneration and adult onset are unknown. Developing therapeutics requires a deeper understanding of how XDP-relevant features vary in health and disease. XDP is possibly due, in part, to a partial loss of TAF1 function. A disease-specific SINE-VNTR-Alu (SVA) retrotransposon insertion occurs within intron 32 of TAF1, a subunit of TFIID involved in transcription initiation. While all XDP males are usually clinically affected, females are heterozygous carriers generally not manifesting the full syndrome. As a resource for disease modeling, we characterized eight iPSC lines from three XDP female carrier individuals for X chromosome inactivation status and identified clonal lines that express either the wild-type X or XDP haplotype. Furthermore, we characterized XDP-relevant transcript expression in neurotypical humans, and found that SVA-F expression decreases after 30 years of age in the brain and that TAF1 is decreased in most female samples. Uniquely in the caudate nucleus, TAF1 expression is not sexually dimorphic and decreased after adolescence. These findings indicate that regional-, age- and sex-specific mechanisms regulate TAF1, highlighting the importance of disease-relevant models and postmortem tissue. We propose that the decreased TAF1 expression in the adult caudate may synergize with the XDP-specific partial loss of TAF1 function in patients, thereby passing a minimum threshold of TAF1 function, and triggering degeneration in the neostriatum.Significance StatementXDP is an inherited, X-linked, adult-onset movement disorder characterized by degeneration in the neostriatum. No therapeutics alter disease progression. Developing therapeutics requires a deeper understanding of how XDP-relevant features vary in health and disease. XDP is possibly due to a partial loss of TAF1 function. While all XDP males are usually affected, females are heterozygous carriers generally not manifesting the full syndrome. As a resource for disease modeling, we characterized eight stem cell lines from XDP female carrier individuals. Furthermore, we found that, uniquely in the caudate nucleus, TAF1 expression decreases after adolescence in healthy humans. We hypothesize that the decrease of TAF1 after adolescence in human caudate, in general, may underlie the vulnerability of the adult neostriatum in XDP.
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Affiliation(s)
- Laura D'Ignazio
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ricardo S Jacomini
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Bareera Qamar
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ria Arora
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Biology, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tomoyo Sawada
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Taylor A Evans
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Aimee R Pankonin
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - William T Hendriks
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University Baltimore, MD 21205, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Apua C M Paquola
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jennifer A Erwin
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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35
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Sosnowski DW, Jaffe AE, Tao R, Deep-Soboslay A, Shu C, Sabunciyan S, Kleinman JE, Hyde TM, Maher BS. Differential expression of NPAS4 in the dorsolateral prefrontal cortex following opioid overdose. Drug Alcohol Depend Rep 2022; 3:100040. [PMID: 36845993 PMCID: PMC9948892 DOI: 10.1016/j.dadr.2022.100040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Although preclinical models reveal the neurobiological pathways altered through opioid abuse, comprehensive assessments of gene expression in human brain samples are needed. Moreover, less is known about gene expression in response to fatal overdose. The primary goal of the present study was to compare gene expression in the dorsolateral prefrontal cortex (DLPFC) between brain samples of individuals who died of acute opioid intoxication and group-matched controls. METHODS Postmortem tissue samples of the DLPFC from 153 deceased individuals (Mage = 35.4; 62% male; 77% European ancestry). Study groups included 72 brain samples from individuals who died of acute opioid intoxication, 53 psychiatric controls, and 28 normal controls. Whole transcriptome RNA-sequencing was used to generate exon counts, and differential expression was tested using limma-voom. Analyses were adjusted for relevant sociodemographic characteristics, technical covariates, and cryptic relatedness using quality surrogate variables. Weighted correlation network analysis and gene set enrichment analyses also were conducted. RESULTS Two genes were differentially expressed in opioid samples compared to control samples. The top gene, NPAS4, was downregulated in opioid samples (log2FC = -2.47, adj. p = .049) and has been implicated in opioid, cocaine, and methamphetamine use. Weighted correlation network analysis revealed 15 gene modules associated with opioid overdose, though no intramodular hub genes were related to opioid overdose, nor were pathways related to opioid overdose enriched for differential expression. CONCLUSIONS Results provide preliminary evidence that NPAS4 is implicated in opioid overdose, and more research is needed to understand its role in opioid abuse and associated outcomes.
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Affiliation(s)
- David W. Sosnowski
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Hampton House, Baltimore, MD 21205, United States
| | - Andrew E. Jaffe
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Hampton House, Baltimore, MD 21205, United States
- Lieber Institute for Brain Development, United States
| | - Ran Tao
- Lieber Institute for Brain Development, United States
| | | | - Chang Shu
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Hampton House, Baltimore, MD 21205, United States
- Department of Pediatrics, Columbia University Irving Medical Center, United States
| | | | - Joel E. Kleinman
- Lieber Institute for Brain Development, United States
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, United States
| | | | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Hampton House, Baltimore, MD 21205, United States
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36
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Mandell KAP, Eagles NJ, Deep-Soboslay A, Tao R, Han S, Wilton R, Szalay AS, Hyde TM, Kleinman JE, Jaffe AE, Weinberger DR. Molecular phenotypes associated with antipsychotic drugs in the human caudate nucleus. Mol Psychiatry 2022; 27:2061-2067. [PMID: 35236959 PMCID: PMC9133054 DOI: 10.1038/s41380-022-01453-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 11/09/2022]
Abstract
Antipsychotic drugs are the current first-line of treatment for schizophrenia and other psychotic conditions. However, their molecular effects on the human brain are poorly studied, due to difficulty of tissue access and confounders associated with disease status. Here we examine differences in gene expression and DNA methylation associated with positive antipsychotic drug toxicology status in the human caudate nucleus. We find no genome-wide significant differences in DNA methylation, but abundant differences in gene expression. These gene expression differences are overall quite similar to gene expression differences between schizophrenia cases and controls. Interestingly, gene expression differences based on antipsychotic toxicology are different between brain regions, potentially due to affected cell type differences. We finally assess similarities with effects in a mouse model, which finds some overlapping effects but many differences as well. As a first look at the molecular effects of antipsychotics in the human brain, the lack of epigenetic effects is unexpected, possibly because long term treatment effects may be relatively stable for extended periods.
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Affiliation(s)
- Kira A. Perzel Mandell
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM), Baltimore, MD 21205, USA
| | - Nicholas J. Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Amy Deep-Soboslay
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Shizhong Han
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA,Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA
| | - Richard Wilton
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA
| | - Alexander S. Szalay
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD, USA,Department of Computer Science, JHSOM, Baltimore, MD, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA,Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA,Department of Neurology, JHSOM, Baltimore, MD, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA,Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM), Baltimore, MD 21205, USA,Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA,Department of Neuroscience, JHSOM, Baltimore, MD, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health (JHBSPH), MD 21205, USA,Department of Biostatistics, JHBSPH, Baltimore, MD, USA
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM), Baltimore, MD 21205, USA,Department of Psychiatry and Behavioral Sciences, JHSOM, Baltimore, MD, USA,Department of Neurology, JHSOM, Baltimore, MD, USA,Department of Neuroscience, JHSOM, Baltimore, MD, USA.,
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37
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Zandi PP, Jaffe AE, Goes FS, Burke EE, Collado-Torres L, Huuki-Myers L, Seyedian A, Lin Y, Seifuddin F, Pirooznia M, Ross CA, Kleinman JE, Weinberger DR, Hyde TM. Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways. Nat Neurosci 2022; 25:381-389. [PMID: 35260864 PMCID: PMC8915427 DOI: 10.1038/s41593-022-01024-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/26/2022] [Indexed: 12/12/2022]
Abstract
Recent genetic studies have identified variants associated with bipolar disorder (BD), but it remains unclear how brain gene expression is altered in BD and how genetic risk for BD may contribute to these alterations. Here, we obtained transcriptomes from subgenual anterior cingulate cortex and amygdala samples from post-mortem brains of individuals with BD and neurotypical controls, including 511 total samples from 295 unique donors. We examined differential gene expression between cases and controls and the transcriptional effects of BD-associated genetic variants. We found two coexpressed modules that were associated with transcriptional changes in BD: one enriched for immune and inflammatory genes and the other with genes related to the postsynaptic membrane. Over 50% of BD genome-wide significant loci contained significant expression quantitative trait loci (QTL) (eQTL), and these data converged on several individual genes, including SCN2A and GRIN2A. Thus, these data implicate specific genes and pathways that may contribute to the pathology of BP.
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Affiliation(s)
- Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Andrew E Jaffe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,The Lieber Institute for Brain Development, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Emily E Burke
- The Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- The Lieber Institute for Brain Development, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Arta Seyedian
- The Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Yian Lin
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Fayaz Seifuddin
- The National Heart, Lung and Blood Institute, the National Institute of Health, Bethesda, MD, USA
| | - Mehdi Pirooznia
- The National Heart, Lung and Blood Institute, the National Institute of Health, Bethesda, MD, USA
| | - Christopher A Ross
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,The Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Daniel R Weinberger
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,The Lieber Institute for Brain Development, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,The Lieber Institute for Brain Development, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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38
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Punzi G, Ursini G, Chen Q, Radulescu E, Tao R, Huuki LA, Di Carlo P, Collado-Torres L, Shin JH, Catanesi R, Jaffe AE, Hyde TM, Kleinman JE, Mackay TFC, Weinberger DR. Genetics and Brain Transcriptomics of Completed Suicide. Am J Psychiatry 2022; 179:226-241. [PMID: 35236118 PMCID: PMC8908792 DOI: 10.1176/appi.ajp.2021.21030299] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The authors sought to study the transcriptomic and genomic features of completed suicide by parsing the method chosen, to capture molecular correlates of the distinctive frame of mind of individuals who die by suicide, while reducing heterogeneity. METHODS The authors analyzed gene expression (RNA sequencing) from postmortem dorsolateral prefrontal cortex of patients who died by suicide with violent compared with nonviolent means, nonsuicide patients with the same psychiatric disorders, and a neurotypical group (total N=329). They then examined genomic risk scores (GRSs) for each psychiatric disorder included, and GRSs for cognition (IQ) and for suicide attempt, testing how they predict diagnosis or traits (total N=888). RESULTS Patients who died by suicide by violent means showed a transcriptomic pattern remarkably divergent from each of the other patient groups but less from the neurotypical group; consistently, their genomic profile of risk was relatively low for their diagnosed illness as well as for suicide attempt, and relatively high for IQ: they were more similar to the neurotypical group than to other patients. Differentially expressed genes (DEGs) associated with patients who died by suicide by violent means pointed to purinergic signaling in microglia, showing similarities to a genome-wide association study of Drosophila aggression. Weighted gene coexpression network analysis revealed that these DEGs were coexpressed in a context of mitochondrial metabolic activation unique to suicide by violent means. CONCLUSIONS These findings suggest that patients who die by suicide by violent means are in part biologically separable from other patients with the same diagnoses, and their behavioral outcome may be less dependent on genetic risk for conventional psychiatric disorders and be associated with an alteration of purinergic signaling and mitochondrial metabolism.
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Affiliation(s)
- Giovanna Punzi
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Eugenia Radulescu
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Louise A Huuki
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Pasquale Di Carlo
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Roberto Catanesi
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Trudy F C Mackay
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore (Punzi, Ursini, Chen, Radulescu, Tao, Huuki, Di Carlo, Collado-Torres, Shin, Jaffe, Hyde, Kleinman, Weinberger); Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore (Ursini, Hyde, Kleinman, Weinberger); Section of Forensic Psychiatry and Criminology, Institute of Legal Medicine, D.I.M., University of Bari "Aldo Moro," Bari, Italy (Catanesi); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Hyde, Weinberger); Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, Greenwood, S.C. (Mackay); Departments of Neuroscience and Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Weinberger)
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Iverson GL, Deep-Soboslay A, Hyde TM, Kleinman JE, Erskine B, Fisher-Hubbard A, deJong JL, Castellani RJ. Suicide in Older Adult Men Is Not Related to a Personal History of Participation in Football. Front Neurol 2021; 12:745824. [PMID: 34899570 PMCID: PMC8662809 DOI: 10.3389/fneur.2021.745824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction: It is reasonable to estimate that tens of millions of men in the United States played high school football. There is societal concern that participation in football confers risk for later-in-life mental health problems. The purpose of this study is to examine whether there is an association between a personal history of playing high school football and death by suicide. Methods: The subjects were obtained from the Lieber Institute for Brain Development (LIBD) brain donation program in collaboration with the Office of the Medical Examiner at Western Michigan University Homer Stryker MD School of Medicine. Donor history was documented via medical records, mental health records, and telephone interviews with the next-of-kin. Results: The sample included 198 men aged 50 or older (median = 65.0 years, interquartile range = 57-75). There were 34.8% who participated in contact sports during high school (including football), and 29.8% participated in high school football. Approximately one-third of the sample had suicide as their manner of death (34.8%). There was no statistically significant difference in the proportions of suicide as a manner of death among those men with a personal history of playing football compared to men who did not play football or who did not play sports (p = 0.070, Odds Ratio, OR = 0.537). Those who played football were significantly less likely to have a lifetime history of a suicide attempt (p = 0.012, OR = 0.352). Men with mood disorders (p < 0.001, OR = 10.712), substance use disorders (p < 0.020, OR = 2.075), and those with a history of suicide ideation (p < 0.001, OR = 8.038) or attempts (p < 0.001, OR = 40.634) were more likely to have suicide as a manner of death. Moreover, those men with a family history of suicide were more likely to have prior suicide attempts (p = 0.031, OR = 2.153) and to have completed suicide (p = 0.001, OR = 2.927). Discussion: Suicide was related to well-established risk factors such as a personal history of a mood disorder, substance abuse disorder, prior suicide ideation, suicide attempts, and a family history of suicide attempts. This study adds to a steadily growing body of evidence suggesting that playing high school football is not associated with increased risk for suicidality or suicide during adulthood.
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Affiliation(s)
- Grant L. Iverson
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Boston, MA, United States
- Spaulding Rehabilitation Hospital, Charlestown, MA, United States
- Spaulding Research Institute, Charlestown, MA, United States
- MassGeneral Hospital for Children Sports Concussion Program, Boston, MA, United States
- Home Base, A Red Sox Foundation and Massachusetts General Hospital Program, Charlestown, MA, United States
| | - Amy Deep-Soboslay
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Brittany Erskine
- Department of Pathology, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Amanda Fisher-Hubbard
- Department of Pathology, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Joyce L. deJong
- Department of Pathology, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Rudolph J. Castellani
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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40
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Takahashi Y, Maynard KR, Tippani M, Jaffe AE, Martinowich K, Kleinman JE, Weinberger DR, Hyde TM. Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain. Mol Psychiatry 2021; 26:3536-3547. [PMID: 33649454 DOI: 10.1038/s41380-021-01046-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/20/2021] [Accepted: 02/02/2021] [Indexed: 11/09/2022]
Abstract
Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with schizophrenia risk. Integration of RNA-sequencing data from postmortem human brains with these risk SNPs identified transcripts associated with increased schizophrenia susceptibility, including a class of exon 9-spliced isoforms of Sorting nexin-19 (SNX19d9) and an isoform of Arsenic methyltransferase (AS3MT) splicing out exons 2 and 3 (AS3MTd2d3). However, the biological function of these transcript variants is unclear. Defining the cell types where these risk transcripts are dominantly expressed is an important step to understand function, in prioritizing specific cell types and/or neural pathways in subsequent studies. To identify the cell type-specific localization of SNX19 and AS3MT in the human dorsolateral prefrontal cortex (DLPFC), we used single-molecule in situ hybridization techniques combined with automated quantification and machine learning approaches to analyze 10 postmortem brains of neurotypical individuals. These analyses revealed that both pan-SNX19 and pan-AS3MT were more highly expressed in neurons than non-neurons in layers II/III and VI of DLPFC. Furthermore, pan-SNX19 was preferentially expressed in glutamatergic neurons, while pan-AS3MT was preferentially expressed in GABAergic neurons. Finally, we utilized duplex BaseScope technology, to delineate the localization of SNX19d9 and AS3MTd2d3 splice variants, revealing consistent trends in spatial gene expression among pan-transcripts and schizophrenia risk-related transcript variants. These findings demonstrate that schizophrenia risk transcripts have distinct localization patterns in the healthy human brains, and suggest that SNX19 transcripts might disrupt the normal function of glutamatergic neurons, while AS3MT may lead to disturbances in the GABAergic system in the pathophysiology of schizophrenia.
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Affiliation(s)
- Yoichiro Takahashi
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Legal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA. .,Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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41
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Shu C, Sosnowski DW, Tao R, Deep-Soboslay A, Kleinman JE, Hyde TM, Jaffe AE, Sabunciyan S, Maher BS. Epigenome-wide study of brain DNA methylation following acute opioid intoxication. Drug Alcohol Depend 2021; 221:108658. [PMID: 33667780 PMCID: PMC8026744 DOI: 10.1016/j.drugalcdep.2021.108658] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/01/2021] [Accepted: 02/18/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Opioid abuse poses significant risk to individuals in the United States and epigenetic changes are a leading potential biomarker of opioid abuse. Current evidence, however, is mostly limited to candidate gene analysis in whole blood. To clarify the association between opioid abuse and DNA methylation, we conducted an epigenome-wide analysis of DNA methylation in brain samples of individuals who died from acute opioid intoxication and group-matched controls. METHODS Tissue samples were extracted from the dorsolateral prefrontal cortex of 153 deceased individuals (Mage = 35.42; 62 % male; 77 % European ancestry). The study included 72 opioid samples, 53 psychiatric controls, and 28 normal controls. The epigenome-wide analysis was implemented using the Illumina MethylationEPIC BeadChip; analyses adjusted for sociodemographic characteristics, negative control principal components, ancestry principal components, cellular composition, and surrogate variables. Horvath's epigenetic age and Levine's PhenoAge were calculated, and gene set enrichment analyses were performed. RESULTS Although no CpG sites survived false-discovery rate correction for multiple testing, 13 sites surpassed a relaxed significance threshold (p < 1.0 × 10-5). One of these sites was located within Netrin-1, a gene implicated in kappa opioid receptor activity. There was an association between opioid use and accelerated PhenoAge (b = 2.24, se = 1.11, p = .045). Gene set enrichment analyses revealed enrichment of differential methylation in GO and KEGG pathways broadly related to substance use. CONCLUSIONS Netrin-1 may be associated with opioid overdose, and future research with larger samples across stages of opioid use will elucidate the complex genomics of opioid abuse.
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Affiliation(s)
- Chang Shu
- Department of Pediatrics, Columbia University Irving Medical Center, United States; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, United States
| | - David W Sosnowski
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, United States.
| | - Ran Tao
- Lieber Institute for Brain Development, United States
| | | | - Joel E Kleinman
- Lieber Institute for Brain Development, United States; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, United States
| | - Thomas M Hyde
- Lieber Institute for Brain Development, United States
| | - Andrew E Jaffe
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, United States; Lieber Institute for Brain Development, United States
| | | | - Brion S Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, United States
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42
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Yeini E, Ofek P, Pozzi S, Albeck N, Ben-Shushan D, Tiram G, Golan S, Kleiner R, Sheinin R, Israeli Dangoor S, Reich-Zeliger S, Grossman R, Ram Z, Brem H, Hyde TM, Magod P, Friedmann-Morvinski D, Madi A, Satchi-Fainaro R. P-selectin axis plays a key role in microglia immunophenotype and glioblastoma progression. Nat Commun 2021; 12:1912. [PMID: 33771989 PMCID: PMC7997963 DOI: 10.1038/s41467-021-22186-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma (GB) is a highly invasive type of brain cancer exhibiting poor prognosis. As such, its microenvironment plays a crucial role in its progression. Among the brain stromal cells, the microglia were shown to facilitate GB invasion and immunosuppression. However, the reciprocal mechanisms by which GB cells alter microglia/macrophages behavior are not fully understood. We propose that these mechanisms involve adhesion molecules such as the Selectins family. These proteins are involved in immune modulation and cancer immunity. We show that P-selectin mediates microglia-enhanced GB proliferation and invasion by altering microglia/macrophages activation state. We demonstrate these findings by pharmacological and molecular inhibition of P-selectin which leads to reduced tumor growth and increased survival in GB mouse models. Our work sheds light on tumor-associated microglia/macrophage function and the mechanisms by which GB cells suppress the immune system and invade the brain, paving the way to exploit P-selectin as a target for GB therapy.
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Affiliation(s)
- Eilam Yeini
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paula Ofek
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sabina Pozzi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nitzan Albeck
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Dikla Ben-Shushan
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Galia Tiram
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sapir Golan
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Kleiner
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Sheinin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sahar Israeli Dangoor
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Rachel Grossman
- Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Zvi Ram
- Department of Neurosurgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Henry Brem
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Prerna Magod
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Sherman Building, Tel Aviv University, Tel Aviv, Israel
| | - Dinorah Friedmann-Morvinski
- Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Sherman Building, Tel Aviv University, Tel Aviv, Israel
| | - Asaf Madi
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Satchi-Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel.
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43
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Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams SR, Catallini JL, Tran MN, Besich Z, Tippani M, Chew J, Yin Y, Kleinman JE, Hyde TM, Rao N, Hicks SC, Martinowich K, Jaffe AE. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nat Neurosci 2021; 24:425-436. [PMID: 33558695 PMCID: PMC8095368 DOI: 10.1038/s41593-020-00787-0] [Citation(s) in RCA: 277] [Impact Index Per Article: 92.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022]
Abstract
We used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral prefrontal cortex. We identified extensive layer-enriched expression signatures and refined associations to previous laminar markers. We overlaid our laminar expression signatures on large-scale single nucleus RNA-sequencing data, enhancing spatial annotation of expression-driven clusters. By integrating neuropsychiatric disorder gene sets, we showed differential layer-enriched expression of genes associated with schizophrenia and autism spectrum disorder, highlighting the clinical relevance of spatially defined expression. We then developed a data-driven framework to define unsupervised clusters in spatial transcriptomics data, which can be applied to other tissues or brain regions in which morphological architecture is not as well defined as cortical laminae. Last, we created a web application for the scientific community to explore these raw and summarized data to augment ongoing neuroscience and spatial transcriptomics research ( http://research.libd.org/spatialLIBD ).
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Affiliation(s)
- Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Lukas M Weber
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Brianna K Barry
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Joseph L Catallini
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matthew N Tran
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zachary Besich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | | | | | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams SR, Catallini JL, Tran MN, Besich Z, Tippani M, Chew J, Yin Y, Kleinman JE, Hyde TM, Rao N, Hicks SC, Martinowich K, Jaffe AE. Publisher Correction: Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nat Neurosci 2021; 24:612. [PMID: 33603232 DOI: 10.1038/s41593-021-00817-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Lukas M Weber
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Brianna K Barry
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Joseph L Catallini
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matthew N Tran
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zachary Besich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | | | | | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA. .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA. .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. .,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA. .,Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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45
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Powers B, Joyce C, Kleinman JE, Hyde TM, Ajilore O, Leow A, Sodhi MS. Sex differences in the transcription of glutamate transporters in major depression and suicide. J Affect Disord 2020; 277:244-252. [PMID: 32836031 DOI: 10.1016/j.jad.2020.07.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 05/29/2020] [Accepted: 07/05/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Accumulating evidence indicates that the glutamate system contributes to the pathophysiology of major depressive disorder (MDD) and suicide. We previously reported higher mRNA expression of glutamate receptors in the dorsolateral prefrontal cortex (DLPFC) of females with MDD. METHODS In the current study, we measured the expression of mRNAs encoding glutamate transporters in the DLPFC of MDD subjects who died by suicide (MDD-S, n = 51), MDD non-suicide subjects (MDD-NS, n = 28), and individuals who did not have a history of neurological illness (CTRL, n = 32). RESULTS Females but not males with MDD showed higher expression of EAATs and VGLUTs relative to CTRLs. VGLUT expression was significantly higher in the female MDD-S group, relative to the other groups. EAAT expression was lower in the male violent suicides. LIMITATIONS This study has limitations common to most human studies, including medication history and demographic differences between the diagnostic groups. We mitigated the effects of confounders by including them as covariates in our analyses. CONCLUSIONS We report sex differences in the expression of glutamate transporter genes in the DLPFC in MDD. Increased neuronal glutamate transporter expression may increase synaptic glutamate, leading to neuronal and glial loss in the DLPFC in MDD. These deficits may lower DLPFC activity, impair problem solving and impair executive function in depression, perhaps increasing vulnerability to suicidal behavior. These data add to accumulating support for the hypothesis that glutamatergic transmission is dysregulated in MDD and suicide. Glutamate transporters may be novel targets for the development of rapidly acting antidepressant therapies.
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Affiliation(s)
- Brian Powers
- Department of Molecular Pharmacology & Neuroscience, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, United States
| | - Cara Joyce
- Biostatistics Collaborative Core, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Joel E Kleinman
- Lieber Institute for Brain Development and Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Thomas M Hyde
- Lieber Institute for Brain Development and Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Johns Hopkins University School of Medicine, Department of Neurology, Baltimore, MD, United States
| | - Olusola Ajilore
- Dept. Psychiatry, University of Illinois at Chicago, Chicago, IL, United States
| | - Alex Leow
- Dept. Psychiatry, University of Illinois at Chicago, Chicago, IL, United States
| | - Monsheel S Sodhi
- Department of Molecular Pharmacology & Neuroscience, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, United States; Dept. Psychiatry, University of Illinois at Chicago, Chicago, IL, United States.
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46
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Spurney CF, Ohuoha DC, Murray AM, Kleinman JE, Hyde TM. The Subnuclear Distribution of 5-HT1A Receptors in the Human Nucleus of the Solitary Tract and Selected Structures of the Caudal Medulla. Mcgill J Med 2020. [DOI: 10.26443/mjm.v3i2.547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The distribution of 5-HT1A receptors in the subnuclei of the human caudal nucleus of solitary tract and adjacent structures in the dorsal vagal complex was studied using [3H]8-OH-DPAT, a highly selective 5-HT1A receptor agonist. The highest binding of the labeled ligand was found in the dorsal motor nucleus of the vagus, followed by the medial, intermediate, and subpostremal subnuclei of the nucleus of solitary tract. Previous animal studies suggest an important role for these structures in the regulation of visceral function, particularly for the gastrointestinal and cardiovascular systems. The results of this study suggest the possibility of an analogous role for 5-HT1A receptors in the regulation of these autonomic pathways in humans as well.
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47
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Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Huestis M, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE, Jaffe AE. Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome. Mol Psychiatry 2020; 25:3267-3277. [PMID: 30131587 PMCID: PMC6438764 DOI: 10.1038/s41380-018-0223-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 01/05/2023]
Abstract
Cigarette smoking during pregnancy is a major public health concern. While there are well-described consequences in early child development, there is very little known about the effects of maternal smoking on human cortical biology during prenatal life. We therefore performed a genome-wide differential gene expression analysis using RNA sequencing (RNA-seq) on prenatal (N = 33; 16 smoking-exposed) as well as adult (N = 207; 57 active smokers) human postmortem prefrontal cortices. Smoking exposure during the prenatal period was directly associated with differential expression of 14 genes; in contrast, during adulthood, despite a much larger sample size, only two genes showed significant differential expression (FDR < 10%). Moreover, 1,315 genes showed significantly different exposure effects between maternal smoking during pregnancy and direct exposure in adulthood (FDR < 10%)-these differences were largely driven by prenatal differences that were enriched for pathways previously implicated in addiction and synaptic function. Furthermore, prenatal and age-dependent differentially expressed genes were enriched for genes implicated in non-syndromic autism spectrum disorder (ASD) and were differentially expressed as a set between patients with ASD and controls in postmortem cortical regions. These results underscore the enhanced sensitivity to the biological effect of smoking exposure in the developing brain and offer insight into how maternal smoking during pregnancy affects gene expression in the prenatal human cortex. They also begin to address the relationship between in utero exposure to smoking and the heightened risks for the subsequent development of neuropsychiatric disorders.
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Affiliation(s)
- Stephen A. Semick
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Center for Computational Biology, Johns Hopkins University,
Baltimore, MD, 21205, USA
| | - Christina A. Markunas
- Behavioral and Urban Health Program, Behavioral Health and
Criminal Justice Division, RTI International, Research Triangle Park, NC, 27709,
USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA
| | - Amy Deep-Soboslay
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA
| | - Marilyn Huestis
- The Lambert Center for the Study of Medicinal Cannabis and
Hemp, Institute of Emerging Health Professions, Thomas Jefferson University,
Philadelphia, PA, USA
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of
Medicine, St. Louis, MO 63110, USA
| | - Brion S. Maher
- Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD, 21205, USA
| | - Eric O. Johnson
- Fellow Program and Behavioral Health and Criminal Justice
Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Department of Psychiatry and Behavioral Sciences, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA,Department of Neurology, Johns Hopkins School of Medicine,
Baltimore, MD, 21205, USA
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Department of Psychiatry and Behavioral Sciences, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA,Department of Neurology, Johns Hopkins School of Medicine,
Baltimore, MD, 21205, USA,Department of Neuroscience, Johns Hopkins School of
Medicine, Baltimore, MD, 21205, USA,McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Dana B. Hancock
- Behavioral and Urban Health Program, Behavioral Health and
Criminal Justice Division, RTI International, Research Triangle Park, NC, 27709,
USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Department of Psychiatry and Behavioral Sciences, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA,Contact: Lieber Institute for Brain Development,
855 N Wolfe St, Ste 300. Baltimore MD 21205. Ph: 1-410-955-1000
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Johns Hopkins
Medical Campus, Baltimore, MD, 21205, USA,Center for Computational Biology, Johns Hopkins University,
Baltimore, MD, 21205, USA,Department of Mental Health, Johns Hopkins Bloomberg School
of Public Health, Baltimore, MD, 21205, USA,McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins School of Medicine, Baltimore, MD 21205, USA,Department of Biostatistics, Johns Hopkins Bloomberg
School of Public Health, Baltimore, MD, 21205, USA,Contact: Lieber Institute for Brain Development, 855
N Wolfe St, Ste 300. Baltimore MD 21205. Ph: 1-410-955-1000
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48
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Zink CF, Barker PB, Sawa A, Weinberger DR, Wang M, Quillian H, Ulrich WS, Chen Q, Jaffe AE, Kleinman JE, Hyde TM, Prettyman GE, Giegerich M, Carta K, van Ginkel M, Bigos KL. Association of Missense Mutation in FOLH1 With Decreased NAAG Levels and Impaired Working Memory Circuitry and Cognition. Am J Psychiatry 2020; 177:1129-1139. [PMID: 33256444 DOI: 10.1176/appi.ajp.2020.19111152] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Altering the metabotropic glutamate receptor 3 (mGluR3) by pharmacology or genetics is associated with differences in learning and memory in animals and humans. GRM3 (the gene coding for mGluR3) is also genome-wide associated with risk for schizophrenia. The neurotransmitter N-acetyl-aspartyl-glutamate (NAAG) is the selective endogenous agonist of mGluR3, and increasing NAAG may improve cognition. Glutamate carboxypeptidase II (GCPII), coded by the gene folate hydrolase 1 (FOLH1), regulates the amount of NAAG in the synapse. The goal of this study was to determine the relationship between FOLH1, NAAG levels, measures of human cognition, and neural activity associated with cognition. METHODS The effects of genetic variation in FOLH1 on mRNA expression in human brain and NAAG levels using 7-T magnetic resonance spectroscopy (MRS) were measured. NAAG levels and FOLH1 genetic variation were correlated with measures of cognition in subjects with psychosis and unaffected subjects. Additionally, FOLH1 genetic variation was correlated with neural activity during working memory, as measured by functional MRI (fMRI). RESULTS A missense mutation in FOLH1 (rs202676 G allele) was associated with increased FOLH1 mRNA in the dorsolateral prefrontal cortex of brains from unaffected subjects and schizophrenia patients. This FOLH1 variant was associated with decreased NAAG levels in unaffected subjects and patients with psychosis. NAAG levels were positively correlated with visual memory performance. Carriers of the FOLH1 variant associated with lower NAAG levels had lower IQ scores. Carriers of this FOLH1 variant had less efficient cortical activity during working memory. CONCLUSIONS These data show that higher NAAG levels are associated with better cognition, suggesting that increasing NAAG levels through FOLH1/GCPII inhibition may improve cognition. Additionally, NAAG levels measured by MRS and cortical efficiency during working memory measured by fMRI have the potential to be neuroimaging biomarkers for future clinical trials.
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Affiliation(s)
- Caroline F Zink
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Peter B Barker
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Akira Sawa
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Daniel R Weinberger
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Min Wang
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Henry Quillian
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - William S Ulrich
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Qiang Chen
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Andrew E Jaffe
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Joel E Kleinman
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Thomas M Hyde
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Greer E Prettyman
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Mellissa Giegerich
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Kayla Carta
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Marcus van Ginkel
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
| | - Kristin L Bigos
- Baltimore Research and Education Foundation, Baltimore (Zink); Lieber Institute for Brain Development, Baltimore (Zink, Weinberger, Quillian, Ulrich, Chen, Jaffe, Kleinman, Hyde, Prettyman, Giegerich, Carta, van Ginkel, Bigos); Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore (Zink, Sawa, Weinberger, Jaffe, Kleinman, Hyde, Bigos); Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore (Barker, Wang); Department of Oncology, Johns Hopkins School of Medicine, Baltimore (Barker); Kennedy Krieger Institute, Baltimore (Barker); Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore (Sawa, Jaffe); Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger); McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (Sawa, Weinberger, Jaffe); Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore (Sawa); Department of Neurology, Johns Hopkins School of Medicine, Baltimore (Weinberger, Hyde); Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore (Jaffe); Center for Computational Biology, Johns Hopkins University, Baltimore (Jaffe); Department of Neuroscience, University of Pennsylvania, Philadelphia (Prettyman); Eating Disorders Center for Treatment and Research, University of California San Diego (Giegerich); Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore (Carta, van Ginkel, Bigos); and Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore (Bigos)
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49
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Perzel Mandell KA, Price AJ, Wilton R, Collado-Torres L, Tao R, Eagles NJ, Szalay AS, Hyde TM, Weinberger DR, Kleinman JE, Jaffe AE. Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex. Epigenetics 2020; 16:1-13. [PMID: 32602773 DOI: 10.1080/15592294.2020.1786304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
DNA methylation (DNAm) is a key epigenetic regulator of gene expression across development. The developing prenatal brain is a highly dynamic tissue, but our understanding of key drivers of epigenetic variability across development is limited. We, therefore, assessed genomic methylation at over 39 million sites in the prenatal cortex using whole-genome bisulfite sequencing and found loci and regions in which methylation levels are dynamic across development. We saw that DNAm at these loci was associated with nearby gene expression and enriched for enhancer chromatin states in prenatal brain tissue. Additionally, these loci were enriched for genes associated with neuropsychiatric disorders and genes involved with neurogenesis. We also found autosomal differences in DNAm between the sexes during prenatal development, though these have less clear functional consequences. We lastly confirmed that the dynamic methylation at this critical period is specifically CpG methylation, with generally low levels of CpH methylation. Our findings provide detailed insight into prenatal brain development as well as clues to the pathogenesis of psychiatric traits seen later in life.
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Affiliation(s)
- Kira A Perzel Mandell
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM) , Baltimore, MD, USA
| | - Amanda J Price
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM) , Baltimore, MD, USA
| | - Richard Wilton
- Department of Physics and Astronomy, Krieger School of Arts and Sciences, Johns Hopkins University , Baltimore, MD, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University , Baltimore, MD, USA
| | - Ran Tao
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA
| | - Nicholas J Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA
| | - Alexander S Szalay
- Department of Physics and Astronomy, Krieger School of Arts and Sciences, Johns Hopkins University , Baltimore, MD, USA.,Department of Computer Science, Whiting School of Engineering, Johns Hopkins University , Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Neurology, JHSOM , Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, JHSOM , Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM) , Baltimore, MD, USA.,Department of Neurology, JHSOM , Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, JHSOM , Baltimore, MD, USA.,Department of Neuroscience, JHSOM , Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, JHSOM , Baltimore, MD, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD, USA.,Department of Genetic Medicine, Johns Hopkins University School of Medicine (JHSOM) , Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University , Baltimore, MD, USA.,Department of Psychiatry and Behavioral Sciences, JHSOM , Baltimore, MD, USA.,Department of Neuroscience, JHSOM , Baltimore, MD, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health (JHBSPH) , Baltimore, MD, USA.,Department of Biostatistics, JHBSPH , Baltimore, MD, USA
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50
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Sawada T, Benjamin KJM, Brandtjen AC, Tietze E, Allen SJ, Paquola ACM, Kleinman JE, Hyde TM, Erwin JA. Generation of four postmortem dura-derived iPS cell lines from four control individuals with genotypic and brain-region-specific transcriptomic data available through the BrainSEQ consortium. Stem Cell Res 2020; 46:101806. [PMID: 32446240 PMCID: PMC10515715 DOI: 10.1016/j.scr.2020.101806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 11/24/2022] Open
Abstract
In this study, we established induced pluripotent stem (iPS) cell lines from postmortem dura-derived fibroblasts of four control individuals with low polygenic risk score for psychiatric disorders including schizophrenia and bipolar disorder. The fibroblasts were reprogrammed into iPS cells using episomal vectors carrying OCT3/4, SOX2, KLF4, L-Myc, LIN28 and shRNA-p53. All iPS cell lines showed the same genotype with parental postmortem brain tissues, expressed pluripotency markers, and exhibited the differentiation potency into three embryonic germ layers.
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Affiliation(s)
- Tomoyo Sawada
- Lieber Institute for Brain Development, Baltimore, Maryland, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
| | - Kynon J M Benjamin
- Lieber Institute for Brain Development, Baltimore, Maryland, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Anna C Brandtjen
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Ethan Tietze
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Samuel J Allen
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Apuã C M Paquola
- Lieber Institute for Brain Development, Baltimore, Maryland, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, Maryland, USA; Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, Maryland, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jennifer A Erwin
- Lieber Institute for Brain Development, Baltimore, Maryland, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
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