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Chen KG, Farley KO, Lassmann T. Mining single-cell data for cell type-disease associations. NAR Genom Bioinform 2024; 6:lqae180. [PMID: 39703426 PMCID: PMC11655289 DOI: 10.1093/nargab/lqae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 11/26/2024] [Accepted: 12/04/2024] [Indexed: 12/21/2024] Open
Abstract
A robust understanding of the cellular mechanisms underlying diseases sets the foundation for the effective design of drugs and other interventions. The wealth of existing single-cell atlases offers the opportunity to uncover high-resolution information on expression patterns across various cell types and time points. To better understand the associations between cell types and diseases, we leveraged previously developed tools to construct a standardized analysis pipeline and systematically explored associations across four single-cell datasets, spanning a range of tissue types, cell types and developmental time periods. We utilized a set of existing tools to identify co-expression modules and temporal patterns per cell type and then investigated these modules for known disease and phenotype enrichments. Our pipeline reveals known and novel putative cell type-disease associations across all investigated datasets. In addition, we found that automatically discovered gene co-expression modules and temporal clusters are enriched for drug targets, suggesting that our analysis could be used to identify novel therapeutic targets.
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Affiliation(s)
- Kevin G Chen
- Precision Health, The Kids Research Institute Australia, 15 Hospital Ave, Nedlands, 6009, WA, Australia
| | - Kathryn O Farley
- Precision Health, The Kids Research Institute Australia, 15 Hospital Ave, Nedlands, 6009, WA, Australia
| | - Timo Lassmann
- Precision Health, The Kids Research Institute Australia, 15 Hospital Ave, Nedlands, 6009, WA, Australia
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2
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Sighencea MG, Popescu RȘ, Trifu SC. From Fundamentals to Innovation in Alzheimer's Disease: Molecular Findings and Revolutionary Therapies. Int J Mol Sci 2024; 25:12311. [PMID: 39596378 PMCID: PMC11594972 DOI: 10.3390/ijms252212311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 11/11/2024] [Accepted: 11/14/2024] [Indexed: 11/28/2024] Open
Abstract
Alzheimer's disease (AD) is a global health concern and the leading cause of dementia in the elderly. The prevalence of this neurodegenerative condition is projected to increase concomitantly with increased life expectancy, resulting in a significant economic burden. With very few FDA-approved disease-modifying drugs available for AD, there is an urgent need to develop new compounds capable of impeding the progression of the disease. Given the unclear etiopathogenesis of AD, this review emphasizes the underlying mechanisms of this condition. It explores not only well-studied aspects, such as the accumulation of Aβ plaques and neurofibrillary tangles, but also novel areas, including glymphatic and lymphatic pathways, microbiota and the gut-brain axis, serotoninergic and autophagy alterations, vascular dysfunction, the metal hypothesis, the olfactory pathway, and oral health. Furthermore, the potential molecular targets arising from all these mechanisms have been reviewed, along with novel promising approaches such as nanoparticle-based therapy, neural stem cell transplantation, vaccines, and CRISPR-Cas9-mediated genome editing techniques. Taking into account the overlap of these various mechanisms, individual and combination therapies emerge as the future direction in the AD strategy.
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Affiliation(s)
| | - Ramona Ștefania Popescu
- Department of Infectious Diseases, “Carol Davila” University of Medicine and Pharmacy Bucharest, 020021 Bucharest, Romania;
| | - Simona Corina Trifu
- Department of Psychiatry, “Carol Davila” University of Medicine and Pharmacy Bucharest, 020021 Bucharest, Romania
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3
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Lin H, Su L, Mao D, Yang G, Huang Q, Lan Y, Zeng J, Song W, Liang G, Wei Q, Zou D, Li R, Zou C. Identification of altered immune cell types and molecular mechanisms in Alzheimer's disease progression by single-cell RNA sequencing. Front Aging Neurosci 2024; 16:1477327. [PMID: 39610716 PMCID: PMC11602448 DOI: 10.3389/fnagi.2024.1477327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 10/24/2024] [Indexed: 11/30/2024] Open
Abstract
Introduction Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by gradual loss of cognitive function. Understanding the molecular mechanisms is crucial for developing effective therapies. Methods Data from single-cell RNA sequencing (scRNA-seq) in the GSE181279 dataset and gene chips in the GSE63060 and GSE63061 datasets were collected and analyzed to identify immune cell types and differentially expressed genes. Cell communication, pseudotime trajectory, enrichment analysis, co- expression network, and short time-series expression miner were analyzed to identify disease-specific molecular and cellular mechanisms. Results We identified eight cell types (B cells, monocytes, natural killer cells, gamma-delta T cells, CD8+ T cells, Tem/Temra cytotoxic T cells, Tem/Trm cytotoxic T cells, and mucosal-associated invariant T cells) using scRNA-seq. AD samples were enriched in monocytes, CD8+ T cells, Tem/Temra cytotoxic T cells, and Tem/Trm cytotoxic T cells, whereas samples from healthy controls were enriched in natural killer and mucosal-associated invariant T cells. Five co-expression modules that were identified through weighted gene correlation network analysis were enriched in immune- inflammatory pathways. Candidate genes with higher area under the receiver operating characteristic curve values were screened, and the expression trend of Ubiquitin-Fold Modifier Conjugating Enzyme 1 (UFC1) gradually decreased from healthy controls to mild cognitive impairment and then to AD. Conclusion Our study suggests that peripheral immune cells may be a potential therapeutic target for AD. Candidate genes, particularly UFC1, may serve as potential biomarkers for progression of AD.
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Affiliation(s)
- Hua Lin
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li Su
- Department of Neurology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Daniel Mao
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Grace Yang
- State College Area High School, State College, PA, United States
| | - Qi Huang
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yating Lan
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jingyi Zeng
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wenyi Song
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Guining Liang
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qingyan Wei
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Donghua Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Rongjie Li
- Department of Geriatrics, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chanhua Zou
- Department of Comprehensive Internal Medicine, Guangxi Medical University Caner Hospital, Nanning, China
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4
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Jiang W, Vogelgsang J, Dan S, Durning P, McCoy TH, Berretta S, Klengel T. Association of RDoC dimensions with post-mortem brain transcriptional profiles in Alzheimer's Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.10.07.24315057. [PMID: 39417104 PMCID: PMC11482973 DOI: 10.1101/2024.10.07.24315057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
INTRODUCTION Neuropsychiatric symptoms are common in people with Alzheimer's disease (AD) across all severity stages. Their heterogeneous presentation and variable temporal association with cognitive decline suggest shared and distinct biological mechanisms. We hypothesized that specific patterns of gene expression associate with distinct NIMH Research Domain Criteria (RDoC) domains in AD. METHODS Post-mortem bulk RNAseq on the insula and anterior cingulate cortex from 60 brain donors representing the spectrum of canonical AD neuropathology combined with natural language processing approaches based on the RDoC Clinical Domains. RESULTS Distinct sets of >100 genes (p FDR <0.05) were specifically associated with at least one clinical domain (Cognitive, Social, Negative, Positive, Arousal). In addition, dysregulation of immune response pathways was shared across domains and brain regions. DISCUSSION Our findings provide evidence for distinct transcriptional profiles associated with RDoC domains suggesting that each dimension is characterized by specific sets of genes providing insight into the underlying mechanisms.
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5
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Xie L, Wu Q, Li K, Khan MAS, Zhang A, Sinha B, Li S, Chang SL, Brody DL, Grinstaff MW, Zhou S, Alterovitz G, Liu P, Wang X. Tryptophan Metabolism in Alzheimer's Disease with the Involvement of Microglia and Astrocyte Crosstalk and Gut-Brain Axis. Aging Dis 2024; 15:2168-2190. [PMID: 38916729 PMCID: PMC11346405 DOI: 10.14336/ad.2024.0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/03/2024] [Indexed: 06/26/2024] Open
Abstract
Alzheimer's disease (AD) is an age-dependent neurodegenerative disease characterized by extracellular Amyloid Aβ peptide (Aβ) deposition and intracellular Tau protein aggregation. Glia, especially microglia and astrocytes are core participants during the progression of AD and these cells are the mediators of Aβ clearance and degradation. The microbiota-gut-brain axis (MGBA) is a complex interactive network between the gut and brain involved in neurodegeneration. MGBA affects the function of glia in the central nervous system (CNS), and microbial metabolites regulate the communication between astrocytes and microglia; however, whether such communication is part of AD pathophysiology remains unknown. One of the potential links in bilateral gut-brain communication is tryptophan (Trp) metabolism. The microbiota-originated Trp and its metabolites enter the CNS to control microglial activation, and the activated microglia subsequently affect astrocyte functions. The present review highlights the role of MGBA in AD pathology, especially the roles of Trp per se and its metabolism as a part of the gut microbiota and brain communications. We (i) discuss the roles of Trp derivatives in microglia-astrocyte crosstalk from a bioinformatics perspective, (ii) describe the role of glia polarization in the microglia-astrocyte crosstalk and AD pathology, and (iii) summarize the potential of Trp metabolism as a therapeutic target. Finally, we review the role of Trp in AD from the perspective of the gut-brain axis and microglia, as well as astrocyte crosstalk, to inspire the discovery of novel AD therapeutics.
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Affiliation(s)
- Lushuang Xie
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
- Acupuncture and Moxibustion College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610075, China.
| | - Qiaofeng Wu
- Acupuncture and Moxibustion College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610075, China.
| | - Kelin Li
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Mohammed A. S. Khan
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Andrew Zhang
- Biomedical Cybernetics Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Bharati Sinha
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Sihui Li
- Acupuncture and Moxibustion College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 610075, China.
| | - Sulie L. Chang
- Department of Biological Sciences, Institute of NeuroImmune Pharmacology, Seton Hall University, South Orange, NJ 07079, USA.
| | - David L. Brody
- Department of Neurology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| | | | - Shuanhu Zhou
- Harvard Medical School, Harvard Stem Cell Institute, Boston, MA 02115, USA.
| | - Gil Alterovitz
- Biomedical Cybernetics Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
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6
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Vilkaite G, Vogel J, Mattsson-Carlgren N. Integrating amyloid and tau imaging with proteomics and genomics in Alzheimer's disease. Cell Rep Med 2024; 5:101735. [PMID: 39293391 PMCID: PMC11525023 DOI: 10.1016/j.xcrm.2024.101735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/28/2024] [Accepted: 08/20/2024] [Indexed: 09/20/2024]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease and is characterized by the aggregation of β-amyloid (Aβ) and tau in the brain. Breakthroughs in disease-modifying treatments targeting Aβ bring new hope for the management of AD. But to effectively modify and someday even prevent AD, a better understanding is needed of the biological mechanisms that underlie and link Aβ and tau in AD. Developments of high-throughput omics, including genomics, proteomics, and transcriptomics, together with molecular imaging of Aβ and tau with positron emission tomography (PET), allow us to discover and understand the biological pathways that regulate the aggregation and spread of Aβ and tau in living humans. The field of integrated omics and PET studies of Aβ and tau in AD is growing rapidly. We here provide an update of this field, both in terms of biological insights and in terms of future clinical implications of integrated omics-molecular imaging studies.
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Affiliation(s)
- Gabriele Vilkaite
- Department of Clinical Sciences Malmö, SciLifeLab, Lund University, Lund, Sweden
| | - Jacob Vogel
- Department of Clinical Sciences Malmö, SciLifeLab, Lund University, Lund, Sweden
| | - Niklas Mattsson-Carlgren
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden; Department of Neurology, Skåne University Hospital, Lund University, Lund, Sweden; Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden.
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7
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Lu M, Li J, Huang Q, Mao D, Yang G, Lan Y, Zeng J, Pan M, Shi S, Zou D. Single-Nucleus Landscape of Glial Cells and Neurons in Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04428-6. [PMID: 39153159 DOI: 10.1007/s12035-024-04428-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease with a projected significant increase in incidence. Therefore, this study analyzed single-nucleus AD data to provide a theoretical basis for the clinical development and treatment of AD. We downloaded AD-related monocyte data from the Gene Expression Omnibus database, annotated cells, compared cell abundance between groups, and investigated glial and neuronal cell biological processes and pathways through functional enrichment analysis. Furthermore, we constructed a global regulatory network for AD based on cell communication and ecological analyses. Our findings revealed increased abundance of Capping Protein Regulator And Myosin 1 linker 1 (CARMIL1)+ astrocytes (AST), Immunoglobulin Superfamily Member 21 (IGSF21)+ microglia (MIC), SRY-Box Transcription Factor 6 (SOX6)+ inhibitory neurons (InNeu), and laminin alpha-2 chain (LAMA2)+ oligodendrocytes (OLI) cell subgroups in tissues of patients with AD, while prostaglandin D2 synthase (PTGDS)+ AST, Src Family Tyrosine Kinase (FYN)+ MIC, and Proteolipid Protein 1 (PLP1)+ InNeu subgroups specifically decreased. We found that the cell phenotype of patients with AD shifted from a simpler to a more complex state compared to the control group. Cell communication analysis revealed strong communication between MIC and NEU. Furthermore, AST, MIC, NEU, and OLI were involved in oxidative stress- and inflammation-related pathways, potentially contributing to disease development. This study provides a theoretical basis for further exploring the specific mechanisms underlying AD.
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Affiliation(s)
- Mengru Lu
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, No 166 Daxuedong Road, Nanning, Guangxi, 530007, China
| | - Jiaxin Li
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Qi Huang
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, No 166 Daxuedong Road, Nanning, Guangxi, 530007, China
| | - Daniel Mao
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Grace Yang
- State College Area High School, State College, PA, 16801, USA
| | - Yating Lan
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, No 166 Daxuedong Road, Nanning, Guangxi, 530007, China
| | - Jingyi Zeng
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, No 166 Daxuedong Road, Nanning, Guangxi, 530007, China
| | - Mika Pan
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, No 166 Daxuedong Road, Nanning, Guangxi, 530007, China
| | - Shengliang Shi
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, No 166 Daxuedong Road, Nanning, Guangxi, 530007, China.
| | - Donghua Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, No 166 Daxuedong Road, Nanning, Guangxi, 530007, China.
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8
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McInvale JJ, Canoll P, Hargus G. Induced pluripotent stem cell models as a tool to investigate and test fluid biomarkers in Alzheimer's disease and frontotemporal dementia. Brain Pathol 2024; 34:e13231. [PMID: 38246596 PMCID: PMC11189780 DOI: 10.1111/bpa.13231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/29/2023] [Indexed: 01/23/2024] Open
Abstract
Neurodegenerative diseases are increasing in prevalence and comprise a large socioeconomic burden on patients and their caretakers. The need for effective therapies and avenues for disease prevention and monitoring is of paramount importance. Fluid biomarkers for neurodegenerative diseases have gained a variety of uses, including informing participant selection for clinical trials, lending confidence to clinical diagnosis and disease staging, determining prognosis, and monitoring therapeutic response. Their role is expected to grow as disease-modifying therapies start to be available to a broader range of patients and as prevention strategies become established. Many of the underlying molecular mechanisms of currently used biomarkers are incompletely understood. Animal models and in vitro systems using cell lines have been extensively employed but face important translatability limitations. Induced pluripotent stem cell (iPSC) technology, where a theoretically unlimited range of cell types can be reprogrammed from peripheral cells sampled from patients or healthy individuals, has gained prominence over the last decade. It is a promising avenue to study physiological and pathological biomarker function and response to experimental therapeutics. Such systems are amenable to high-throughput drug screening or multiomics readouts such as transcriptomics, lipidomics, and proteomics for biomarker discovery, investigation, and validation. The present review describes the current state of biomarkers in the clinical context of neurodegenerative diseases, with a focus on Alzheimer's disease and frontotemporal dementia. We include a discussion of how iPSC models have been used to investigate and test biomarkers such as amyloid-β, phosphorylated tau, neurofilament light chain or complement proteins, and even nominate novel biomarkers. We discuss the limitations of current iPSC methods, mentioning alternatives such as coculture systems and three-dimensional organoids which address some of these concerns. Finally, we propose exciting prospects for stem cell transplantation paradigms using animal models as a preclinical tool to study biomarkers in the in vivo context.
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Affiliation(s)
- Julie J. McInvale
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNew YorkUSA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia UniversityNew YorkNew YorkUSA
- Medical Scientist Training Program, Columbia UniversityNew YorkNew YorkUSA
| | - Peter Canoll
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNew YorkUSA
| | - Gunnar Hargus
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNew YorkUSA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia UniversityNew YorkNew YorkUSA
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9
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Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. Science 2024; 384:eadi5199. [PMID: 38781369 PMCID: PMC11365579 DOI: 10.1126/science.adi5199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multiomics datasets into a resource comprising >2.8 million nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550,000 cell type-specific regulatory elements and >1.4 million single-cell expression quantitative trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
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Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Chicago, IL 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | | | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - 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
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, 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
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, 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
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
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10
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Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X, Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Single-cell genomics and regulatory networks for 388 human brains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585576. [PMID: 38562822 PMCID: PMC10983939 DOI: 10.1101/2024.03.18.585576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
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Affiliation(s)
- Prashant S Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jason J Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Declan Clarke
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Matthew Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Chirag Gupta
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Cagatay Dursun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yuhang Chen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zhiyuan Chu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
- Mathematical, Computational and Systems Biology, University of California, Irvine, CA, 92697, USA
| | - Yunyang Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Xiao Zhou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lucy Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Tanima Chatterjee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Opthalmology, Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi Dai
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Ziheng Duan
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | | | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Gancz
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Diego Garrido-Martín
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Sophia Gaynor-Gillett
- Tempus Labs, Inc., Chicago, IL, 60654, USA
- Department of Biology, Cornell College, Mount Vernon, IA, 52314, USA
| | - Jennifer Grundman
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Natalie Hawken
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Ella Henry
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Ao Huang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Ting Jin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, CA, 90095, USA
| | - Saniya Khullar
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jianyin Liu
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Junhao Liu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Shuang Liu
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Michael Margolis
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Samantha Mazariegos
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | | | - Eric Nguyen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Milos Pjanic
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Henry Pratt
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Diana Quintero
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | | | - Tiernon R Riesenmy
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Manman Shi
- Tempus Labs, Inc., Chicago, IL, 60654, USA
| | | | - Rosemarie Terwilliger
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
| | | | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Gaoyuan Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Yan Xia
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Shaohua Xiao
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Andrew C Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Suchen Zheng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - 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
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University, New Haven, CT, 06510, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Kevin P White
- Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Matthew J Girgenti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06520, USA
- Wu Tsai Institute, Yale University, New Haven, CT, 06520, USA
- Clinical Neuroscience Division, National Center for Posttraumatic Stress Disorder, Veterans Affairs Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, 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
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA
- Department of Statistics & Data Science, Yale University, New Haven, CT, 06520, USA
- Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT, 06520, USA
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11
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Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove R, Glymour M, Aghaeepour N, Oskotsky TT, Miller Z, Allen IE, Sanders SJ, Baranzini S, Sirota M. Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights. NATURE AGING 2024; 4:379-395. [PMID: 38383858 PMCID: PMC10950787 DOI: 10.1038/s43587-024-00573-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
Identification of Alzheimer's disease (AD) onset risk can facilitate interventions before irreversible disease progression. We demonstrate that electronic health records from the University of California, San Francisco, followed by knowledge networks (for example, SPOKE) allow for (1) prediction of AD onset and (2) prioritization of biological hypotheses, and (3) contextualization of sex dimorphism. We trained random forest models and predicted AD onset on a cohort of 749 individuals with AD and 250,545 controls with a mean area under the receiver operating characteristic of 0.72 (7 years prior) to 0.81 (1 day prior). We further harnessed matched cohort models to identify conditions with predictive power before AD onset. Knowledge networks highlight shared genes between multiple top predictors and AD (for example, APOE, ACTB, IL6 and INS). Genetic colocalization analysis supports AD association with hyperlipidemia at the APOE locus, as well as a stronger female AD association with osteoporosis at a locus near MS4A6A. We therefore show how clinical data can be utilized for early AD prediction and identification of personalized biological hypotheses.
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Affiliation(s)
- Alice S Tang
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, San Francisco and Berkeley, CA, USA.
| | - Katherine P Rankin
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriel Cerono
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Silvia Miramontes
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Hunter Mills
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jacquelyn Roger
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Billy Zeng
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Charlotte Nelson
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Karthik Soman
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah Woldemariam
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Yaqiao Li
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Albert Lee
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Riley Bove
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Maria Glymour
- Department of Anesthesiology, Pain, and Perioperative Medicine, Stanford University, Palo Alto, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Pain, and Perioperative Medicine, Stanford University, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University, Palo Alto, CA, USA
- Department of Biomedical Data Science, Stanford University, Palo Alto, CA, USA
| | - Tomiko T Oskotsky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Zachary Miller
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Isabel E Allen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Stephan J Sanders
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Sergio Baranzini
- Weill Institute for Neuroscience. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Pediatrics, University of California, San Francisco, CA, USA.
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12
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Zhang X, Qazi AA, Deshmukh S, Lobato Ventura R, Mukim A, Beliakova-Bethell N. Single-cell RNA sequencing reveals common and unique gene expression profiles in primary CD4+ T cells latently infected with HIV under different conditions. Front Cell Infect Microbiol 2023; 13:1286168. [PMID: 38156317 PMCID: PMC10754520 DOI: 10.3389/fcimb.2023.1286168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Background The latent HIV reservoir represents the major barrier to a cure. One curative strategy is targeting diseased cells for elimination based on biomarkers that uniquely define these cells. Single-cell RNA sequencing (scRNA-seq) has enabled the identification of gene expression profiles associated with disease at the single-cell level. Because HIV provirus in many cells during latency is not entirely silent, it became possible to determine gene expression patterns in a subset of cells latently infected with HIV. Objective The primary objective of this study was the identification of the gene expression profiles of single latently infected CD4+ T cells using scRNA-seq. Different conditions of latency establishment were considered. The identified profiles were then explored to prioritize the identified genes for future experimental validation. Methods To facilitate gene prioritization, three approaches were used. First, we characterized and compared the gene expression profiles of HIV latency established in different environments: in cells that encountered an activation stimulus and then returned to quiescence, and in resting cells that were infected directly via cell-to-cell viral transmission from autologous activated, productively infected cells. Second, we characterized and compared the gene expression profiles of HIV latency established with viruses of different tropisms, using an isogenic pair of CXCR4- and CCR5-tropic viruses. Lastly, we used proviral expression patterns in cells from people with HIV to more accurately define the latently infected cells in vitro. Results Our analyses demonstrated that a subset of genes is expressed differentially between latently infected and uninfected cells consistently under most conditions tested, including cells from people with HIV. Our second important observation was the presence of latency signatures, associated with variable conditions when latency was established, including cellular exposure and responsiveness to a T cell receptor stimulus and the tropism of the infecting virus. Conclusion Common signatures, specifically genes that encode proteins localized to the cell surface, should be prioritized for further testing at the protein level as biomarkers for the ability to enrich or target latently infected cells. Cell- and tropism-dependent biomarkers may need to be considered in developing targeting strategies to ensure that all the different reservoir subsets are eliminated.
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Affiliation(s)
- Xinlian Zhang
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, CA, United States
| | - Andrew A. Qazi
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Savitha Deshmukh
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Roni Lobato Ventura
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Amey Mukim
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
| | - Nadejda Beliakova-Bethell
- Veterans Affairs (VA), San Diego Healthcare System and Veterans Medical Research Foundation, San Diego, CA, United States
- Department of Medicine, University of California, San Diego, CA, United States
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13
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Guido G, Mangano K, Tancheva L, Kalfin R, Leone GM, Saraceno A, Fagone P, Nicoletti F, Petralia MC. Evaluation of Cell-Specific Alterations in Alzheimer's Disease and Relevance of In Vitro Models. Genes (Basel) 2023; 14:2187. [PMID: 38137009 PMCID: PMC10743149 DOI: 10.3390/genes14122187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder classically characterized by two neuropathological hallmarks: β-amyloid plaques and tau tangles in the brain. However, the cellular and molecular mechanisms involved in AD are still elusive, which dampens the possibility of finding new and more effective therapeutic interventions. Current in vitro models are limited in modelling the complexity of AD pathogenesis. In this study, we aimed to characterize the AD expression signature upon a meta-analysis of multiple human datasets, including different cell populations from various brain regions, and compare cell-specific alterations in AD patients and in vitro models to highlight the appropriateness and the limitations of the currently available models in recapitulating AD pathology. The meta-analysis showed consistent enrichment of the Rho GTPases signaling pathway among different cell populations and in the models. The accuracy of in vitro models was higher for neurons and lowest for astrocytes. Our study underscores the particularly low fidelity in modelling down-regulated genes across all cell populations. The top enriched pathways arising from meta-analysis of human data differ from the enriched pathways arising from the overlap. We hope that our data will prove useful in indicating a starting point in the development of future, more complex, 3D in vitro models.
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Affiliation(s)
- Giorgio Guido
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (G.G.); (K.M.); (G.M.L.); (A.S.)
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (G.G.); (K.M.); (G.M.L.); (A.S.)
| | - Lyubka Tancheva
- Department of Biological Effects of Natural and Synthetic Substances, Institute of Neurobiology, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str. Block 23, 1113 Sofia, Bulgaria; (L.T.); (R.K.)
| | - Reni Kalfin
- Department of Biological Effects of Natural and Synthetic Substances, Institute of Neurobiology, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str. Block 23, 1113 Sofia, Bulgaria; (L.T.); (R.K.)
- Department of Healthcare, South-West University “Neofit Rilski”, Ivan Mihailov Str. 66, 2700 Blagoevgrad, Bulgaria
| | - Gian Marco Leone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (G.G.); (K.M.); (G.M.L.); (A.S.)
| | - Andrea Saraceno
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (G.G.); (K.M.); (G.M.L.); (A.S.)
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (G.G.); (K.M.); (G.M.L.); (A.S.)
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 89, 95123 Catania, Italy; (G.G.); (K.M.); (G.M.L.); (A.S.)
| | - Maria Cristina Petralia
- Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy
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14
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Jeffries AM, Yu T, Ziegenfuss JS, Tolles AK, Kim Y, Weng Z, Lodato MA. Single-cell transcriptomic and genomic changes in the aging human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566050. [PMID: 37986960 PMCID: PMC10659272 DOI: 10.1101/2023.11.07.566050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Aging brings dysregulation of various processes across organs and tissues, often stemming from stochastic damage to individual cells over time. Here, we used a combination of single-nucleus RNA-sequencing and single-cell whole-genome sequencing to identify transcriptomic and genomic changes in the prefrontal cortex of the human brain across life span, from infancy to centenarian. We identified infant-specific cell clusters enriched for the expression of neurodevelopmental genes, and a common down-regulation of cell-essential homeostatic genes that function in ribosomes, transport, and metabolism during aging across cell types. Conversely, expression of neuron-specific genes generally remains stable throughout life. We observed a decrease in specific DNA repair genes in aging, including genes implicated in generating brain somatic mutations as indicated by mutation signature analysis. Furthermore, we detected gene-length-specific somatic mutation rates that shape the transcriptomic landscape of the aged human brain. These findings elucidate critical aspects of human brain aging, shedding light on transcriptomic and genomics dynamics.
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Affiliation(s)
- Ailsa M. Jeffries
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tianxiong Yu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jennifer S. Ziegenfuss
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Allie K. Tolles
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Yerin Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael A. Lodato
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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15
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Vanrobaeys Y, Peterson ZJ, Walsh EN, Chatterjee S, Lin LC, Lyons LC, Nickl-Jockschat T, Abel T. Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation. Nat Commun 2023; 14:7095. [PMID: 37925446 PMCID: PMC10625558 DOI: 10.1038/s41467-023-42751-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Sleep deprivation has far-reaching consequences on the brain and behavior, impacting memory, attention, and metabolism. Previous research has focused on gene expression changes in individual brain regions, such as the hippocampus or cortex. Therefore, it is unclear how uniformly or heterogeneously sleep loss affects the brain. Here, we use spatial transcriptomics to define the impact of a brief period of sleep deprivation across the brain in male mice. We find that sleep deprivation induced pronounced differences in gene expression across the brain, with the greatest changes in the hippocampus, neocortex, hypothalamus, and thalamus. Both the differentially expressed genes and the direction of regulation differed markedly across regions. Importantly, we developed bioinformatic tools to register tissue sections and gene expression data into a common anatomical space, allowing a brain-wide comparison of gene expression patterns between samples. Our results suggest that distinct molecular mechanisms acting in discrete brain regions underlie the biological effects of sleep deprivation.
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Affiliation(s)
- Yann Vanrobaeys
- Interdisciplinary Graduate Program in Genetics, University of Iowa, 357 Medical Research Center Iowa City, Iowa, IA, USA
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
| | - Zeru J Peterson
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emily N Walsh
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, 356 Medical Research Center, Iowa City, IA, USA
| | - Snehajyoti Chatterjee
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
| | - Li-Chun Lin
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA
- Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Lisa C Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Thomas Nickl-Jockschat
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA.
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA.
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.
| | - Ted Abel
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, Iowa City, IA, USA.
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 51 Newton Road, 2-417B Bowen Science Building, Iowa City, IA, USA.
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16
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Pomeshchik Y, Velasquez E, Gil J, Klementieva O, Gidlöf R, Sydoff M, Bagnoli S, Nacmias B, Sorbi S, Westergren-Thorsson G, Gouras GK, Rezeli M, Roybon L. Proteomic analysis across patient iPSC-based models and human post-mortem hippocampal tissue reveals early cellular dysfunction and progression of Alzheimer's disease pathogenesis. Acta Neuropathol Commun 2023; 11:150. [PMID: 37715247 PMCID: PMC10504768 DOI: 10.1186/s40478-023-01649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
The hippocampus is a primary region affected in Alzheimer's disease (AD). Because AD postmortem brain tissue is not available prior to symptomatic stage, we lack understanding of early cellular pathogenic mechanisms. To address this issue, we examined the cellular origin and progression of AD pathogenesis by comparing patient-based model systems including iPSC-derived brain cells transplanted into the mouse brain hippocampus. Proteomic analysis of the graft enabled the identification of pathways and network dysfunction in AD patient brain cells, associated with increased levels of Aβ-42 and β-sheet structures. Interestingly, the host cells surrounding the AD graft also presented alterations in cellular biological pathways. Furthermore, proteomic analysis across human iPSC-based models and human post-mortem hippocampal tissue projected coherent longitudinal cellular changes indicative of early to end stage AD cellular pathogenesis. Our data showcase patient-based models to study the cell autonomous origin and progression of AD pathogenesis.
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Affiliation(s)
- Yuriy Pomeshchik
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden.
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden.
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden.
| | - Erika Velasquez
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, BMC D13, Lund University, 22184, Lund, Sweden
| | - Oxana Klementieva
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Medical Micro-Spectroscopy, Department of Experimental Medical Science, BMC B10, Lund University, 22184, Lund, Sweden
| | - Ritha Gidlöf
- Lund University BioImaging Centre, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Marie Sydoff
- Lund University BioImaging Centre, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Silvia Bagnoli
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Benedetta Nacmias
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Sandro Sorbi
- Laboratorio Di Neurogenetica, Dipartimento Di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino- NEUROFARBA, Università degli Studi di Firenze, 50134, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Gunilla Westergren-Thorsson
- Department of Experimental Medical Science, BMC C12, Faculty of Medicine, Lund University, 22142, Lund, Sweden
| | - Gunnar K Gouras
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden
- Experimental Dementia Research Unit, Department of Experimental Medical Science, BMC B11, Lund University, 22184, Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, BMC D13, Lund University, 22184, Lund, Sweden
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, 22184, Lund, Sweden
| | - Laurent Roybon
- iPSC Laboratory for CNS Disease Modelling, Department of Experimental Medical Science, BMC D10, Lund University, 22184, Lund, Sweden.
- Strategic Research Area MultiPark, Lund University, 22184, Lund, Sweden.
- Lund Stem Cell Center, Lund University, 22184, Lund, Sweden.
- Department of Neurodegenerative Science, The MiND Program, Van Andel Institute, Grand Rapids, MI, USA.
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17
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Ch'ng TH, Augustine GJ. Alzheimer's Disease: Effects on brain circuits and synapses. Semin Cell Dev Biol 2023; 139:1-2. [PMID: 35931594 DOI: 10.1016/j.semcdb.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Toh Hean Ch'ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - George J Augustine
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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18
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Vanrobaeys Y, Peterson ZJ, Walsh EN, Chatterjee S, Lin LC, Lyons LC, Nickl-Jockschat T, Abel T. Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524406. [PMID: 36712009 PMCID: PMC9882298 DOI: 10.1101/2023.01.18.524406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Sleep deprivation has far-reaching consequences on the brain and behavior, impacting memory, attention, and metabolism. Previous research has focused on gene expression changes in individual brain regions, such as the hippocampus or cortex. Therefore, it is unclear how uniformly or heterogeneously sleep loss affects the brain. Here, we use spatial transcriptomics to define the impact of a brief period of sleep deprivation across the brain. We find that sleep deprivation induced pronounced differences in gene expression across the brain, with the greatest changes in the hippocampus, neocortex, hypothalamus, and thalamus. Both the differentially expressed genes and the direction of regulation differed markedly across regions. Importantly, we developed bioinformatic tools to register tissue sections and gene expression data into a common anatomical space, allowing a brain-wide comparison of gene expression patterns between samples. Our results suggest that distinct molecular mechanisms acting in discrete brain regions underlie the biological effects of sleep deprivation.
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Affiliation(s)
- Yann Vanrobaeys
- Interdisciplinary Graduate Program in Genetics, University of Iowa, 357 Medical Research Center Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
| | - Zeru J. Peterson
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Emily. N. Walsh
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, 356 Medical Research Center, Iowa City, IA 52242, USA
| | - Snehajyoti Chatterjee
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
| | - Li-Chun Lin
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Lisa C. Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Thomas Nickl-Jockschat
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Iowa Neuroscience Institute, Carver College of Medicine, 169 Newton Road, 2312 Pappajohn Biomedical Discovery Building, University of Iowa, Iowa City, IA 52242, USA
- Department of Neuroscience and Pharmacology, Carver College of Medicine, 51 Newton Road, 2-417B Bowen Science Building, University of Iowa, Iowa City, IA 52242, USA
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19
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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: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [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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