1
|
Wen J, Skampardoni I, Tian YE, Yang Z, Cui Y, Erus G, Hwang G, Varol E, Boquet-Pujadas A, Chand GB, Nasrallah IM, Satterthwaite TD, Shou H, Shen L, Toga AW, Zalesky A, Davatzikos C. Neuroimaging endophenotypes reveal underlying mechanisms and genetic factors contributing to progression and development of four brain disorders. Nat Biomed Eng 2025:10.1038/s41551-025-01412-w. [PMID: 40481237 DOI: 10.1038/s41551-025-01412-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/24/2025] [Indexed: 06/11/2025]
Abstract
Recent work leveraging artificial intelligence has offered promise to dissect disease heterogeneity by identifying complex intermediate brain phenotypes, called dimensional neuroimaging endophenotypes (DNEs). We advance the argument that these DNEs capture the degree of expression of respective neuroanatomical patterns measured, offering a dimensional neuroanatomical representation for studying disease heterogeneity and similarities of neurologic and neuropsychiatric diseases. We investigate the presence of nine DNEs derived from independent yet harmonized studies on Alzheimer's disease, autism spectrum disorder, late-life depression and schizophrenia in the UK Biobank study. Phenome-wide associations align with genome-wide associations, revealing 31 genomic loci (P < 5 × 10-8/9) associated with the nine DNEs. The nine DNEs, along with their polygenic risk scores, significantly enhanced the predictive accuracy for 14 systemic disease categories, particularly for conditions related to mental health and the central nervous system, as well as mortality outcomes. These findings underscore the potential of the nine DNEs to capture the expression of disease-related brain phenotypes in individuals of the general population and to relate such measures with genetics, lifestyle factors and chronic diseases.
Collapse
Affiliation(s)
- Junhao Wen
- Laboratory of AI and Biomedical Science (LABS), Columbia University, New York, NY, USA.
- Department of Radiology, Columbia University, New York, NY, USA.
- New York Genome Center (NYGC), New York, NY, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Data Science Institute (DSI), Columbia University, New York, NY, USA.
- Center for Innovation in Imaging Biomarkers and Integrated Diagnostics (CIMBID), Department of Radiology, Columbia University, New York, NY, USA.
- Zuckerman Institute, Columbia University, New York, NY, USA.
| | - Ioanna Skampardoni
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ye Ella Tian
- Systems Lab, Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Zhijian Yang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuhan Cui
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guray Erus
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gyujoon Hwang
- Department of Psychiatry and Behavioral Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Erdem Varol
- Department of Computer Science and Engineering, New York University, New York, NY, USA
| | - Aleix Boquet-Pujadas
- Laboratory of AI and Biomedical Science (LABS), Columbia University, New York, NY, USA
| | - Ganesh B Chand
- Department of Radiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Ilya M Nasrallah
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haochang Shou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology and Informatics University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging (LONI), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Andrew Zalesky
- Systems Lab, Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christos Davatzikos
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
2
|
Zheng M, Bao N, Wang Z, Song C, Jin Y. Alternative splicing in autism spectrum disorder: Recent insights from mechanisms to therapy. Asian J Psychiatr 2025; 108:104501. [PMID: 40273800 DOI: 10.1016/j.ajp.2025.104501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 04/11/2025] [Accepted: 04/12/2025] [Indexed: 04/26/2025]
Abstract
Alternative splicing (AS) is a vital and highly dynamic RNA regulatory mechanism that allows a single gene to generate multiple mRNA and protein isoforms. Dysregulation of AS has been identified as a key contributor to the pathogenesis of autism spectrum disorders (ASD). A comprehensive understanding of aberrant splicing mechanisms and their functional consequences in ASD can help uncover the molecular basis of the disorder and facilitate the development of therapeutic strategies. This review focuses on the major aberrant splicing events and key splicing regulators associated with ASD, highlighting their roles in linking defective splicing to ASD pathogenesis. In addition, a discussion of how emerging technologies, such as long-read sequencing, single-cell sequencing, spatial transcriptomics and CRISPR-Cas systems are offering novel insights into the role and mechanisms of AS in ASD is presented. Finally, the RNA splicing-based therapeutic strategies are evaluated, emphasizing their potential to address unmet clinical needs in ASD treatment.
Collapse
Affiliation(s)
- Mixue Zheng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
| | - Nengcheng Bao
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zhechao Wang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Chao Song
- Department of Developmental and Behavioral Pediatrics, the Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Centre for Child Health, Hangzhou 310052, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
3
|
Wang M, Zhang X, Zhong L, Zeng L, Li L, Yao P. Understanding autism: Causes, diagnosis, and advancing therapies. Brain Res Bull 2025; 227:111411. [PMID: 40449388 DOI: 10.1016/j.brainresbull.2025.111411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 05/28/2025] [Accepted: 05/28/2025] [Indexed: 06/03/2025]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental condition marked by difficulties in social communication, languages, and repetitive behaviors. Its rising prevalence has made it a critical global public health issue. ASD is believed to arise from a combination of genetic and environmental influences. While some gene mutations associated with ASD have been identified, most cases lack clear genetic explanations. Evidence increasingly points to early-life environmental factors as key contributors to ASD, including advanced parental age, maternal diabetes during pregnancy, infections, hormonal imbalances, certain medications, and exposure to air pollution. Currently, ASD diagnosis relies on behavioral assessments, but the absence of specific molecular biomarkers poses significant obstacles to early detection and targeted therapies. Encouragingly, research has identified potential biomarkers, such as neuroimaging classifiers, electroencephalography patterns, eye-tracking data, digital analytics, gene expression profiles, inflammatory and chemokine markers, proteomic and metabolomic profiles, and gut microbiota characteristics. Potential therapeutical strategies under investigation include digital therapies, non-invasive brain stimulation, antioxidants, oxytocin, AVPR1a antagonists, PPAR agonists, and mTOR inhibitors. This review explores ASD across five areas: epidemiological trends, genetic mechanisms, early-life environmental factors and their potential roles, diagnostic biomarkers, and therapeutic approaches.
Collapse
Affiliation(s)
- Min Wang
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 570206, PR China
| | - Xiaozhuang Zhang
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 570206, PR China
| | - Liyan Zhong
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 570206, PR China
| | - Liqin Zeng
- Department of gynecology, Sun Yat-Sen University Affiliated No.8 Hospital, Shenzhen 518033, PR China
| | - Ling Li
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 570206, PR China.
| | - Paul Yao
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 570206, PR China.
| |
Collapse
|
4
|
Rynard KM, Han K, Wainberg M, Calarco JA, Lee HO, Lipshitz HD, Smibert CA, Tripathy SJ. ASiDentify (ASiD): a machine learning model to predict new autism spectrum disorder risk genes. Genetics 2025; 230:iyaf040. [PMID: 40088463 DOI: 10.1093/genetics/iyaf040] [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: 10/08/2024] [Accepted: 02/26/2025] [Indexed: 03/17/2025] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects nearly 3% of children and has a strong genetic component. While hundreds of ASD risk genes have been identified through sequencing studies, the genetic heterogeneity of ASD makes identifying additional risk genes using these methods challenging. To predict candidate ASD risk genes, we developed a simple machine learning model, ASiDentify (ASiD), using human genomic, RNA- and protein-based features. ASiD identified over 1,300 candidate ASD risk genes, over 300 of which have not been previously predicted. ASiD made accurate predictions of ASD risk genes using 6 features predictive of ASD risk gene status, including mutational constraint, synapse localization and gene expression in neurons, astrocytes and non-brain tissues. Particular functional groups of proteins found to be strongly implicated in ASD include RNA-binding proteins (RBPs) and chromatin regulators. We constructed additional logistic regression models to make predictions and assess informative features specific to RBPs, including mutational constraint, or chromatin regulators, for which both expression level in excitatory neurons and mutational constraint were informative. The fact that RBPs and chromatin regulators had informative features distinct from all protein-coding genes suggests that specific biological pathways connect risk genes with different molecular functions to ASD.
Collapse
Affiliation(s)
- Katherine M Rynard
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kara Han
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Krembil Institute for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
| | - Michael Wainberg
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Krembil Institute for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
| | - John A Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Hyun O Lee
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shreejoy J Tripathy
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Krembil Institute for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
5
|
Hayakawa Y, Ozaki H. A practical guide for single-cell transcriptome data analysis in neuroscience. Neurosci Res 2025; 214:9-15. [PMID: 40164433 DOI: 10.1016/j.neures.2025.03.006] [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: 01/23/2025] [Revised: 03/03/2025] [Accepted: 03/19/2025] [Indexed: 04/02/2025]
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the single-cell level, providing unprecedented insights into cellular heterogeneity, rare cell populations, and dynamic cellular processes. In neuroscience, scRNA-seq has enabled the identification of diverse brain cell types, elucidation of developmental pathways, and discovery of mechanisms underlying neurological diseases. This tutorial provides a practical guide to scRNA-seq data analysis in neuroscience, focusing on the essential workflows and theoretical foundations. Key steps covered include quality control, data preprocessing, integration, cell clustering, and differential expression analysis. Using the Seurat R package, the tutorial demonstrates a comparative analysis approach for identifying differentially expressed genes between conditions, emphasizing the biological interpretation of results. By addressing the unique challenges of scRNA-seq data and illustrating methods for robust analysis, this work aims to enhance the reliability and reproducibility of scRNA-seq studies in neuroscience, supporting the exploration of cellular mechanisms and advancing research into brain function and disease.
Collapse
Affiliation(s)
- Yoshinori Hayakawa
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Center for Artificial Intelligence Research, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| |
Collapse
|
6
|
Atterton C, Trew I, Cale JM, Aung-Htut MT, Grens K, Kiernan J, Delagrammatikas CG, Piper M. Overgrowth-intellectual disability disorders: progress in biology, patient advocacy and innovative therapies. Dis Model Mech 2025; 18:dmm052300. [PMID: 40353642 DOI: 10.1242/dmm.052300] [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] [Indexed: 05/14/2025] Open
Abstract
Overgrowth-intellectual disability (OGID) syndromes encompass a group of rare neurodevelopmental disorders that frequently share common clinical presentations. Although the genetic causes of many OGID syndromes are now known, we lack a clear mechanistic understanding of how such variants disrupt developmental processes and ultimately culminate in overgrowth and neurological symptoms. Patient advocacy groups, such as the Overgrowth Syndromes Alliance (OSA), are mobilising patients, families, clinicians and researchers to work together towards a deeper understanding of the clinical needs of patients with OGID, as well as to understand the fundamental biology of the relevant genes, with the goal of developing treatments. In this Review, we summarise three OGID syndromes encompassed by the OSA, namely Sotos syndrome, Malan syndrome and Tatton-Brown-Rahman syndrome. We discuss similarities and differences in the biology behind each disorder and explore future approaches that could potentially provide a way to ameliorate some of the unmet clinical needs of patients with OGID.
Collapse
Affiliation(s)
- Cooper Atterton
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Isabella Trew
- Personalised Medicine Centre, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Jessica M Cale
- Personalised Medicine Centre, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - May T Aung-Htut
- Personalised Medicine Centre, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Kerry Grens
- TBRS Community, Stanfordville, NY 12581, USA
| | | | | | - Michael Piper
- The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- The Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
7
|
Ju J, Pan Y, Yang X, Li X, Chen J, Wu S, Hou ST. The "don't eat me" signal CD47 is associated with microglial phagocytosis defects and autism-like behaviors in 16p11.2 deletion mice. Proc Natl Acad Sci U S A 2025; 122:e2411080122. [PMID: 40238451 PMCID: PMC12036979 DOI: 10.1073/pnas.2411080122] [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: 06/08/2024] [Accepted: 03/13/2025] [Indexed: 04/18/2025] Open
Abstract
Various pathological characteristics of autism spectrum disorder (ASD) stem from abnormalities in brain resident immune cells, specifically microglia, to prune unnecessary synapses or neural connections during early development. Animal models of ASD exhibit an abundance of synapses in different brain regions, which is strongly linked to the appearance of ASD behaviors. Overexpression of CD47 on neurons acts as a "don't eat me" signal, safeguarding synapses from inappropriate pruning by microglia. Indeed, CD47 overexpression occurs in 16p11.2 deletion carriers, causing decreased synaptic phagocytosis and the manifestation of ASD characteristics. However, the role of CD47 in synaptic pruning impairment leading to ASD phenotypes in the 16p11.2 deletion mouse model is unclear. Moreover, whether blocking CD47 can alleviate ASD mice's behavioral deficits remains unknown. Here, we demonstrate a strong link between increased CD47 expression, decreased microglia phagocytosis capacity, and increased impairment in social novelty preference in the 16p11.2 deletion mice. The reduction in microglia phagocytosis caused a rise in excitatory synapses and transmission in the prefrontal cortex of 16p11.2 deletion mice. Importantly, blocking CD47 using a specific CD47 antibody or reducing CD47 expression using a specific short hairpin RNA (shRNA) enhanced the microglia phagocytosis and reduced excitatory transmission. Reduction in CD47 expression improved social novelty preference deficits in 16p11.2 mice. These findings demonstrate that CD47 is associated with the ASD phenotypes in the 16p11.2 deletion mice and could be a promising target for the development of treatment for ASD.
Collapse
Affiliation(s)
- Jun Ju
- Brain Research Centre, Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Nanshan District, Shenzhen, Guangdong1088, People’s Republic of China
| | - Yifan Pan
- Brain Research Centre, Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Nanshan District, Shenzhen, Guangdong1088, People’s Republic of China
| | - Xinyi Yang
- Brain Research Centre, Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Nanshan District, Shenzhen, Guangdong1088, People’s Republic of China
| | - Xuanyi Li
- Brain Research Centre, Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Nanshan District, Shenzhen, Guangdong1088, People’s Republic of China
| | - Jinghong Chen
- Brain Research Centre, Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Nanshan District, Shenzhen, Guangdong1088, People’s Republic of China
| | - Shiyu Wu
- Brain Research Centre, Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Nanshan District, Shenzhen, Guangdong1088, People’s Republic of China
| | - Sheng-Tao Hou
- Brain Research Centre, Department of Neurobiology, School of Life Sciences, Southern University of Science and Technology, Nanshan District, Shenzhen, Guangdong1088, People’s Republic of China
| |
Collapse
|
8
|
Binan L, Jiang A, Danquah SA, Valakh V, Simonton B, Bezney J, Manguso RT, Yates KB, Nehme R, Cleary B, Farhi SL. Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits. Cell 2025; 188:2141-2158.e18. [PMID: 40081369 DOI: 10.1016/j.cell.2025.02.012] [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: 11/30/2023] [Revised: 10/24/2024] [Accepted: 02/14/2025] [Indexed: 03/16/2025]
Abstract
Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but they have not yet leveraged the power of highly plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present a combination of imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs (Perturb-FISH). Perturb-FISH recovers intracellular effects that are consistent with single-cell RNA-sequencing-based readouts of perturbation effects (Perturb-seq) in a screen of lipopolysaccharide response in cultured monocytes, and it uncovers intercellular and density-dependent regulation of the innate immune response. Similarly, in three-dimensional xenograft models, Perturb-FISH identifies tumor-immune interactions altered by genetic knockout. When paired with a functional readout in a separate screen of autism spectrum disorder risk genes in human-induced pluripotent stem cell (hIPSC) astrocytes, Perturb-FISH shows common calcium activity phenotypes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a general method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.
Collapse
Affiliation(s)
- Loϊc Binan
- Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aiping Jiang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02144, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Serwah A Danquah
- Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vera Valakh
- Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brooke Simonton
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jon Bezney
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert T Manguso
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02144, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Kathleen B Yates
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02144, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA 02215, USA; Department of Biology, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Program in Bioinformatics, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA.
| | - Samouil L Farhi
- Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
9
|
Dougherty JD, Sarafinovska S, Chaturvedi SM, Law TE, Akinwe TM, Gabel HW. Single-cell technology grows up: Leveraging high-resolution omics approaches to understand neurodevelopmental disorders. Curr Opin Neurobiol 2025; 92:102990. [PMID: 40036988 DOI: 10.1016/j.conb.2025.102990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 01/30/2025] [Accepted: 02/05/2025] [Indexed: 03/06/2025]
Abstract
The identification of hundreds of neurodevelopmental disorder (NDD) genes in the last decade led to numerous genetic models for understanding NDD gene mutation consequences and delineating putative neurobiological mediators of disease. In parallel, single-cell and single-nucleus genomic technologies have been developed and implemented to create high-resolution atlases of cell composition, gene expression, and circuit connectivity in the brain. Here, we discuss the opportunities to leverage mutant models (or human tissue, where available) and genomics approaches to systematically define NDD etiology at cellular resolution. We review progress in applying single-cell and spatial transcriptomics to interrogate developmental trajectories, cellular composition, circuit activity, and connectivity across human tissue and NDD models. We discuss considerations for implementing these approaches at scale to maximize insights and facilitate reproducibility. Finally, we highlight how standardized application of these technologies promises to not only define etiologies of individual disorders but also identify molecular, cellular, and circuit level convergence across NDDs.
Collapse
Affiliation(s)
- Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Simona Sarafinovska
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sneha M Chaturvedi
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Saint Louis, MO, USA
| | - Travis E Law
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Saint Louis, MO, USA
| | - Titilope M Akinwe
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Saint Louis, MO, USA
| |
Collapse
|
10
|
Clarence T, Bendl J, Cao X, Wang X, Zheng S, Hoffman GE, Kozlenkov A, Hong A, Iskhakova M, Jaiswal MK, Murphy S, Yu A, Haroutunian V, Dracheva S, Akbarian S, Fullard JF, Yuan GC, Lee D, Roussos P. Multiomic single-cell profiling identifies critical regulators of postnatal brain. Nat Genet 2025; 57:591-603. [PMID: 39962241 DOI: 10.1038/s41588-025-02083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 01/08/2025] [Indexed: 03/15/2025]
Abstract
Human brain development spans from embryogenesis to adulthood, with dynamic gene expression controlled by cell-type-specific cis-regulatory element activity and three-dimensional genome organization. To advance our understanding of postnatal brain development, we simultaneously profiled gene expression and chromatin accessibility in 101,924 single nuclei from four brain regions across ten donors, covering five key postnatal stages from infancy to late adulthood. Using this dataset and chromosome conformation capture data, we constructed enhancer-based gene regulatory networks to identify cell-type-specific regulators of brain development and interpret genome-wide association study loci for ten main brain disorders. Our analysis connected 2,318 cell-specific loci to 1,149 unique genes, representing 41% of loci linked to the investigated traits, and highlighted 55 genes influencing several disease phenotypes. Pseudotime analysis revealed distinct stages of postnatal oligodendrogenesis and their regulatory programs. These findings provide a comprehensive dataset of cell-type-specific gene regulation at critical timepoints in postnatal brain development.
Collapse
Affiliation(s)
- Tereza Clarence
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuan Cao
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xinyi Wang
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shiwei Zheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexey Kozlenkov
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aram Hong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marina Iskhakova
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manoj K Jaiswal
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, USA
| | - Sarah Murphy
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander Yu
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vahram Haroutunian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, USA
| | - Stella Dracheva
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Donghoon Lee
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, USA.
- Center for Precision Medicine and Translational Therapeutics, James J. Peters VA Medical Center, Bronx, NY, USA.
| |
Collapse
|
11
|
Starr AL, Fraser HB. A general principle of neuronal evolution reveals a human-accelerated neuron type potentially underlying the high prevalence of autism in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.02.606407. [PMID: 39131279 PMCID: PMC11312593 DOI: 10.1101/2024.08.02.606407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types found in the mammalian brain, is a key characteristic of multicellular life. While it has been observed that some cell types are far more evolutionarily conserved than others, the factors driving these differences in evolutionary rate remain unknown. Here, we hypothesized that highly abundant neuronal cell types may be under greater selective constraint than rarer neuronal types, leading to variation in their rates of evolution. To test this, we leveraged recently published cross-species single-nucleus RNA-sequencing datasets from three distinct regions of the mammalian neocortex. We found a strikingly consistent relationship where more abundant neuronal subtypes show greater gene expression conservation between species, which replicated across three independent datasets covering >106 neurons from six species. Based on this principle, we discovered that the most abundant type of neocortical neurons-layer 2/3 intratelencephalic excitatory neurons-has evolved exceptionally quickly in the human lineage compared to other apes. Surprisingly, this accelerated evolution was accompanied by the dramatic down-regulation of autism-associated genes, which was likely driven by polygenic positive selection specific to the human lineage. In sum, we introduce a general principle governing neuronal evolution and suggest that the exceptionally high prevalence of autism in humans may be a direct result of natural selection for lower expression of a suite of genes that conferred a fitness benefit to our ancestors while also rendering an abundant class of neurons more sensitive to perturbation.
Collapse
Affiliation(s)
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
12
|
Vartiainen E, Liyanage D, Mazureac I, Battaglia RA, Tegtmeyer M, He JX, Räsänen N, Sealock J, McCarroll S, Nehme R, Pietiläinen O. Astrocytic-supplied cholesterol drives synaptic gene expression programs in developing neurons and downstream astrocytic transcriptional programs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.28.635252. [PMID: 39975161 PMCID: PMC11838310 DOI: 10.1101/2025.01.28.635252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Astrocytes participate in neuronal synaptic programs that are enriched for genetic associations in schizophrenia and autism spectrum disorders (ASD). To better understand how these co-regulated cellular programs are induced during early neuronal development, we studied astrocytes and iPSC-derived neurons in co-cultures and mono-cultures at 16 time points spanning 0.5 hours to 8 days. We found that upregulation in astrocytes of genes involved in cholesterol biosynthesis preceded the activation of synaptic gene programs in neurons and upregulation of the astrocytic Nrxn1. Neuronal knockdown of key cholesterol receptors led to downregulation of neuronal synaptic genes and induced a robust transcriptional response in the astrocytes, including further upregulation of Nrxn1. This suggests that astrocyte-supplied cholesterol drives these neuronal changes and that bi-directional signalling is occuring. The genes upregulated in neurons were enriched for deleterious variants in schizophrenia and neurodevelopmental disorders, suggesting that their pathogenic effect may be, in part, mediated by reduced buffering capacity for changes in the astrocyte cholesterol supply to neurons. These findings highlight the critical role of astrocyte-neuron interactions in psychiatric and neurodevelopmental disorders, particularly in relation to lipid metabolism and synaptic plasticity.
Collapse
Affiliation(s)
- Emilia Vartiainen
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Dhara Liyanage
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Illinca Mazureac
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rachel A Battaglia
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Matthew Tegtmeyer
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jax Xu He
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Noora Räsänen
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Julia Sealock
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Steven McCarroll
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ralda Nehme
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olli Pietiläinen
- Neuroscience Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- The Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Cambridge, MA, USA
| |
Collapse
|
13
|
Bendl J, Fullard JF, Girdhar K, Dong P, Kosoy R, Zeng B, Hoffman GE, Roussos P. Chromatin accessibility provides a window into the genetic etiology of human brain disease. Trends Genet 2025:S0168-9525(25)00001-0. [PMID: 39855972 DOI: 10.1016/j.tig.2025.01.001] [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: 11/18/2024] [Revised: 01/02/2025] [Accepted: 01/03/2025] [Indexed: 01/27/2025]
Abstract
Neuropsychiatric and neurodegenerative diseases have a significant genetic component. Risk variants often affect the noncoding genome, altering cis-regulatory elements (CREs) and chromatin structure, ultimately impacting gene expression. Chromatin accessibility profiling methods, especially assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), have been used to pinpoint disease-associated SNPs and link them to affected genes and cell types in the brain. The integration of single-cell technologies with genome-wide association studies (GWAS) and transcriptomic data has further advanced our understanding of cell-specific chromatin dynamics. This review discusses recent findings regarding the role played by chromatin accessibility in brain disease, highlighting the need for high-quality data and rigorous computational tools. Future directions include spatial chromatin studies and CRISPR-based functional validation to bridge genetic discovery and clinical applications, paving the way for targeted gene-regulatory therapies.
Collapse
Affiliation(s)
- 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
| | - 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
| | - Kiran Girdhar
- 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
| | - Pengfei Dong
- 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
| | - Roman Kosoy
- 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
| | - Biao Zeng
- 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
| | - 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 (MIRECC), 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
| | - 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 (MIRECC), 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.
| |
Collapse
|
14
|
Marcassa G, Dascenco D, Lorente-Echeverría B, Daaboul D, Vandensteen J, Leysen E, Baltussen L, Howden AJM, de Wit J. Synaptic signatures and disease vulnerabilities of layer 5 pyramidal neurons. Nat Commun 2025; 16:228. [PMID: 39747884 PMCID: PMC11697078 DOI: 10.1038/s41467-024-55470-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 12/12/2024] [Indexed: 01/04/2025] Open
Abstract
Cortical layer 5 (L5) intratelencephalic (IT) and pyramidal tract (PT) neurons are embedded in distinct information processing pathways. Their morphology, connectivity, electrophysiological properties, and role in behavior have been extensively analyzed. However, the molecular composition of their synapses remains largely uncharacterized. Here, we dissect the protein composition of the excitatory postsynaptic compartment of mouse L5 neurons in intact somatosensory circuits, using an optimized proximity biotinylation workflow with high spatial accuracy. We find distinct synaptic signatures of L5 IT and PT neurons that are defined by proteins regulating synaptic organization and transmission, including cell-surface proteins (CSPs), neurotransmitter receptors and ion channels. In addition, we find a differential vulnerability to disease, with a marked enrichment of autism risk genes in the synaptic signature of L5 IT neurons compared to PT neurons. These results align with human studies and suggest that the excitatory postsynaptic compartment of L5 IT neurons is susceptible in autism. Our approach is versatile and can be broadly applied to other neuron types to create a protein-based, synaptic atlas of cortical circuits.
Collapse
Affiliation(s)
- Gabriele Marcassa
- VIB Center for Brain & Disease Research, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Dan Dascenco
- VIB Center for Brain & Disease Research, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Blanca Lorente-Echeverría
- VIB Center for Brain & Disease Research, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Danie Daaboul
- VIB Center for Brain & Disease Research, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Jeroen Vandensteen
- VIB Center for Brain & Disease Research, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Elke Leysen
- VIB Center for Brain & Disease Research, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Lucas Baltussen
- VIB Center for Brain & Disease Research, Leuven, Belgium
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | | | - Joris de Wit
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.
| |
Collapse
|
15
|
Cui J, Li H, Hu C, Zhang F, Li Y, Weng Y, Yang L, Li Y, Yao M, Li H, Luo X, Hao Y. Unraveling pathogenesis and potential biomarkers for autism spectrum disorder associated with HIF1A pathway based on machine learning and experiment validation. Neurobiol Dis 2025; 204:106763. [PMID: 39657846 DOI: 10.1016/j.nbd.2024.106763] [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: 08/04/2024] [Revised: 10/05/2024] [Accepted: 12/04/2024] [Indexed: 12/12/2024] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a high social burden and limited treatments. Hypoxic condition of the brain is considered an important pathological mechanism of ASD. HIF1A is a key participant in brain hypoxia, but its contribution to the pathophysiological landscape of ASD remains unclear. METHODS ASD-related datasets were obtained from GEO database, and HIF1A-related genes from GeneCards. Co-expression module analysis identified module genes, which were intersected with HIF1A-related genes to identify common genes. Machine learning identified hub genes from intersection genes and PPI networks were constructed to explore relationships among hub and HIF1A. Single-cell RNA sequencing analyzed hub gene distribution across cell clusters. ASD mouse model was created by inducing maternal immune activation (MIA) with poly(I:C) injections, verified through behavioral tests. Validation of HIF1A pathway and hub genes was confirmed through Western Blot, qPCR, and immunofluorescence in ASD mice and microglia BV-2 cells. RESULTS Using CEMiTool and GeneCards, 45 genes associated with ASD and HIF1A pathway were identified. Machine learning identified CDKN1A, ETS2, LYN, and SLC16A3 as potential ASD diagnostic markers. Single-cell sequencing pinpointed activated microglia as key immune cells. Behavioral tests showed MIA offspring mice exhibited typical ASD-like behaviors. Immunofluorescence confirmed the activation of microglia and HIF1A pathway in frontal cortex of ASD mice. Additionally, IL-6 contributed to ASD by activating JUN/HIF1A pathway, affecting CDKN1A, LYN, and SLC16A3 expression in microglia. CONCLUSIONS HIF1A-related genes CDKN1A, ETS2, LYN, and SLC16A3 are strong diagnostic markers for ASD and the activation of IL-6/JUN/HIF1A pathway in microglia contributes to the pathogenesis of ASD.
Collapse
Affiliation(s)
- Jinru Cui
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Heli Li
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Cong Hu
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Feiyan Zhang
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yunjie Li
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ying Weng
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liping Yang
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yingying Li
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Minglan Yao
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hao Li
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoping Luo
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yan Hao
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| |
Collapse
|
16
|
Natowicz MR, Bauman ML, Edelson SM. A most important gift: the critical role of postmortem brain tissue in autism science. Front Neurol 2024; 15:1486227. [PMID: 39726759 PMCID: PMC11670190 DOI: 10.3389/fneur.2024.1486227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Accepted: 11/13/2024] [Indexed: 12/28/2024] Open
Affiliation(s)
- Marvin R. Natowicz
- Pathology and Laboratory Medicine, Genomic Medicine, Neurological and Pediatrics Institutes, Cleveland Clinic, Cleveland, OH, United States
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, United States
| | - Margaret L. Bauman
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, United States
| | | |
Collapse
|
17
|
Séjourné G, Eroglu C. Astrocyte-neuron crosstalk in neurodevelopmental disorders. Curr Opin Neurobiol 2024; 89:102925. [PMID: 39357429 DOI: 10.1016/j.conb.2024.102925] [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: 06/25/2024] [Revised: 09/06/2024] [Accepted: 09/08/2024] [Indexed: 10/04/2024]
Abstract
A fundamental feature shared across neurodevelopmental disorders (NDDs) is the disruption of synaptic circuit formation and homeostasis. During early life, non-neuronal cells called astrocytes tightly regulate the establishment of circuits by controlling formation, remodeling, stabilization, and maturation of synapses. Concurrently, astrocytes mature to meet the evolving needs of the developing brain. Bidirectional astrocyte-neuron communication synchronizes astrocyte maturation with synapse development. An emerging body of evidence supports the hypothesis that in NDDs, deficits in astrocyte-neuron communication underlie errors in synaptic circuit development. Here we will review and discuss these findings, with the aim of inspiring future research and guiding translational studies.
Collapse
Affiliation(s)
- Gabrielle Séjourné
- The Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
| | - Cagla Eroglu
- The Department of Cell Biology, Duke University Medical Center, Durham, NC, USA; The Department of Neurobiology, Duke University Medical Center, Durham, NC, USA; Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA.
| |
Collapse
|
18
|
Zhang T, Li Y, Pan L, Sha J, Bailey M, Faure-Kumar E, Williams CK, Wohlschlegel J, Magaki S, Niu C, Lee Y, Su YC, Li X, Vinters HV, Geschwind DH. Brain-wide alterations revealed by spatial transcriptomics and proteomics in COVID-19 infection. NATURE AGING 2024; 4:1598-1618. [PMID: 39543407 PMCID: PMC11867587 DOI: 10.1038/s43587-024-00730-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/25/2024] [Indexed: 11/17/2024]
Abstract
Understanding the pathophysiology of neurological symptoms observed after severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection is essential to optimizing outcomes and therapeutics. To date, small sample sizes and narrow molecular profiling have limited the generalizability of findings. In this study, we profiled multiple cortical and subcortical regions in postmortem brains of patients with coronavirus disease 2019 (COVID-19) and controls with matched pulmonary pathology (total n = 42) using spatial transcriptomics, bulk gene expression and proteomics. We observed a multi-regional antiviral response without direct active SARS-CoV2 infection. We identified dysregulation of mitochondrial and synaptic pathways in deep-layer excitatory neurons and upregulation of neuroinflammation in glia, consistent across both mRNA and protein. Remarkably, these alterations overlapped substantially with changes in age-related neurodegenerative diseases, including Parkinson's disease and Alzheimer's disease. Our work, combining multiple experimental and analytical methods, demonstrates the brain-wide impact of severe acute/subacute COVID-19, involving both cortical and subcortical regions, shedding light on potential therapeutic targets within pathways typically associated with pathological aging and neurodegeneration.
Collapse
Affiliation(s)
- Ting Zhang
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yunfeng Li
- Translational Pathology Core Laboratory, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Liuliu Pan
- Technology Access Program, Bruker Spatial Technology, Seattle, WA, USA
- Duality Biologics, Shanghai, China
| | - Jihui Sha
- Proteome Research Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael Bailey
- Proof of Principle Team, Translational Science, Bruker Spatial Technology, Seattle, WA, USA
| | - Emmanuelle Faure-Kumar
- Center for Systems Biomedicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher Kazu Williams
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - James Wohlschlegel
- Proteome Research Center, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shino Magaki
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chao Niu
- Technology Center for Genomics & Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yoojin Lee
- Technology Center for Genomics & Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yu-Chyuan Su
- Technology Center for Genomics & Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xinmin Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Technology Center for Genomics & Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Harry V Vinters
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
19
|
Gora C, Dudas A, Vaugrente O, Drobecq L, Pecnard E, Lefort G, Pellissier LP. Deciphering autism heterogeneity: a molecular stratification approach in four mouse models. Transl Psychiatry 2024; 14:416. [PMID: 39366951 PMCID: PMC11452541 DOI: 10.1038/s41398-024-03113-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 09/19/2024] [Accepted: 09/23/2024] [Indexed: 10/06/2024] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by impairments in social interaction and communication, as well as restrained or stereotyped behaviors. The inherent heterogeneity within the autism spectrum poses challenges for developing effective pharmacological treatments targeting core features. Successful clinical trials require the identification of robust markers to enable patient stratification. In this study, we identified molecular markers within the oxytocin and immediate early gene families across five interconnected brain structures of the social circuit. We used wild-type and four heterogeneous mouse models, each exhibiting unique autism-like behaviors modeling the autism spectrum. While dysregulations in the oxytocin family were model-specific, immediate early genes displayed widespread alterations, reflecting global changes across the four models. Through integrative analysis, we identified Egr1, Foxp1, Homer1a, Oxt, and Oxtr as five robust and discriminant molecular markers that allowed the successful stratification of the four models. Importantly, our stratification demonstrated predictive values when challenged with a fifth mouse model or identifying subgroups of mice potentially responsive to oxytocin treatment. Beyond providing insights into oxytocin and immediate early gene mRNA dynamics, this proof-of-concept study represents a significant step toward the potential stratification of individuals with ASD. This work has implications for the success of clinical trials and the development of personalized medicine in autism.
Collapse
Affiliation(s)
- Caroline Gora
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | - Ana Dudas
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | | | - Lucile Drobecq
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | | | - Gaëlle Lefort
- INRAE, CNRS, Université de Tours, PRC, 37380, Nouzilly, France
| | | |
Collapse
|
20
|
Rexach JE, Cheng Y, Chen L, Polioudakis D, Lin LC, Mitri V, Elkins A, Han X, Yamakawa M, Yin A, Calini D, Kawaguchi R, Ou J, Huang J, Williams C, Robinson J, Gaus SE, Spina S, Lee EB, Grinberg LT, Vinters H, Trojanowski JQ, Seeley WW, Malhotra D, Geschwind DH. Cross-disorder and disease-specific pathways in dementia revealed by single-cell genomics. Cell 2024; 187:5753-5774.e28. [PMID: 39265576 PMCID: PMC12017262 DOI: 10.1016/j.cell.2024.08.019] [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: 07/15/2023] [Revised: 05/29/2024] [Accepted: 08/09/2024] [Indexed: 09/14/2024]
Abstract
The development of successful therapeutics for dementias requires an understanding of their shared and distinct molecular features in the human brain. We performed single-nuclear RNA-seq and ATAC-seq in Alzheimer's disease (AD), frontotemporal dementia (FTD), and progressive supranuclear palsy (PSP), analyzing 41 participants and ∼1 million cells (RNA + ATAC) from three brain regions varying in vulnerability and pathological burden. We identify 32 shared, disease-associated cell types and 14 that are disease specific. Disease-specific cell states represent glial-immune mechanisms and selective neuronal vulnerability impacting layer 5 intratelencephalic neurons in AD, layer 2/3 intratelencephalic neurons in FTD, and layer 5/6 near-projection neurons in PSP. We identify disease-associated gene regulatory networks and cells impacted by causal genetic risk, which differ by disorder. These data illustrate the heterogeneous spectrum of glial and neuronal compositional and gene expression alterations in different dementias and identify therapeutic targets by revealing shared and disease-specific cell states.
Collapse
Affiliation(s)
- Jessica E Rexach
- Program in Neurogenetics, Department of Neurology, 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.
| | - Yuyan Cheng
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lawrence Chen
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Li-Chun Lin
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Vivianne Mitri
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew Elkins
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Han
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mai Yamakawa
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Yin
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniela Calini
- Neuroscience and Rare Diseases, Roche Pharma Research and Early Development, F. Hoffman-LaRoche Ltd., Basel, Switzerland
| | - Riki Kawaguchi
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jing Ou
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jerry Huang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher Williams
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John Robinson
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie E Gaus
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Salvatore Spina
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Edward B Lee
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lea T Grinberg
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Harry Vinters
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John Q Trojanowski
- Department of Pathology & Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William W Seeley
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Dheeraj Malhotra
- Neuroscience and Rare Diseases, Roche Pharma Research and Early Development, F. Hoffman-LaRoche Ltd., Basel, Switzerland
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, 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 of Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
21
|
Tang W, Wang Q, Sun M, Liu C, Huang Y, Zhou M, Zhang X, Meng Z, Zhang J. The gut microbiota-oligodendrocyte axis: A promising pathway for modulating oligodendrocyte homeostasis and demyelination-associated disorders. Life Sci 2024; 354:122952. [PMID: 39127317 DOI: 10.1016/j.lfs.2024.122952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/22/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
The bidirectional regulation between the gut microbiota and brain, known as gut-brain axis, has received significant attention. The myelin sheath, produced by oligodendrocytes or Schwann cells, is essential for efficient nervous signal transmission and the maintenance of brain function. Growing evidence shows that both oligodendrogenesis and myelination are modulated by gut microbiota and its metabolites, and when dysbiosis occurs, changes in the microbiota composition and/or associated metabolites may impact developmental myelination and the occurrence of neurodevelopmental disabilities. Although the link between the microbiota and demyelinating disease such as multiple sclerosis has been extensively studied, our knowledge about the role of the microbiota in other myelin-related disorders, such as neurodegenerative diseases, is limited. Mechanistically, the microbiota-oligodendrocyte axis is primarily mediated by factors such as inflammation, the vagus nerve, endocrine hormones, and microbiota metabolites as evidenced by metagenomics, metabolomics, vagotomy, and morphological and molecular approaches. Treatments targeting this axis include probiotics, prebiotics, microbial metabolites, herbal bioactive compounds, and specific dietary management. In addition to the commonly used approaches, viral vector-mediated tracing and gene manipulation, integrated multiomics and multicenter clinical trials will greatly promote the mechanistic and interventional studies and ultimately, the development of new preventive and therapeutic strategies against gut-oligodendrocyte axis-mediated brain impairments. Interestingly, recent findings showed that microbiota dysbiosis can be induced by hippocampal myelin damage and is reversible by myelin-targeted drugs, which provides new insights into understanding how hippocampus-based functional impairment (such as in neurodegenerative Alzheimer's disease) regulates the peripheral homeostasis of microbiota and associated systemic disorders.
Collapse
Affiliation(s)
- Wen Tang
- Department of Gastroenterology, Chongqing Western Hospital, Chongqing 400052, China
| | - Qi Wang
- Department of Neurobiology, Army Medical University, Chongqing 400038, China
| | - Mingguang Sun
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China; Department of Neurology, Beijing Hospital of Integrated Traditional Chinese and Western Medicine, Beijing University of Chinese Medicine, Beijing 100853, China
| | - Chang''e Liu
- Department of Nutrition, The Seventh Medical Center of Chinese PLA General Hospital, Beijing 100700, China
| | - Yonghua Huang
- Department of Neurology, The Seventh Medical Center of Chinese PLA General Hospital, Beijing 100700, China
| | - Maohu Zhou
- Department of Neurobiology, Army Medical University, Chongqing 400038, China
| | - Xuan Zhang
- Department of Neurobiology, Army Medical University, Chongqing 400038, China
| | - Zhaoyou Meng
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China.
| | - Jiqiang Zhang
- Department of Neurobiology, Army Medical University, Chongqing 400038, China.
| |
Collapse
|
22
|
Wang X, Lalli M, Thopte U, Buxbaum JD. A scalable, high-throughput neural development platform identifies shared impact of ASD genes on cell fate and differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.25.614184. [PMID: 39386704 PMCID: PMC11463611 DOI: 10.1101/2024.09.25.614184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Background Deleterious mutations in hundreds of genes confer high risk for neurodevelopmental disorders (NDDs), posing significant challenges for therapeutic development. Identifying convergent pathways shared across NDD genes could reveal high-impact therapeutic targets. Methods To identity convergent pathways in NDD genes, we optimized Perturb-seq, a method combining CRISPR perturbation with single-cell RNA sequencing (scRNA-seq), and applied structural topic modeling (STM) to simultaneously assess impact on cell fate and developmental stage. We then studied a subset of autism spectrum disorder (ASD) genes implicated in regulation of gene expression using these improved molecular and analytical approaches. Results Results from targeting 60 high-confidence ASD risk genes revealed significant effects on neural development. As expected, ASD risk genes impacted both progenitor fate and/or neuronal differentiation. Using STM, we could identify latent topics jointly capturing cell types, cell fate, and differentiation stages. Repression of ASD risk genes led to changes in topic proportions and effects of four genes (DEAF1, KMT2A, MED13L, and MYT1L) were validated in an independent dataset. Conclusions Our optimized Perturb-seq method, combined with a novel analytical approach, provides a powerful, cost-effective framework for uncovering convergent mechanisms among genes involved in complex neurodevelopmental processes. Application of these methods advanced understanding of the impact of ASD mutations on multiple dimensions of neural development, and provides a framework for a broader examination of the function of NDD risk genes.
Collapse
Affiliation(s)
- Xuran Wang
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Matthew Lalli
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Urvashi Thopte
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York NY, USA
| |
Collapse
|
23
|
Garcia MF, Retallick-Townsley K, Pruitt A, Davidson E, Dai Y, Fitzpatrick SE, Sen A, Cohen S, Livoti O, Khan S, Dossou G, Cheung J, Deans PJM, Wang Z, Huckins L, Hoffman E, Brennand K. Dynamic convergence of autism disorder risk genes across neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609190. [PMID: 39229156 PMCID: PMC11370590 DOI: 10.1101/2024.08.23.609190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Over a hundred risk genes underlie risk for autism spectrum disorder (ASD) but the extent to which they converge on shared downstream targets to increase ASD risk is unknown. To test the hypothesis that cellular context impacts the nature of convergence, here we apply a pooled CRISPR approach to target 29 ASD loss-of-function genes in human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells, glutamatergic neurons, and GABAergic neurons. Two distinct approaches (gene-level and network-level analyses) demonstrate that convergence is greatest in mature glutamatergic neurons. Convergent effects are dynamic, varying in strength, composition, and biological role between cell types, increasing with functional similarity of the ASD genes examined, and driven by cell-type-specific gene co-expression patterns. Stratification of ASD genes yield targeted drug predictions capable of reversing gene-specific convergent signatures in human cells and ASD-related behaviors in zebrafish. Altogether, convergent networks downstream of ASD risk genes represent novel points of individualized therapeutic intervention.
Collapse
Affiliation(s)
- Meilin Fernandez Garcia
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Kayla Retallick-Townsley
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - April Pruitt
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
| | - Elizabeth Davidson
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Yi Dai
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Sarah E Fitzpatrick
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
| | - Annabel Sen
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Sophie Cohen
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Olivia Livoti
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Suha Khan
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Grace Dossou
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Jen Cheung
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - P J Michael Deans
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
| | - Zuoheng Wang
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Laura Huckins
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ellen Hoffman
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Kristen Brennand
- Departments of Psychiatry and Genetics, Division of Molecular Psychiatry, Department of Genetics, Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06511
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06511
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| |
Collapse
|
24
|
Yim KM, Baumgartner M, Krenzer M, Rosales Larios MF, Hill-Terán G, Nottoli T, Muhle RA, Noonan JP. Cell type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.608000. [PMID: 39185167 PMCID: PMC11343218 DOI: 10.1101/2024.08.14.608000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Disruptive variants in the chromodomain helicase CHD8, which acts as a transcriptional regulator during neurodevelopment, are strongly associated with risk for autism spectrum disorder (ASD). Loss of CHD8 function is hypothesized to perturb gene regulatory networks in the developing brain, thereby contributing to ASD etiology. However, insight into the cell type-specific transcriptional effects of CHD8 loss of function remains limited. We used single-cell and single-nucleus RNA-sequencing to globally profile gene expression and identify dysregulated genes in the embryonic and juvenile wild type and Chd8 +/- mouse cortex, respectively. Chd8 and other ASD risk-associated genes showed a convergent expression trajectory that was largely conserved between the mouse and human developing cortex, increasing from the progenitor zones to the cortical plate. Genes associated with risk for neurodevelopmental disorders and genes involved in neuron projection development, chromatin remodeling, signaling, and migration were dysregulated in Chd8 +/- embryonic day (E) 12.5 radial glia. Genes implicated in synaptic organization and activity were dysregulated in Chd8 +/- postnatal day (P) 25 deep- and upper-layer excitatory cortical neurons, suggesting a delay in synaptic maturation or impaired synaptogenesis due to CHD8 loss of function. Our findings reveal a complex pattern of transcriptional dysregulation in Chd8 +/- developing cortex, potentially with distinct biological impacts on progenitors and maturing neurons in the excitatory neuronal lineage.
Collapse
Affiliation(s)
- Kristina M. Yim
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Martina Krenzer
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Mount Sinai School of Medicine, Brookdale Department of Geriatrics and Palliative Medicine, New York, NY 10029, USA
| | - María F. Rosales Larios
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Social Studies of Science and Technology, Department of Evolutionary Biology, School of Sciences, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Guillermina Hill-Terán
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Present address: Higher Institute of Biological Research (INSIBIO, CONICET-UNT), Institute of Biology, National University of Tucumán, T4000 San Miguel de Tucumán, Argentina
| | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Rebecca A. Muhle
- Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA
- Present address: New York State Psychiatric Institute and Columbia University Department of Psychiatry, New York, NY 10032, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
| |
Collapse
|
25
|
von Maydell D, Wright S, Bonner JM, Staab C, Spitaleri A, Liu L, Pao PC, Yu CJ, Scannail AN, Li M, Boix CA, Mathys H, Leclerc G, Menchaca GS, Welch G, Graziosi A, Leary N, Samaan G, Kellis M, Tsai LH. Single-cell atlas of ABCA7 loss-of-function reveals impaired neuronal respiration via choline-dependent lipid imbalances. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.05.556135. [PMID: 38979214 PMCID: PMC11230156 DOI: 10.1101/2023.09.05.556135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Loss-of-function (LoF) variants in the lipid transporter ABCA7 significantly increase the risk of Alzheimer's disease (odds ratio ∼2), yet the pathogenic mechanisms and the neural cell types affected by these variants remain largely unknown. Here, we performed single-nuclear RNA sequencing of 36 human post-mortem samples from the prefrontal cortex of 12 ABCA7 LoF carriers and 24 matched non-carrier control individuals. ABCA7 LoF was associated with gene expression changes in all major cell types. Excitatory neurons, which expressed the highest levels of ABCA7, showed transcriptional changes related to lipid metabolism, mitochondrial function, cell cycle-related pathways, and synaptic signaling. ABCA7 LoF-associated transcriptional changes in neurons were similarly perturbed in carriers of the common AD missense variant ABCA7 p.Ala1527Gly (n = 240 controls, 135 carriers), indicating that findings from our study may extend to large portions of the at-risk population. Consistent with ABCA7's function as a lipid exporter, lipidomic analysis of isogenic iPSC-derived neurons (iNs) revealed profound intracellular triglyceride accumulation in ABCA7 LoF, which was accompanied by a relative decrease in phosphatidylcholine abundance. Metabolomic and biochemical analyses of iNs further indicated that ABCA7 LoF was associated with disrupted mitochondrial bioenergetics that suggested impaired lipid breakdown by uncoupled respiration. Treatment of ABCA7 LoF iNs with CDP-choline (a rate-limiting precursor of phosphatidylcholine synthesis) reduced triglyceride accumulation and restored mitochondrial function, indicating that ABCA7 LoF-induced phosphatidylcholine dyshomeostasis may directly disrupt mitochondrial metabolism of lipids. Treatment with CDP-choline also rescued intracellular amyloid β -42 levels in ABCA7 LoF iNs, further suggesting a link between ABCA7 LoF metabolic disruptions in neurons and AD pathology. This study provides a detailed transcriptomic atlas of ABCA7 LoF in the human brain and mechanistically links ABCA7 LoF-induced lipid perturbations to neuronal energy dyshomeostasis. In line with a growing body of evidence, our study highlights the central role of lipid metabolism in the etiology of Alzheimer's disease.
Collapse
|