Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

被引：0

作者：

Boyan Bonev ^{[1
]}

Gonçalo Castelo-Branco ^{[2
]}

Fei Chen ^{[3
]}

Simone Codeluppi ^{[4
]}

M. Ryan Corces ^{[5
]}

Jean Fan ^{[6
]}

Myriam Heiman ^{[7
]}

Kenneth Harris ^{[8
]}

Fumitaka Inoue ^{[9
]}

Manolis Kellis ^{[10
]}

Ariel Levine ^{[11
]}

Mo Lotfollahi ^{[12
]}

Chongyuan Luo ^{[13
]}

Kristen R. Maynard ^{[4
]}

Mor Nitzan ^{[14
]}

Vijay Ramani ^{[15
]}

Rahul Satijia ^{[16
]}

Lucas Schirmer ^{[17
]}

Yin Shen ^{[18
]}

Na Sun ^{[19
]}

Gilad S. Green ^{[20
]}

Fabian Theis ^{[21
]}

Xiao Wang ^{[22
]}

Joshua D. Welch ^{[23
]}

Ozgun Gokce ^{[24
]}

Genevieve Konopka ^{[7
]}

Shane Liddelow ^{[25
]}

Evan Macosko ^{[26
]}

Omer Ali Bayraktar ^{[27
]}

Naomi Habib ^{[28
]}

Tomasz J. Nowakowski ^{[29
]}

机构：

[1] Helmholtz Zentrum München,Helmholtz Pioneer Campus

[2] Ludwig-Maximilians-Universität München,Physiological Genomics, Biomedical Center

[3] Karolinska Institutet,Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics

[4] The Broad Institute of MIT and Harvard,Department of Neurology

[5] Moleculent,Department of Biomedical Engineering

[6] Gladstone Institute of Neurological Disease,Department of Brain and Cognitive Sciences

[7] Gladstone Institute of Data Science and Biotechnology,The Picower Institute for Learning and Memory

[8] University of California,UCL Queen Square Institute of Neurology

[9] San Francisco,Institute for the Advanced Study of Human Biology (WPI

[10] Johns Hopkins University,ASHBi)

[11] MIT,Computer Science and Artificial Intelligence Lab

[12] MIT,Spinal Circuits and Plasticity Unit

[13] University College London,Institute of Computational Biology

[14] Kyoto University,Wellcome Sanger Institute

[15] Massachusetts Institute of Technology,Department of Human Genetics

[16] National Institute of Neurological Disorders and Stroke,Department of Psychiatry

[17] Helmholtz Center Munich – German Research Center for Environmental Health,Department of Neuroscience

[18] Wellcome Genome Campus,School of Computer Science and Engineering

[19] University of California,Racah Institute of Physics

[20] Los Angeles,Faculty of Medicine

[21] Lieber Institute for Brain Development,Department of Biochemistry and Biophysics

[22] Johns Hopkins School of Medicine,Center for Genomics and Systems Biology

[23] Johns Hopkins School of Medicine,Department of Neurology, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim

[24] The Hebrew University of Jerusalem,Institute for Human Genetics

[25] The Hebrew University of Jerusalem,Weill Institute for Neurosciences

[26] The Hebrew University of Jerusalem,The Edmond and Lily Safra Center for Brain Sciences

[27] University of California,Department of Chemistry

[28] San Francisco,Stanley Center for Psychiatric Research

[29] Bakar Computational Health Sciences Institute,Department of Computational Medicine and Bioinformatics

[30] New York Genome Center,Department of Neurodegenerative Diseases and Geriatric Psychiatry

[31] New York University,Department of Neuroscience

[32] Heidelberg University,Peter O’Donnell Jr. Brain Institute

[33] University of California,Neuroscience Institute

[34] San Francisco,Department of Neuroscience & Physiology

[35] University of California,Parekh Center for Interdisciplinary Neurology

[36] San Francisco,Department of Ophthalmology

[37] The Hebrew University of Jerusalem,Department of Neurobiology

[38] Massachusetts Institute of Technology,Department of Psychiatry

[39] Broad Institute of MIT and Harvard,Department of Neurological Surgery

[40] University of Michigan,Department of Anatomy

[41] German Center for Neurodegenerative Diseases (DZNE),Department of Psychiatry and Behavioral Sciences

[42] University Hospital Bonn,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research

[43] UT Southwestern Medical Center,undefined

[44] UT Southwestern Medical Center,undefined

[45] NYU Grossman School of Medicine,undefined

[46] NYU Grossman School of Medicine,undefined

[47] NYU Grossman School of Medicine,undefined

[48] NYU Grossman School of Medicine,undefined

[49] Harvard Medical School,undefined

[50] Massachusetts General Hospital,undefined

来源：

Nature Neuroscience | 2024年 / 27卷 / 12期

关键词：

D O I：

10.1038/s41593-024-01806-0

中图分类号：

学科分类号：

摘要：

Over the past decade, single-cell genomics technologies have allowed scalable profiling of cell-type-specific features, which has substantially increased our ability to study cellular diversity and transcriptional programs in heterogeneous tissues. Yet our understanding of mechanisms of gene regulation or the rules that govern interactions between cell types is still limited. The advent of new computational pipelines and technologies, such as single-cell epigenomics and spatially resolved transcriptomics, has created opportunities to explore two new axes of biological variation: cell-intrinsic regulation of cell states and expression programs and interactions between cells. Here, we summarize the most promising and robust technologies in these areas, discuss their strengths and limitations and discuss key computational approaches for analysis of these complex datasets. We highlight how data sharing and integration, documentation, visualization and benchmarking of results contribute to transparency, reproducibility, collaboration and democratization in neuroscience, and discuss needs and opportunities for future technology development and analysis.

引用

页码：2292 / 2309

页数：17

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Simone Codeluppi
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