Review

. 2024 Dec;27(12):2292-2309.

doi: 10.1038/s41593-024-01806-0. Epub 2024 Dec 3.

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

Boyan Bonev^{1

2}, Gonçalo Castelo-Branco³, Fei Chen⁴, Simone Codeluppi⁵, M Ryan Corces^{6

7

8}, Jean Fan⁹, Myriam Heiman^{10

11}, Kenneth Harris¹², Fumitaka Inoue¹³, Manolis Kellis^{4

14}, Ariel Levine¹⁵, Mo Lotfollahi^{16

17}, Chongyuan Luo¹⁸, Kristen R Maynard^{19

20

21}, Mor Nitzan^{22

23

24}, Vijay Ramani^{7

25

26}, Rahul Satijia^{27

28}, Lucas Schirmer²⁹, Yin Shen^{8

30

31}, Na Sun^{4

14}, Gilad S Green³², Fabian Theis^{17

18}, Xiao Wang^{4

33

34}, Joshua D Welch³⁵, Ozgun Gokce^{36

37}, Genevieve Konopka^{38

39}, Shane Liddelow^{40

41

42

43}, Evan Macosko^{44

45

46

47}, Omer Ali Bayraktar⁴⁸, Naomi Habib⁴⁹, Tomasz J Nowakowski^{50

51

52

53

54}

Affiliations

¹ Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
² Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.
³ Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
⁴ The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁵ Moleculent, Stockholm, Sweden.
⁶ Gladstone Institute of Neurological Disease, San Francisco, CA, USA.
⁷ Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
⁸ Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
⁹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
¹⁰ Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
¹¹ The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
¹² UCL Queen Square Institute of Neurology, University College London, London, UK.
¹³ Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
¹⁴ Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁵ Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
¹⁶ Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany.
¹⁷ Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
¹⁸ Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
¹⁹ Lieber Institute for Brain Development, Baltimore, MD, USA.
²⁰ Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
²¹ Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
²² School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
²³ Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel.
²⁴ Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
²⁵ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
²⁶ Bakar Computational Health Sciences Institute, San Francisco, CA, USA.
²⁷ New York Genome Center, New York, NY, USA.
²⁸ Center for Genomics and Systems Biology, New York University, New York, NY, USA.
²⁹ Department of Neurology, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
³⁰ Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
³¹ Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
³² The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
³³ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
³⁴ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³⁵ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
³⁶ German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany. Ozgun.Goekce@ukbonn.de.
³⁷ Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany. Ozgun.Goekce@ukbonn.de.
³⁸ Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA. genevieve.konopka@utsouthwestern.edu.
³⁹ Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA. genevieve.konopka@utsouthwestern.edu.
⁴⁰ Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴¹ Department of Neuroscience & Physiology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴² Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴³ Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴⁴ The Broad Institute of MIT and Harvard, Cambridge, MA, USA. emacosko@broadinstitute.org.
⁴⁵ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. emacosko@broadinstitute.org.
⁴⁶ Department of Neurobiology, Harvard Medical School, Boston, MA, USA. emacosko@broadinstitute.org.
⁴⁷ Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA. emacosko@broadinstitute.org.
⁴⁸ Wellcome Sanger Institute, Hinxton, UK. ob5@sanger.ac.uk.
⁴⁹ The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. naomi.habib@mail.huji.ac.il.
⁵⁰ Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁵¹ Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁵² Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁵³ Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁵⁴ The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.

PMID: 39627587
PMCID: PMC11999325
DOI: 10.1038/s41593-024-01806-0

Review

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

Boyan Bonev et al. Nat Neurosci. 2024 Dec.

. 2024 Dec;27(12):2292-2309.

doi: 10.1038/s41593-024-01806-0. Epub 2024 Dec 3.

Authors

Affiliations

¹ Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
² Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.
³ Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
⁴ The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁵ Moleculent, Stockholm, Sweden.
⁶ Gladstone Institute of Neurological Disease, San Francisco, CA, USA.
⁷ Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
⁸ Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
⁹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
¹⁰ Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
¹¹ The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
¹² UCL Queen Square Institute of Neurology, University College London, London, UK.
¹³ Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
¹⁴ Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁵ Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
¹⁶ Institute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany.
¹⁷ Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
¹⁸ Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
¹⁹ Lieber Institute for Brain Development, Baltimore, MD, USA.
²⁰ Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD, USA.
²¹ Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
²² School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
²³ Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel.
²⁴ Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
²⁵ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
²⁶ Bakar Computational Health Sciences Institute, San Francisco, CA, USA.
²⁷ New York Genome Center, New York, NY, USA.
²⁸ Center for Genomics and Systems Biology, New York University, New York, NY, USA.
²⁹ Department of Neurology, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
³⁰ Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
³¹ Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
³² The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
³³ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
³⁴ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³⁵ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
³⁶ German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany. Ozgun.Goekce@ukbonn.de.
³⁷ Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany. Ozgun.Goekce@ukbonn.de.
³⁸ Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA. genevieve.konopka@utsouthwestern.edu.
³⁹ Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA. genevieve.konopka@utsouthwestern.edu.
⁴⁰ Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴¹ Department of Neuroscience & Physiology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴² Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴³ Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴⁴ The Broad Institute of MIT and Harvard, Cambridge, MA, USA. emacosko@broadinstitute.org.
⁴⁵ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. emacosko@broadinstitute.org.
⁴⁶ Department of Neurobiology, Harvard Medical School, Boston, MA, USA. emacosko@broadinstitute.org.
⁴⁷ Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA. emacosko@broadinstitute.org.
⁴⁸ Wellcome Sanger Institute, Hinxton, UK. ob5@sanger.ac.uk.
⁴⁹ The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. naomi.habib@mail.huji.ac.il.
⁵⁰ Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁵¹ Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁵² Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁵³ Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁵⁴ The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.

PMID: 39627587
PMCID: PMC11999325
DOI: 10.1038/s41593-024-01806-0

Erratum in

Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
Bonev B, Castelo-Branco G, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M, Levine A, Lotfollahi M, Luo C, Maynard KR, Nitzan M, Ramani V, Satijia R, Schirmer L, Shen Y, Sun N, Green GS, Theis F, Wang X, Welch JD, Gokce O, Konopka G, Liddelow S, Macosko E, Ali Bayraktar O, Habib N, Nowakowski TJ. Bonev B, et al. Nat Neurosci. 2025 Jan;28(1):216. doi: 10.1038/s41593-024-01858-2. Nat Neurosci. 2025. PMID: 39681663 Free PMC article. No abstract available.

Abstract

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.

PubMed Disclaimer

Conflict of interest statement

Competing interests: S.A.L. declares a financial interest in AstronauTx and Synapticure. All other authors declare no competing interests.

Figures

**Figure 1.**
Biological considerations: cellular architecture and research questions. Emerging single cell atlas studies have created reference resources for defining cell types in normal and pathological brain tissue. Cell types and states defined by these studies exist in complex and dynamic communities *in vivo* and more disease associated states and types may emerge in the future. Advent of spatial transcriptomics technologies helps to define cellular neighborhoods and identify candidate networks of molecular interactions, while advanced single cell genomic technologies can provide insights into dynamic intracellular pathways underlying cellular transitions.

**Figure 2.**
Outline of key considerations involved in designing high-throughput single-cell and spatial transcriptomics studies.

**Figure 3.**
Outline of computational design of high-throughput single-cell/nucleus and spatial omics studies. TF - Transcription factor; CHIP - chromatin immunoprecipitation.

**Figure 4.**
Epigenomic technologies. a) Overview of the major modalities regulating gene expression currently studied using high-throughput single cell technologies. b) Summary of key single-cell epigenomics technologies. Tn5 – hyperactive Tn5 transposase, Me – methyl group, Ac- acetyl group.

**Box 1 Fig.**
Quality control (QC) in sc/snRNAseq involves evaluating both cells and genes.

See this image and copyright information in PMC

References

1. Siletti K et al. Transcriptomic diversity of cell types across the adult human brain. Science 382, eadd7046 (2023). - PubMed
1. Kim SS et al. Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types. Nat. Commun. 15, 563 (2024). - PMC - PubMed
1. Sun N et al. Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer’s disease. Nat. Neurosci. 26, 970–982 (2023). - PMC - PubMed
1. Cain A et al. Multicellular communities are perturbed in the aging human brain and Alzheimer’s disease. Nat. Neurosci. 26, 1267–1280 (2023). - PMC - PubMed
1. Kim CN, Shin D, Wang A & Nowakowski TJ Spatiotemporal molecular dynamics of the developing human thalamus. Science 382, (2023). - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Erratum in

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous