Implementation and validation of single-cell genomics experiments in neuroscience

Marco Colonna; Genevieve Konopka; Shane A Liddelow; Tomasz Nowakowski; Rajeshwar Awatramani; Helen S Bateup; Cathryn R Cadwell; Emre Caglayan; Jerry L Chen; Jesse Gillis; Martin Kampmann; Fenna Krienen; Samuel E Marsh; Michelle Monje; Michael R O'Dea; Rickie Patani; Alex A Pollen; Francisco J Quintana; Marissa Scavuzzo; Matthew Schmitz; Steven A Sloan; Paul J Tesar; Jessica Tollkuhn; Maria Antonietta Tosches; Madeleine E Urbanek; Jonathan M Werner; Omer A Bayraktar; Ozgun Gokce; Naomi Habib

doi:10.1038/s41593-024-01814-0

Implementation and validation of single-cell genomics experiments in neuroscience

Nat Neurosci. 2024 Dec;27(12):2310-2325. doi: 10.1038/s41593-024-01814-0. Epub 2024 Dec 3.

Authors

Marco Colonna¹, Genevieve Konopka², Shane A Liddelow^{3

4

5

6}, Tomasz Nowakowski^{7

8

9

10}, Rajeshwar Awatramani¹¹, Helen S Bateup^{12

13

14}, Cathryn R Cadwell^{15

16

17

18}, Emre Caglayan¹⁹, Jerry L Chen^{20

21

22

23}, Jesse Gillis^{24

25}, Martin Kampmann^{26

27}, Fenna Krienen²⁸, Samuel E Marsh^{29

30

31}, Michelle Monje^{32

33}, Michael R O'Dea³⁴, Rickie Patani^{35

36}, Alex A Pollen^{37

38}, Francisco J Quintana^{39

40}, Marissa Scavuzzo^{41

42}, Matthew Schmitz³⁷, Steven A Sloan⁴³, Paul J Tesar^{41

42}, Jessica Tollkuhn²⁵, Maria Antonietta Tosches⁴⁴, Madeleine E Urbanek⁴⁵, Jonathan M Werner^{24

25}, Omer A Bayraktar⁴⁶, Ozgun Gokce^{47

48}, Naomi Habib⁴⁹

Affiliations

¹ Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA. mcolonna@wustl.edu.
² Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA. genevieve.konopka@utsouthwestern.edu.
³ Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁴ Department of Neuroscience & Physiology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁵ Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁶ Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.
⁷ Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁸ Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
⁹ Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
¹⁰ Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.
¹¹ Department of Microbiology and Immunology, Northwestern University, Chicago, IL, USA.
¹² Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA, USA.
¹³ Department of Neuroscience, University of California, Berkeley, Berkeley, CA, USA.
¹⁴ Chan Zuckerberg Biohub, San Francisco, CA, USA.
¹⁵ Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
¹⁶ Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
¹⁷ Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
¹⁸ Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
¹⁹ Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
²⁰ Department of Biomedical Engineering, Boston University, Boston, MA, USA.
²¹ Center for Neurophotonics, Boston University, Boston, MA, USA.
²² Department of Biology, Boston University, Boston, MA, USA.
²³ Center for Systems Neuroscience, Boston University, Boston, MA, USA.
²⁴ Department of Physiology and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
²⁵ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
²⁶ Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
²⁷ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
²⁸ Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.
²⁹ F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
³⁰ Harvard Medical School, Boston, MA, USA.
³¹ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³² Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
³³ Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
³⁴ Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA.
³⁵ Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK.
³⁶ The Francis Crick Institute, Human Stem Cells and Neurodegeneration Laboratory, London, UK.
³⁷ Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
³⁸ Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
³⁹ Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
⁴⁰ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁴¹ Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, OH, USA.
⁴² Institute for Glial Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
⁴³ Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
⁴⁴ Department of Biological Sciences, Columbia University, New York, NY, USA.
⁴⁵ Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
⁴⁶ Wellcome Sanger Institute, Cambridge, UK. ob5@sanger.ac.uk.
⁴⁷ Department of Old Age Psychiatry and Cognitive Disorders, University Hospital Bonn, Bonn, Germany. ozgun.goekce@ukbonn.de.
⁴⁸ German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany. ozgun.goekce@ukbonn.de.
⁴⁹ Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. naomi.habib@mail.huji.ac.il.

PMID: 39627589
DOI: 10.1038/s41593-024-01814-0

Abstract

Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.

Publication types

Review

MeSH terms

Animals
Gene Expression Profiling / methods
Genomics* / methods
Humans
Neurosciences* / methods
Single-Cell Analysis* / methods
Transcriptome