Barcoded viral tracing of single-cell interactions in central nervous system inflammation

Iain C Clark; Cristina Gutiérrez-Vázquez; Michael A Wheeler; Zhaorong Li; Veit Rothhammer; Mathias Linnerbauer; Liliana M Sanmarco; Lydia Guo; Manon Blain; Stephanie E J Zandee; Chun-Cheih Chao; Katelyn V Batterman; Marius Schwabenland; Peter Lotfy; Amalia Tejeda-Velarde; Patrick Hewson; Carolina Manganeli Polonio; Michael W Shultis; Yasmin Salem; Emily C Tjon; Pedro H Fonseca-Castro; Davis M Borucki; Kalil Alves de Lima; Agustin Plasencia; Adam R Abate; Douglas L Rosene; Kevin J Hodgetts; Marco Prinz; Jack P Antel; Alexandre Prat; Francisco J Quintana

doi:10.1126/science.abf1230

Barcoded viral tracing of single-cell interactions in central nervous system inflammation

Science. 2021 Apr 23;372(6540):eabf1230. doi: 10.1126/science.abf1230.

Authors

Iain C Clark^#^{1

2}, Cristina Gutiérrez-Vázquez^#¹, Michael A Wheeler^#^{1

3}, Zhaorong Li^{1

3}, Veit Rothhammer^{1

4}, Mathias Linnerbauer^{1

4}, Liliana M Sanmarco¹, Lydia Guo¹, Manon Blain⁵, Stephanie E J Zandee⁶, Chun-Cheih Chao¹, Katelyn V Batterman⁷, Marius Schwabenland⁸, Peter Lotfy^{1

3}, Amalia Tejeda-Velarde¹, Patrick Hewson¹, Carolina Manganeli Polonio¹, Michael W Shultis¹, Yasmin Salem¹, Emily C Tjon¹, Pedro H Fonseca-Castro¹, Davis M Borucki¹, Kalil Alves de Lima¹, Agustin Plasencia¹, Adam R Abate^{9

10}, Douglas L Rosene⁷, Kevin J Hodgetts¹, Marco Prinz^{8

11

12}, Jack P Antel⁵, Alexandre Prat⁶, Francisco J Quintana^{13

3}

Affiliations

¹ Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
² Department of Bioengineering, University of California, Berkeley, California Institute for Quantitative Biosciences, Berkeley, CA 94720, USA.
³ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁴ Department of Neurology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany.
⁵ Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada.
⁶ Neuroimmunology Research Laboratory, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada.
⁷ Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA.
⁸ Institute of Neuropathology, University of Freiburg, D-79106 Freiburg, Germany.
⁹ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA.
¹⁰ Chan Zuckerberg Biohub, San Francisco, CA, USA.
¹¹ Signaling Research Centres BIOSS and CIBSS, University of Freiburg, D-79106 Freiburg, Germany.
¹² Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, D-79106 Freiburg, Germany.
¹³ Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. fquintana@bwh.harvard.edu.

^# Contributed equally.

Abstract

Cell-cell interactions control the physiology and pathology of the central nervous system (CNS). To study astrocyte cell interactions in vivo, we developed rabies barcode interaction detection followed by sequencing (RABID-seq), which combines barcoded viral tracing and single-cell RNA sequencing (scRNA-seq). Using RABID-seq, we identified axon guidance molecules as candidate mediators of microglia-astrocyte interactions that promote CNS pathology in experimental autoimmune encephalomyelitis (EAE) and, potentially, multiple sclerosis (MS). In vivo cell-specific genetic perturbation EAE studies, in vitro systems, and the analysis of MS scRNA-seq datasets and CNS tissue established that Sema4D and Ephrin-B3 expressed in microglia control astrocyte responses via PlexinB2 and EphB3, respectively. Furthermore, a CNS-penetrant EphB3 inhibitor suppressed astrocyte and microglia proinflammatory responses and ameliorated EAE. In summary, RABID-seq identified microglia-astrocyte interactions and candidate therapeutic targets.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Antigens, CD / metabolism
Astrocytes / physiology*
Brain / pathology
Brain / physiopathology
Cell Communication*
Central Nervous System / pathology*
Central Nervous System / physiopathology
Encephalomyelitis, Autoimmune, Experimental / pathology
Encephalomyelitis, Autoimmune, Experimental / physiopathology*
Ephrin-B3 / metabolism
Herpesvirus 1, Suid / genetics
Humans
Male
Mice
Mice, Inbred C57BL
Microglia / physiology*
Mitochondria / metabolism
Multiple Sclerosis / pathology
Multiple Sclerosis / physiopathology*
NF-kappa B / metabolism
Nerve Tissue Proteins / metabolism
RNA-Seq
Reactive Oxygen Species / metabolism
Receptor, EphB3 / antagonists & inhibitors
Receptor, EphB3 / metabolism
Receptors, Cell Surface / metabolism
Semaphorins / metabolism
Signal Transduction
Single-Cell Analysis*
T-Lymphocytes / physiology
TOR Serine-Threonine Kinases / metabolism

Substances

Antigens, CD
CD100 antigen
Ephrin-B3
NF-kappa B
Nerve Tissue Proteins
PLXNB1 protein, human
PLXNB2 protein, human
Plxnb1 protein, mouse
Plxnb2 protein, mouse
Reactive Oxygen Species
Receptors, Cell Surface
Sema4d protein, mouse
Semaphorins
mTOR protein, mouse
Receptor, EphB3
TOR Serine-Threonine Kinases

Abstract

Publication types

MeSH terms

Substances

Grants and funding