Michael A. Wheeler1,2†, Iain C. Clark1,3†, Hong-Gyun Lee1†, Zhaorong Li1,2, Mathias Linnerbauer1, Joseph M. Rone1, Manon Blain4, Camilo Faust Akl1, Gavin Piester1,5, Federico Giovannoni1, Marc Charabati1, Joon-Hyuk Lee1, Yoon-Chul Kye1,6, Joshua Choi1,6, Liliana M. Sanmarco1, Lena Srun1, Elizabeth N. Chung1, Lucas E. Flausino1, Brian M. Andersen1,7, Veit Rothhammer1,8, Hiroshi Yano9, Tomer Illouz1, Stephanie E. J. Zandee10, Carolin Daniel11,12,13, David Artis9,14, Marco Prinz15,16,17, Adam R. Abate18,19, Vijay K. Kuchroo1,2,6, Jack P. Antel4, Alexandre Prat10, Francisco J. Quintana1,2*
1Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA.
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
3Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, USA.
4Neuroimmunology Unit,Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 2B4, Canada.
5Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA.
6Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA.
7Department of Neurology, Jamaica Plain Veterans Affairs Hospital, Harvard Medical School, Boston, MA 02130, USA.
8Department of Neurology, University Hospital Erlangen, Friedrich-AlexanderUniversity Erlangen-Nuernberg, Erlangen, Germany.
9Jill Roberts Institute for Research in Inflammatory Bowel Disease, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
10Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Universitéde Montréal, Montreal, QC H2X 0A9, Canada.
11Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, 80939 Munich, Germany.
12Deutsches Zentrum für Diabetesforschung, 85764 Munich-Neuherberg, Germany.
13Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, 80337 Munich, Germany.
14Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, NewYork, NY 10021, USA.
15Institute of Neuropathology, University of Freiburg, D-79106 Freiburg, Germany.
16Signaling Research Centres BIOSS and CIBSS, University of Freiburg, D-79106 Freiburg, Germany.
17Center for Basics in Neuro Modulation, Faculty of Medicine, University of Freiburg, D-79106 Freiburg, Germany.
18Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA.
19Chan Zuckerberg Biohub, San Francisco, CA, USA.
*Corresponding author: Francisco J. Quintana
†These authors contributed equally to this work.
Cell-cell interactions in the central nervous system play important roles in neurologic diseases. However, little is known about the specific molecular pathways involved, and methods for their systematic identification are limited. Here, we developed a forward genetic screening platform that combines CRISPR-Cas9 perturbations, cell coculture in picoliter droplets, and microfluidic-based fluorescence-activated droplet sorting to identify mechanisms of cell-cell communication. We used SPEAC-seq (systematic perturbation of encapsulated associated cells followed by sequencing), in combination with in vivo genetic perturbations, to identify microglia-produced amphiregulin as a suppressor of disease-promoting astrocyte responses in multiple sclerosis preclinical models and clinical samples. Thus, SPEAC-seq enables the high-throughput systematic identification of cell-cell communication mechanisms.