Department of Bioengineering, Stanford University, Stanford, United States; Department of Applied Physics, Stanford University, Stanford, United States
Drew Friedmann
Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, United States
Jiawei Zeng
National Institute of Biological Science, Beijing, China
Sophie M Grutzner
Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, United States
Albert Pun
Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, United States
Grace Q Zhao
Department of Neurobiology, Stanford University School of Medicine, Stanford, United States
Sai Saroja Kolluru
Department of Bioengineering, Stanford University, Stanford, United States; Department of Applied Physics, Stanford University, Stanford, United States
Ruiyu Wang
National Institute of Biological Science, Beijing, China
Rui Lin
National Institute of Biological Science, Beijing, China
Pengcheng Li
Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology (HUST), Wuhan, China; HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
Anan Li
Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology (HUST), Wuhan, China; HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology (HUST), Wuhan, China
Department of Bioengineering, Stanford University, Stanford, United States; Department of Applied Physics, Stanford University, Stanford, United States; Chan Zuckerberg Biohub, San Francisco, United States
Serotonin neurons of the dorsal and median raphe nuclei (DR, MR) collectively innervate the entire forebrain and midbrain, modulating diverse physiology and behavior. To gain a fundamental understanding of their molecular heterogeneity, we used plate-based single-cell RNA-sequencing to generate a comprehensive dataset comprising eleven transcriptomically distinct serotonin neuron clusters. Systematic in situ hybridization mapped specific clusters to the principal DR, caudal DR, or MR. These transcriptomic clusters differentially express a rich repertoire of neuropeptides, receptors, ion channels, and transcription factors. We generated novel intersectional viral-genetic tools to access specific subpopulations. Whole-brain axonal projection mapping revealed that DR serotonin neurons co-expressing vesicular glutamate transporter-3 preferentially innervate the cortex, whereas those co-expressing thyrotropin-releasing hormone innervate subcortical regions in particular the hypothalamus. Reconstruction of 50 individual DR serotonin neurons revealed diverse and segregated axonal projection patterns at the single-cell level. Together, these results provide a molecular foundation of the heterogenous serotonin neuronal phenotypes.
