학술논문
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Document Type
Report
Author
Yao, Zizhen; van Velthoven, Cindy T.J.; Nguyen, Thuc Nghi; Goldy, Jeff; Sedeno-Cortes, Adriana E.; Baftizadeh, Fahimeh; Bertagnolli, Darren; Casper, Tamara; Chiang, Megan; Crichton, Kirsten; Ding, Song-Lin; Fong, Olivia; Garren, Emma; Glandon, Alexandra; Gouwens, Nathan W.; Gray, James; Graybuck, Lucas T.; Hawrylycz, Michael J.; Hirschstein, Daniel; Kroll, Matthew; Lathia, Kanan; Lee, Changkyu; Levi, Boaz; McMillen, Delissa; Mok, Stephanie; Pham, Thanh; Ren, Qingzhong; Rimorin, Christine; Shapovalova, Nadiya; Sulc, Josef; Sunkin, Susan M.; Tieu, Michael; Torkelson, Amy; Tung, Herman; Ward, Katelyn; Dee, Nick; Smith, Kimberly A.; Tasic, Bosiljka; Zeng, Hongkui
Source
Cell. June 10, 2021, Vol. 184 Issue 12, 3222
Subject
Language
English
ISSN
0092-8674
Abstract
Keywords single-cell RNA sequencing; single-cell transcriptomics; cell type; cortex; hippocampus; glutamatergic; GABAergic; excitatory neuron; interneuron Highlights * Single-cell transcriptomics from >1.3 million cells in the mouse cortex and hippocampus * Many neuron types specific to associational cortex and hippocampal regions are identified * Parallel cell-type and laminar organization between isocortex and hippocampal formation * Large-scale continuous neuron-type variation in isocortex and hippocampus/subiculum Summary The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion, and learning. We profiled ~1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic cell-type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and the isocortex share a common circuit organization. We also identify large-scale continuous and graded variations of cell types along isocortical depth, across the isocortical sheet, and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of the mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity, and function of these two brain structures. Author Affiliation: (1) Allen Institute for Brain Science, Seattle, WA 98109, USA * Corresponding author Article History: Received 2 April 2020; Revised 9 February 2021; Accepted 14 April 2021 (miscellaneous) Published: May 17, 2021 (footnote)2 Lead contact Byline: Zizhen Yao (1), Cindy T.J. van Velthoven (1), Thuc Nghi Nguyen (1), Jeff Goldy (1), Adriana E. Sedeno-Cortes (1), Fahimeh Baftizadeh (1), Darren Bertagnolli (1), Tamara Casper (1), Megan Chiang (1), Kirsten Crichton (1), Song-Lin Ding (1), Olivia Fong (1), Emma Garren (1), Alexandra Glandon (1), Nathan W. Gouwens (1), James Gray (1), Lucas T. Graybuck (1), Michael J. Hawrylycz (1), Daniel Hirschstein (1), Matthew Kroll (1), Kanan Lathia (1), Changkyu Lee (1), Boaz Levi (1), Delissa McMillen (1), Stephanie Mok (1), Thanh Pham (1), Qingzhong Ren (1), Christine Rimorin (1), Nadiya Shapovalova (1), Josef Sulc (1), Susan M. Sunkin (1), Michael Tieu (1), Amy Torkelson (1), Herman Tung (1), Katelyn Ward (1), Nick Dee (1), Kimberly A. Smith (1), Bosiljka Tasic (1), Hongkui Zeng [hongkuiz@alleninstitute.org] (1,2,*)