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Conserved cell types with divergent features between human and mouse cortex

Rebecca D Hodge, Trygve E Bakken, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, Lucas T Graybuck, Jennie L Close, Brian Long, Osnat Penn, Zizhen Yao, Jeroen Eggermont, Thomas Hollt, Boaz P Levi, Soraya I Shehata, Brian Aevermann, Allison Beller, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Charles Cobbs, Rachel Dalley, Nick Dee, Song-Lin Ding, Richard G Ellenbogen, Olivia Fong, Emma Garren, Jeff Goldy, Ryder P Gwinn, Daniel Hirschstein, C Dirk Keene, Mohamed Keshk, Andrew L Ko, Kanan Lathia, Ahmed Mahfouz, Zoe Maltzer, Medea McGraw, Thuc Nghi Nguyen, Julie Nyhus, Jeffrey G Ojemann, Aaron Oldre, Sheana Parry, Shannon Reynolds, Christine Rimorin, Nadiya V Shapovalova, Saroja Somasundaram, Aaron Szafer, Elliot R Thomsen, Michael Tieu, Richard H Scheuermann, Rafael Yuste, Susan M Sunkin, Boudewijn Lelieveldt, David Feng, Lydia Ng, Amy Bernard, Michael Hawrylycz, John W. Phillips, Bosiljka Tasic, Hongkui Zeng, Allan R Jones, Christof Koch, Ed S Lein
doi: https://doi.org/10.1101/384826
Rebecca D Hodge
1Allen Institute for Brain Science, Seattle, WA, USA
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Trygve E Bakken
1Allen Institute for Brain Science, Seattle, WA, USA
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Jeremy A Miller
1Allen Institute for Brain Science, Seattle, WA, USA
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Kimberly A Smith
1Allen Institute for Brain Science, Seattle, WA, USA
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Eliza R Barkan
1Allen Institute for Brain Science, Seattle, WA, USA
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Lucas T Graybuck
1Allen Institute for Brain Science, Seattle, WA, USA
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Jennie L Close
1Allen Institute for Brain Science, Seattle, WA, USA
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Brian Long
1Allen Institute for Brain Science, Seattle, WA, USA
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Osnat Penn
1Allen Institute for Brain Science, Seattle, WA, USA
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Zizhen Yao
1Allen Institute for Brain Science, Seattle, WA, USA
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Jeroen Eggermont
2Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
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Thomas Hollt
2Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
3Department of Intelligent Systems, Delft University of Technology, Delft, the Netherlands
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Boaz P Levi
1Allen Institute for Brain Science, Seattle, WA, USA
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Soraya I Shehata
1Allen Institute for Brain Science, Seattle, WA, USA
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Brian Aevermann
4J. Craig Venter Institute, La Jolla, CA, USA
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Allison Beller
5Department of Pathology, University of Washington, Seattle, WA, USA
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Darren Bertagnolli
1Allen Institute for Brain Science, Seattle, WA, USA
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Krissy Brouner
1Allen Institute for Brain Science, Seattle, WA, USA
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Tamara Casper
1Allen Institute for Brain Science, Seattle, WA, USA
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Charles Cobbs
6The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
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Rachel Dalley
1Allen Institute for Brain Science, Seattle, WA, USA
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Nick Dee
1Allen Institute for Brain Science, Seattle, WA, USA
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Song-Lin Ding
1Allen Institute for Brain Science, Seattle, WA, USA
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Richard G Ellenbogen
7Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA
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Olivia Fong
1Allen Institute for Brain Science, Seattle, WA, USA
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Emma Garren
1Allen Institute for Brain Science, Seattle, WA, USA
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Jeff Goldy
1Allen Institute for Brain Science, Seattle, WA, USA
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Ryder P Gwinn
8Epilepsy Surgery and Functional Neurosurgery, Swedish Neuroscience Institute, Seattle, WA, USA
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Daniel Hirschstein
1Allen Institute for Brain Science, Seattle, WA, USA
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C Dirk Keene
5Department of Pathology, University of Washington, Seattle, WA, USA
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Mohamed Keshk
4J. Craig Venter Institute, La Jolla, CA, USA
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Andrew L Ko
7Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA
9Regional Epilepsy Center at Harborview Medical Center, Seattle, WA, USA
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Kanan Lathia
1Allen Institute for Brain Science, Seattle, WA, USA
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Ahmed Mahfouz
2Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
3Department of Intelligent Systems, Delft University of Technology, Delft, the Netherlands
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Zoe Maltzer
1Allen Institute for Brain Science, Seattle, WA, USA
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Medea McGraw
1Allen Institute for Brain Science, Seattle, WA, USA
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Thuc Nghi Nguyen
1Allen Institute for Brain Science, Seattle, WA, USA
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Julie Nyhus
1Allen Institute for Brain Science, Seattle, WA, USA
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Jeffrey G Ojemann
7Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA
9Regional Epilepsy Center at Harborview Medical Center, Seattle, WA, USA
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Aaron Oldre
1Allen Institute for Brain Science, Seattle, WA, USA
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Sheana Parry
1Allen Institute for Brain Science, Seattle, WA, USA
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Shannon Reynolds
1Allen Institute for Brain Science, Seattle, WA, USA
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Christine Rimorin
1Allen Institute for Brain Science, Seattle, WA, USA
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Nadiya V Shapovalova
1Allen Institute for Brain Science, Seattle, WA, USA
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Saroja Somasundaram
1Allen Institute for Brain Science, Seattle, WA, USA
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Aaron Szafer
1Allen Institute for Brain Science, Seattle, WA, USA
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Elliot R Thomsen
1Allen Institute for Brain Science, Seattle, WA, USA
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Michael Tieu
1Allen Institute for Brain Science, Seattle, WA, USA
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Richard H Scheuermann
4J. Craig Venter Institute, La Jolla, CA, USA
10Department of Pathology, University of California, San Diego, CA, USA
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Rafael Yuste
11Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA
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Susan M Sunkin
1Allen Institute for Brain Science, Seattle, WA, USA
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Boudewijn Lelieveldt
2Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
3Department of Intelligent Systems, Delft University of Technology, Delft, the Netherlands
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David Feng
1Allen Institute for Brain Science, Seattle, WA, USA
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Lydia Ng
1Allen Institute for Brain Science, Seattle, WA, USA
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Amy Bernard
1Allen Institute for Brain Science, Seattle, WA, USA
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Michael Hawrylycz
1Allen Institute for Brain Science, Seattle, WA, USA
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John W. Phillips
1Allen Institute for Brain Science, Seattle, WA, USA
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Bosiljka Tasic
1Allen Institute for Brain Science, Seattle, WA, USA
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Hongkui Zeng
1Allen Institute for Brain Science, Seattle, WA, USA
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Allan R Jones
1Allen Institute for Brain Science, Seattle, WA, USA
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Christof Koch
1Allen Institute for Brain Science, Seattle, WA, USA
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Ed S Lein
1Allen Institute for Brain Science, Seattle, WA, USA
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  • For correspondence: edl@alleninstitute.org
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Abstract

Elucidating the cellular architecture of the human neocortex is central to understanding our cognitive abilities and susceptibility to disease. Here we applied single nucleus RNA-sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cerebral cortex. We identify a highly diverse set of excitatory and inhibitory neuronal types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to a similar mouse cortex single cell RNA-sequencing dataset revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous human and mouse cell types, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 05, 2018.
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Conserved cell types with divergent features between human and mouse cortex
Rebecca D Hodge, Trygve E Bakken, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, Lucas T Graybuck, Jennie L Close, Brian Long, Osnat Penn, Zizhen Yao, Jeroen Eggermont, Thomas Hollt, Boaz P Levi, Soraya I Shehata, Brian Aevermann, Allison Beller, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Charles Cobbs, Rachel Dalley, Nick Dee, Song-Lin Ding, Richard G Ellenbogen, Olivia Fong, Emma Garren, Jeff Goldy, Ryder P Gwinn, Daniel Hirschstein, C Dirk Keene, Mohamed Keshk, Andrew L Ko, Kanan Lathia, Ahmed Mahfouz, Zoe Maltzer, Medea McGraw, Thuc Nghi Nguyen, Julie Nyhus, Jeffrey G Ojemann, Aaron Oldre, Sheana Parry, Shannon Reynolds, Christine Rimorin, Nadiya V Shapovalova, Saroja Somasundaram, Aaron Szafer, Elliot R Thomsen, Michael Tieu, Richard H Scheuermann, Rafael Yuste, Susan M Sunkin, Boudewijn Lelieveldt, David Feng, Lydia Ng, Amy Bernard, Michael Hawrylycz, John W. Phillips, Bosiljka Tasic, Hongkui Zeng, Allan R Jones, Christof Koch, Ed S Lein
bioRxiv 384826; doi: https://doi.org/10.1101/384826
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Conserved cell types with divergent features between human and mouse cortex
Rebecca D Hodge, Trygve E Bakken, Jeremy A Miller, Kimberly A Smith, Eliza R Barkan, Lucas T Graybuck, Jennie L Close, Brian Long, Osnat Penn, Zizhen Yao, Jeroen Eggermont, Thomas Hollt, Boaz P Levi, Soraya I Shehata, Brian Aevermann, Allison Beller, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Charles Cobbs, Rachel Dalley, Nick Dee, Song-Lin Ding, Richard G Ellenbogen, Olivia Fong, Emma Garren, Jeff Goldy, Ryder P Gwinn, Daniel Hirschstein, C Dirk Keene, Mohamed Keshk, Andrew L Ko, Kanan Lathia, Ahmed Mahfouz, Zoe Maltzer, Medea McGraw, Thuc Nghi Nguyen, Julie Nyhus, Jeffrey G Ojemann, Aaron Oldre, Sheana Parry, Shannon Reynolds, Christine Rimorin, Nadiya V Shapovalova, Saroja Somasundaram, Aaron Szafer, Elliot R Thomsen, Michael Tieu, Richard H Scheuermann, Rafael Yuste, Susan M Sunkin, Boudewijn Lelieveldt, David Feng, Lydia Ng, Amy Bernard, Michael Hawrylycz, John W. Phillips, Bosiljka Tasic, Hongkui Zeng, Allan R Jones, Christof Koch, Ed S Lein
bioRxiv 384826; doi: https://doi.org/10.1101/384826

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