1
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Kim MH, Radaelli C, Thomsen ER, Monet D, Chartrand T, Jorstad NL, Mahoney JT, Taormina MJ, Long B, Baker K, Bakken TE, Campagnola L, Casper T, Clark M, Dee N, D'Orazi F, Gamlin C, Kalmbach BE, Kebede S, Lee BR, Ng L, Trinh J, Cobbs C, Gwinn RP, Keene CD, Ko AL, Ojemann JG, Silbergeld DL, Sorensen SA, Berg J, Smith KA, Nicovich PR, Jarsky T, Zeng H, Ting JT, Levi BP, Lein E. Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex. eLife 2023; 12:e81863. [PMID: 37249212 PMCID: PMC10332811 DOI: 10.7554/elife.81863] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Rodent studies have demonstrated that synaptic dynamics from excitatory to inhibitory neuron types are often dependent on the target cell type. However, these target cell-specific properties have not been well investigated in human cortex, where there are major technical challenges in reliably obtaining healthy tissue, conducting multiple patch-clamp recordings on inhibitory cell types, and identifying those cell types. Here, we take advantage of newly developed methods for human neurosurgical tissue analysis with multiple patch-clamp recordings, post-hoc fluorescent in situ hybridization (FISH), machine learning-based cell type classification and prospective GABAergic AAV-based labeling to investigate synaptic properties between pyramidal neurons and PVALB- vs. SST-positive interneurons. We find that there are robust molecular differences in synapse-associated genes between these neuron types, and that individual presynaptic pyramidal neurons evoke postsynaptic responses with heterogeneous synaptic dynamics in different postsynaptic cell types. Using molecular identification with FISH and classifiers based on transcriptomically identified PVALB neurons analyzed by Patch-seq, we find that PVALB neurons typically show depressing synaptic characteristics, whereas other interneuron types including SST-positive neurons show facilitating characteristics. Together, these data support the existence of target cell-specific synaptic properties in human cortex that are similar to rodent, thereby indicating evolutionary conservation of local circuit connectivity motifs from excitatory to inhibitory neurons and their synaptic dynamics.
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Affiliation(s)
- Mean-Hwan Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Deja Monet
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | | | - Brian Long
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Tamara Casper
- Allen Institute for Brain ScienceSeattleUnited States
| | - Michael Clark
- Allen Institute for Brain ScienceSeattleUnited States
| | - Nick Dee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | - Clare Gamlin
- Allen Institute for Brain ScienceSeattleUnited States
| | - Brian E Kalmbach
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology & Biophysics, School of Medicine, University of WashingtonSeattleUnited States
| | - Sara Kebede
- Allen Institute for Brain ScienceSeattleUnited States
| | - Brian R Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lindsay Ng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jessica Trinh
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - C Dirk Keene
- Department of Laboratory Medicine & Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - Andrew L Ko
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | - Daniel L Silbergeld
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | | | - Jim Berg
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jonathan T Ting
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology & Biophysics, School of Medicine, University of WashingtonSeattleUnited States
| | - Boaz P Levi
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Laboratory Medicine & Pathology, School of Medicine, University of WashingtonSeattleUnited States
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
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2
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Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification. Nature 2022; 601:E12. [PMID: 34992294 PMCID: PMC8770134 DOI: 10.1038/s41586-021-04322-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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3
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Muñoz-Castañeda R, Zingg B, Matho KS, Chen X, Wang Q, Foster NN, Li A, Narasimhan A, Hirokawa KE, Huo B, Bannerjee S, Korobkova L, Park CS, Park YG, Bienkowski MS, Chon U, Wheeler DW, Li X, Wang Y, Naeemi M, Xie P, Liu L, Kelly K, An X, Attili SM, Bowman I, Bludova A, Cetin A, Ding L, Drewes R, D'Orazi F, Elowsky C, Fischer S, Galbavy W, Gao L, Gillis J, Groblewski PA, Gou L, Hahn JD, Hatfield JT, Hintiryan H, Huang JJ, Kondo H, Kuang X, Lesnar P, Li X, Li Y, Lin M, Lo D, Mizrachi J, Mok S, Nicovich PR, Palaniswamy R, Palmer J, Qi X, Shen E, Sun YC, Tao HW, Wakemen W, Wang Y, Yao S, Yuan J, Zhan H, Zhu M, Ng L, Zhang LI, Lim BK, Hawrylycz M, Gong H, Gee JC, Kim Y, Chung K, Yang XW, Peng H, Luo Q, Mitra PP, Zador AM, Zeng H, Ascoli GA, Josh Huang Z, Osten P, Harris JA, Dong HW. Cellular anatomy of the mouse primary motor cortex. Nature 2021; 598:159-166. [PMID: 34616071 PMCID: PMC8494646 DOI: 10.1038/s41586-021-03970-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 08/27/2021] [Indexed: 12/24/2022]
Abstract
An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.
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Affiliation(s)
| | - Brian Zingg
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | - Xiaoyin Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nicholas N Foster
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | | | - Karla E Hirokawa
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Bingxing Huo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Laura Korobkova
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Chris Sin Park
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Young-Gyun Park
- Institute for Medical Engineering and Science, Department of Chemical Engineering, Picower Institute for Learning and Memory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Michael S Bienkowski
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Uree Chon
- Department of Neural and Behavioral Sciences, College of Medicine, Penn State University, Hershey, PA, USA
| | - Diek W Wheeler
- Center for Neural Informatics, Structures and Plasticity, Bioengineering Department and Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Yun Wang
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Peng Xie
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Lijuan Liu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Kathleen Kelly
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xu An
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Sarojini M Attili
- Center for Neural Informatics, Structures and Plasticity, Bioengineering Department and Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Ian Bowman
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | - Ali Cetin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Liya Ding
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Rhonda Drewes
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Corey Elowsky
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | - Lei Gao
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Lin Gou
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Joel D Hahn
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Joshua T Hatfield
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Houri Hintiryan
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Junxiang Jason Huang
- Center for Neural Circuits and Sensory Processing Disorders, Zilkha Neurogenetics Institute (ZNI), Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hideki Kondo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xiuli Kuang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | - Xu Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yaoyao Li
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Mengkuan Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Darrick Lo
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | | | - Philip R Nicovich
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | | | - Jason Palmer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xiaoli Qi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elise Shen
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Yu-Chi Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Huizhong W Tao
- Center for Neural Circuits and Sensory Processing Disorders, Zilkha Neurogenetics Institute (ZNI), Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Yimin Wang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Huiqing Zhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Muye Zhu
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Li I Zhang
- Center for Neural Circuits and Sensory Processing Disorders, Zilkha Neurogenetics Institute (ZNI), Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Byung Kook Lim
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
- Division of Biological Science, Neurobiology section, University of California San Diego, San Diego, CA, USA
| | | | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - James C Gee
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, College of Medicine, Penn State University, Hershey, PA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Department of Chemical Engineering, Picower Institute for Learning and Memory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Partha P Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures and Plasticity, Bioengineering Department and Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA.
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA, USA.
- Cajal Neuroscience, Seattle, WA, USA.
| | - Hong-Wei Dong
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
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Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Human neocortical expansion involves glutamatergic neuron diversification. Nature 2021; 598:151-158. [PMID: 34616067 PMCID: PMC8494638 DOI: 10.1038/s41586-021-03813-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/07/2021] [Indexed: 11/09/2022]
Abstract
The neocortex is disproportionately expanded in human compared with mouse1,2, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers composed of neurons that selectively make connections within the neocortex and with other telencephalic structures. Single-cell transcriptomic analyses of human and mouse neocortex show an increased diversity of glutamatergic neuron types in supragranular layers in human neocortex and pronounced gradients as a function of cortical depth3. Here, to probe the functional and anatomical correlates of this transcriptomic diversity, we developed a robust platform combining patch clamp recording, biocytin staining and single-cell RNA-sequencing (Patch-seq) to examine neurosurgically resected human tissues. We demonstrate a strong correspondence between morphological, physiological and transcriptomic phenotypes of five human glutamatergic supragranular neuron types. These were enriched in but not restricted to layers, with one type varying continuously in all phenotypes across layers 2 and 3. The deep portion of layer 3 contained highly distinctive cell types, two of which express a neurofilament protein that labels long-range projection neurons in primates that are selectively depleted in Alzheimer's disease4,5. Together, these results demonstrate the explanatory power of transcriptomic cell-type classification, provide a structural underpinning for increased complexity of cortical function in humans, and implicate discrete transcriptomic neuron types as selectively vulnerable in disease.
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Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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