Connecting single-cell transcriptomes to projectomes in mouse visual cortex-Reference-Cited by-同舟云学术

Connecting single-cell transcriptomes to projectomes in mouse visual cortex

Published:2023-11-27 Issue: Volume: Page:
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Sorensen Staci A.^ORCID,Gouwens Nathan W.^ORCID,Wang Yun,Mallory Matt^ORCID,Budzillo Agata^ORCID,Dalley Rachel^ORCID,Lee Brian,Gliko Olga^ORCID,Kuo Hsien-chi,Kuang Xiuli^ORCID,Mann Rusty^ORCID,Ahmadinia Leila,Alfiler Lauren,Baftizadeh Fahimeh^ORCID,Baker Katherine^ORCID,Bannick Sarah,Bertagnolli Darren^ORCID,Bickley Kris^ORCID,Bohn Phil,Brown Dillan,Bomben Jasmine^ORCID,Brouner Krissy^ORCID,Chen Chao,Chen Kai^ORCID,Chvilicek Maggie,Collman Forrest^ORCID,Daigle Tanya^ORCID,Dawes Tim,de Frates Rebecca^ORCID,Dee Nick^ORCID,DePartee Maxwell,Egdorf Tom^ORCID,El-Hifnawi Laila,Enstrom Rachel,Esposito Luke^ORCID,Farrell Colin^ORCID,Gala Rohan^ORCID,Glomb Andrew,Gamlin Clare^ORCID,Gary Amanda^ORCID,Goldy Jeff^ORCID,Gu Hong^ORCID,Hadley Kristen^ORCID,Hawrylycz Mike^ORCID,Henry Alex^ORCID,Hill Dijon^ORCID,Hirokawa Karla E.^ORCID,Huang Zili^ORCID,Johnson Katelyn,Juneau Zoe,Kebede Sara^ORCID,Kim Lisa^ORCID,Lee Changkyu^ORCID,Lesnar Phil^ORCID,Li Anan,Glomb Andrew,Li Yaoyao^ORCID,Liang Elizabeth^ORCID,Link Katie,Maxwell Michelle^ORCID,McGraw Medea^ORCID,McMillen Delissa A.^ORCID,Mukora Alice^ORCID,Ng Lindsay,Ochoa Thomas,Oldre Aaron^ORCID,Park Daniel^ORCID,Pom Christina Alice^ORCID,Popovich Zoran,Potekhina Lydia^ORCID,Rajanbabu Ram,Ransford Shea^ORCID,Reding Melissa^ORCID,Ruiz Augustin^ORCID,Sandman David^ORCID,Siverts La’Akea^ORCID,Smith Kimberly A.^ORCID,Stoecklin Michelle,Sulc Josef^ORCID,Tieu Michael^ORCID,Ting Jonathan^ORCID,Trinh Jessica^ORCID,Vargas Sara,Vumbaco Dave,Walker Miranda^ORCID,Wang Micheal^ORCID,Wanner Adrian^ORCID,Waters Jack^ORCID,Williams Grace^ORCID,Wilson Julia^ORCID,Xiong Wei,Lein Ed^ORCID,Berg Jim^ORCID,Kalmbach Brian^ORCID,Yao Shenqin,Gong Hui^ORCID,Luo Qingming^ORCID,Ng Lydia^ORCID,Sümbül Uygar^ORCID,Jarsky Tim^ORCID,Yao Zizhen^ORCID,Tasic Bosiljka^ORCID,Zeng Hongkui^ORCID

Abstract

Abstract The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neuron’s role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morphoelectric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.

Publisher

Cold Spring Harbor Laboratory

Reference75 articles.

1. Sulla strutura della sostanza grigia del cervello;Gazzeta Medica Italiana, Lombardia,1873

2. Cajal S R. y. Histologie du systéme nerveux de l’homme et des vertébrés (1911).

3. Yao, Z. et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain preprint (bioRxiv, 2023).

4. Dorkenwald, S. et al. CAVE: Connectome Annotation Versioning Engine preprint (Neuroscience, 2023).

5. Single-neuron projectome of mouse prefrontal cortex