IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-34590-1.html
   My bibliography  Save this article

Identification of visual cortex cell types and species differences using single-cell RNA sequencing

Author

Listed:
  • Jia-Ru Wei

    (Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science)

  • Zhao-Zhe Hao

    (Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science)

  • Chuan Xu

    (Wellcome Genome Campus)

  • Mengyao Huang

    (Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science)

  • Lei Tang

    (Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science)

  • Nana Xu

    (Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science)

  • Ruifeng Liu

    (Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science)

  • Yuhui Shen

    (Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science)

  • Sarah A. Teichmann

    (Wellcome Genome Campus
    University of Cambridge)

  • Zhichao Miao

    (Guangzhou Medical University
    Wellcome Genome Campus)

  • Sheng Liu

    (Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science
    Guangdong Province Key Laboratory of Brain Function and Disease)

Abstract

The primate neocortex exerts high cognitive ability and strong information processing capacity. Here, we establish a single-cell RNA sequencing dataset of 133,454 macaque visual cortical cells. It covers major cortical cell classes including 25 excitatory neuron types, 37 inhibitory neuron types and all glial cell types. We identified layer-specific markers including HPCAL1 and NXPH4, and also identified two cell types, an NPY-expressing excitatory neuron type that expresses the dopamine receptor D3 gene; and a primate specific activity-dependent OSTN + sensory neuron type. Comparisons of our dataset with humans and mice show that the gene expression profiles differ between species in relation to genes that are implicated in the synaptic plasticity and neuromodulation of excitatory neurons. The comparisons also revealed that glutamatergic neurons may be more diverse across species than GABAergic neurons and non-neuronal cells. These findings pave the way for understanding how the primary cortex fulfills the high-cognitive functions.

Suggested Citation

  • Jia-Ru Wei & Zhao-Zhe Hao & Chuan Xu & Mengyao Huang & Lei Tang & Nana Xu & Ruifeng Liu & Yuhui Shen & Sarah A. Teichmann & Zhichao Miao & Sheng Liu, 2022. "Identification of visual cortex cell types and species differences using single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34590-1
    DOI: 10.1038/s41467-022-34590-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-34590-1
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-34590-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Ryan S. Ziffra & Chang N. Kim & Jayden M. Ross & Amy Wilfert & Tychele N. Turner & Maximilian Haeussler & Alex M. Casella & Pawel F. Przytycki & Kathleen C. Keough & David Shin & Derek Bogdanoff & Ana, 2021. "Single-cell epigenomics reveals mechanisms of human cortical development," Nature, Nature, vol. 598(7879), pages 205-213, October.
    2. Matthew T. Schmitz & Kadellyn Sandoval & Christopher P. Chen & Mohammed A. Mostajo-Radji & William W. Seeley & Tomasz J. Nowakowski & Chun Jimmie Ye & Mercedes F. Paredes & Alex A. Pollen, 2022. "The development and evolution of inhibitory neurons in primate cerebrum," Nature, Nature, vol. 603(7903), pages 871-877, March.
    3. Bosiljka Tasic & Zizhen Yao & Lucas T. Graybuck & Kimberly A. Smith & Thuc Nghi Nguyen & Darren Bertagnolli & Jeff Goldy & Emma Garren & Michael N. Economo & Sarada Viswanathan & Osnat Penn & Trygve B, 2018. "Shared and distinct transcriptomic cell types across neocortical areas," Nature, Nature, vol. 563(7729), pages 72-78, November.
    4. Aparna Bhaduri & Carmen Sandoval-Espinosa & Marcos Otero-Garcia & Irene Oh & Raymund Yin & Ugomma C. Eze & Tomasz J. Nowakowski & Arnold R. Kriegstein, 2021. "An atlas of cortical arealization identifies dynamic molecular signatures," Nature, Nature, vol. 598(7879), pages 200-204, October.
    5. Katherine S. Matho & Dhananjay Huilgol & William Galbavy & Miao He & Gukhan Kim & Xu An & Jiangteng Lu & Priscilla Wu & Daniela J. Bella & Ashwin S. Shetty & Ramesh Palaniswamy & Joshua Hatfield & Ric, 2021. "Genetic dissection of the glutamatergic neuron system in cerebral cortex," Nature, Nature, vol. 598(7879), pages 182-187, October.
    6. Daniel E. Michele & Rita Barresi & Motoi Kanagawa & Fumiaki Saito & Ronald D. Cohn & Jakob S. Satz & James Dollar & Ichizo Nishino & Richard I. Kelley & Hannu Somer & Volker Straub & Katherine D. Math, 2002. "Post-translational disruption of dystroglycan–ligand interactions in congenital muscular dystrophies," Nature, Nature, vol. 418(6896), pages 417-421, July.
    7. Trygve E. Bakken & Jeremy A. Miller & Song-Lin Ding & Susan M. Sunkin & Kimberly A. Smith & Lydia Ng & Aaron Szafer & Rachel A. Dalley & Joshua J. Royall & Tracy Lemon & Sheila Shapouri & Kaylynn Aion, 2016. "A comprehensive transcriptional map of primate brain development," Nature, Nature, vol. 535(7612), pages 367-375, July.
    8. Hansruedi Mathys & Jose Davila-Velderrain & Zhuyu Peng & Fan Gao & Shahin Mohammadi & Jennie Z. Young & Madhvi Menon & Liang He & Fatema Abdurrob & Xueqiao Jiang & Anthony J. Martorell & Richard M. Ra, 2019. "Single-cell transcriptomic analysis of Alzheimer’s disease," Nature, Nature, vol. 570(7761), pages 332-337, June.
    9. Zizhen Yao & Hanqing Liu & Fangming Xie & Stephan Fischer & Ricky S. Adkins & Andrew I. Aldridge & Seth A. Ament & Anna Bartlett & M. Margarita Behrens & Koen Berge & Darren Bertagnolli & Hector Roux , 2021. "A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex," Nature, Nature, vol. 598(7879), pages 103-110, October.
    10. Lei Han & Xiaoyu Wei & Chuanyu Liu & Giacomo Volpe & Zhenkun Zhuang & Xuanxuan Zou & Zhifeng Wang & Taotao Pan & Yue Yuan & Xiao Zhang & Peng Fan & Pengcheng Guo & Yiwei Lai & Ying Lei & Xingyuan Liu , 2022. "Cell transcriptomic atlas of the non-human primate Macaca fascicularis," Nature, Nature, vol. 604(7907), pages 723-731, April.
    11. Federico Scala & Dmitry Kobak & Matteo Bernabucci & Yves Bernaerts & Cathryn René Cadwell & Jesus Ramon Castro & Leonard Hartmanis & Xiaolong Jiang & Sophie Laturnus & Elanine Miranda & Shalaka Mulher, 2021. "Phenotypic variation of transcriptomic cell types in mouse motor cortex," Nature, Nature, vol. 598(7879), pages 144-150, October.
    12. Rebecca D. Hodge & Trygve E. Bakken & Jeremy A. Miller & Kimberly A. Smith & Eliza R. Barkan & Lucas T. Graybuck & Jennie L. Close & Brian Long & Nelson Johansen & Osnat Penn & Zizhen Yao & Jeroen Egg, 2019. "Conserved cell types with divergent features in human versus mouse cortex," Nature, Nature, vol. 573(7772), pages 61-68, September.
    13. Fenna M. Krienen & Melissa Goldman & Qiangge Zhang & Ricardo C. H. Rosario & Marta Florio & Robert Machold & Arpiar Saunders & Kirsten Levandowski & Heather Zaniewski & Benjamin Schuman & Carolyn Wu &, 2020. "Author Correction: Innovations present in the primate interneuron repertoire," Nature, Nature, vol. 588(7837), pages 17-17, December.
    14. Jordan W. Squair & Matthieu Gautier & Claudia Kathe & Mark A. Anderson & Nicholas D. James & Thomas H. Hutson & Rémi Hudelle & Taha Qaiser & Kaya J. E. Matson & Quentin Barraud & Ariel J. Levine & Gio, 2021. "Confronting false discoveries in single-cell differential expression," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    15. Trygve E. Bakken & Nikolas L. Jorstad & Qiwen Hu & Blue B. Lake & Wei Tian & Brian E. Kalmbach & Megan Crow & Rebecca D. Hodge & Fenna M. Krienen & Staci A. Sorensen & Jeroen Eggermont & Zizhen Yao & , 2021. "Comparative cellular analysis of motor cortex in human, marmoset and mouse," Nature, Nature, vol. 598(7879), pages 111-119, October.
    16. Fenna M. Krienen & Melissa Goldman & Qiangge Zhang & Ricardo del Rosario & Marta Florio & Robert Machold & Arpiar Saunders & Kirsten Levandowski & Heather Zaniewski & Benjamin Schuman & Carolyn Wu & A, 2020. "Innovations present in the primate interneuron repertoire," Nature, Nature, vol. 586(7828), pages 262-269, October.
    17. Hansruedi Mathys & Jose Davila-Velderrain & Zhuyu Peng & Fan Gao & Shahin Mohammadi & Jennie Z. Young & Madhvi Menon & Liang He & Fatema Abdurrob & Xueqiao Jiang & Anthony J. Martorell & Richard M. Ra, 2019. "Author Correction: Single-cell transcriptomic analysis of Alzheimer’s disease," Nature, Nature, vol. 571(7763), pages 1-1, July.
    18. Rebecca D. Hodge & Jeremy A. Miller & Mark Novotny & Brian E. Kalmbach & Jonathan T. Ting & Trygve E. Bakken & Brian D. Aevermann & Eliza R. Barkan & Madeline L. Berkowitz-Cerasano & Charles Cobbs & F, 2020. "Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    19. Velina Kozareva & Caroline Martin & Tomas Osorno & Stephanie Rudolph & Chong Guo & Charles Vanderburg & Naeem Nadaf & Aviv Regev & Wade G. Regehr & Evan Macosko, 2021. "A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types," Nature, Nature, vol. 598(7879), pages 214-219, October.
    20. Daniela J. Di Bella & Ehsan Habibi & Robert R. Stickels & Gabriele Scalia & Juliana Brown & Payman Yadollahpour & Sung Min Yang & Catherine Abbate & Tommaso Biancalani & Evan Z. Macosko & Fei Chen & A, 2021. "Molecular logic of cellular diversification in the mouse cerebral cortex," Nature, Nature, vol. 595(7868), pages 554-559, July.
    21. Steven A. Moore & Fumiaki Saito & Jianguo Chen & Daniel E. Michele & Michael D. Henry & Albee Messing & Ronald D. Cohn & Susan E. Ross-Barta & Steve Westra & Roger A. Williamson & Toshinori Hoshi & Ke, 2002. "Deletion of brain dystroglycan recapitulates aspects of congenital muscular dystrophy," Nature, Nature, vol. 418(6896), pages 422-425, July.
    22. Jim Berg & Staci A. Sorensen & Jonathan T. Ting & Jeremy A. Miller & Thomas Chartrand & Anatoly Buchin & Trygve E. Bakken & Agata Budzillo & Nick Dee & Song-Lin Ding & Nathan W. Gouwens & Rebecca D. H, 2021. "Human neocortical expansion involves glutamatergic neuron diversification," Nature, Nature, vol. 598(7879), pages 151-158, October.
    23. Christian Mayer & Christoph Hafemeister & Rachel C. Bandler & Robert Machold & Renata Batista Brito & Xavier Jaglin & Kathryn Allaway & Andrew Butler & Gord Fishell & Rahul Satija, 2018. "Developmental diversification of cortical inhibitory interneurons," Nature, Nature, vol. 555(7697), pages 457-462, March.
    24. Gioele La Manno & Kimberly Siletti & Alessandro Furlan & Daniel Gyllborg & Elin Vinsland & Alejandro Mossi Albiach & Christoffer Mattsson Langseth & Irina Khven & Alex R. Lederer & Lisa M. Dratva & An, 2021. "Molecular architecture of the developing mouse brain," Nature, Nature, vol. 596(7870), pages 92-96, August.
    25. Daniela J. Di Bella & Ehsan Habibi & Robert R. Stickels & Gabriele Scalia & Juliana Brown & Payman Yadollahpour & Sung Min Yang & Catherine Abbate & Tommaso Biancalani & Evan Z. Macosko & Fei Chen & A, 2021. "Author Correction: Molecular logic of cellular diversification in the mouse cerebral cortex," Nature, Nature, vol. 596(7873), pages 11-11, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ying Lei & Mengnan Cheng & Zihao Li & Zhenkun Zhuang & Liang Wu & Yunong sun & Lei Han & Zhihao Huang & Yuzhou Wang & Zifei Wang & Liqin Xu & Yue Yuan & Shang Liu & Taotao Pan & Jiarui Xie & Chuanyu L, 2022. "Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    2. Nelson Johansen & Hongru Hu & Gerald Quon, 2023. "Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Leonardo D. Garma & Lisbeth Harder & Juan M. Barba-Reyes & Sergio Marco Salas & Mónica Díez-Salguero & Mats Nilsson & Alberto Serrano-Pozo & Bradley T. Hyman & Ana B. Muñoz-Manchado, 2024. "Interneuron diversity in the human dorsal striatum," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    4. BaDoi N. Phan & Madelyn H. Ray & Xiangning Xue & Chen Fu & Robert J. Fenster & Stephen J. Kohut & Jack Bergman & Suzanne N. Haber & Kenneth M. McCullough & Madeline K. Fish & Jill R. Glausier & Qiao S, 2024. "Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    5. Wendy Xueyi Wang & Julie L. Lefebvre, 2022. "Morphological pseudotime ordering and fate mapping reveal diversification of cerebellar inhibitory interneurons," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    6. Tingting Bo & Jie Li & Ganlu Hu & Ge Zhang & Wei Wang & Qian Lv & Shaoling Zhao & Junjie Ma & Meng Qin & Xiaohui Yao & Meiyun Wang & Guang-Zhong Wang & Zheng Wang, 2023. "Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    7. Ian Covert & Rohan Gala & Tim Wang & Karel Svoboda & Uygar Sümbül & Su-In Lee, 2023. "Predictive and robust gene selection for spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    8. Yueqi Wang & Simone Chiola & Guang Yang & Chad Russell & Celeste J. Armstrong & Yuanyuan Wu & Jay Spampanato & Paisley Tarboton & H. M. Arif Ullah & Nicolas U. Edgar & Amelia N. Chang & David A. Harmi, 2022. "Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes," Nature Communications, Nature, vol. 13(1), pages 1-25, December.
    9. Malosree Maitra & Haruka Mitsuhashi & Reza Rahimian & Anjali Chawla & Jennie Yang & Laura M. Fiori & Maria Antonietta Davoli & Kelly Perlman & Zahia Aouabed & Deborah C. Mash & Matthew Suderman & Nagu, 2023. "Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    10. Zeinab Asgarian & Marcio Guiomar Oliveira & Agata Stryjewska & Ioannis Maragkos & Anna Noren Rubin & Lorenza Magno & Vassilis Pachnis & Mohammadmersad Ghorbani & Scott Wayne Hiebert & Myrto Denaxa & N, 2022. "MTG8 interacts with LHX6 to specify cortical interneuron subtype identity," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    11. Yuqiu Zhou & Wei He & Weizhen Hou & Ying Zhu, 2024. "Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    12. Arpiar Saunders & Kee Wui Huang & Cassandra Vondrak & Christina Hughes & Karina Smolyar & Harsha Sen & Adrienne C. Philson & James Nemesh & Alec Wysoker & Seva Kashin & Bernardo L. Sabatini & Steven A, 2022. "Ascertaining cells’ synaptic connections and RNA expression simultaneously with barcoded rabies virus libraries," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    13. Yina Wei & Anirban Nandi & Xiaoxuan Jia & Joshua H. Siegle & Daniel Denman & Soo Yeun Lee & Anatoly Buchin & Werner Geit & Clayton P. Mosher & Shawn Olsen & Costas A. Anastassiou, 2023. "Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    14. Özkan İş & Xue Wang & Joseph S. Reddy & Yuhao Min & Elanur Yilmaz & Prabesh Bhattarai & Tulsi Patel & Jeremiah Bergman & Zachary Quicksall & Michael G. Heckman & Frederick Q. Tutor-New & Birsen Can De, 2024. "Gliovascular transcriptional perturbations in Alzheimer’s disease reveal molecular mechanisms of blood brain barrier dysfunction," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    15. Xuelong Yao & Zongyang Lu & Zhanying Feng & Lei Gao & Xin Zhou & Min Li & Suijuan Zhong & Qian Wu & Zhenbo Liu & Haofeng Zhang & Zeyuan Liu & Lizhi Yi & Tao Zhou & Xudong Zhao & Jun Zhang & Yong Wang , 2022. "Comparison of chromatin accessibility landscapes during early development of prefrontal cortex between rhesus macaque and human," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    16. Daniel J. Lodge & Hannah B. Elam & Angela M. Boley & Jennifer J. Donegan, 2023. "Discrete hippocampal projections are differentially regulated by parvalbumin and somatostatin interneurons," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    17. Abhijit Chakraborty & Jeffrey G. Wang & Ferhat Ay, 2022. "dcHiC detects differential compartments across multiple Hi-C datasets," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    18. Christopher T. Rhodes & Joyce J. Thompson & Apratim Mitra & Dhanya Asokumar & Dongjin R. Lee & Daniel J. Lee & Yajun Zhang & Eva Jason & Ryan K. Dale & Pedro P. Rocha & Timothy J. Petros, 2022. "An epigenome atlas of neural progenitors within the embryonic mouse forebrain," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    19. Yuzhou Chang & Jixin Liu & Yi Jiang & Anjun Ma & Yao Yu Yeo & Qi Guo & Megan McNutt & Jordan E. Krull & Scott J. Rodig & Dan H. Barouch & Garry P. Nolan & Dong Xu & Sizun Jiang & Zihai Li & Bingqiang , 2024. "Graph Fourier transform for spatial omics representation and analyses of complex organs," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    20. Qingnan Liang & Yuefan Huang & Shan He & Ken Chen, 2023. "Pathway centric analysis for single-cell RNA-seq and spatial transcriptomics data with GSDensity," Nature Communications, Nature, vol. 14(1), pages 1-17, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34590-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.