A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

Nature

Volumn 555, Issue 7697, 2018, Pages 524-528

  Zhong, Suijuan ^a,b   Zhang, Shu ^c   Fan, Xiaoying ^c   Wu, Qian ^a,b   Yan, Liying ^c   Dong, Ji ^c   Zhang, Haofeng ^d   Li, Long ^b   Sun, Le ^a   Pan, Na ^a   Xu, Xiaohui ^d   Tang, Fuchou ^c,e   Zhang, Jun ^d   Qiao, Jie ^c,e   Wang, Xiaoqun ^a,b,f  

^a Shenzhen Fundamental Research Institutions   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c PEKING UNIVERSITY   (China)

^d CAPITAL MEDICAL UNIVERSITY   (China)

^e BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

^f BEIJING INSTITUTE FOR BRAIN DISORDERS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BRAIN; CELL; COGNITION; DEVELOPMENTAL BIOLOGY; EMBRYONIC DEVELOPMENT; MAMMAL; MOLECULAR ANALYSIS; NERVOUS SYSTEM; NERVOUS SYSTEM DISORDER; RNA;

ARTICLE; BRAIN DEVELOPMENT; CELL MATURATION; EMBRYO; FETUS; GENE; GESTATIONAL AGE; HUMAN; HUMAN CELL; HUMAN TISSUE; INTERNEURON; NERVE CELL STIMULATION; NERVOUS SYSTEM DEVELOPMENT; NEURAL STEM CELL; PREFRONTAL CORTEX; PRIORITY JOURNAL; RNA SEQUENCE; SIGNAL TRANSDUCTION; SINGLE CELL ANALYSIS; TRANSCRIPTOMICS; CELL DIFFERENTIATION; CLASSIFICATION; CYTOLOGY; EMBRYOLOGY; GENETICS; METABOLISM; NERVE CELL; SEQUENCE ANALYSIS;

MAMMALIA;

RNA;

CELL DIFFERENTIATION; HUMANS; INTERNEURONS; NEURAL STEM CELLS; NEUROGENESIS; NEURONS; PREFRONTAL CORTEX; RNA; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION; SINGLE-CELL ANALYSIS;

EID: 85044277334     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature25980     Document Type: Article

References (45)

1. Roth, G. &Dicke, U. Evolution of the brain and intelligence in primates. Prog. Brain Res. 195, 413-430 (2012).
2. O'Rahilly, R. &Müller, F. Significant features in the early prenatal development of the human brain. Ann. Anat. 190, 105-118 (2008).
3. Rakic, P. Evolution of the neocortex: a perspective from developmental biology. Nat. Rev. Neurosci. 10, 724-735 (2009).
4. Masserdotti, G., Gascón, S. &Götz, M. Direct neuronal reprogramming: learning from and for development. Development 143, 2494-2510 (2016).
5. Satija, R., Farrell, J. A., Gennert, D., Schier, A. F. &Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495-502 (2015).
6. Lake, B. B. et al. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science 352, 1586-1590 (2016).
7. Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381-386 (2014).
8. Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979-982 (2017).
9. Qiu, X. et al. Single-cell mRNA quantification and differential analysis with Census. Nat. Methods 14, 309-315 (2017).
10. Ma, T. et al. Subcortical origins of human and monkey neocortical interneurons. Nat. Neurosci. 16, 1588-1597 (2013).
11. Sandberg, M. et al. Transcriptional networks controlled by NKX2-1 in the development of forebrain GABAergic neurons. Neuron 91, 1260-1275 (2016).
12. Radonjić, N. V. et al. Diversity of cortical interneurons in primates: the role of the dorsal proliferative niche. Cell Rep. 9, 2139-2151 (2014).
13. Kierdorf, K. et al. Microglia emerge from erythromyeloid precursors via Pu.1-and Irf8-dependent pathways. Nat. Neurosci. 16, 273-280 (2013).
14. Prinz, M. &Priller, J. Microglia and brain macrophages in the molecular age: from origin to neuropsychiatric disease. Nat. Rev. Neurosci. 15, 300-312 (2014).
15. Hong, S. et al. Complement and microglia mediate early synapse loss in Alzheimer mouse models. Science 352, 712-716 (2016).
16. Vasek, M. J. et al. A complement-microglial axis drives synapse loss during virus-induced memory impairment. Nature 534, 538-543 (2016).
17. Pollen, A. A. et al. Molecular identity of human outer radial glia during cortical development. Cell 163, 55-67 (2015).
18. Lewitus, E., Kelava, I. &Huttner, W. B. Conical expansion of the outer subventricular zone and the role of neocortical folding in evolution and development. Front. Hum. Neurosci. 7, 424 (2013).
19. Noctor, S. C., Martínez-Cerdeño, V., Ivic, L. &Kriegstein, A. R. Cortical neurons arise in symmetric and asymmetric division zones and migrate through specific phases. Nat. Neurosci. 7, 136-144 (2004).
20. Homem, C. C., Repic, M. &Knoblich, J. A. Proliferation control in neural stem and progenitor cells. Nat. Rev. Neurosci. 16, 647-659 (2015).
21. Kowalczyk, T. et al. Intermediate neuronal progenitors (basal progenitors) produce pyramidal-projection neurons for all layers of cerebral cortex. Cereb. Cortex 19, 2439-2450 (2009).
22. Noctor, S. C., Martinez-Cerdeno, V. &Kriegstein, A. R. Contribution of intermediate progenitor cells to cortical histogenesis. Arch Neurol. 64, 639-642 (2007).
23. Vasistha, N. A. et al. Cortical and clonal contribution of Tbr2 expressing progenitors in the developing mouse brain. Cereb. Cortex 25, 3290-3302 (2015).
24. Lui, J. H., Hansen, D. V. &Kriegstein, A. R. Development and evolution of the human neocortex. Cell 146, 18-36 (2011).
25. Bandler, R. C., Mayer, C. &Fishell, G. Cortical interneuron specification: the juncture of genes, time and geometry. Curr. Opin. Neurobiol. 42, 17-24 (2017).
26. Shi, G. X., Han, J. &Andres, D. A. Rin GTPase couples nerve growth factor signaling to p38 and b-Raf/ERK pathways to promote neuronal differentiation. J. Biol. Chem. 280, 37599-37609 (2005).
27. Canitano, R. &Pallagrosi, M. Autism spectrum disorders and schizophrenia spectrum disorders: excitation/inhibition imbalance and developmental trajectories. Front. Psychiatry 8, 69 (2017).
28. Bicks, L. K., Koike, H., Akbarian, S. &Morishita, H. Prefrontal cortex and social cognition in mouse and man. Front. Psychol. 6, 1805 (2015).
29. Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171-181 (2014).
30. Guo, F. et al. The tanscriptome and DNA methylome landscapes of human primordial germ cells. Cell 161, 1437-1452 (2015).
31. Li, L. et al. Single-cell RNA-seq analysis maps development of human germline cells and gonadal niche interactions. Cell Stem Cell 20, 891-892 (2017).
32. Trapnell, C., Pachter, L. &Salzberg, S. L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105-1111 (2009).
33. Hinrichs, A. S. et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 37, D590-D598 (2006).
34. Anders, S., Pyl, P. T. &Huber, W. HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
35. Love, M. I., Huber, W. &Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
36. Huang, W., Sherman, B. T. &Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13 (2009).
37. Huang, W., Sherman, B. T. &Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
38. Tripathi, S. et al. Meta-and orthogonal integration of influenza 'omics' data defines a role for UBR4 in virus budding. Cell Host Microbe 18, 723-735 (2015).
39. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
40. Ogata, H. et al. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27, 29-34 (1999).
41. The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-29 (2000).
42. Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 27, 1739-1740 (2011).
43. Tirosh, I. et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352, 189-196 (2016).
44. Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214 (2015).
45. Palop, J. J., Roberson, E. D. &Cobos, I. Step-by-step in situ hybridization method for localizing gene expression changes in the brain. Methods Mol. Biol. 670, 207-230 (2011).