Lineage-specific laminar organization of cortical GABAergic interneurons


In the cerebral cortex, pyramidal cells and interneurons are generated in distant germinal zones, and so the mechanisms that control their precise assembly into specific microcircuits remain an enigma. Here we report that cortical interneurons labeled at the clonal level do not distribute randomly but rather have a strong tendency to cluster in the mouse neocortex. This behavior is common to different classes of interneurons, independently of their origin. Interneuron clusters are typically contained within one or two adjacent cortical layers, are largely formed by isochronically generated neurons and populate specific layers, as revealed by unbiased hierarchical clustering methods. Our results suggest that different progenitor cells give rise to interneurons populating infra- and supragranular cortical layers, which challenges current views of cortical neurogenesis. Thus, specific lineages of cortical interneurons seem to be produced to primarily mirror the laminar structure of the cerebral cortex, rather than its columnar organization.

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Figure 1: Region-specific labeling of progenitor cells with conditional retroviruses.
Figure 2: Clustering of MGE/POA-derived interneurons in the cerebral cortex.
Figure 3: Spatial organization of MGE/POA-derived interneuron clusters.
Figure 4: Electrophysiological and neurochemical characterization of MGE/POA-derived interneuron clusters.
Figure 5: Clustering of PV+ interneurons in the cerebral cortex.
Figure 6: Clustering of SST+ interneurons in the cerebral cortex.
Figure 7: Clustering of VIP+ interneurons in the cerebral cortex.
Figure 8: Late born MGE/POA-derived interneurons cluster in superficial cortical layers.

Change history

  • 18 August 2013

    In the version of this article initially published online, author Z. Josh Huang's name was misspelled Josh Z. Huang. The error has been corrected for the print, PDF and HTML versions of this article.


  1. 1

    Klausberger, T. & Somogyi, P. Neuronal diversity and temporal dynamics: the unity of hippocampal circuit operations. Science 321, 53–57 (2008).

  2. 2

    Isaacson, J.S. & Scanziani, M. How inhibition shapes cortical activity. Neuron 72, 231–243 (2011).

  3. 3

    DeFelipe, J. & Fariñas, I. The pyramidal neuron of the cerebral cortex: morphological and chemical characteristics of the synaptic inputs. Prog. Neurobiol. 39, 563–607 (1992).

  4. 4

    Mountcastle, V.B. The columnar organization of the neocortex. Brain 120, 701–722 (1997).

  5. 5

    Jones, E.G. & Rakic, P. Radial columns in cortical architecture: it is the composition that counts. Cereb. Cortex 20, 2261–2264 (2010).

  6. 6

    Silberberg, G., Gupta, A. & Markram, H. Stereotypy in neocortical microcircuits. Trends Neurosci. 25, 227–230 (2002).

  7. 7

    Rakic, P. Guidance of neurons migrating to the fetal monkey neocortex. Brain Res. 33, 471–476 (1971).

  8. 8

    Noctor, S.C., Flint, A.C., Weissman, T.A., Dammerman, R.S. & Kriegstein, A.R. Neurons derived from radial glial cells establish radial units in neocortex. Nature 409, 714–720 (2001).

  9. 9

    Anderson, S.A., Eisenstat, D.D., Shi, L. & Rubenstein, J.L.R. Interneuron migration from basal forebrain to neocortex: dependence on Dlx genes. Science 278, 474–476 (1997).

  10. 10

    Marín, O. & Rubenstein, J.L.R. A long, remarkable journey: tangential migration in the telencephalon. Nat. Rev. Neurosci. 2, 780–790 (2001).

  11. 11

    Butt, S.J. et al. The temporal and spatial origins of cortical interneurons predict their physiological subtype. Neuron 48, 591–604 (2005).

  12. 12

    Flames, N. et al. Delineation of multiple subpallial progenitor domains by the combinatorial expression of transcriptional codes. J. Neurosci. 27, 9682–9695 (2007).

  13. 13

    Fogarty, M. et al. Spatial genetic patterning of the embryonic neuroepithelium generates GABAergic interneuron diversity in the adult cortex. J. Neurosci. 27, 10935–10946 (2007).

  14. 14

    Xu, Q., Tam, M. & Anderson, S.A. Fate mapping Nkx2.1-lineage cells in the mouse telencephalon. J. Comp. Neurol. 506, 16–29 (2008).

  15. 15

    Gelman, D.M. et al. The embryonic preoptic area is a novel source of cortical GABAergic interneurons. J. Neurosci. 29, 9380–9389 (2009).

  16. 16

    Wichterle, H., Turnbull, D.H., Nery, S., Fishell, G. & Alvarez-Buylla, A. In utero fate mapping reveals distinct migratory pathways and fates of neurons born in the mammalian basal forebrain. Development 128, 3759–3771 (2001).

  17. 17

    Nery, S., Fishell, G. & Corbin, J.G. The caudal ganglionic eminence is a source of distinct cortical and subcortical cell populations. Nat. Neurosci. 5, 1279–1287 (2002).

  18. 18

    Yozu, M., Tabata, H. & Nakajima, K. The caudal migratory stream: a novel migratory stream of interneurons derived from the caudal ganglionic eminence in the developing mouse forebrain. J. Neurosci. 25, 7268–7277 (2005).

  19. 19

    Rymar, V.V. & Sadikot, A.F. Laminar fate of cortical GABAergic interneurons is dependent on both birthdate and phenotype. J. Comp. Neurol. 501, 369–380 (2007).

  20. 20

    Miyoshi, G. & Fishell, G. GABAergic interneuron lineages selectively sort into specific cortical layers during early postnatal development. Cereb. Cortex 21, 845–852 (2011).

  21. 21

    Wonders, C.P. & Anderson, S.A. The origin and specification of cortical interneurons. Nat. Rev. Neurosci. 7, 687–696 (2006).

  22. 22

    Hendry, S.H., Jones, E.G. & Emson, P.C. Morphology, distribution, and synaptic relations of somatostatin- and neuropeptide Y-immunoreactive neurons in rat and monkey neocortex. J. Neurosci. 4, 2497–2517 (1984).

  23. 23

    Cavanagh, M.E. & Parnavelas, J.G. Development of vasoactive-intestinal-polypeptide-immunoreactive neurons in the rat occipital cortex: a combined immunohistochemical-autoradiographic study. J. Comp. Neurol. 284, 637–645 (1989).

  24. 24

    Ma, Y., Hu, H., Berrebi, A.S., Mathers, P.H. & Agmon, A. Distinct subtypes of somatostatin-containing neocortical interneurons revealed in transgenic mice. J. Neurosci. 26, 5069–5082 (2006).

  25. 25

    Miller, M.W. Cogeneration of retrogradely labeled corticocortical projection and GABA-immunoreactive local circuit neurons in cerebral cortex. Brain Res. 355, 187–192 (1985).

  26. 26

    Fairén, A., Cobas, A. & Fonseca, M. Times of generation of glutamic acid decarboxylase immunoreactive neurons in mouse somatosensory cortex. J. Comp. Neurol. 251, 67–83 (1986).

  27. 27

    Ang, E.S. Jr., Haydar, T.F., Gluncic, V. & Rakic, P. Four-dimensional migratory coordinates of GABAergic interneurons in the developing mouse cortex. J. Neurosci. 23, 5805–5815 (2003).

  28. 28

    Tanaka, D.H. et al. Random walk behavior of migrating cortical interneurons in the marginal zone: time-lapse analysis in flat-mount cortex. J. Neurosci. 29, 1300–1311 (2009).

  29. 29

    Brown, K.N. et al. Clonal production and organization of inhibitory interneurons in the neocortex. Science 334, 480–486 (2011).

  30. 30

    Walsh, C. & Cepko, C.L. Clonally related cortical cells show several migration patterns. Science 241, 1342–1345 (1988).

  31. 31

    Sussel, L., Marín, O., Kimura, S. & Rubenstein, J.L. Loss of Nkx2.1 homeobox gene function results in a ventral to dorsal molecular respecification within the basal telencephalon: evidence for a transformation of the pallidum into the striatum. Development 126, 3359–3370 (1999).

  32. 32

    Cepko, C.L. et al. Lineage analysis using retroviral vectors. Methods 14, 393–406 (1998).

  33. 33

    Valcanis, H. & Tan, S.S. Layer specification of transplanted interneurons in developing mouse neocortex. J. Neurosci. 23, 5113–5122 (2003).

  34. 34

    Pla, R., Borrell, V., Flames, N. & Marín, O. Layer acquisition by cortical GABAergic interneurons is independent of Reelin signaling. J. Neurosci. 26, 6924–6934 (2006).

  35. 35

    Kawaguchi, Y. & Kubota, Y. GABAergic cell subtypes and their synaptic connections in rat frontal cortex. Cereb. Cortex 7, 476–486 (1997).

  36. 36

    Miyoshi, G. et al. Genetic fate mapping reveals that the caudal ganglionic eminence produces a large and diverse population of superficial cortical interneurons. J. Neurosci. 30, 1582–1594 (2010).

  37. 37

    Xu, Q., Cobos, I., De La Cruz, E., Rubenstein, J.L. & Anderson, S.A. Origins of cortical interneuron subtypes. J. Neurosci. 24, 2612–2622 (2004).

  38. 38

    Rakic, P. Specification of cerebral cortical areas. Science 241, 170–176 (1988).

  39. 39

    Miyoshi, G., Butt, S.J., Takebayashi, H. & Fishell, G. Physiologically distinct temporal cohorts of cortical interneurons arise from telencephalic Olig2-expressing precursors. J. Neurosci. 27, 7786–7798 (2007).

  40. 40

    Hensch, T.K. Critical period plasticity in local cortical circuits. Nat. Rev. Neurosci. 6, 877–888 (2005).

  41. 41

    Turrigiano, G. Too many cooks? Intrinsic and synaptic homeostatic mechanisms in cortical circuit refinement. Annu. Rev. Neurosci. 34, 89–103 (2011).

  42. 42

    Molyneaux, B.J., Arlotta, P., Menezes, J.R. & Macklis, J.D. Neuronal subtype specification in the cerebral cortex. Nat. Rev. Neurosci. 8, 427–437 (2007).

  43. 43

    Markram, H. et al. Interneurons of the neocortical inhibitory system. Nat. Rev. Neurosci. 5, 793–807 (2004).

  44. 44

    Yu, Y.C., Bultje, R.S., Wang, X. & Shi, S.H. Specific synapses develop preferentially among sister excitatory neurons in the neocortex. Nature 458, 501–504 (2009).

  45. 45

    Li, Y. et al. Clonally related visual cortical neurons show similar stimulus feature selectivity. Nature 486, 118–121 (2012).

  46. 46

    Ohtsuki, G. et al. Similarity of visual selectivity among clonally related neurons in visual cortex. Neuron 75, 65–72 (2012).

  47. 47

    Stancik, E.K., Navarro-Quiroga, I., Sellke, R. & Haydar, T.F. Heterogeneity in ventricular zone neural precursors contributes to neuronal fate diversity in the postnatal neocortex. J. Neurosci. 30, 7028–7036 (2010).

  48. 48

    Franco, S.J. et al. Fate-restricted neural progenitors in the mammalian cerebral cortex. Science 337, 746–749 (2012).

  49. 49

    Hevner, R.F., Daza, R.A., Englund, C., Kohtz, J. & Fink, A. Postnatal shifts of interneuron position in the neocortex of normal and reeler mice: evidence for inward radial migration. Neuroscience 124, 605–618 (2004).

  50. 50

    Lodato, S. et al. Excitatory projection neuron subtypes control the distribution of local inhibitory interneurons in the cerebral cortex. Neuron 69, 763–779 (2011).

  51. 51

    Taniguchi, H. et al. A resource of Cre driver lines for genetic targeting of GABAergic neurons in cerebral cortex. Neuron 71, 995–1013 (2011).

  52. 52

    Hippenmeyer, S. et al. A developmental switch in the response of DRG neurons to ETS transcription factor signaling. PLoS Biol. 3, e159 (2005).

  53. 53

    Sousa, V.H., Miyoshi, G., Hjerling-Leffler, J., Karayannis, T. & Fishell, G. Characterization of Nkx6–2-derived neocortical interneuron lineages. Cereb. Cortex 19 (suppl. 1), i1–i10 (2009).

  54. 54

    Cardin, J.A. et al. Driving fast-spiking cells induces gamma rhythm and controls sensory responses. Nature 459, 663–667 (2009).

  55. 55

    Sakaue-Sawano, A. et al. Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132, 487–498 (2008).

  56. 56

    Tashiro, A., Sandler, V.M., Toni, N., Zhao, C. & Gage, F.H. NMDA-receptor-mediated, cell-specific integration of new neurons in adult dentate gyrus. Nature 442, 929–933 (2006).

  57. 57

    Gaiano, N., Kohtz, J.D., Turnbull, D.H. & Fishell, G. A method for rapid gain-of-function studies in the mouse embryonic nervous system. Nat. Neurosci. 2, 812–819 (1999).

  58. 58

    Ascoli, G.A. et al. Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex. Nat. Rev. Neurosci. 9, 557–568 (2008).

  59. 59

    Carugo, O. Clustering criteria and algorithms. Methods Mol. Biol. 609, 175–196 (2010).

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We thank A. Casillas, T. Gil and M. Pérez for excellent technical assistance, D. Gelman for contributing to the development of conditional retroviruses, S.A. Anderson (University of Pennsylvania School of Medicine; Nkx2-1-Cre), S. Arber (University of Basel; PV-Cre), and A. Barco (Instituto de Neurociencias; Nestin-Cre) for mouse strains, F.H. Gage (The Salk Institute for Biological Studies) for retroviral vectors and N. Tamamaki (Kumamoto University) for the CAG-Fucci-G plasmid. We are grateful to members of the Marín and Rico laboratories for discussions and ideas. Supported by grants from Spanish Ministry of Economy and Innovation (MINECO) SAF2011-28845 to O.M., BFU2011-23049 to M.M. and CONSOLIDER CSD2007-00023 to O.M. and M.M., and from the European Research Council (ERC-2011-AdG 293683) to O.M. G.C. and I.S. are recipients of “Formación de Personal Investigador” (FPI) fellowships from the MINECO. N.D. is the recipient of a European Molecular Biology Organization (EMBO) long-term fellowship.

Author information

G.C., M.M. and O.M. designed the project; G.C., N.D. and I.S. performed the research and analyzed the results; Z.J.H., M.M. and O.M. provided analytical tools, reagents and transgenic mice. G.C., M.M. and O.M. interpreted the data and wrote the paper.

Correspondence to Miguel Maravall or Oscar Marín.

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Ciceri, G., Dehorter, N., Sols, I. et al. Lineage-specific laminar organization of cortical GABAergic interneurons. Nat Neurosci 16, 1199–1210 (2013) doi:10.1038/nn.3485

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