Abstract
Different interneuron classes have distinct laminar distribution patterns which contribute to the layer-specific organization of cortical microcircuits. However, laminar differences within the same interneuron classes are not well recognized. Despite systematic efforts towards neuron cell-type taxonomy in the neocortex by single-cell transcriptomics, less attention has been driven towards laminar differences in interneurons compared to projection neurons. VIP+ interneurons are the major interneuron class that mostly populate superficial layers and mediate disinhibition. A few reports noted the morphological and electrophysiological differences between VIP+ interneurons residing in layers I–III (upper layer) and layers IV–VI (deeper layer), but little is known about their molecular differences. Here, we delineated the laminar difference in their transcriptome employing single-cell RNA sequencing (scRNAseq) data from public databases. Analysis of 1175 high-quality VIP+ interneurons in the primary visual cortex (VISp) showed that the upper layer and deeper layer VIP+ interneurons are transcriptionally distinct distinguished by genes implicated in synapse organization and regulation of membrane potential. Similar differences are also observed in the anterior lateral motor cortex (ALM) and primary motor cortex (MOp). Cross-comparing between the top 10 differentially expressed genes (DEGs) with Allen Mouse Brain in situ hybridization database, we identified Tac2 and CxCl14 as potential marker genes of upper layer VIP+ interneurons across most cortical regions. Importantly, such expression patterns are conserved in the human brain. Together, we revealed significant laminar differences in transcriptomic profiles within VIP+ interneurons, which provided new insight into their molecular heterogeneity that may contribute to their functional diversity.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data Availability
The data that support the findings of this study are included in the supplementary materials.
References
Adachi M, Lin PY, Pranav H, Monteggia LM (2016) Postnatal loss of Mef2c results in dissociation of effects on synapse number and learning and memory. Biol Psychiatry 80(2):140–148. https://doi.org/10.1016/j.biopsych.2015.09.018
Andero R, Dias BG, Ressler KJ (2014) A role for Tac2, NkB, and Nk3 receptor in normal and dysregulated fear memory consolidation. Neuron 83(2):444–454. https://doi.org/10.1016/j.neuron.2014.05.028
Bandler RC, Vitali I, Delgado RN, Ho MC, Dvoretskova E, Ibarra Molinas JS, Mayer C (2022) Single-cell delineation of lineage and genetic identity in the mouse brain. Nature 601(7893):404–409. https://doi.org/10.1038/s41586-021-04237-0
Cacace R, Heeman B, Van Mossevelde S, De Roeck A, Hoogmartens J, De Rijk P, Consortium B (2019) Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability. Acta Neuropathol 137(6):901–918. https://doi.org/10.1007/s00401-019-01976-3
Chang M, Suzuki N, Kawai HD (2018) Laminar specific gene expression reveals differences in postnatal laminar maturation in mouse auditory, visual, and somatosensory cortex. J Comp Neurol 526(14):2257–2284. https://doi.org/10.1002/cne.24481
den Boon FS, Werkman TR, Schaafsma-Zhao Q, Houthuijs K, Vitalis T, Kruse CG, Chameau P (2015) Activation of type-1 cannabinoid receptor shifts the balance between excitation and inhibition towards excitation in layer II/III pyramidal neurons of the rat prelimbic cortex. Pflugers Arch 467(7):1551–1564. https://doi.org/10.1007/s00424-014-1586-z
Economo MN, Viswanathan S, Tasic B, Bas E, Winnubst J, Menon V, Svoboda K (2018) Distinct descending motor cortex pathways and their roles in movement. Nature 563(7729):79–84. https://doi.org/10.1038/s41586-018-0642-9
Fishell G, Kepecs A (2020) Interneuron types as attractors and controllers. Annu Rev Neurosci 43:1–30. https://doi.org/10.1146/annurev-neuro-070918-050421
Florido A, Velasco ER, Soto-Faguas CM, Gomez-Gomez A, Perez-Caballero L, Molina P, Andero R (2021) Sex differences in fear memory consolidation via Tac2 signaling in mice. Nat Commun 12(1):2496. https://doi.org/10.1038/s41467-021-22911-9
Fu Y, Tucciarone JM, Espinosa JS, Sheng N, Darcy DP, Nicoll RA, Stryker MP (2014) A cortical circuit for gain control by behavioral state. Cell 156(6):1139–1152. https://doi.org/10.1016/j.cell.2014.01.050
Gan KJ, Sudhof TC (2019) Specific factors in blood from young but not old mice directly promote synapse formation and NMDA-receptor recruitment. Proc Natl Acad Sci U S A 116(25):12524–12533. https://doi.org/10.1073/pnas.1902672116
Gan KJ, Sudhof TC (2020) SPARCL1 Promotes excitatory but not inhibitory synapse formation and function independent of neurexins and neuroligins. J Neurosci 40(42):8088–8102. https://doi.org/10.1523/JNEUROSCI.0454-20.2020
Garcia-Junco-Clemente P, Ikrar T, Tring E, Xu X, Ringach DL, Trachtenberg JT (2017) An inhibitory pull-push circuit in frontal cortex. Nat Neurosci 20(3):389–392. https://doi.org/10.1038/nn.4483
Gasselin C, Hohl B, Vernet A, Crochet S, Petersen CCH (2021) Cell-type-specific nicotinic input disinhibits mouse barrel cortex during active sensing. Neuron 109(5):778-787 e773. https://doi.org/10.1016/j.neuron.2020.12.018
Hagemann-Jensen M, Ziegenhain C, Chen P, Ramskold D, Hendriks GJ, Larsson AJM, Sandberg R (2020) Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat Biotechnol 38(6):708–714. https://doi.org/10.1038/s41587-020-0497-0
He M, Tucciarone J, Lee S, Nigro MJ, Kim Y, Levine JM, Huang ZJ (2016) Strategies and tools for combinatorial targeting of GABAergic neurons in mouse cerebral cortex. Neuron 92(2):555. https://doi.org/10.1016/j.neuron.2016.10.009
Hoshina N, Tanimura A, Yamasaki M, Inoue T, Fukabori R, Kuroda T, Yamamoto T (2013) Protocadherin 17 regulates presynaptic assembly in topographic corticobasal Ganglia circuits. Neuron 78(5):839–854. https://doi.org/10.1016/j.neuron.2013.03.031
Hu JS, Vogt D, Sandberg M, Rubenstein JL (2017) Cortical interneuron development: a tale of time and space. Development 144(21):3867–3878. https://doi.org/10.1242/dev.132852
Kamath SP, Chen AI (2019) Myocyte enhancer factor 2c regulates dendritic complexity and connectivity of cerebellar purkinje cells. Mol Neurobiol 56(6):4102–4119. https://doi.org/10.1007/s12035-018-1363-7
Kamigaki T, Dan Y (2017) Delay activity of specific prefrontal interneuron subtypes modulates memory-guided behavior. Nat Neurosci 20(6):854–863. https://doi.org/10.1038/nn.4554
Kepecs A, Fishell G (2014) Interneuron cell types are fit to function. Nature 505(7483):318–326. https://doi.org/10.1038/nature12983
Kim JH, Jung HG, Kim A, Shim HS, Hyeon SJ, Lee YS, Suk K (2021) Hevin-calcyon interaction promotes synaptic reorganization after brain injury. Cell Death Differ 28(9):2571–2588. https://doi.org/10.1038/s41418-021-00772-5
Kim Y, Yang GR, Pradhan K, Venkataraju KU, Bota M, Garcia Del Molino LC, Osten P (2017) Brain-wide maps reveal stereotyped cell-type-based cortical architecture and subcortical sexual dimorphism. Cell 171(2):456-469 e422. https://doi.org/10.1016/j.cell.2017.09.020
Lee S, Kruglikov I, Huang ZJ, Fishell G, Rudy B (2013) A disinhibitory circuit mediates motor integration in the somatosensory cortex. Nat Neurosci 16(11):1662–1670. https://doi.org/10.1038/nn.3544
Leu B, Koch E, Schmidt JT (2010) GAP43 phosphorylation is critical for growth and branching of retinotectal arbors in zebrafish. Dev Neurobiol 70(13):897–911. https://doi.org/10.1002/dneu.20829
Lodato S, Arlotta P (2015) Generating neuronal diversity in the mammalian cerebral cortex. Annu Rev Cell Dev Biol 31:699–720. https://doi.org/10.1146/annurev-cellbio-100814-125353
Lummis SC (2012) 5-HT(3) receptors. J Biol Chem 287(48):40239–40245. https://doi.org/10.1074/jbc.R112.406496
Madisen L, Zwingman TA, Sunkin SM, Oh SW, Zariwala HA, Gu H, Zeng H (2010) A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat Neurosci 13(1):133–140. https://doi.org/10.1038/nn.2467
Mar L, Yang FC, Ma Q (2012) Genetic marking and characterization of Tac2-expressing neurons in the central and peripheral nervous system. Mol Brain 5:3. https://doi.org/10.1186/1756-6606-5-3
Mathewson ND, Ashenberg O, Tirosh I, Gritsch S, Perez EM, Marx S, Wucherpfennig KW (2021) Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis. Cell 184(5):1281-1298 e1226. https://doi.org/10.1016/j.cell.2021.01.022
Matho KS, Huilgol D, Galbavy W, He M, Kim G, An X, Huang ZJ (2021) Genetic dissection of the glutamatergic neuron system in cerebral cortex. Nature 598(7879):182–187. https://doi.org/10.1038/s41586-021-03955-9
Matt L, Kirk LM, Chenaux G, Speca DJ, Puhger KR, Pride MC, Diaz E (2018) SynDIG4/Prrt1 is required for excitatory synapse development and plasticity underlying cognitive function. Cell Rep 22(9):2246–2253. https://doi.org/10.1016/j.celrep.2018.02.026
Mu Q, Chen Y, Wang J (2019) Deciphering brain complexity using single-cell sequencing. Genomics Proteomics Bioinformatics 17(4):344–366. https://doi.org/10.1016/j.gpb.2018.07.007
Paul A, Crow M, Raudales R, He M, Gillis J, Huang ZJ (2017) Transcriptional architecture of synaptic communication delineates GABAergic neuron identity. Cell 171(3):522-539 e520. https://doi.org/10.1016/j.cell.2017.08.032
Pi HJ, Hangya B, Kvitsiani D, Sanders JI, Huang ZJ, Kepecs A (2013) Cortical interneurons that specialize in disinhibitory control. Nature 503(7477):521–524. https://doi.org/10.1038/nature12676
Pronneke A, Scheuer B, Wagener RJ, Mock M, Witte M, Staiger JF (2015) Characterizing VIP neurons in the barrel cortex of VIPcre/tdTomato mice reveals layer-specific differences. Cereb Cortex 25(12):4854–4868. https://doi.org/10.1093/cercor/bhv202
Pronneke A, Witte M, Mock M, Staiger JF (2019) Neuromodulation leads to a burst-tonic switch in a subset of VIP neurons in mouse primary somatosensory (barrel) cortex. Cereb Cortex. https://doi.org/10.1093/cercor/bhz102
Ranneva SV, Maksimov VF, Korostyshevskaja IM, Lipina TV (2020) Lack of synaptic protein, calsyntenin-2, impairs morphology of synaptic complexes in mice. Synapse 74(2):e22132. https://doi.org/10.1002/syn.22132
Scala F, Kobak D, Bernabucci M, Bernaerts Y, Cadwell CR, Castro JR, Tolias AS (2021) Phenotypic variation of transcriptomic cell types in mouse motor cortex. Nature 598(7879):144–150. https://doi.org/10.1038/s41586-020-2907-3
Segal-Hayoun Y, Cohen A, Zilberberg N (2010) Molecular mechanisms underlying membrane-potential-mediated regulation of neuronal K2P2.1 channels. Mol Cell Neurosci 43(1):117–126. https://doi.org/10.1016/j.mcn.2009.10.002
Skrapits K, Borsay BA, Herczeg L, Ciofi P, Liposits Z, Hrabovszky E (2015) Neuropeptide co-expression in hypothalamic kisspeptin neurons of laboratory animals and the human. Front Neurosci 9:29. https://doi.org/10.3389/fnins.2015.00029
Staiger JF, Petersen CCH (2021) Neuronal circuits in barrel cortex for whisker sensory perception. Physiol Rev 101(1):353–415. https://doi.org/10.1152/physrev.00019.2019
Tanegashima K, Okamoto S, Nakayama Y, Taya C, Shitara H, Ishii R, Hara T (2010) CXCL14 deficiency in mice attenuates obesity and inhibits feeding behavior in a novel environment. PLoS ONE 5(4):e10321. https://doi.org/10.1371/journal.pone.0010321
Tao W, Diaz-Alonso J, Sheng N, Nicoll RA (2018) Postsynaptic delta1 glutamate receptor assembles and maintains hippocampal synapses via Cbln2 and neurexin. Proc Natl Acad Sci U S A 115(23):E5373–E5381. https://doi.org/10.1073/pnas.1802737115
Tasic B, Menon V, Nguyen TN, Kim TK, Jarsky T, Yao Z, Zeng H (2016) Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat Neurosci 19(2):335–346. https://doi.org/10.1038/nn.4216
Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Zeng H (2018) Shared and distinct transcriptomic cell types across neocortical areas. Nature 563(7729):72–78. https://doi.org/10.1038/s41586-018-0654-5
Tremblay R, Lee S, Rudy B (2016) GABAergic interneurons in the neocortex: from cellular properties to circuits. Neuron 91(2):260–292. https://doi.org/10.1016/j.neuron.2016.06.033
Vucurovic K, Gallopin T, Ferezou I, Rancillac A, Chameau P, van Hooft JA, Vitalis T (2010) Serotonin 3A receptor subtype as an early and protracted marker of cortical interneuron subpopulations. Cereb Cortex 20(10):2333–2347. https://doi.org/10.1093/cercor/bhp310
Wang S, Zhang AP, Kurada L, Matsui T, Lei S (2011) Cholecystokinin facilitates neuronal excitability in the entorhinal cortex via activation of TRPC-like channels. J Neurophysiol 106(3):1515–1524. https://doi.org/10.1152/jn.00025.2011
Wang Z, Jiang C, Yao H, Chen O, Rahman S, Gu Y, Ji RR (2021) Central opioid receptors mediate morphine-induced itch and chronic itch via disinhibition. Brain 144(2):665–681. https://doi.org/10.1093/brain/awaa430
Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Yu G (2021) clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (N Y) 2(3):100141. https://doi.org/10.1016/j.xinn.2021.100141
Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Mukamel EA (2021) A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 598(7879):103–110. https://doi.org/10.1038/s41586-021-03500-8
Yetman MJ, Washburn E, Hyun JH, Osakada F, Hayano Y, Zeng H, Taniguchi H (2019) Intersectional monosynaptic tracing for dissecting subtype-specific organization of GABAergic interneuron inputs. Nat Neurosci 22(3):492–502. https://doi.org/10.1038/s41593-018-0322-y
Yu J, Hu H, Agmon A, Svoboda K (2019) Recruitment of GABAergic interneurons in the barrel cortex during active tactile behavior. Neuron 104(2):412-427 e414. https://doi.org/10.1016/j.neuron.2019.07.027
Zelikowsky M, Hui M, Karigo T, Choe A, Yang B, Blanco MR, Anderson DJ (2018) The neuropeptide Tac2 controls a distributed brain state induced by chronic social isolation stress. Cell 173(5):1265-1279 e1219. https://doi.org/10.1016/j.cell.2018.03.037
Zhang S, Xu M, Kamigaki T, Hoang Do JP, Chang WC, Jenvay S, Dan Y (2014) Selective attention. Long-range and local circuits for top-down modulation of visual cortex processing. Science 345(6197):660–665. https://doi.org/10.1126/science.1254126
Zhou X, Rickmann M, Hafner G, Staiger JF (2017) Subcellular targeting of VIP boutons in mouse barrel cortex is layer-dependent and not restricted to interneurons. Cereb Cortex 27(11):5353–5368. https://doi.org/10.1093/cercor/bhx220
Acknowledgements
We thank Dr. Wei He and Prof. Yin Zhu from Institutes of Brain Science, Fudan University for their technical assistance and insightful advice throughout the course of this study. We thank Profs. Qiufu Ma from Harvard Medical School and Longzhen Chen from Southern University of Science and Technology for providing Tac2Cre mice.
Funding
This work was supported by funds from the National Key R&D Program of China (2018YFA0108000), National Natural Science Foundation of China (32171087, 31771196, 31970971), Shanghai Municipal Science and Technology Major Project (No. 2018SHZDZX01), and ZJLab.
Author information
Authors and Affiliations
Contributions
JW and MH conceived and designed the study. MH provided the funding. JW conducted all the experiments, analyses, prepared all the figures, and wrote the drafts of the manuscript. ZZ and MH were involved in a substantive review of the manuscript. YS assisted with mouse breeding. All the authors read and approved the final manuscript.
Corresponding author
Ethics declarations
Conflict of Interest
The authors declare no competing interests.
Competing Interests
The authors declare no competing interests.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Wu, J., Zhao, Z., Shi, Y. et al. Cortical VIP+ Interneurons in the Upper and Deeper Layers Are Transcriptionally Distinct. J Mol Neurosci 72, 1779–1795 (2022). https://doi.org/10.1007/s12031-022-02040-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12031-022-02040-8