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Axonal Tree Morphology and Signal Propagation Dynamics Improve Interneuron Classification

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Abstract

Neurons are diverse and can be differentiated by their morphological, electrophysiological, and molecular properties. Current morphology-based classification approaches largely rely on the dendritic tree structure or on the overall axonal projection layout. Here, we use data from public databases of neuronal reconstructions and membrane properties to study the characteristics of the axonal and dendritic trees for interneuron classification. We show that combining signal propagation patterns observed by biophysical simulations of the activity along ramified axonal trees with morphological parameters of the axonal and dendritic trees, significantly improve classification results compared to previous approaches. The classification schemes introduced here can be utilized for robust neuronal classification. Our work paves the way for understanding and utilizing form-function principles in realistic neuronal reconstructions.

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References

  • Akram, M.A., Nanda, S., Maraver, P., Armañanzas, R, & Ascoli, G.A. (2018). An open repository for single-cell reconstructions of the brain forest. Scientific data, 5, 180006.

    Article  PubMed  PubMed Central  Google Scholar 

  • Alcami, P., & El Hady, A. (2019). Axonal computations. Frontiers in Cellular Neuroscience, 13, 413.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Angotzi, G.N., Boi, F., Lecomte, A., Miele, E., Malerba, M., Zucca, S., Casile, A., & Berdondini, L. (2019). Sinaps: an implantable active pixel sensor cmos-probe for simultaneous large-scale neural recordings. Biosensors and Bioelectronics, 126, 355–364.

    Article  CAS  PubMed  Google Scholar 

  • Armañanzas, R, & Ascoli, G.A. (2015). Towards the automatic classification of neurons. Trends in Neurosciences, 38(5), 307–318.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Avena-Koenigsberger, A., Misic, B., & Sporns, O. (2018). Communication dynamics in complex brain networks. Nature Reviews Neuroscience, 19(1), 17.

    Article  CAS  Google Scholar 

  • Bakkum, D.J., Obien, M.E.J., Radivojevic, M., Jäckel, D, Frey, U., Takahashi, H., & Hierlemann, A. (2019). The axon initial segment is the dominant contributor to the neuron’s extracellular electrical potential landscape. Advanced Biosystems, 3(2), 1800308.

    Article  Google Scholar 

  • Bono, J., Wilmes, K.A., & Clopath, C. (2017). Modelling plasticity in dendrites: from single cells to networks. Current Opinion in Neurobiology, 46, 136–141.

    Article  CAS  PubMed  Google Scholar 

  • Casale, A.E., Foust, A.J., Bal, T., & McCormick, D.A. (2015). Cortical interneuron subtypes vary in their axonal action potential properties. Journal of Neuroscience, 35(47), 15555–15567.

    Article  CAS  PubMed  Google Scholar 

  • Chen, G., Zhang, Y., Li, X., Zhao, X., Ye, Q., Lin, Y., Tao, H.W., Rasch, M.J., & Zhang, X. (2017). Distinct inhibitory circuits orchestrate cortical beta and gamma band oscillations. Neuron, 96 (6), 1403–1418.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chevée, M, Robertson, J.D.J., Cannon, G.H., Brown, S.P., & Goff, L.A. (2018). Variation in activity state, axonal projection, and position define the transcriptional identity of individual neocortical projection neurons. Cell Reports, 22(2), 441–455.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Debanne, D., Campanac, E., Bialowas, A., Carlier, E., & Alcaraz, G. (2011). Axon physiology. Physiological Reviews, 91(2), 555–602.

    Article  CAS  PubMed  Google Scholar 

  • DeFelipe, J., López-Cruz, P.L., Benavides-Piccione, R., Bielza, C., Larrañaga, P, Anderson, S., Burkhalter, A., Cauli, B., Fairén, A, Feldmeyer, D., & et al. (2013). New insights into the classification and nomenclature of cortical gabaergic interneurons. Nature Reviews Neuroscience, 14(3), 202.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Druckmann, S., Hill, S., Schürmann, F, Markram, H., & Segev, I. (2012). A hierarchical structure of cortical interneuron electrical diversity revealed by automated statistical analysis. Cerebral Cortex, 23(12), 2994–3006.

    Article  PubMed  Google Scholar 

  • Dumitriu, D., Cossart, R., Huang, J., & Yuste, R. (2006). Correlation between axonal morphologies and synaptic input kinetics of interneurons from mouse visual cortex. Cerebral Cortex, 17(1), 81–91.

    Article  PubMed  Google Scholar 

  • Emmenegger, V, Qi, G, Wang, H, & Feldmeyer, D. (2018). Morphological and functional characterization of non-fast-spiking gabaergic interneurons in layer 4 microcircuitry of rat barrel cortex. Cerebral Cortex.

  • Eyal, G., Mansvelder, H.D., de Kock, C.P., & Segev, I. (2014). Dendrites impact the encoding capabilities of the axon. Journal of Neuroscience, 34(24), 8063–8071.

    Article  CAS  PubMed  Google Scholar 

  • Feldmeyer, D., Qi, G., Emmenegger, V., & Staiger, J.F. (2018). Inhibitory interneurons and their circuit motifs in the many layers of the barrel cortex. Neuroscience, 368, 132–151.

    Article  CAS  PubMed  Google Scholar 

  • Ferrante, M., Tahvildari, B., Duque, A., Hadzipasic, M., Salkoff, D., Zagha, E.W., Hasselmo, M.E., & McCormick, D.A. (2016). Distinct functional groups emerge from the intrinsic properties of molecularly identified entorhinal interneurons and principal cells. Cerebral Cortex, 27(6), 3186–3207.

    Google Scholar 

  • Gillette, T.A., & Ascoli, G.A. (2015). Topological characterization of neuronal arbor morphology via sequence representation: I-motif analysis. BMC Bioinformatics, 16(1), 216.

    Article  PubMed  PubMed Central  Google Scholar 

  • Goldstein, S.S., & Rall, W. (1974). Changes of action potential shape and velocity for changing core conductor geometry. Biophysical Journal, 14(10), 731–757.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gouwens, N.W., Berg, J., Feng, D., Sorensen, S.A., Zeng, H., Hawrylycz, M.J., Koch, C., & Arkhipov, A. (2018). Systematic generation of biophysically detailed models for diverse cortical neuron types. Nature Communications, 9(1), 710.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gouwens, N.W., Sorensen, S.A., Berg, J., Lee, C., Jarsky, T., Ting, J., Sunkin, S.M., Feng, D., Anastassiou, C., Barkan, E., Bickley, K., Blesie, N., Braun, T., Brouner, K., Budzillo, A., Caldejon, S., Casper, T., Casteli, D., Chong, P., Crichton, K., Cuhaciyan, C., Daigle, T., Dalley, R., Dee, N., Desta, T., Dingman, S., Doperalski, A., Dotson, N., Egdorf, T., Fisher, M., de Frates, R.A., Garren, E., Garwood, M., Gary, A., Gaudreault, N., Godfrey, K., Gorham, M., Gu, H., Habel, C., Hadley, K., Harrington, J., Harris, J., Henry, A., Hill, D., Josephsen, S., Kebede, S., Kim, L., Kroll, M., Lee, B., Lemon, T., Liu, X., Long, B., Mann, R., McGraw, M., Mihalas, S., Mukora, A., Murphy, G.J., Ng, L., Ngo, K., Nguyen, T.N., Nicovich, P.R., Oldre, A., Park, D., Parry, S., Perkins, J., Potekhina, L., Reid, D., Robertson, M., Sandman, D., Schroedter, M., Slaughterbeck, C., Soler-Llavina, G., Sulc, J., Szafer, A., Tasic, B., Taskin, N., Teeter, C., Thatra, N., Tung, H., Wakeman, W., Williams, G., Young, R., Zhou, Z., Farrell, C., Peng, H., Hawrylycz, M.J., Lein, E., Ng, L., Arkhipov, A., Bernard, A., Phillips, J.W., Zeng, H., & Koch, C. (2019). Classification of electrophysiological and morphological neuron types in the mouse visual cortex. Nature Neuroscience, 22(7), 1182–1195.

    Article  CAS  PubMed  Google Scholar 

  • Gouwens, NW, Sorensen, SA, Baftizadeh, F, Budzillo, A, Lee, BR, Jarsky, T, Alfiler, L, Arkhipov, A, Baker, K, Barkan, E, Berry, K, Bertagnolli, D, Bickley, K, Bomben, J, Braun, T, Brouner, K, Casper, T, Crichton, K, Daigle, TL, Dalley, R, de Frates, R, Dee, N, Desta, T, Lee, SD, Dotson, N, Egdorf, T, Ellingwood, L, Enstrom, R, Esposito, L, Farrell, C, Feng, D, Fong, O, Gala, R, Gamlin, C, Gary, A, Glandon, A, Goldy, J, Gorham, M, Graybuck, L, Gu, H, Hadley, K, Hawrylycz, MJ, Henry, AM, Hill, D, Hupp, M, Kebede, S, Kim, TK, Kim, L, Kroll, M, Lee, C, Link, KE, Mallory, M, Mann, R, Maxwell, M, McGraw, M, McMillen, D, Mukora, A, Ng, L, Ng, L, Ngo, K, Nicovich, PR, Oldre, A, Park, D, Peng, H, Penn, O, Pham, T, Pom, A, Potekhina, L, Rajanbabu, R, Ransford, S, Reid, D, Rimorin, C, Robertson, M, Ronellenfitch, K, Ruiz, A, Sandman, D, Smith, K, Sulc, J, Sunkin, SM, Szafer, A, Tieu, M, Torkelson, A, Trinh, J, Tung, H, Wakeman, W, War, K, Williams, G, Zhou, Z, Ting, J, Sumbul, U, Lein, E, Koch, C, Yao, Z, Tasic, B, Berg, J, Murphy, GJ, & Zeng, H. (2020). Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual gabaergic cortical neurons. bioRxiv.

  • Han, S., Yang, W., & Yuste, R. (2019). Two-color volumetric imaging of neuronal activity of cortical columns. Cell Reports, 27(7), 2229–2240.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harris, K.D., & Shepherd, G.M. (2015). The neocortical circuit: themes and variations. Nature Neuroscience, 18(2), 170.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Helmstaedter, M., Sakmann, B., & Feldmeyer, D. (2008). The relation between dendritic geometry, electrical excitability, and axonal projections of l2/3 interneurons in rat barrel cortex. Cerebral Cortex, 19(4), 938–950.

    Article  PubMed  Google Scholar 

  • Hernández-Pérez, L.A, Delgado-Castillo, D., Martín-Pérez, R, Orozco-Morales, R, & Lorenzo-Ginori, J.V. (2019). New features for neuron classification. Neuroinformatics, 17(1), 5–25.

    Article  PubMed  Google Scholar 

  • Hill, M.O. (1973). Diversity and evenness: a unifying notation and its consequences. Ecology, 54(2), 427–432.

    Article  Google Scholar 

  • Hines, M.L., Davison, A.P., & Muller, E. (2009). Neuron and python. Frontiers in neuroinformatics, 3.

  • Jiang, X, Shen, S, Cadwell, CR, Berens, P, Sinz, F, Ecker, AS, Patel, S, & Tolias, AS. (2015). Principles of connectivity among morphologically defined cell types in adult neocortex. Science, 350(6264), aac9462.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kanari, L., Ramaswamy, S., Shi, Y., Morand, S., Meystre, J., Perin, R., Abdellah, M., Wang, Y., Hess, K, & Markram, H. (2019). Objective morphological classification of neocortical pyramidal cells. Cerebral Cortex.

  • Kepecs, A., & Fishell, G. (2014). Interneuron cell types are fit to function. Nature, 505(7483), 318–326.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kirch, C, & Gollo, LL. (2019). Spatially resolved dendritic integration: Towards a functional classification of neurons. bioRxiv p 657403.

  • Krimer, L.S., Zaitsev, A.V., Czanner, G., Kroner, S., González-Burgos, G, Povysheva, N.V., Iyengar, S., Barrionuevo, G., & Lewis, D.A. (2005). Cluster analysis–based physiological classification and morphological properties of inhibitory neurons in layers 2–3 of monkey dorsolateral prefrontal cortex. Journal of Neurophysiology, 94(5), 3009– 3022.

    Article  PubMed  Google Scholar 

  • Li, T., Tian, C., Scalmani, P., Frassoni, C., Mantegazza, M., Wang, Y., Yang, M., Wu, S., & Shu, Y. (2014). Action potential initiation in neocortical inhibitory interneurons. PLoS Biology, 12(9), e1001944.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • López-Cabrera, JD, & Lorenzo-Ginori, JV. (2018). Feature selection for the classification of traced neurons. Journal of Neuroscience Methods.

  • Luo, C., Keown, C.L., Kurihara, L., Zhou, J., He, Y., Li, J., Castanon, R., Lucero, J., Nery, J.R., Sandoval, J.P., & et al. (2017). Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science, 357(6351), 600–604.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Manor, Y., Koch, C., & Segev, I. (1991). Effect of geometrical irregularities on propagation delay in axonal trees. Biophysical Journal, 60(6), 1424–1437.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Markram, H., Muller, E., Ramaswamy, S., Reimann, M.W., Abdellah, M., Sanchez, C.A., Ailamaki, A., Alonso-Nanclares, L., Antille, N., Arsever, S., & et al. (2015). Reconstruction and simulation of neocortical microcircuitry. Cell, 163(2), 456–492.

    Article  CAS  PubMed  Google Scholar 

  • Mihaljević, B, Larrañaga, P, Benavides-Piccione, R., Hill, S., DeFelipe, J., & Bielza, C. (2018). Towards a supervised classification of neocortical interneuron morphologies. BMC Bioinformatics, 19(1), 511.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ofer, N., & Shefi, O. (2016). Axonal geometry as a tool for modulating firing patterns. Applied Mathematical Modelling, 40(4), 3175–3184.

    Article  Google Scholar 

  • Ofer, N., Shefi, O., & Yaari, G. (2017). Branching morphology determines signal propagation dynamics in neurons. Scientific Reports, 7.

  • Overstreet-Wadiche, L., & McBain, C.J. (2015). Neurogliaform cells in cortical circuits. Nature Reviews Neuroscience, 16(8), 458.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Papoutsi, A., Kastellakis, G., & Poirazi, P. (2017). Basal tree complexity shapes functional pathways in the prefrontal cortex. Journal of Neurophysiology, 118(4), 1970–1983.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V., & et al. (2011). Scikit-learn: machine learning in python. Journal of Machine Learning Research, 12, 2825–2830.

    Google Scholar 

  • Ramaswamy, S., Courcol, J.D., Abdellah, M., Adaszewski, S.R., Antille, N., Arsever, S., Atenekeng, G., Bilgili, A., Brukau, Y., Chalimourda, A., & et al. (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in Neural Circuits, 9.

  • Tasic, B., Menon, V., Nguyen, T.N., Kim, T.K., Jarsky, T., Yao, Z., Levi, B., Gray, L.T., Sorensen, S.A., Dolbeare, T., & et al. (2016). Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nature Neuroscience, 19(2), 335–346.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teeter, C., Iyer, R., Menon, V., Gouwens, N., Feng, D., Berg, J., Szafer, A., Cain, N., Zeng, H., Hawrylycz, M., & et al. (2018). Generalized leaky integrate-and-fire models classify multiple neuron types. Nature Communications, 9(1), 709.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tremblay, R., Lee, S., & Rudy, B. (2016). Gabaergic interneurons in the neocortex: from cellular properties to circuits. Neuron, 91(2), 260–292.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tuomisto, H. (2010). A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity. Ecography, 33(1), 2–22.

    Article  Google Scholar 

  • Wan, Y., Long, F., Qu, L., Xiao, H., Hawrylycz, M., Myers, E.W., & Peng, H. (2015). Blastneuron for automated comparison, retrieval and clustering of 3d neuron morphologies. Neuroinformatics, 13(4), 487–499.

    Article  PubMed  Google Scholar 

  • Wang, B., Ke, W., Guang, J., Chen, G., Yin, L., Deng, S., He, Q., Liu, Y., He, T., Zheng, R., & et al. (2016). Firing frequency maxima of fast-spiking neurons in human, monkey, and mouse neocortex. Frontiers in Cellular Neuroscience, 10.

  • Yuste, R, Hawrylycz, M, Aalling, N, Arendt, D, Armananzas, R, Ascoli, G, Bielza, C, Bokharaie, V, Bergmann, T, Bystron, I, Capogna, M, Chang, Y, Clemens, A, de Kock, C, DeFelipe, J, Santos, SD, Dunville, K, Feldmeyer, D, Fiath, R, Fishell, G, Foggetti, A, Gao, X, Ghaderi, P, Gunturkun, O, Hall, VJ, Helmstaedter, M, Herculano-Houzel, S, Hilscher, M, Hirase, H, Hjerling-Leffler, J, Hodge, R, Huang, ZJ, Huda, R, Juan, Y, Khodosevich, K, Kiehn, O, Koch, H, Kuebler, E, Kuhnemund, M, Larranaga, P, Lelieveldt, B, Louth, EL, Lui, J, Mansvelder, H, Marin, O, Martínez-Trujillo, J, Moradi, H, Goriounova, N, Mohapatra, A, Nedergaard, M, Němec, P, Ofer, N, Pfisterer, U, Pontes, S, Redmond, W, Rossier, J, Sanes, J, Scheuermann, R, Saiz, ES, Somogyi, P, Tamás, G, Tolias, A, Tosches, M, Garcia, MT, Aguilar-Valles, A, Munguba, H, Wozny, C, Wuttke, T, Yong, L, Zeng, H, & Lein, ES. (2019). A community-based transcriptomics classification and nomenclature of neocortical cell types. arXiv:https://arxiv.org/abs/190903083.

  • Zeisel, A., Muñoz-Manchado, A.B., Codeluppi, S., Lönnerberg, P, La Manno, G., Juréus, A, Marques, S., Munguba, H., He, L., Betsholtz, C., & et al. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell rna-seq. Science, 347(6226), 1138–1142.

    Article  CAS  Google Scholar 

  • Zeng, H., & Sanes, J.R. (2017). Neuronal cell-type classification: challenges, opportunities and the path forward. Nature Reviews Neuroscience, 18(9), 530.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work has been partially supported by the Israel Science Foundation. Orit Shefi (1053/15) and Gur Yaari (832/16).

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Ofer, N., Shefi, O. & Yaari, G. Axonal Tree Morphology and Signal Propagation Dynamics Improve Interneuron Classification. Neuroinform 18, 581–590 (2020). https://doi.org/10.1007/s12021-020-09466-8

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