DOI QR코드

DOI QR Code

Finding Needles in a Haystack with Light: Resolving the Microcircuitry of the Brain with Fluorescence Microscopy

  • Rah, Jong-Cheol (Laboratory of Neurophysiology, Korea Brain Research Institute) ;
  • Choi, Joon Ho (Laboratory of Neurophysiology, Korea Brain Research Institute)
  • 투고 : 2021.11.14
  • 심사 : 2021.12.20
  • 발행 : 2022.02.28

초록

To understand the microcircuitry of the brain, the anatomical and functional connectivity among neurons must be resolved. One of the technical hurdles to achieving this goal is that the anatomical connections, or synapses, are often smaller than the diffraction limit of light and thus are difficult to resolve by conventional microscopy, while the microcircuitry of the brain is on the scale of 1 mm or larger. To date, the gold standard method for microcircuit reconstruction has been electron microscopy (EM). However, despite its rapid development, EM has clear shortcomings as a method for microcircuit reconstruction. The greatest weakness of this method is arguably its incompatibility with functional and molecular analysis. Fluorescence microscopy, on the other hand, is readily compatible with numerous physiological and molecular analyses. We believe that recent advances in various fluorescence microscopy techniques offer a new possibility for reliable synapse detection in large volumes of neural circuits. In this minireview, we summarize recent advances in fluorescence-based microcircuit reconstruction. In the same vein as these studies, we introduce our recent efforts to analyze the long-range connectivity among brain areas and the subcellular distribution of synapses of interest in relatively large volumes of cortical tissue with array tomography and superresolution microscopy.

키워드

과제정보

This work was supported by grants from the KBRI Research Program (21-BR-01-01, 21-BR-01-04, and 21-BR-03-01), from the DGIST R&D Program (21-IJRP-01), and from the Brain Research Program through the National Research Foundation of Korea (NRF) of the Ministry of Science and ICT (NRF-2017M3C7A1048086 and No. 2017M3A9G8084463).

참고문헌

  1. Adams, S.R., Mackey, M.R., Ramachandra, R., Palida Lemieux, S.F., Steinbach, P., Bushong, E.A., Butko, M.T., Giepmans, B.N.G., Ellisman, M.H., and Tsien, R.Y. (2016). Multicolor electron microscopy for simultaneous visualization of multiple molecular species. Cell Chem. Biol. 23, 1417-1427. https://doi.org/10.1016/j.chembiol.2016.10.006
  2. Andermann, M.L., Gilfoy, N.B., Goldey, G.J., Sachdev, R.N.S., Wolfel, M., McCormick, D.A., Reid, R.C., and Levene, M.J. (2013). Chronic cellular imaging of entire cortical columns in awake mice using microprisms. Neuron 80, 900-913. https://doi.org/10.1016/j.neuron.2013.07.052
  3. Atasoy, D., Betley, J.N., Li, W.P., Su, H.H., Sertel, S.M., Scheffer, L.K., Simpson, J.H., Fetter, R.D., and Sternson, S.M. (2014). A genetically specified connectomics approach applied to long-range feeding regulatory circuits. Nat. Neurosci. 17, 1830-1839. https://doi.org/10.1038/nn.3854
  4. Bae, J.A., Mu, S., Kim, J.S., Turner, N.L., Tartavull, I., Kemnitz, N., Jordan, C.S., Norton, A.D., Silversmith, W.M., Prentki, R., et al. (2018). Digital museum of retinal ganglion cells with dense anatomy and physiology. Cell 173, 1293-1306.e19. https://doi.org/10.1016/j.cell.2018.04.040
  5. Beier, T., Pape, C., Rahaman, N., Prange, T., Berg, S., Bock, D.D., Cardona, A., Knott, G.W., Plaza, S.M., Scheffer, L.K., et al. (2017). Multicut brings automated neurite segmentation closer to human performance. Nat. Methods 14, 101-102. https://doi.org/10.1038/nmeth.4151
  6. Betzig, E., Patterson, G.H., Sougrat, R., Lindwasser, O.W., Olenych, S., Bonifacino, J.S., Davidson, M.W., Lippincott-Schwartz, J., and Hess, H.F. (2006). Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642-1645. https://doi.org/10.1126/science.1127344
  7. Bloss, E.B., Cembrowski, M.S., Karsh, B., Colonell, J., Fetter, R.D., and Spruston, N. (2016). Structured dendritic inhibition supports branch-selective integration in CA1 pyramidal cells. Neuron 89, 1016-1030. https://doi.org/10.1016/j.neuron.2016.01.029
  8. Bock, D.D., Lee, W.C.A., Kerlin, A.M., Andermann, M.L., Hood, G., Wetzel, A.W., Yurgenson, S., Soucy, E.R., Kim, H.S., and Reid, R.C. (2011). Network anatomy and in vivo physiology of visual cortical neurons. Nature 471, 177-182. https://doi.org/10.1038/nature09802
  9. Briggman, K.L. and Bock, D.D. (2012). Volume electron microscopy for neuronal circuit reconstruction. Curr. Opin. Neurobiol. 22, 154-161. https://doi.org/10.1016/j.conb.2011.10.022
  10. Briggman, K.L. and Denk, W. (2006). Towards neural circuit reconstruction with volume electron microscopy techniques. Curr. Opin. Neurobiol. 16, 562-570. https://doi.org/10.1016/j.conb.2006.08.010
  11. Briggman, K.L., Helmstaedter, M., and Denk, W. (2011). Wiring specificity in the direction-selectivity circuit of the retina. Nature 471, 183-188. https://doi.org/10.1038/nature09818
  12. Burgers, J., Pavlova, I., Rodriguez-Gatica, J.E., Henneberger, C., Oeller, M., Ruland, J.A., Siebrasse, J.P., Kubitscheck, U., and Schwarz, M.K. (2019). Light-sheet fluorescence expansion microscopy: fast mapping of neural circuits at super resolution. Neurophotonics 6, 015005.
  13. Cai, D., Cohen, K.B., Luo, T., Lichtman, J.W., and Sanes, J.R. (2013). Improved tools for the Brainbow toolbox. Nat. Methods 10, 540-547. https://doi.org/10.1038/nmeth.2450
  14. Chen, F., Tillberg, P.W., and Boyden, E.S. (2015). Optical imaging. Expansion microscopy. Science 347, 543-548. https://doi.org/10.1126/science.1260088
  15. de Mena, L., Rizk, P., and Rincon-Limas, D.E. (2018). Bringing light to transcription: the optogenetics repertoire. Front. Genet. 9, 518. https://doi.org/10.3389/fgene.2018.00518
  16. Dorkenwald, S., Turner, N.L., Macrina, T., Lee, K., Lu, R., Wu, J., Bodor, A.L., Bleckert, A.A., Brittain, D., Kemnitz, N., et al. (2019). Binary and analog variation of synapses between cortical pyramidal neurons. BioRxiv, https://doi.org/10.1101/2019.12.29.890319
  17. Eichler, K., Li, F., Litwin-Kumar, A., Park, Y., Andrade, I., Schneider-Mizell, C.M., Saumweber, T., Huser, A., Eschbach, C., Gerber, B., et al. (2017). The complete connectome of a learning and memory centre in an insect brain. Nature 548, 175-182. https://doi.org/10.1038/nature23455
  18. Fiala, J.C. and Harris, K.M. (1999). Dendrite structure. In Dendrites, G. Stuart, N. Spruston, and M. Hausser, eds. (Oxford, UK: Oxford University Press), pp. 1-34.
  19. Fiolka, R. (2013). Three-dimensional live microscopy beyond the diffraction limit. J. Opt. 15, 094002. https://doi.org/10.1088/2040-8986/15/9/094002
  20. Gustafsson, M.G.L. (2000). Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198, 82-87. https://doi.org/10.1046/j.1365-2818.2000.00710.x
  21. Gustafsson, M.G.L. (2005). Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. Proc. Natl. Acad. Sci. U. S. A. 102, 13081-13086. https://doi.org/10.1073/pnas.0406877102
  22. Han, C., Wang, D., Soba, P., Zhu, S., Lin, X., Jan, L.Y., and Jan, Y.N. (2012). Integrins regulate repulsion-mediated dendritic patterning of drosophila sensory neurons by restricting dendrites in a 2D space. Neuron 73, 64-78. https://doi.org/10.1016/j.neuron.2011.10.036
  23. Hecht, E. (2016). Optics (5th Edition) (Boston: Pearson Education).
  24. Helmstaedter, M., Briggman, K.L., and Denk, W. (2008). 3D structural imaging of the brain with photons and electrons. Curr. Opin. Neurobiol. 18, 633-641. https://doi.org/10.1016/j.conb.2009.03.005
  25. Hildebrand, D.G.C., Cicconet, M., Torres, R.M., Choi, W., Quan, T.M., Moon, J., Wetzel, A.W., Scott Champion, A., Graham, B.J., Randlett, O., et al. (2017). Whole-brain serial-section electron microscopy in larval zebrafish. Nature 545, 345-349. https://doi.org/10.1038/nature22356
  26. Hobert, O., Glenwinkel, L., and White, J. (2016). Revisiting neuronal cell type classification in Caenorhabditis elegans. Curr. Biol. 26, R1197-R1203. https://doi.org/10.1016/j.cub.2016.10.027
  27. Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J., and Stelzer, E.H.K. (2004). Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305, 1007-1009. https://doi.org/10.1126/science.1100035
  28. Huszka, G. and Gijs, M.A.M. (2019). Super-resolution optical imaging: a comparison. Micro Nano Eng. 2, 7-28. https://doi.org/10.1016/j.mne.2018.11.005
  29. Januszewski, M., Kornfeld, J., Li, P.H., Pope, A., Blakely, T., Lindsey, L., Maitin-Shepard, J., Tyka, M., Denk, W., and Jain, V. (2018). High-precision automated reconstruction of neurons with flood-filling networks. Nat. Methods 15, 605-610. https://doi.org/10.1038/s41592-018-0049-4
  30. Jarrell, T.A., Wang, Y., Bloniarz, A.E., Brittin, C.A., Xu, M., Thomson, J.N., Albertson, D.G., Hall, D.H., and Emmons, S.W. (2012). The connectome of a decision-making neural network. Science 337, 437-444. https://doi.org/10.1126/science.1221762
  31. Jenett, A., Rubin, G.M., Ngo, T.T.B., Shepherd, D., Murphy, C., Dionne, H., Pfeiffer, B.D., Cavallaro, A., Hall, D., Jeter, J., et al. (2012). A GAL4-driver line resource for Drosophila neurobiology. Cell Rep. 2, 991-1001. https://doi.org/10.1016/j.celrep.2012.09.011
  32. Ji, N., Shroff, H., Zhong, H., and Betzig, E. (2008). Advances in the speed and resolution of light microscopy. Curr. Opin. Neurobiol. 18, 605-616. https://doi.org/10.1016/j.conb.2009.03.009
  33. Kasthuri, N., Hayworth, K.J., Berger, D.R., Schalek, R.L., Conchello, J.A., Knowles-Barley, S., Lee, D., Vazquez-Reina, A., Kaynig, V., Jones, T.R., et al. (2015). Saturated reconstruction of a volume of neocortex. Cell 162, 648-661. https://doi.org/10.1016/j.cell.2015.06.054
  34. Khater, I.M., Nabi, I.R., and Hamarneh, G. (2020). A review of super-resolution single-molecule localization microscopy cluster analysis and quantification methods. Patterns (N. Y.) 1, 100038. https://doi.org/10.1016/j.patter.2020.100038
  35. Kim, G., Bahn, S.K., Kim, N., Choi, J.H., Kim, J.S., and Rah, J.C. (2021a). Efficient and accurate synapse detection with selective structured illumination microscopy on the putative regions of interest of ultrathin serial sections. Front. Neuroanat. 15, 759816. https://doi.org/10.3389/fnana.2021.759816
  36. Kim, J.S., Greene, M.J., Zlateski, A., Lee, K., Richardson, M., Turaga, S.C., Purcaro, M., Balkam, M., Robinson, A., Behabadi, B.F., et al. (2014). Space-time wiring specificity supports direction selectivity in the retina. Nature 509, 331-336. https://doi.org/10.1038/nature13240
  37. Kim, N., Bahn, S., Choi, J.H., Kim, J.S., and Rah, J.C. (2021b). Synapses from the motor cortex and a high-order thalamic nucleus are spatially clustered in proximity to each other in the distal tuft dendrites of mouse somatosensory cortex. Cereb. Cortex 2021 Aug 5 [Epub]. https://doi.org/10.1093/cercor/bhab236
  38. Ko, H., Hofer, S.B., Pichler, B., Buchanan, K.A., Sjostrom, P.J., and Mrsic-Flogel, T.D. (2011). Functional specificity of local synaptic connections in neocortical networks. Nature 473, 87-91. https://doi.org/10.1038/nature09880
  39. Kubota, Y., Sohn, J., and Kawaguchi, Y. (2018). Large volume electron microscopy and neural microcircuit analysis. Front. Neural Circuits 12, 98. https://doi.org/10.3389/fncir.2018.00098
  40. Lee, D., Hyun, J.H., Jung, K., Hannan, P., and Kwon, H.B. (2017). A calcium- and light-gated switch to induce gene expression in activated neurons. Nat. Biotechnol. 35, 858-863. https://doi.org/10.1038/nbt.3902
  41. Li, F., Lindsey, J., Marin, E.C., Otto, N., Dreher, M., Dempsey, G., Stark, I., Shakeel Bates, A., William Pleijzier, M., Schlegel, P., et al. (2020). The connectome of the adult Drosophila mushroom body: implications for function. BioRxiv, https://doi.org/10.1101/2020.08.29.273276
  42. Li, J., Wang, Y., Chiu, S.L., and Cline, H.T. (2010). Membrane targeted horseradish peroxidase as a marker for correlative fluorescence and electron microscopy studies. Front. Neural Circuits 4, 6. https://doi.org/10.3389/neuro.04.006.2010
  43. Lin, T.Y., Luo, J., Shinomiya, K., Ting, C.Y., Lu, Z., Meinertzhagen, I.A., and Lee, C.H. (2016). Mapping chromatic pathways in the Drosophila visual system. J. Comp. Neurol. 524, 213-227. https://doi.org/10.1002/cne.23857
  44. Livet, J., Weissman, T.A., Kang, H., Draft, R.W., Lu, J., Bennis, R.A., Sanes, J.R., and Lichtman, J.W. (2007). Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56-62. https://doi.org/10.1038/nature06293
  45. Loulier, K., Barry, R., Mahou, P., Le Franc, Y., Supatto, W., Matho, K.S., Ieng, S., Fouquet, S., Dupin, E., Benosman, R., et al. (2014). Multiplex cell and lineage tracking with combinatorial labels. Neuron 81, 505-520. https://doi.org/10.1016/j.neuron.2013.12.016
  46. Maglione, M. and Sigrist, S.J. (2013). Seeing the forest tree by tree: super-resolution light microscopy meets the neurosciences. Nat. Neurosci. 16, 790-797. https://doi.org/10.1038/nn.3403
  47. Martell, J.D., Deerinck, T.J., Lam, S.S., Ellisman, M.H., and Ting, A.Y. (2017). Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. Nat. Protoc. 12, 1792-1816. https://doi.org/10.1038/nprot.2017.065
  48. Micheva, K.D., Busse, B., Weiler, N.C., O'Rourke, N., and Smith, S.J. (2010a). Single-synapse analysis of a diverse synapse population: proteomic imaging methods and markers. Neuron 68, 639-653. https://doi.org/10.1016/j.neuron.2010.09.024
  49. Micheva, K.D., Kiraly, M., Perez, M.M., and Madison, D.V. (2021). Extensive structural remodeling of the axonal arbors of parvalbumin basket cells during development in mouse neocortex. J. Neurosci. 41, 9326-9339. https://doi.org/10.1523/JNEUROSCI.0871-21.2021
  50. Micheva, K.D., O'Rourke, N., Busse, B., and Smith, S.J. (2010b). Array tomography: immunostaining and antibody elution. Cold Spring Harb. Protoc. 2010, pdb.prot5525. https://doi.org/10.1101/pdb.prot5525
  51. Micheva, K.D. and Smith, S.J. (2007). Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron 55, 25-36. https://doi.org/10.1016/j.neuron.2007.06.014
  52. Motta, A., Berning, M., Boergens, K.M., Staffler, B., Beining, M., Loomba, S., Hennig, P., Wissler, H., and Helmstaedter, M. (2019). Dense connectomic reconstruction in layer 4 of the somatosensory cortex. Science 366, eaay3134. https://doi.org/10.1126/science.aay3134
  53. Ohyama, T., Schneider-Mizell, C.M., Fetter, R.D., Aleman, J.V., Franconville, R., Rivera-Alba, M., Mensh, B.D., Branson, K.M., Simpson, J.H., Truman, J.W., et al. (2015). A multilevel multimodal circuit enhances action selection in Drosophila. Nature 520, 633-639. https://doi.org/10.1038/nature14297
  54. Peng, H., Xie, P., Liu, L., Kuang, X., Wang, Y., Qu, L., Gong, H., Jiang, S., Li, A., Ruan, Z., et al. (2021). Morphological diversity of single neurons in molecularly defined cell types. Nature 598, 174-181. https://doi.org/10.1038/s41586-021-03941-1
  55. Rae, J., Ferguson, C., Ariotti, N., Webb, R.I., Cheng, H.H., Mead, J.L., Riches, J.D., Hunter, D.J.B., Martel, N., Baltos, J., et al. (2021). A robust method for particulate detection of a genetic tag for 3D electron microscopy. Elife 10, e64630. https://doi.org/10.7554/eLife.64630
  56. Rah, J.C., Bas, E., Colonell, J., Mishchenko, Y., Karsh, B., Fetter, R.D., Myers E.W., Chklovskii, D.B., Svoboda, K., Harris, T.D., et al. (2013). Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography. Front. Neural Circuits 7, 177.
  57. Rah, J.C., Feng, L., Druckmann, S., Lee, H., and Kim, J. (2015). From a meso- to micro-scale connectome: array tomography and mGRASP. Front. Neuroanat. 9, 78. https://doi.org/10.3389/fnana.2015.00078
  58. Sahl, S.J., Hell, S.W., and Jakobs, S. (2017). Fluorescence nanoscopy in cell biology. Nat. Rev. Mol. Cell Biol. 18, 685-701. https://doi.org/10.1038/nrm.2017.71
  59. Scheffer, L.K., Xu, C.S., Januszewski, M., Lu, Z., Takemura, S.Y., Hayworth, K.J., Huang, G.B., Shinomiya, K., Maitin-Shepard, J., Berg, S., et al. (2020). A connectome and analysis of the adult Drosophila central brain. Elife 9, e57443. https://doi.org/10.7554/elife.57443
  60. Schikorski, T., Young, S.M., Jr., and Hu, Y. (2007). Horseradish peroxidase cDNA as a marker for electron microscopy in neurons. J. Neurosci. Methods 165, 210-215. https://doi.org/10.1016/j.jneumeth.2007.06.004
  61. Shapson-Coe, A., Januszewski, M., Berger, D.R., Pope, A., Wu, Y., Blakely, T., Schalek, R.L., Li, P.H., Wang, S., Maitin-Shepard, J., et al. (2021). A connectomic study of a petascale fragment of human cerebral cortex. BioRxiv, https://doi.org/10.1101/2021.05.29.446289
  62. Shepherd, G.M.G. and Harris, K.M. (1998). Three-dimensional structure and composition of CA3-->CA1 axons in rat hippocampal slices: implications for presynaptic connectivity and compartmentalization. J. Neurosci. 18, 8300-8310. https://doi.org/10.1523/jneurosci.18-20-08300.1998
  63. Takemura, S.Y., Xu, C.S., Lu, Z., Rivlin, P.K., Parag, T., Olbris, D.J., Plaza, S., Zhao, T., Katz, W.T., Umayam, L., et al. (2015). Synaptic circuits and their variations within different columns in the visual system of Drosophila. Proc. Natl. Acad. Sci. U. S. A. 112, 13711-13716. https://doi.org/10.1073/pnas.1509820112
  64. Tao, C., Xia, C., Chen, X., Hong Zhou, Z., and Bi, G. (2012). Ultrastructural analysis of neuronal synapses using state-of-the-art nano-imaging techniques. Neurosci. Bull. 28, 321-332. https://doi.org/10.1007/s12264-012-1249-z
  65. Thorn, K. (2016). A quick guide to light microscopy in cell biology. Mol. Biol. Cell 27, 219-222. https://doi.org/10.1091/mbc.E15-02-0088
  66. Tobin, W.F., Wilson, R.I., and Allen Lee, W.C. (2017). Wiring variations that enable and constrain neural computation in a sensory microcircuit. Elife 6, e24838. https://doi.org/10.7554/elife.24838
  67. Truckenbrodt, S., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., and Rizzoli, S.O. (2018). X10 expansion microscopy enables 25-nm resolution on conventional microscopes. EMBO Rep. 19, e45836. https://doi.org/10.15252/embr.201845836
  68. Vicidomini, G., Bianchini, P., and Diaspro, A. (2018). STED super-resolved microscopy. Nat. Methods 15, 173-182. https://doi.org/10.1038/nmeth.4593
  69. Vishwanathan, A., Daie, K., Ramirez, A.D., Lichtman, J.W., Aksay, E.R.F., and Seung, H.S. (2017). Electron microscopic reconstruction of functionally identified cells in a neural integrator. Curr. Biol. 27, 2137-2147.e3. https://doi.org/10.1016/j.cub.2017.06.028
  70. Wassie, A.T., Zhao, Y., and Boyden, E.S. (2019). Expansion microscopy: principles and uses in biological research. Nat. Methods 16, 33-41. https://doi.org/10.1038/s41592-018-0219-4
  71. White, J.G., Southgate, E., Thomson, J.N., and Brenner, S. (1986). The structure of the nervous system of the nematode Caenorhabditis elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 314, 1-340. https://doi.org/10.1098/rstb.1986.0056
  72. Wu, Y., Christensen, R., Colon-Ramos, D., and Shroff, H. (2013). Advanced optical imaging techniques for neurodevelopment. Curr. Opin. Neurobiol. 23, 1090-1097. https://doi.org/10.1016/j.conb.2013.06.008
  73. Yemini, E., Lin, A., Nejatbakhsh, A., Varol, E., Sun, R., Mena, G.E., Samuel, A.D.T., Paninski, L., Venkatachalam, V., and Hobert, O. (2021). NeuroPAL: a multicolor atlas for whole-brain neuronal identification in C. elegans. Cell 184, 272-288.e11. https://doi.org/10.1016/j.cell.2020.12.012
  74. York, A.G., Parekh, S.H., Nogare, D.D., Fischer, R.S., Temprine, K., Mione, M., Chitnis, A.B., Combs, C.A., and Shroff, H. (2012). Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy. Nat. Methods 9, 749-754. https://doi.org/10.1038/nmeth.2025
  75. Zeng, H. and Sanes, J.R. (2017). Neuronal cell-type classification: challenges, opportunities and the path forward. Nat. Rev. Neurosci. 18, 530-546. https://doi.org/10.1038/nrn.2017.85
  76. Zhang, Q., Lee, W.C.A., Paul, D.L., and Ginty, D.D. (2019). Multiplexed peroxidase-based electron microscopy labeling enables simultaneous visualization of multiple cell types. Nat. Neurosci. 22, 828-839. https://doi.org/10.1038/s41593-019-0358-7
  77. Zheng, Z., Lauritzen, J.S., Perlman, E., Robinson, C.G., Nichols, M., Milkie, D., Torrens, O., Price, J., Fisher, C.B., Sharifi, N., et al. (2018). A complete electron microscopy volume of the brain of adult Drosophila melanogaster. Cell 174, 730-743.e22. https://doi.org/10.1016/j.cell.2018.06.019