Tools for mapping the molecular architecture and wiring of the brain
Biological systems such as brain circuits are complex structures made out of nanoscale building blocks such as proteins, RNAs, DNA, lipids, sugars, and other biomolecules, which take a great many forms, and are often organized with nanoscale precision. This presents a fundamental tension in biology – to understand a biological system like a brain circuit, you might need to map a large diversity of nanoscale building blocks, with great precision, across 3D spatial expanses. We are developing a suite of tools that enable the mapping of the location and identity of the molecular building blocks of biological systems such as the brain, aiming to map out the architecture of such systems with enough precision to understand how the structures of biological systems lead to function and dysfunction. One of the technologies we are developing, expansion microscopy (ExM), enables specimens to be imaged with nanoscale precision on ordinary microscopes, by physically expanding preserved biological systems (in contrast to all previous microscopies, that magnify images of specimens via lenses). We are working to improve expansion microscopy further, improving resolution and multiplexing capability, and are working, often in interdisciplinary collaborations, on a suite of new labeling and analysis techniques that exploit the biochemical freedom enabled by the expanded state. We are working, for example, on ways to perform in situ RNA and DNA sequencing in intact biological systems. We share all such tools as freely as possible, aiming to democratize multiplexed, nanoresolution imaging by making it as powerful and inexpensive as possible. We are also applying expansion microscopy to the scalable mapping of biological systems, such as brain circuits. Such brain circuit maps may be detailed enough someday to enable detailed computer simulations of brain functions, starting with small organisms such as C. elegans and zebrafish. Finally, we are extending and applying such tools to the early detection and understanding of complex diseases such as cancers and immune diseases, and to the analysis of aging.
Expansion microscopy using a single anchor molecule for high-yield multiplexed imaging of proteins and RNAsPLoS One | 2023
Cui Y*, Yang G*, Goodwin DR, O'Flanagan CH, Sinha A, Zhang C, Kitko KE, Shin TW, Park D, Aparicio S; CRUK IMAXT Grand Challenge Consortium; Boyden ES (2023) Expansion microscopy using a single anchor molecule for high-yield multiplexed imaging of proteins and RNAs, PLoS One 18(9):e0291506. (*, contributed equally)
Lauenburg L, Lin Z, Zhang R, Santos MD, Huang S, Arganda-Carreras I, Boyden ES, Pfister H, Wei D (2023) 3D Domain Adaptive Instance Segmentation via Cyclic Segmentation GANs, IEEE Journal of Biomedical and Health Informatics 27(8):4018-4027.
Günay KA, Chang TL, Skillin NP, Rao VV, Macdougall LJ, Cutler AA, Silver JS, Brown TE, Zhang C, Yu CJ, Olwin BB, Boyden ES, Anseth KS (2023) Photo-expansion microscopy enables super-resolution imaging of cells embedded in 3D hydrogels, Nature Materials 22(6):777-785.
Deblina Sarkar*, Jinyoung Kang*, Asmamaw T. Wassie*, Margaret E. Schroeder, Zhuyu Peng, Tyler B. Tarr, Ai-Hui Tang, Emily D. Niederst, Jennie Z. Young, Hanquan Su, Demian Park, Peng Yin, Li-Huei Tsai**, Thomas A. Blanpied** & Edward S. Boyden** (2022) Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy, Nature Biomedical Engineering 6:1057–1073. (*, contributed equally; **, co-corresponding)
Skuhersky M, Wu T, Yemini E, Nejatbakhsh A, Boyden E, Tegmark M (2022) Toward a more accurate 3D atlas of C. elegans neurons, BMC Bioinformatics 23(1):195.
Yu CJ*, Orozco Cosio DM*, Boyden ES (2022) ExCel: Super-Resolution Imaging of C. elegans with Expansion Microscopy, Methods in Molecular Biology 2468:141-203. (* contributed equally)
Decrowding Expansion Pathology: Unmasking Previously Invisible Nanostructures and Cells in Intact Human Brain Pathology SpecimensbioRxiv | 2021
Pablo A. Valdes, Chih-Chieh (Jay) Yu, Jenna Aronson, Yongxin Zhao, Joshua D. Bernstock, Deepak Bhere, Bobae An, Mariano S. Viapiano, Khalid Shah, E. Antonio Chiocca, Edward S. Boyden (2021) Decrowding Expansion Pathology: Unmasking Previously Invisible Nanostructures and Cells in Intact Human Brain Pathology Specimens, bioRxiv 2021.12.05.471271; doi: https://doi.org/10.1101/2021.12.05.471271.
Lee H, Yu CC, Boyden ES, Zhuang X, Kosuri P (2021) Tetra-gel enables superior accuracy in combined super-resolution imaging and expansion microscopy, Scientific Reports 11(1):16944.
A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopyNature Nanotechnology | 2021
Gao R*, Yu CJ*, Gao L, Piatkevich KD, Neve RL, Munro JB, Upadhyayula S, Boyden ES (2021) A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy, Nature Nanotechnology 16:698–707. (*, equal contribution)
Liu S, Punthambaker S, Iyer EPR, Ferrante T, Goodwin D, Fürth D, Pawlowski AC, Jindal K, Tam JM, Mifflin L, Alon S, Sinha A, Wassie AT, Chen F, Cheng A, Willocq V, Meyer K, Ling KH, Camplisson CK, Kohman RE, Aach J, Lee JH, Yankner BA, Boyden ES, Church GM (2021) Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses, Nucleic Acids Research 49(10):e58.
Alon S*, Goodwin DR*, Sinha A*, Wassie AT*, Chen F*, Daugharthy ER**, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A; IMAXT Consortium, Church GM***+, Marblestone AH***, Boyden ES***+ (2021) Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems, Science 371(6528):eaax2656. (* equal contribution, ** key contributions to early stages of project, *** equal contribution, +co-corresponding authors)
Payne AC*, Chiang ZD*, Reginato PL*, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES**, Buenrostro JD**, Chen F** (2020) In situ genome sequencing resolves DNA sequence and structure in intact biological samples, Science 371(6532):eaay3446. (* equal contribution, **co-corresponding)
Shen FY, Harrington MM, Walker LA, Cheng HPJ, Boyden ES, Cai D (2020) Light microscopy based approach for mapping connectivity with molecular specificity, Nature Communications 11(1):4632.
Zhang C*, Kang JS*, Asano SM, Gao R, Boyden ES (2020) Expansion Microscopy for Beginners: Visualizing Microtubules in Expanded Cultured HeLa Cells, Current Protocols in Neuroscience 92(1):e96. (*, contributed equally)
Yu CJ, Barry NC, Wassie AT, Sinha A, Bhattacharya A, Asano S, Zhang C, Chen F, Hobert O, Goodman MB, Haspel G, Boyden ES (2020) Expansion microscopy of C. elegans, eLife 9:e46249.
Emmanouil D. Karagiannis*, Jeong Seuk Kang*, Tay Won Shin, Amauche Emenari, Shoh Asano, Leanne Lin, Emma K. Costa, IMAXT Grand Challenge Consortium, Adam H. Marblestone, Narayanan Kasthuri, Edward S. Boyden (2019) Expansion Microscopy of Lipid Membranes, bioRxiv 829903. (*, equal contribution)
Guo SM, Veneziano R, Gordonov S, Li L, Danielson E, Perez de Arce K, Park D, Kulesa AB, Wamhoff EC, Blainey PC, Boyden ES, Cottrell JR, Bathe M (2019) Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes, Nature Communications 10(1):4377.
Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P (2019) Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues, Nature Biotechnology 37(9):1080-1090.
Rodriques SG, Marblestone AH, Boyden ES (2019) A theoretical analysis of single molecule protein sequencing via weak binding spectra, PLoS One 14(3):e0212868.
Ruixuan Gao*, Shoh M. Asano*, Srigokul Upadhyayula*, Igor Pisarev, Daniel E. Milkie, Tsung-Li Liu, Ved Singh, Austin Graves, Grace H. Huynh, Yongxin Zhao, John Bogovic, Jennifer Colonell, Carolyn M. Ott, Christopher Zugates, Susan Tappan, Alfredo Rodriguez, Kishore R. Mosaliganti, Shu-Hsien Sheu, H. Amalia Pasolli, Song Pang, C. Shan Xu, Sean G. Megason, Harald Hess, Jennifer Lippincott-Schwartz, Adam Hantman, Gerald M. Rubin, Tom Kirchhausen, Stephan Saalfeld, Yoshinori Aso, Edward S. Boyden**, Eric Betzig** (2019) Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution, Science 363(6424):eaau8302. (*, equal contribution, **, co-corresponding)
Wassie AT*, Zhao Y*, Boyden ES (2019) Expansion microscopy: principles and uses in biological research, Nature Methods 16(1):33-41. (*, equal contributors)
Gambarotto D, Zwettler FU, Le Guennec M, Schmidt-Cernohorska M, Fortun D, Borgers S, Heine J, Schloetel JG, Reuss M, Unser M, Boyden ES, Sauer M, Hamel V, Guichard P (2019) Imaging cellular ultrastructures using expansion microscopy (U-ExM), Nature Methods 16(1):71-74.
Michihiro Igarashi, Motohiro Nozumi, Ling-Gang Wu, Francesca Cella Zanacchi, István Katona, László Barna, Pingyong Xu, Mingshu Zhang, Fudong Xue, Edward Boyden (2018) New observations in neuroscience using superresolution microscopy, Journal of Neuroscience 38 (44) 9459-9467.
Boyden, E. S. (2018) Physical magnification of objects, Materials Horizons 6:11-13.
Asano SM*, Gao R*, Wassie AT*, Tillberg PW, Chen F, Boyden ES (2018) Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues, Current Protocols in Cell Biology 80(1):e56. (*, co-first authors)
Alon, S.*, Huynh, G. H.*, Boyden, E. S. (2018) Expansion Microscopy: Enabling Single Cell Analysis In Intact Biological Systems, The FEBS Journal 286(8):1482-1494. (*, co-first authors)
Migliori B, Datta MS, Dupre C, Apak MC, Asano S, Gao R, Boyden ES, Hermanson O, Yuste R, Tomer R (2018) Light sheet theta microscopy for rapid high-resolution imaging of large biological samples, BMC Biology 16(1):57.
Karagiannis ED, Boyden ES (2018) Expansion microscopy: development and neuroscience applications, Current Opinion in Neurobiology 50:56-63.
Freifeld L, Odstrcil I, Förster D, Ramirez A, Gagnon JA, Randlett O, Costa EK, Asano S, Celiker OT, Gao R, Martin-Alarcon DA, Reginato P, Dick C, Chen L, Schoppik D, Engert F, Baier H, Boyden ES (2017) Expansion microscopy of zebrafish for neuroscience and developmental biology studies, Proceedings of the National Academy of Sciences 114(50):E10799-E10808.
Glyoxal as an alternative fixative to formaldehyde in immunostaining and super-resolution microscopyThe EMBO Journal | 2017
Richter KN, Revelo NH, Seitz KJ, Helm MS, Sarkar D, Saleeb RS, D'Este E, Eberle J, Wagner E, Vogl C, Lazaro DF, Richter F, Coy-Vergara J, Coceano G, Boyden ES, Duncan RR, Hell SW, Lauterbach MA, Lehnart SE, Moser T, Outeiro T, Rehling P, Schwappach B, Testa I, Zapiec B, Rizzoli SO (2017) Glyoxal as an alternative fixative to formaldehyde in immunostaining and super-resolution microscopy, The EMBO Journal 37(1):139-159.
Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided AgglomerationFrontiers in Computational Neuroscience | 2017
Yoon YG, Dai P, Wohlwend J, Chang JB, Marblestone AH, Boyden ES (2017) Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration, Frontiers in Computational Neuroscience 11:97.
Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RCJ, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P (2017) Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues, Nano Letters 17(10):6131-6139.
Gao R.*, Asano S.M.*, Boyden E.S. (2017) Q&A: Expansion microscopy, BMC Biology 15:50. (*, co-first authors)
Chang, J.-B., Chen, F., Yoon, Y.-G., Jung, E. E., Babcock H., Kang J.-S., Asano S., Suk H.-J., Pak N., Tillberg P.W., Wassie A., Cai D., Boyden E.S. (2017) Iterative expansion microscopy, Nature Methods 14:593-599.
Chen, F.*, Wassie, A.T.*, Cote, A.J., Sinha, A., Alon, S., Asano, S., Daugharthy, E.R., Chang, J.-B., Marblestone, A., Church, G.M., Raj, A., Boyden, E.S. (2016) Nanoscale Imaging of RNA with Expansion Microscopy, Nature Methods 13(8):679-84. (*, co-first authors)
Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodiesNature Biotechnology | 2016
Tillberg, P.W.*, Chen, F.*, Piatkevich, K.D., Zhao, Y., Yu, C.-C., English, B.P., Gao, L., Martorell, A., Suk, H.-J., Yoshida, F., DeGennaro, E.M., Roossien, D.H., Gong, G., Seneviratne, U., Tannenbaum, S.R., Desimone, R., Cai, D., Boyden, E.S. (2016) Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies, Nature Biotechnology 34:987-992. (*, co-first authors)
Uygar Sümbül, Douglas Roossien, Dawen Cai, Fei Chen, Nicholas Barry, John P. Cunningham, Edward Boyden, Liam Paninski (2016) Automated scalable segmentation of neurons from multispectral images, Advances in Neural Information Processing Systems 29 (NIPS 2016).
Adamala, K.P.*, Martin-Alarcon, D. A.*, Boyden E. S. (2016) Programmable RNA-binding protein composed of repeats of a single modular unit, Proceedings of the National Academy of Sciences 113(19):E2579–E2588. (*, co-first authors)
Chen, F.*, Tillberg, P.W.*, Boyden, E.S. (2015) Expansion Microscopy, Science 347(6221):543-548. (*, equal contribution)