دورية أكاديمية

Ultrastructure expansion microscopy (U-ExM) of mouse and human kidneys for analysis of subcellular structures.

التفاصيل البيبلوغرافية
العنوان: Ultrastructure expansion microscopy (U-ExM) of mouse and human kidneys for analysis of subcellular structures.
المؤلفون: Langner E; Department of Medicine, Washington University, St. Louis, Missouri, USA., Puapatanakul P; Department of Medicine, Washington University, St. Louis, Missouri, USA.; Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand., Pudlowski R; Department of Biology, Washington University, St. Louis, Missouri, USA., Alsabbagh DY; Department of Medicine, Washington University, St. Louis, Missouri, USA., Miner JH; Department of Medicine, Washington University, St. Louis, Missouri, USA., Horani A; Department of Pediatrics, Washington University, St. Louis, Missouri, USA., Dutcher SK; Department of Genetics, Washington University, St. Louis, Missouri, USA., Brody SL; Department of Medicine, Washington University, St. Louis, Missouri, USA., Wang JT; Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand., Suleiman HY; Department of Medicine, Washington University, St. Louis, Missouri, USA., Mahjoub MR; Department of Medicine, Washington University, St. Louis, Missouri, USA.; Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri, USA.
المصدر: Cytoskeleton (Hoboken, N.J.) [Cytoskeleton (Hoboken)] 2024 May 07. Date of Electronic Publication: 2024 May 07.
Publication Model: Ahead of Print
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 101523844 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1949-3592 (Electronic) Linking ISSN: 19493592 NLM ISO Abbreviation: Cytoskeleton (Hoboken) Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Hoboken, NJ : Wiley-Liss, 2010-
مستخلص: Ultrastructure expansion microscopy (U-ExM) involves the physical magnification of specimens embedded in hydrogels, which allows for super-resolution imaging of subcellular structures using a conventional diffraction-limited microscope. Methods for expansion microscopy exist for several organisms, organs, and cell types, and used to analyze cellular organelles and substructures in nanoscale resolution. Here, we describe a simple step-by-step U-ExM protocol for the expansion, immunostaining, imaging, and analysis of cytoskeletal and organellar structures in kidney tissue. We detail the critical modified steps to optimize isotropic kidney tissue expansion, and preservation of the renal cell structures of interest. We demonstrate the utility of the approach using several markers of renal cell types, centrioles, cilia, the extracellular matrix, and other cytoskeletal elements. Finally, we show that the approach works well on mouse and human kidney samples that were preserved using different fixation and embedding conditions. Overall, this protocol provides a simple and cost-effective approach to analyze both preclinical and clinical renal samples in high detail, using conventional lab supplies and standard widefield or confocal microscopy.
(© 2024 Wiley Periodicals LLC.)
التعليقات: Update of: bioRxiv. 2024 Feb 17;:. (PMID: 38405695)
References: Arsenijevic, Y., Chang, N., Mercey, O., Fersioui, Y. E., Koskiniemi‐Kuendig, H., Joubert, C., Bemelmans, A.‐P., Rivolta, C., Banin, E., Sharon, D., Guichard, P., Hamel, V., & Kostic, C. (2023). Fine‐tuning FAM161A gene augmentation therapy to restore retinal function. bioRxiv, 2023.2010.2006.561164. https://doi.org/10.1101/2023.10.06.561164.
Atchou, K., Berger, B. M., Heussler, V., & Ochsenreiter, T. (2023). Pre‐gelation staining expansion microscopy for visualisation of the plasmodium liver stage. Journal of Cell Science, 136(22), 1‐9. https://doi.org/10.1242/jcs.261377.
Avidor‐Reiss, T., & Gopalakrishnan, J. (2013). Building a centriole. Current Opinion in Cell Biology, 25(1), 72–77. https://doi.org/10.1016/j.ceb.2012.10.016.
Bai, Y., Zhu, B., Oliveria, J. P., Cannon, B. J., Feyaerts, D., Bosse, M., Vijayaragavan, K., Greenwald, N. F., Phillips, D., Schürch, C. M., Naik, S. M., Ganio, E. A., Gaudilliere, B., Rodig, S. J., Miller, M. B., Angelo, M., Bendall, S. C., Rovira‐Clavé, X., Nolan, G. P., & Jiang, S. (2023). Expanded vacuum‐stable gels for multiplexed high‐resolution spatial histopathology. Nature Communications, 14(1), 4013. https://doi.org/10.1038/s41467-023-39616-w.
Bandeira, P. T., Ortiz, S., Benchimol, M., & de Souza, W. (2023). Expansion microscopy of trichomonads. Experimental Parasitology, 255, 108629. https://doi.org/10.1016/j.exppara.2023.108629.
Bastos, A. P., & Onuchic, L. F. (2011). Molecular and cellular pathogenesis of autosomal dominant polycystic kidney disease. Brazilian Journal of Medical and Biological Research, 44, 606–617.
Battini, L., Macip, S., Fedorova, E., Dikman, S., Somlo, S., Montagna, C., & Gusella, G. L. (2008). Loss of polycystin‐1 causes centrosome amplification and genomic instability. Human Molecular Genetics, 17(18), 2819–2833. https://doi.org/10.1093/hmg/ddn180.
Berbari, N. F., Sharma, N., Malarkey, E. B., Pieczynski, J. N., Boddu, R., Gaertig, J., Guay‐Woodford, L., & Yoder, B. K. (2013). Microtubule modifications and stability are altered by cilia perturbation and in cystic kidney disease. Cytoskeleton, 70(1), 24–31. https://doi.org/10.1002/cm.21088.
Betleja, E., Nanjundappa, R., Cheng, T., & Mahjoub, M. R. (2018). A novel Cep120‐dependent mechanism inhibits centriole maturation in quiescent cells. eLife, 7, 1‐20. https://doi.org/10.7554/eLife.35439.
Bucur, O., & Zhao, Y. (2018). Nanoscale imaging of kidney glomeruli using expansion pathology [protocols]. Frontiers in Medicine, 5, 1‐9. https://doi.org/10.3389/fmed.2018.00322.
Burtey, S., Riera, M., Ribe, É., Pennenkamp, P., Rance, R., Luciani, J., Dworniczak, B., Mattei, M. G., & Fontés, M. (2008). Centrosome overduplication and mitotic instability in PKD2 transgenic lines. Cell Biology International, 32(10), 1193–1198. https://doi.org/10.1016/j.cellbi.2008.07.021.
Campbell, L. A., Pannoni, K. E., Savory, N. A., Lal, D., & Farris, S. (2021). Protein‐retention expansion microscopy for visualizing subcellular organelles in fixed brain tissue. Journal of Neuroscience Methods, 361, 109285. https://doi.org/10.1016/j.jneumeth.2021.109285.
Chang, G. H., Wu, M. Y., Yen, L. H., Huang, D. Y., Lin, Y. H., Luo, Y. R., Liu, Y. D., Xu, B., Leong, K. W., Lai, W. S., Chiang, A. S., Wang, K. C., Lin, C. H., Wang, S. L., & Chu, L. A. (2024). Isotropic multi‐scale neuronal reconstruction from high‐ratio expansion microscopy with contrastive unsupervised deep generative models. Computer Methods and Programs in Biomedicine, 244, 107991. https://doi.org/10.1016/j.cmpb.2023.107991.
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. T., Cai, D., & Boyden, E. S. (2017). Iterative expansion microscopy. Nature Methods, 14(6), 593–599. https://doi.org/10.1038/nmeth.4261.
Chen, F., Tillberg, P. W., & Boyden, E. S. (2015). Expansion microscopy. Science, 347(6221), 543–548. https://doi.org/10.1126/science.1260088.
Cheng, T., Mariappan, A., Langner, E., Shim, K., Gopalakrishnan, J., & Mahjoub, M. R. (2024). Inhibiting centrosome clustering reduces cystogenesis and improves kidney function in autosomal dominant polycystic kidney disease. JCI Insight, 9, 1‐20. https://doi.org/10.1172/jci.insight.172047.
Cheng, Z., Stefani, C., Skillman, T., Klimas, A., Lee, A., DiBernardo, E. F., Brown, K. M., Milman, T., Wang, Y., Gallagher, B. R., Lagree, K., Jena, B. P., Pulido, J. S., Filler, S. G., Mitchell, A. P., Hiller, N. L., Lacy‐Hulbert, A., & Zhao, Y. (2023). MicroMagnify: A multiplexed expansion microscopy method for pathogens and infected tissues. Advanced Science, 10(30), 2302249. https://doi.org/10.1002/advs.202302249.
Ching, K., Wang, J. T., & Stearns, T. (2022). Long‐range migration of centrioles to the apical surface of the olfactory epithelium. eLife, 11, 1‐23. https://doi.org/10.7554/eLife.74399.
Chozinski, T. J., Halpern, A. R., Okawa, H., Kim, H. J., Tremel, G. J., Wong, R. O., & Vaughan, J. C. (2016). Expansion microscopy with conventional antibodies and fluorescent proteins. Nature Methods, 13(6), 485–488. https://doi.org/10.1038/nmeth.3833.
Chozinski, T. J., Mao, C., Halpern, A. R., Pippin, J. W., Shankland, S. J., Alpers, C. E., Najafian, B., & Vaughan, J. C. (2018). Volumetric, nanoscale optical imaging of mouse and human kidney via expansion microscopy. Scientific Reports, 8(1), 10396. https://doi.org/10.1038/s41598-018-28694-2.
Dahl, K. D., Sankaran, D. G., Bayless, B. A., Pinter, M. E., Galati, D. F., Heasley, L. R., Giddings, T. H., Jr., & Pearson, C. G. (2015). A short CEP135 splice isoform controls centriole duplication. Current Biology, 25(19), 2591–2596. https://doi.org/10.1016/j.cub.2015.08.039.
Damstra, H. G. J., Mohar, B., Eddison, M., Akhmanova, A., Kapitein, L. C., & Tillberg, P. W. (2022). Visualizing cellular and tissue ultrastructure using ten‐fold robust expansion microscopy (TREx). eLife, 11, e73775. https://doi.org/10.7554/eLife.73775.
Damstra, H. G. J., Passmore, J. B., Serweta, A. K., Koutlas, I., Burute, M., Meye, F. J., Akhmanova, A., & Kapitein, L. C. (2023). GelMap: Intrinsic calibration and deformation mapping for expansion microscopy. Nature Methods, 20(10), 1573–1580. https://doi.org/10.1038/s41592-023-02001-y.
Devlin, L. A., & Sayer, J. A. (2019). Renal ciliopathies. Current Opinion in Genetics & Development, 56, 49–60. https://doi.org/10.1016/j.gde.2019.07.005.
Dionne, L. K., Shim, K., Hoshi, M., Cheng, T., Wang, J., Marthiens, V., Knoten, A., Basto, R., Jain, S., & Mahjoub, M. R. (2018). Centrosome amplification disrupts renal development and causes cystogenesis. Journal of Cell Biology, 217(7), 2485–2501. https://doi.org/10.1083/jcb.201710019.
Dos Santos Pacheco, N., & Soldati‐Favre, D. (2021). Coupling auxin‐inducible degron system with ultrastructure expansion microscopy to accelerate the discovery of gene function in toxoplasma gondii. Methods in Molecular Biology, 2369, 121–137. https://doi.org/10.1007/978-1-0716-1681-9_8.
Fan, Y., Lim, Y., Wyss, L. S., Park, S., Xu, C., Fu, H., Fei, J., Hong, Y., & Wang, B. (2021). Mechanical expansion microscopy. Methods in Cell Biology, 161, 125–146. https://doi.org/10.1016/bs.mcb.2020.04.013.
Fleming, L. R., Doherty, D. A., Parisi, M. A., Glass, I. A., Bryant, J., Fischer, R., Turkbey, B., Choyke, P., Daryanani, K., Vemulapalli, M., Mullikin, J. C., Malicdan, M. C., Vilboux, T., Sayer, J. A., Gahl, W. A., & Gunay‐Aygun, M. (2017). Prospective evaluation of kidney disease in Joubert syndrome. Clinical Journal of the American Society of Nephrology, 12(12), 1962–1973. https://doi.org/10.2215/cjn.05660517.
Fragiadaki, M., Macleod, F. M., & Ong, A. C. M. (2020). The controversial role of fibrosis in autosomal dominant polycystic kidney disease. International Journal of Molecular Sciences, 21(23), 1‐15. https://doi.org/10.3390/ijms21238936.
Gallagher, B. R., & Zhao, Y. (2021). Expansion microscopy: A powerful nanoscale imaging tool for neuroscientists. Neurobiology of Disease, 154, 105362. https://doi.org/10.1016/j.nbd.2021.105362.
Gambarotto, D., Hamel, V., & Guichard, P. (2021). Ultrastructure expansion microscopy (U‐ExM). Methods in Cell Biology, 161, 57–81. https://doi.org/10.1016/bs.mcb.2020.05.006.
Gambarotto, D., Zwettler, F. U., Le Guennec, M., Schmidt‐Cernohorska, M., Fortun, D., Borgers, S., Heine, J., Schloetel, J.‐G., Reuss, M., Unser, M., Boyden, E. S., Sauer, M., Hamel, V., & Guichard, P. (2019). Imaging cellular ultrastructures using expansion microscopy (U‐ExM). Nature Methods, 16(1), 71–74. https://doi.org/10.1038/s41592-018-0238-1.
Gaudreau‐Lapierre, A., Mulatz, K., Béïque, J. C., & Trinkle‐Mulcahy, L. (2021). Expansion microscopy‐based imaging of nuclear structures in cultured cells. STAR Protocols, 2(3), 100630. https://doi.org/10.1016/j.xpro.2021.100630.
Grantham, J. J., Mulamalla, S., & Swenson‐Fields, K. I. (2011). Why kidneys fail in autosomal dominant polycystic kidney disease. Nature Reviews. Nephrology, 7(10), 556–566. https://doi.org/10.1038/nrneph.2011.109.
Hamel, V., & Guichard, P. (2021). Improving the resolution of fluorescence nanoscopy using post‐expansion labeling microscopy. Methods in Cell Biology, 161, 297–315. https://doi.org/10.1016/bs.mcb.2020.07.002.
Hoshi, M., Wang, J., Jain, S., & Mahjoub, M. R. (2015). Imaging centrosomes and cilia in the mouse kidney. Methods in Cell Biology, 127, 1–17. https://doi.org/10.1016/bs.mcb.2014.12.008.
Hou, X., Mrug, M., Yoder, B. K., Lefkowitz, E. J., Kremmidiotis, G., D'Eustachio, P., Beier, D. R., & Guay‐Woodford, L. M. (2002). Cystin, a novel cilia‐associated protein, is disrupted in the cpk mouse model of polycystic kidney disease. The Journal of Clinical Investigation, 109(4), 533–540. https://doi.org/10.1172/JCI14099.
Huang, L., & Lipschutz, J. H. (2014). Cilia and polycystic kidney disease, kith and kin. Birth Defects Research. Part C, Embryo Today, 102(2), 174–185. https://doi.org/10.1002/bdrc.21066.
Ishikawa, H., Kubo, A., Tsukita, S., & Tsukita, S. (2005). Odf2‐deficient mother centrioles lack distal/subdistal appendages and the ability to generate primary cilia. Nature Cell Biology, 7(5), 517–524. https://doi.org/10.1038/ncb1251.
Jurriens, D., van Batenburg, V., Katrukha, E. A., & Kapitein, L. C. (2021). Chapter 6—Mapping the neuronal cytoskeleton using expansion microscopy. In P. Guichard & V. Hamel (Eds.), Methods in cell biology (Vol. 161, pp. 105–124). Academic Press. https://doi.org/10.1016/bs.mcb.2020.04.018.
Kerjaschki, D., Sharkey, D. J., & Farquhar, M. G. (1984). Identification and characterization of podocalyxin—The major sialoprotein of the renal glomerular epithelial cell. The Journal of Cell Biology, 98(4), 1591–1596. https://doi.org/10.1083/jcb.98.4.1591.
Khodjakov, A., & Rieder, C. L. (1999). The sudden recruitment of γ‐tubulin to the centrosome at the onset of mitosis and its dynamic exchange throughout the cell cycle, do not require microtubules. Journal of Cell Biology, 146(3), 585–596. https://doi.org/10.1083/jcb.146.3.585.
Kieferle, S., Fong, P., Bens, M., Vandewalle, A., & Jentsch, T. J. (1994). Two highly homologous members of the ClC chloride channel family in both rat and human kidney. Proceedings of the National Academy of Sciences of the United States of America, 91(15), 6943–6947. https://doi.org/10.1073/pnas.91.15.6943.
Klimas, A., Gallagher, B. R., Wijesekara, P., Fekir, S., DiBernardo, E. F., Cheng, Z., Stolz, D. B., Cambi, F., Watkins, S. C., Brody, S. L., Horani, A., Barth, A. L., Moore, C. I., Ren, X., & Zhao, Y. (2023). Magnify is a universal molecular anchoring strategy for expansion microscopy. Nature Biotechnology, 41(6), 858–869. https://doi.org/10.1038/s41587-022-01546-1.
Kong, D., & Loncarek, J. (2021). Analyzing centrioles and cilia by expansion microscopy. Methods in Molecular Biology, 2329, 249–263. https://doi.org/10.1007/978-1-0716-1538-6_18.
Kraft, N., Muenz, T. S., Reinhard, S., Werner, C., Sauer, M., Groh, C., & Rössler, W. (2023). Expansion microscopy in honeybee brains for high‐resolution neuroanatomical analyses in social insects. Cell and Tissue Research, 393(3), 489–506. https://doi.org/10.1007/s00441-023-03803-4.
Kriz, W., Shirato, I., Nagata, M., LeHir, M., & Lemley, K. V. (2013). The podocyte's response to stress: The enigma of foot process effacement. American Journal of Physiology—Renal Physiology, 304(4), F333–F347. https://doi.org/10.1152/ajprenal.00478.2012.
Ku, T., Swaney, J., Park, J. Y., Albanese, A., Murray, E., Cho, J. H., Park, Y. G., Mangena, V., Chen, J., & Chung, K. (2016). Multiplexed and scalable super‐resolution imaging of three‐dimensional protein localization in size‐adjustable tissues. Nature Biotechnology, 34(9), 973–981. https://doi.org/10.1038/nbt.3641.
Kunz, T. C., Götz, R., Sauer, M., & Rudel, T. (2019). Detection of chlamydia developmental forms and secreted effectors by expansion microscopy. Frontiers in Cellular and Infection Microbiology, 9, 276. https://doi.org/10.3389/fcimb.2019.00276.
Kunz, T. C., Rühling, M., Moldovan, A., Paprotka, K., Kozjak‐Pavlovic, V., Rudel, T., & Fraunholz, M. (2021). The Expandables: Cracking the staphylococcal cell wall for expansion microscopy. Frontiers in Cellular and Infection Microbiology, 11, 644750. https://doi.org/10.3389/fcimb.2021.644750.
Kylies, D., Zimmermann, M., Haas, F., Schwerk, M., Kuehl, M., Brehler, M., Czogalla, J., Hernandez, L. C., Konczalla, L., Okabayashi, Y., Menzel, J., Edenhofer, I., Mezher, S., Aypek, H., Dumoulin, B., Wu, H., Hofmann, S., Kretz, O., Wanner, N., … Puelles, V. G. (2023). Expansion‐enhanced super‐resolution radial fluctuations enable nanoscale molecular profiling of pathology specimens. Nature Nanotechnology, 18(4), 336–342. https://doi.org/10.1038/s41565-023-01328-z.
Lachapelle, M., & Bendayan, M. (1991). Contractile proteins in podocytes: Immunocytochemical localization of actin and alpha‐actinin in normal and nephrotic rat kidneys. Virchows Archiv B, 60(1), 105–111. https://doi.org/10.1007/BF02899534.
Larkins, C. E., Aviles, G. D., East, M. P., Kahn, R. A., & Caspary, T. (2011). Arl13b regulates ciliogenesis and the dynamic localization of Shh signaling proteins. Molecular Biology of the Cell, 22(23), 4694–4703. https://doi.org/10.1091/mbc.E10-12-0994.
Lee, S. H., & Somlo, S. (2014). Cyst growth, polycystins, and primary cilia in autosomal dominant polycystic kidney disease. Kidney Research and Clinical Practice, 33(2), 73–78. https://doi.org/10.1016/j.krcp.2014.05.002.
LeGuennec, M., Klena, N., Aeschlimann, G., Hamel, V., & Guichard, P. (2021). Overview of the centriole architecture. Current Opinion in Structural Biology, 66, 58–65. https://doi.org/10.1016/j.sbi.2020.09.015.
Liffner, B., Cepeda Diaz, A. K., Blauwkamp, J., Anaguano, D., Frolich, S., Muralidharan, V., Wilson, D. W., Dvorin, J. D., & Absalon, S. (2023). Atlas of Plasmodium falciparum intraerythrocytic development using expansion microscopy. eLife, 12, 1‐39. https://doi.org/10.7554/eLife.88088.
Lin, C. H., Lin, T. Y., Hsu, S. C., & Hsu, H. J. (2022). Expansion microscopy‐based imaging for visualization of mitochondria in Drosophila ovarian germline stem cells. FEBS Open Bio, 12(12), 2102–2110. https://doi.org/10.1002/2211-5463.13506.
Louvel, V., Haase, R., Mercey, O., Laporte, M. H., Eloy, T., Baudrier, É., Fortun, D., Soldati‐Favre, D., Hamel, V., & Guichard, P. (2023). iU‐ExM: Nanoscopy of organelles and tissues with iterative ultrastructure expansion microscopy. Nature Communications, 14(1), 7893. https://doi.org/10.1038/s41467-023-43582-8.
Ma, M., Gallagher, A. R., & Somlo, S. (2017). Ciliary mechanisms of cyst formation in polycystic kidney disease. Cold Spring Harbor Perspectives in Biology, 9(11), 1–18. https://doi.org/10.1101/cshperspect.a028209.
Mahjoub, M. R., Xie, Z., & Stearns, T. (2010). Cep120 is asymmetrically localized to the daughter centriole and is essential for centriole assembly. The Journal of Cell Biology, 191(2), 331–346. https://doi.org/10.1083/jcb.201003009.
Mäntylä, E., Montonen, T., Azzari, L., Mattola, S., Hannula, M., Vihinen‐Ranta, M., Hyttinen, J., Vippola, M., Foi, A., Nymark, S., & Ihalainen, T. O. (2023). Iterative immunostaining combined with expansion microscopy and image processing reveals nanoscopic network organization of nuclear lamina. Molecular Biology of the Cell, 34(9), br13. https://doi.org/10.1091/mbc.E22-09-0448.
McConnachie, D. J., Stow, J. L., & Mallett, A. J. (2021). Ciliopathies and the kidney: A review. American Journal of Kidney Diseases, 77(3), 410–419. https://doi.org/10.1053/j.ajkd.2020.08.012.
Middelhauve, V., Siebrasse, J. P., & Kubitscheck, U. (2023). Expansion microscopy of Bacillus subtilis. Methods in Molecular Biology, 2601, 191–202. https://doi.org/10.1007/978-1-0716-2855-3_10.
Miner, J. H. (1999). Renal basement membrane components. Kidney International, 56(6), 2016–2024. https://doi.org/10.1046/j.1523-1755.1999.00785.x.
Moye, A. R., Robichaux, M. A., & Wensel, T. (2023). Expansion microscopy of mouse photoreceptor cilia. Advances in Experimental Medicine and Biology, 1415, 395–402. https://doi.org/10.1007/978-3-031-27681-1_58.
Mundel, P., Heid, H. W., Mundel, T. M., Krüger, M., Reiser, J., & Kriz, W. (1997). Synaptopodin: An actin‐associated protein in telencephalic dendrites and renal podocytes. The Journal of Cell Biology, 139(1), 193–204. https://doi.org/10.1083/jcb.139.1.193.
Murakami, T. C., Mano, T., Saikawa, S., Horiguchi, S. A., Shigeta, D., Baba, K., Sekiya, H., Shimizu, Y., Tanaka, K. F., Kiyonari, H., Iino, M., Mochizuki, H., Tainaka, K., & Ueda, H. R. (2018). A three‐dimensional single‐cell‐resolution whole‐brain atlas using CUBIC‐X expansion microscopy and tissue clearing. Nature Neuroscience, 21(4), 625–637. https://doi.org/10.1038/s41593-018-0109-1.
Norman, J. (2011). Fibrosis and progression of autosomal dominant polycystic kidney disease (ADPKD). Biochimica et Biophysica Acta, 1812(10), 1327–1336. https://doi.org/10.1016/j.bbadis.2011.06.012.
Park, H.‐E., Choi, D., Park, J. S., Sim, C., Park, S., Kang, S., Yim, H., Lee, M., Kim, J., Pac, J., Rhee, K., Lee, J., Lee, Y., Lee, Y., & Kim, S.‐Y. (2019). Scalable and isotropic expansion of tissues with simply tunable expansion ratio. Advanced Science, 6(22), 1901673. https://doi.org/10.1002/advs.201901673.
Park, J., Khan, S., Yun, D. H., Ku, T., Villa, K. L., Lee, J. E., Zhang, Q., Park, J., Feng, G., Nedivi, E., & Chung, K. (2021). Epitope‐preserving magnified analysis of proteome (eMAP). Science Advances, 7(46), eabf6589. https://doi.org/10.1126/sciadv.abf6589.
Parveen, S., Jones, N. W., Millerschultz, I., & Paré, A. C. (2023). Using expansion microscopy to physically enlarge whole‐mount drosophila embryos for super‐resolution imaging. Journal of Visualized Experiments, 194, 1‐16. https://doi.org/10.3791/64662.
Perelsman, O., Asano, S., & Freifeld, L. (2022). Expansion microscopy of larval zebrafish brains and zebrafish embryos. Methods in Molecular Biology, 2440, 211–222. https://doi.org/10.1007/978-1-0716-2051-9_13.
Pernal, S. P., Liyanaarachchi, A., Gatti, D. L., Formosa, B., Pulvender, R., Kuhn, E. R., Ramos, R., Naik, A. R., George, K., Arslanturk, S., Taatjes, D. J., & Jena, B. P. (2020). Nanoscale imaging using differential expansion microscopy. Histochemistry and Cell Biology, 153(6), 469–480. https://doi.org/10.1007/s00418-020-01869-7.
Pesce, L., Cozzolino, M., Lanzanò, L., Diaspro, A., & Bianchini, P. (2019). Measuring expansion from macro‐ to nanoscale using NPC as intrinsic reporter. Journal of Biophotonics, 12(8), e201900018. https://doi.org/10.1002/jbio.201900018.
Ponjavić, I., Vukušić, K., & Tolić, I. M. (2021). Expansion microscopy of the mitotic spindle. Methods in Cell Biology, 161, 247–274. https://doi.org/10.1016/bs.mcb.2020.04.014.
Prozialeck, W. C., Lamar, P. C., & Appelt, D. M. (2004). Differential expression of E‐cadherin, N‐cadherin and beta‐catenin in proximal and distal segments of the rat nephron. BMC Physiology, 4(1), 10. https://doi.org/10.1186/1472-6793-4-10.
Reiter, J. F., & Leroux, M. R. (2017). Genes and molecular pathways underpinning ciliopathies. Nature Reviews. Molecular Cell Biology, 18(9), 533–547. https://doi.org/10.1038/nrm.2017.60.
Rodriguez‐Gatica, J. E., Iefremova, V., Sokhranyaeva, L., Au Yeung, S. W. C., Breitkreuz, Y., Brüstle, O., Schwarz, M. K., & Kubitscheck, U. (2022). Imaging three‐dimensional brain organoid architecture from meso‐ to nanoscale across development. Development, 149(20), 1‐12. https://doi.org/10.1242/dev.200439.
Roselli, S., Gribouval, O., Boute, N., Sich, M., Benessy, F., Attié, T., Gubler, M. C., & Antignac, C. (2002). Podocin localizes in the kidney to the slit diaphragm area. The American Journal of Pathology, 160(1), 131–139. https://doi.org/10.1016/s0002-9440(10)64357-x.
Ruotsalainen, V., Ljungberg, P., Wartiovaara, J., Lenkkeri, U., Kestilä, M., Jalanko, H., Holmberg, C., & Tryggvason, K. (1999). Nephrin is specifically located at the slit diaphragm of glomerular podocytes. Proceedings of the National Academy of Sciences of the United States of America, 96(14), 7962–7967. https://doi.org/10.1073/pnas.96.14.7962.
Sahabandu, N., Kong, D., Magidson, V., Nanjundappa, R., Sullenberger, C., Mahjoub, M. R., & Loncarek, J. (2019). Expansion microscopy for the analysis of centrioles and cilia. Journal of Microscopy, 276(3), 145–159. https://doi.org/10.1111/jmi.12841.
Salisbury, J. L. (1995). Centrin, centrosomes, and mitotic spindle poles. Current Opinion in Cell Biology, 7(1), 39–45. https://doi.org/10.1016/0955-0674(95)80043-3.
Shao, L., El‐Jouni, W., Kong, F., Ramesh, J., Kumar, R. S., Shen, X., Ren, J., Devendra, S., Dorschel, A., Wu, M., Barrera, I., Tabari, A., Hu, K., Haque, N., Yambayev, I., Li, S., Kumar, A., Behera, T. R., McDonough, G., … Zhou, J. (2020). Genetic reduction of cilium length by targeting intraflagellar transport 88 protein impedes kidney and liver cyst formation in mouse models of autosomal polycystic kidney disease. Kidney International, 98(5), 1225–1241. https://doi.org/10.1016/j.kint.2020.05.049.
Siegerist, F., Drenic, V., Koppe, T.‐M., Telli, N., & Endlich, N. (2022). Super‐resolution microscopy: A technique to revolutionize research and diagnosis of glomerulopathies. Glomerular Diseases, 3(1), 19–28. https://doi.org/10.1159/000528713.
Song, C. J., Zimmerman, K. A., Henke, S. J., & Yoder, B. K. (2017). Inflammation and fibrosis in polycystic kidney disease. Results and Problems in Cell Differentiation, 60, 323–344. https://doi.org/10.1007/978-3-319-51436-9_12.
Srivastava, S., Molinari, E., Raman, S., & Sayer, J. A. (2018). Many genes—One disease? Genetics of nephronophthisis (NPHP) and NPHP‐associated disorders [review]. Frontiers in Pediatrics, 5, 1‐15. https://doi.org/10.3389/fped.2017.00287.
Stamenkovic, I., Skalli, O., & Gabbiani, G. (1986). Distribution of intermediate filament proteins in normal and diseased human glomeruli. The American Journal of Pathology, 125(3), 465–475.
Steib, E., Tetley, R., Laine, R. F., Norris, D. P., Mao, Y., & Vermot, J. (2022). TissUExM enables quantitative ultrastructural analysis in whole vertebrate embryos by expansion microscopy. Cell Reports Methods, 2(10), 100311. https://doi.org/10.1016/j.crmeth.2022.100311.
Tillberg, P. W., & Chen, F. (2019). Expansion microscopy: Scalable and convenient super‐resolution microscopy. Annual Review of Cell and Developmental Biology, 35, 683–701. https://doi.org/10.1146/annurev-cellbio-100818-125320.
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(9), 987–992. https://doi.org/10.1038/nbt.3625.
Unnersjö‐Jess, D., Butt, L., Höhne, M., Witasp, A., Kühne, L., Hoyer, P. F., Patrakka, J., Brinkkötter, P. T., Wernerson, A., Schermer, B., Benzing, T., Scott, L., Brismar, H., & Blom, H. (2021). A fast and simple clearing and swelling protocol for 3D in‐situ imaging of the kidney across scales. Kidney International, 99(4), 1010–1020. https://doi.org/10.1016/j.kint.2020.10.039.
Unnersjö‐Jess, D., Scott, L., Sevilla, S. Z., Patrakka, J., Blom, H., & Brismar, H. (2018). Confocal super‐resolution imaging of the glomerular filtration barrier enabled by tissue expansion. Kidney International, 93(4), 1008–1013. https://doi.org/10.1016/j.kint.2017.09.019.
Verkman, A. S. (2002). Renal concentrating and diluting function in deficiency of specific aquaporin genes. Experimental Nephrology, 10(4), 235–240. https://doi.org/10.1159/000063697.
Vlijm, R., Li, X., Panic, M., Rüthnick, D., Hata, S., Herrmannsdörfer, F., Kuner, T., Heilemann, M., Engelhardt, J., Hell, S. W., & Schiebel, E. (2018). STED nanoscopy of the centrosome linker reveals a CEP68‐organized, periodic rootletin network anchored to a C‐Nap1 ring at centrioles. Proceedings of the National Academy of Sciences of the United States of America, 115(10), E2246–e2253. https://doi.org/10.1073/pnas.1716840115.
Wainman, A. (2021). Expansion microscopy on Drosophila spermatocyte centrioles. Methods in Cell Biology, 161, 217–245. https://doi.org/10.1016/bs.mcb.2020.06.008.
Wang, Y., Yu, Z., Cahoon, C. K., Parmely, T., Thomas, N., Unruh, J. R., Slaughter, B. D., & Hawley, R. S. (2018). Combined expansion microscopy with structured illumination microscopy for analyzing protein complexes. Nature Protocols, 13(8), 1869–1895. https://doi.org/10.1038/s41596-018-0023-8.
Wartiovaara, J., Öfverstedt, L.‐G., Khoshnoodi, J., Zhang, J., Mäkelä, E., Sandin, S., Ruotsalainen, V., Cheng, R. H., Jalanko, H., Skoglund, U., & Tryggvason, K. (2004). Nephrin strands contribute to a porous slit diaphragm scaffold as revealed by electron tomography. The Journal of Clinical Investigation, 114(10), 1475–1483. https://doi.org/10.1172/JCI22562.
Wassie, A. T., Zhao, Y., & Boyden, E. S. (2019). Expansion microscopy: Principles and uses in biological research. Nature Methods, 16(1), 33–41. https://doi.org/10.1038/s41592-018-0219-4.
Wen, G., Leen, V., Rohand, T., Sauer, M., & Hofkens, J. (2023). Current Progress in expansion microscopy: Chemical strategies and applications. Chemical Reviews, 123(6), 3299–3323. https://doi.org/10.1021/acs.chemrev.2c00711.
Wilmerding, A., Espana‐Bonilla, P., Giakoumakis, N. N., & Saade, M. (2023). Expansion microscopy of the chick embryo neural tube to overcome molecular crowding at the centrosomes‐cilia. STAR Protocols, 4(1), 101997. https://doi.org/10.1016/j.xpro.2022.101997.
Wilson, P. D. (2004). Polycystic kidney disease. The New England Journal of Medicine, 350(2), 151–164. https://doi.org/10.1056/NEJMra022161.
Wilson, P. D., Hreniuk, D., & Gabow, P. A. (1992). Abnormal extracellular matrix and excessive growth of human adult polycystic kidney disease epithelia. Journal of Cellular Physiology, 150(2), 360–369. https://doi.org/10.1002/jcp.1041500220.
Wloga, D., Joachimiak, E., Louka, P., & Gaertig, J. (2017). Posttranslational modifications of tubulin and cilia. Cold Spring Harbor Perspectives in Biology, 9(6), 1‐14. https://doi.org/10.1101/cshperspect.a028159.
Woo, J., Seo, J.‐M., Lee, M., Kim, J., Min, S., Kim, S.‐T., Ku, S., & Park, J.‐Y. (2020). A modified magnified analysis of proteome (MAP) method for super‐resolution cell imaging that retains fluorescence. Scientific Reports, 10(1), 4186. https://doi.org/10.1038/s41598-020-61156-2.
Wunderlich, L. C. S., Ströhl, F., Ströhl, S., Vanderpoorten, O., Mascheroni, L., & Kaminski, C. F. (2021). Superresolving the kidney‐a practical comparison of fluorescence nanoscopy of the glomerular filtration barrier. Analytical and Bioanalytical Chemistry, 413(4), 1203–1214. https://doi.org/10.1007/s00216-020-03084-8.
Yanda, M. K., Ciobanu, C., Guggino, W. B., & Cebotaru, L. (2023). CFTR and PC2, partners in the primary cilia in autosomal dominant polycystic kidney disease. American Journal of Physiology. Cell Physiology, 325(3), C682–c693. https://doi.org/10.1152/ajpcell.00197.2023.
Yang, J., Liu, X., Yue, G., Adamian, M., Bulgakov, O., & Li, T. (2002). Rootletin, a novel coiled‐coil protein, is a structural component of the ciliary rootlet. The Journal of Cell Biology, 159(3), 431–440. https://doi.org/10.1083/jcb.200207153.
Yoder, B. K., Hou, X., & Guay‐Woodford, L. M. (2002). The polycystic kidney disease proteins, polycystin‐1, polycystin‐2, Polaris, and cystin, are co‐localized in renal cilia. Journal of the American Society of Nephrology, 13(10), 2508–2516. https://doi.org/10.1097/01.Asn.0000029587.47950.25.
Yu, C. J., Orozco Cosio, D. M., & Boyden, E. S. (2022). ExCel: Super‐resolution imaging of C. elegans with expansion microscopy. Methods in Molecular Biology, 2468, 141–203. https://doi.org/10.1007/978-1-0716-2181-3_9.
Zhang, Y. S., Chang, J. B., Alvarez, M. M., Trujillo‐de Santiago, G., Aleman, J., Batzaya, B., Krishnadoss, V., Ramanujam, A. A., Kazemzadeh‐Narbat, M., Chen, F., Tillberg, P. W., Dokmeci, M. R., Boyden, E. S., & Khademhosseini, A. (2016). Hybrid microscopy: Enabling inexpensive high‐performance imaging through combined physical and optical magnifications. Scientific Reports, 6, 22691. https://doi.org/10.1038/srep22691.
Zhao, Y., Bucur, O., Irshad, H., Chen, F., Weins, A., Stancu, A. L., Oh, E. Y., DiStasio, M., Torous, V., Glass, B., Stillman, I. E., Schnitt, S. J., Beck, A. H., & Boyden, E. S. (2017). Nanoscale imaging of clinical specimens using pathology‐optimized expansion microscopy. Nature Biotechnology, 35(8), 757–764. https://doi.org/10.1038/nbt.3892.
Zhou, X., Fan, L. X., Li, K., Ramchandran, R., Calvet, J. P., & Li, X. (2014). SIRT2 regulates ciliogenesis and contributes to abnormal centrosome amplification caused by loss of polycystin‐1. Human Molecular Genetics, 23(6), 1644–1655. https://doi.org/10.1093/hmg/ddt556.
Zhu, C., Wang, A., Chen, L., Guo, L., Ye, J., Chen, Q., Wang, Q., Yao, G., Xia, Q., Cai, T., Guo, J., Yang, Z., Sun, Z., Xu, Y., Lu, G., Zhang, Z., Cao, J., Liu, Y., & Xu, H. (2021). Measurement of expansion factor and distortion for expansion microscopy using isolated renal glomeruli as landmarks. Journal of Biophotonics, 14(7), e202100001. https://doi.org/10.1002/jbio.202100001.
Zhuang, Y., & Shi, X. (2024). Label‐retention expansion microscopy (LR‐ExM) for enhanced fluorescent signals using trifunctional probes. Current Protocols, 4(1), e973. https://doi.org/10.1002/cpz1.973.
معلومات مُعتمدة: R01 HL128370 United States HL NHLBI NIH HHS; NIH DK131177 United States DK NIDDK NIH HHS; NIH HL128370 United States HL NHLBI NIH HHS
فهرسة مساهمة: Keywords: basement membrane; centriole; cilium; nephron; podocytes; polycystic kidney disease; renal
تواريخ الأحداث: Date Created: 20240508 Latest Revision: 20240520
رمز التحديث: 20240520
DOI: 10.1002/cm.21870
PMID: 38715433
قاعدة البيانات: MEDLINE
الوصف
تدمد:1949-3592
DOI:10.1002/cm.21870