Journal Home > Volume 16 , Issue 1

Cell membrane integrity is fundamental to the normal activities of cells and is involved in both acute and chronic pathologies. Here, we report a probe for analyzing cell membrane integrity developed from a 9 nm-sized protein nanocage named Dps via fluorophore conjugation with high spatial precision to avoid self-quenching. The probe cannot enter normal live cells but can accumulate in dead or live cells with damaged membranes, which, interestingly, leads to weak cytoplasmic and strong nuclear staining. This differential staining is found attributed to the high affinity of Dps for histones rather than DNA, providing a staining mechanism different from those of known membrane exclusion probes (MEPs). Moreover, the Dps nanoprobe is larger in size and thus applies a more stringent criterion for identifying severe membrane damage than currently available MEPs. This study shows the potential of Dps as a new bioimaging platform for biological and medical analyses.


menu
Abstract
Full text
Outline
Electronic supplementary material
About this article

Probing cell membrane integrity using a histone-targeting protein nanocage displaying precisely positioned fluorophores

Show Author's information Ti Fang1,2Chaoqun Li2,5Ao Liang2,5Hui Zhang2Fan Zhang2Xian-En Zhang3,4,5Yi-Yu Yang1( )Feng Li2,5( )
Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510120, China
State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
University of Chinese Academy of Sciences, Beijing 100049, China

Abstract

Cell membrane integrity is fundamental to the normal activities of cells and is involved in both acute and chronic pathologies. Here, we report a probe for analyzing cell membrane integrity developed from a 9 nm-sized protein nanocage named Dps via fluorophore conjugation with high spatial precision to avoid self-quenching. The probe cannot enter normal live cells but can accumulate in dead or live cells with damaged membranes, which, interestingly, leads to weak cytoplasmic and strong nuclear staining. This differential staining is found attributed to the high affinity of Dps for histones rather than DNA, providing a staining mechanism different from those of known membrane exclusion probes (MEPs). Moreover, the Dps nanoprobe is larger in size and thus applies a more stringent criterion for identifying severe membrane damage than currently available MEPs. This study shows the potential of Dps as a new bioimaging platform for biological and medical analyses.

Keywords: nanoparticles, fluorescent probes, protein engineering, cell membrane damage, ferritin superfamily

References(56)

[1]

Ammendolia, D. A.; Bement, W. M.; Brumell, J. H. Plasma membrane integrity: Implications for health and disease. BMC Biol. 2021, 19, 71.

[2]

Dias, C.; Nylandsted, J. Plasma membrane integrity in health and disease: Significance and therapeutic potential. Cell Discov. 2021, 7, 4.

[3]

Gu, L. S.; Li, Y. Y.; Zhang, S. W.; Zhou, M. G.; Xue, Y. H.; Li, W. X.; Xu, T.; Ji, W. Molecular-scale axial localization by repetitive optical selective exposure. Nat. Methods 2021, 18, 369–373.

[4]

Cheng, Y.; Borum, R. M.; Clark, A. E.; Jin, Z. C.; Moore, C.; Fajtová, P.; O'Donoghue, A. J.; Carlin, A. F.; Jokerst, J. V. A dual-color fluorescent probe allows simultaneous imaging of main and papain-like proteases of SARS-CoV-2-infected cells for accurate detection and rapid inhibitor screening. Angew. Chem., Int. Ed. 2022, 61, e202113617.

[5]

Lee, S.; Zhang, Z. H.; Yu, Y. Real-time simultaneous imaging of acidification and proteolysis in single phagosomes using bifunctional janus-particle probes. Angew. Chem., Int. Ed. 2021, 60, 26734–26739.

[6]

Williams, N. D.; Landajuela, A.; Kasula, R. K.; Zhou, W. J.; Powell, J. T.; Xi, Z. Q.; Isaacs, F. J.; Berro, J.; Toomre, D.; Karatekin, E. et al. DNA-origami-based fluorescence brightness standards for convenient and fast protein counting in live cells. Nano Lett. 2020, 20, 8890–8896.

[7]

Othmer, M.; Zepp, F. Flow cytometric immunophenotyping: Principles and pitfalls. Eur. J. Pediatr. 1992, 151, 398–406.

[8]

Schmid, I.; Krall, W. J.; Uittenbogaart, C. H.; Braun, J.; Giorgi, J. V. Dead cell discrimination with 7-amino-actinomycin D in combination with dual color immunofluorescence in single laser flow cytometry. Cytometry 1992, 13, 204–208.

[9]
Perfetto, S. P.; Chattopadhyay, P. K.; Lamoreaux, L.; Nguyen, R.; Ambrozak, D.; Koup, R. A.; Roederer, M. Amine-reactive dyes for dead cell discrimination in fixed samples. Curr. Protoc. Cytom. 2010, Chapter 9, Unit 9.34.
[10]

Chen, S. J.; Liu, J. Z.; Zhang, S. X.; Zhao, E. G.; Yu, C. Y. Y.; Hushiarian, R.; Hong, Y. N.; Tang, B. Z. Biochromic silole derivatives: A single dye for differentiation, quantitation and imaging of live/dead cells. Mater. Horiz. 2018, 5, 969–978.

[11]

Martinić, I.; Eliseeva, S. V.; Nguyen, T. N.; Pecoraro, V. L.; Petoud, S. Near-infrared optical imaging of necrotic cells by photostable lanthanide-based metallacrowns. J. Am. Chem. Soc. 2017, 139, 8388–8391.

[12]

Ouyang, C.; Li, Y. G.; Rees, T. W.; Liao, X. X.; Jia, J. H.; Chen, Y.; Zhang, X. T.; Ji, L. N.; Chao, H. Supramolecular assembly of an organoplatinum(II) complex with ratiometric dual emission for two-photon bioimaging. Angew. Chem., Int. Ed. 2021, 60, 4150–4157.

[13]

Shen, L. Y.; Bing, T.; Zhang, N.; Wang, L. L.; Wang, J. Y.; Liu, X. J.; Shangguan, D. H. A Nucleus-targeting DNA aptamer for dead cell indication. ACS Sens. 2019, 4, 1612–1618.

[14]

Tian, M. G.; Ma, Y. Y.; Lin, W. Y. Fluorescent probes for the visualization of cell viability. Acc. Chem. Res. 2019, 52, 2147–2157.

[15]

Davey, H. M.; Hexley, P. Red but not dead? Membranes of stressed Saccharomyces cerevisiae are permeable to propidium iodide. Environ. Microbiol. 2011, 13, 163–171.

[16]

Shi, L.; Günther, S.; Hübschmann, T.; Wick, L. Y.; Harms, H.; Müller, S. Limits of propidium iodide as a cell viability indicator for environmental bacteria. Cytometry 2007, 71A, 592–598.

[17]

Kirchhoff, C.; Cypionka, H. Propidium ion enters viable cells with high membrane potential during live-dead staining. J. Microbiol. Methods 2017, 142, 79–82.

[18]

Shirakashi, R.; Sukhorukov, V. L.; Tanasawa, I.; Zimmermann, U. Measurement of the permeability and resealing time constant of the electroporated mammalian cell membranes. Int. J. Heat Mass Transf. 2004, 47, 4517–4524.

[19]

Rieger, A. M.; Hall, B. E.; Luong, L. T.; Schang, L. M.; Barreda, D. R. Conventional apoptosis assays using propidium iodide generate a significant number of false positives that prevent accurate assessment of cell death. J. Immunol. Methods 2010, 358, 81–92.

[20]

Yang, Y. G.; Xiang, Y. B.; Xu, M. Y. From red to green: The propidium iodide-permeable membrane of Shewanella decolorationis S12 is repairable. Sci. Rep. 2015, 5, 18583.

[21]

Vitale, M.; Zamai, L.; Mazzotti, G.; Cataldi, A.; Falcieri, E. Differential kinetics of propidium iodide uptake in apoptotic and necrotic thymocytes. Histochemistry 1993, 100, 223–229.

[22]

Sayas, E.; García-López, F.; Serrano, R. Toxicity, mutagenicity and transport in Saccharomyces cerevisiae of three popular DNA intercalating fluorescent dyes. Yeast 2015, 32, 595–606.

[23]

Ferguson, L. R.; Denny, W. A. Genotoxicity of non-covalent interactions: DNA intercalators. Mutat. Res. Fund. Mol. Mech. Mutagen. 2007, 623, 14–23.

[24]

Chi, Z. X.; Liu, R. T.; Sun, Y. J.; Wang, M. J.; Zhang, P. J.; Gao, C. Z. Investigation on the toxic interaction of toluidine blue with calf thymus DNA. J. Hazard. Mater. 2010, 175, 274–278.

[25]

Banerjee, A.; Majumder, P.; Sanyal, S.; Singh, J.; Jana, K.; Das, C.; Dasgupta, D. The DNA intercalators ethidium bromide and propidium iodide also bind to core histones. FEBS Open Bio 2014, 4, 251–259.

[26]

Choi, H. S.; Frangioni, J. V. Nanoparticles for biomedical imaging: Fundamentals of clinical translation. Mol. Imaging 2010, 9, 291–310.

[27]

Liu, X. Y.; Wu, W. J.; Cui, D. X.; Chen, X. Y.; Li, W. W. Functional micro-/nanomaterials for multiplexed biodetection. Adv. Mater. 2021, 33, 2004734.

[28]

Maassen, S. J.; van der Ham, A. M.; Cornelissen, J. J. L. M. Combining protein cages and polymers: From understanding self-assembly to functional materials. ACS Macro Lett. 2016, 5, 987–994.

[29]

Sun, H. C.; Luo, Q.; Hou, C. X.; Liu, J. Q. Nanostructures based on protein self-assembly: From hierarchical construction to bioinspired materials. Nano Today 2017, 14, 16–41.

[30]

Luo, Q.; Hou, C. X.; Bai, Y. S.; Wang, R. B.; Liu, J. Q. Protein assembly: Versatile approaches to construct highly ordered nanostructures. Chem. Rev. 2016, 116, 13571–13632.

[31]

Miao, Y.; Yang, T.; Yang, S. X.; Yang, M. Y.; Mao, C. B. Protein nanoparticles directed cancer imaging and therapy. Nano Converg. 2022, 9, 2.

[32]

Allen, M.; Willits, D.; Mosolf, J.; Young, M.; Douglas, T. Protein cage constrained synthesis of ferrimagnetic iron oxide nanoparticles. Adv. Mater. 2002, 14, 1562–1565.

DOI
[33]

Wu, Q. Y.; Wu, L.; Wang, Y. Z.; Zhu, Z.; Song, Y. L.; Tan, Y. Y.; Wang, X. F.; Li, J. X.; Kang, D. Z.; Yang, C. J. Evolution of DNA aptamers for malignant brain tumor gliosarcoma cell recognition and clinical tissue imaging. Biosens. Bioelectron. 2016, 80, 1–8.

[34]

Collot, M.; Schild, J.; Fam, K. T.; Bouchaala, R.; Klymchenko, A. S. stealth and bright monomolecular fluorescent organic nanoparticles based on folded amphiphilic polymer. ACS Nano 2020, 14, 13924–13937.

[35]

Panchuk-Voloshina, N.; Haugland, R. P.; Bishop-Stewart, J.; Bhalgat, M. K.; Millard, P. J.; Mao, F.; Leung, W. Y.; Haugland, R. P. Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates. J. Histochem. Cytochem. 1999, 47, 1179–1188.

[36]

Zhao, H.; Xu, J. B.; Feng, C.; Ren, J. Y.; Bao, L.; Zhao, Y. B.; Tao, W.; Zhao, Y. L.; Yang, X. L. Tailoring aggregation extent of photosensitizers to boost phototherapy potency for eliciting systemic antitumor immunity. Adv. Mater. 2022, 34, 2106390.

[37]

Zhao, H.; Xu, J. B.; Wang, Y. Q.; Sun, C. Y.; Bao, L.; Zhao, Y. B.; Yang, X. L.; Zhao, Y. L. A photosensitizer discretely loaded nanoaggregate with robust photodynamic effect for local treatment triggers systemic antitumor responses. ACS Nano 2022, 16, 3070–3080.

[38]

Khalin, I.; Heimburger, D.; Melnychuk, N.; Collot, M.; Groschup, B.; Hellal, F.; Reisch, A.; Plesnila, N.; Klymchenko, A. S. Ultrabright fluorescent polymeric nanoparticles with a stealth pluronic shell for live tracking in the mouse brain. ACS Nano 2020, 14, 9755–9770.

[39]

Chen, W. Y.; Young, L. J.; Lu, M.; Zaccone, A.; Ströhl, F.; Yu, N.; Schierle, G. S. K.; Kaminski, C. F. Fluorescence self-quenching from reporter dyes informs on the structural properties of amyloid clusters formed in vitro and in cells. Nano Lett. 2017, 17, 143–149.

[40]

Kim, Y.; Ho, S. O.; Gassman, N. R.; Korlann, Y.; Landorf, E. V.; Collart, F. R.; Weiss, S. Efficient site-specific labeling of proteins via cysteines. Bioconjugate Chem. 2008, 19, 786–791.

[41]

Li, J.; Dai, J. B.; Jiang, S. X.; Xie, M.; Zhai, T. T.; Guo, L. J.; Cao, S. T.; Xing, S.; Qu, Z. B.; Zhao, Y. et al. Encoding quantized fluorescence states with fractal DNA frameworks. Nat. Commun. 2020, 11, 2185.

[42]

Milosevic, A. M.; Haeni, L.; Hirschi, L. A.; Vanni, S.; Campomanes-Ramos, P.; Rothen-Rutishauser, B.; Rodriguez-Lorenzo, L.; Petri-Fink, A. The choice of nanoparticle surface-coupled fluorescent dyes impacts cellular interaction. ChemNanoMat 2022, 8, e202100443.

[43]

Cilliers, C.; Nessler, I.; Christodolu, N.; Thurber, G. M. Tracking antibody distribution with near-infrared fluorescent dyes: Impact of dye structure and degree of labeling on plasma clearance. Mol. Pharmaceutics 2017, 14, 1623–1633.

[44]

Xu, Y.; Wang, Q. B.; He, P.; Dong, Q. M.; Liu, F.; Liu, Y.; Lin, L.; Yan, H.; Zhao, X. H. Cell nucleus penetration by quantum dots induced by nuclear staining organic fluorophore and UV-irradiation. Adv. Mater. 2008, 20, 3468–3473.

[45]

Bozzi, M.; Mignogna, G.; Stefanini, S.; Barra, D.; Longhi, C.; Valenti, P.; Chiancone, E. A novel non-heme iron-binding ferritin related to the DNA-binding proteins of the Dps family in Listeria innocua. J. Biol. Chem. 1997, 272, 3259–3265.

[46]

Winterbourn, C. C. The biological chemistry of hydrogen peroxide. Methods Enzymol. 2013, 528, 3–25.

[47]

Shinji, T.; Tetsuji, T.; Hirotoshi, M.; Eijiro, O.; Takeshi, M.; Yasuyoshi, O. Hydrogen peroxide-induced apoptosis and necrosis in human lung fibroblasts: Protective roles of glutathione. Jpn. J. Pharmacol. 1999, 79, 33–40.

[48]

Chu, K. F.; Dupuy, D. E. Thermal ablation of tumours: Biological mechanisms and advances in therapy. Nat. Rev. Cancer 2014, 14, 199–208.

[49]

Tang, H. M.; Tang, H. L. Anastasis: Recovery from the brink of cell death. R. Soc. Open Sci. 2018, 5, 180442.

[50]

Campos, E. I.; Fillingham, J.; Li, G. H.; Zheng, H. Y.; Voigt, P.; Kuo, W. H. W.; Seepany, H.; Gao, Z. H.; Day, L. A.; Greenblatt, J. F. et al. The program for processing newly synthesized histones H3.1 and H4. Nat. Struct. Mol. Biol. 2010, 17, 1343–1351.

[51]

Bernardes, N. E.; Chook, Y. M. Nuclear import of histones. Biochem. Soc. Trans. 2020, 48, 2753–2767.

[52]

Zierhut, C.; Jenness, C.; Kimura, H.; Funabiki, H. Nucleosomal regulation of chromatin composition and nuclear assembly revealed by histone depletion. Nat. Struct. Mol. Biol. 2014, 21, 617–625.

[53]

Vepris, O.; Eich, C.; Feng, Y. S.; Fuentes, G.; Zhang, H.; Kaijzel, E. L.; Cruz, L. J. Optically coupled PtOEP and DPA molecules encapsulated into PLGA-nanoparticles for cancer bioimaging. Biomedicines 2022, 10, 1070.

[54]

Gandra, N.; Wang, D. D.; Zhu, Y.; Mao, C. B. Virus-mimetic cytoplasm-cleavable magnetic/silica nanoclusters for enhanced gene delivery to mesenchymal stem cells. Angew. Chem., Int. Ed. 2013, 52, 11278–11281.

[55]

Finck, A. V.; Blanchard, T.; Roselle, C. P.; Golinelli, G.; June, C. H. Engineered cellular immunotherapies in cancer and beyond. Nat. Med. 2022, 28, 678–689.

[56]

Bush, L. M.; Healy, C. P.; Javdan, S. B.; Emmons, J. C.; Deans, T. L. Biological cells as therapeutic delivery vehicles. Trends Pharmacol. Sci. 2021, 42, 106–118.

File
12274_2022_4785_MOESM1_ESM.pdf (4.6 MB)
Publication history
Copyright
Acknowledgements

Publication history

Received: 07 May 2022
Revised: 13 July 2022
Accepted: 18 July 2022
Published: 02 September 2022
Issue date: January 2023

Copyright

© Tsinghua University Press 2022

Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (No. 31771103), Chinese Academy of Sciences (CAS) Emergency Project of African Swine Fever (ASF) Research (No. KJZD-SW-L07), and the Scientific Instrument Developing Project of the CAS (No. YJKYYQ20190057). We thank Juan Min and Ding Gao at the Core Facility and Technical Support of Wuhan Institute of Virology for assistance in tissue imaging, confocal microscopy, and transmission electron microscopy.

Return