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A DNA nanomachine chemically resolves lysosomes in live cells

Abstract

Lysosomes are multifunctional, subcellular organelles with roles in plasma membrane repair, autophagy, pathogen degradation and nutrient sensing. Dysfunctional lysosomes underlie Alzheimer’s disease, Parkinson’s disease and rare lysosomal storage diseases, but their contributions to these pathophysiologies are unclear. Live imaging has revealed lysosome subpopulations with different physical characteristics including dynamics, morphology or cellular localization. Here, we chemically resolve lysosome subpopulations using a DNA-based combination reporter that quantitatively images pH and chloride simultaneously in the same lysosome while retaining single-lysosome information in live cells. We call this technology two-ion measurement or 2-IM. 2-IM of lysosomes in primary skin fibroblasts derived from healthy individuals shows two main lysosome populations, one of which is absent in primary cells derived from patients with Niemann–Pick disease. When patient cells are treated with relevant therapeutics, the second population re-emerges. Chemically resolving lysosomes by 2-IM could enable decoding the mechanistic underpinnings of lysosomal diseases, monitoring disease progression or evaluating therapeutic efficacy.

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Fig. 1: Design and characterization of ChloropHore.
Fig. 2: Trafficking pathway of ChloropHore in human dermal fibroblasts.
Fig. 3: Intracellular calibration of ChloropHore and ChloropHoreLy.
Fig. 4: 2-IM chemically resolves lysosome populations.

Data availability

The data that support the plots within this paper and the findings of this study are available from the corresponding author upon reasonable request.

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Acknowledgements

This work was supported by the University of Chicago Women’s Board, Pilot and Feasibility award from an NIDDK center grant P30DK42086 to the University of Chicago Digestive Diseases Research Core Center, MRSEC grant no. DMR-1420709, Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust, C-084, ANL-UChicago collaborative grant and University of Chicago start-up funds to Y.K. Y.K. is a Brain Research Foundation Fellow.

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K.L., K.C., A.S. and Y.K. designed the project. K.L., K.C. and A.S. performed experiments. K.L., K.C., A.S. and Y.K. analysed the data. K.L., K.C., A.S. and Y.K. wrote the paper. All authors discussed the results and gave input on the manuscript.

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Correspondence to Yamuna Krishnan.

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Leung, K., Chakraborty, K., Saminathan, A. et al. A DNA nanomachine chemically resolves lysosomes in live cells. Nature Nanotech 14, 176–183 (2019). https://doi.org/10.1038/s41565-018-0318-5

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