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Cited by 1,113Cellular transport and secretionAdvanced Fluorescence Microscopy TechniquesCell Image Analysis Techniques

Applying systems-level spectral imaging and analysis to reveal the organelle interactome

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Valm, Alex M., Cohen, Sarah, Legant, Wesley R., Melunis, Justin, Hershberg, Uri, Wait, Eric, Cohen, Andrew R., Davidson, Michael W. +2 more·2017·Nature
DOI 10.1038/nature22369PMC PMC5536967
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Abstract

The organization of the eukaryotic cell into discrete membrane-bound organelles allows for the separation of incompatible biochemical processes, but the activities of these organelles must be coordinated. For example, lipid metabolism is distributed between the endoplasmic reticulum for lipid synthesis, lipid droplets for storage and transport, mitochondria and peroxisomes for β-oxidation, and lysosomes for lipid hydrolysis and recycling. It is increasingly recognized that organelle contacts have a vital role in diverse cellular functions. However, the spatial and temporal organization of organelles within the cell remains poorly characterized, as fluorescence imaging approaches are limited in the number of different labels that can be distinguished in a single image. Here we present a systems-level analysis of the organelle interactome using a multispectral image acquisition method that overcomes the challenge of spectral overlap in the fluorescent protein palette. We used confocal and lattice light sheet instrumentation and an imaging informatics pipeline of five steps to achieve mapping of organelle numbers, volumes, speeds, positions and dynamic inter-organelle contacts in live cells from a monkey fibroblast cell line. We describe the frequency and locality of two-, three-, four- and five-way interactions among six different membrane-bound organelles (endoplasmic reticulum, Golgi, lysosome, peroxisome, mitochondria and lipid droplet) and show how these relationships change over time. We demonstrate that each organelle has a characteristic distribution and dispersion pattern in three-dimensional space and that there is a reproducible pattern of contacts among the six organelles, that is affected by microtubule and cell nutrient status. These live-cell confocal and lattice light sheet spectral imaging approaches are applicable to any cell system expressing multiple fluorescent probes, whether in normal conditions or when cells are exposed to disturbances such as drugs, pathogens or stress. This methodology thus offers a powerful descriptive tool and can be used to develop hypotheses about cellular organization and dynamics.

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  • Lipid droplets communicate closely through contact sites with other cellular organelles, including peroxisomes.

    “To perform their functions efficiently, LDs communicate closely through contact sites with other cellular organelles, including peroxisomes [429,430].”

    From Revisiting the Pathogenesis of X-Linked Adrenoleukodystrophy (2025) · cites this paper as [429]

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Research works printed but not linked: 36

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Authors
Valm, A. M., Cohen, S., Legant, W. R., Melunis, J., Hershberg, U., Wait, E., Cohen, A. R., Davidson, M. W., Betzig, E., & Lippincott-Schwartz, J.
Affiliations
  • National Institutes of Health (US)
  • Howard Hughes Medical Institute (US)
  • Drexel University (US)
  • Florida State University (US)
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2017-05-24
Volume
546
Issue
7656
Pages
162-167
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature22369
PMC
PMC5536967
OpenAlex
W2617667835
Cited by
1,113
References
0
Citations by year
2026: 102 · 2025: 130 · 2024: 119 · 2023: 119 · 2022: 162 · 2021: 133 · 2020: 145 · 2019: 108 · 2018: 72 · 2017: 22 · 2016: 1
FWCI
50.66
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • Howard Hughes Medical Institute
  • National Institute on Aging (R01AG041861)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
Keywords
multispectral imaging, spectral overlap, lattice light-sheet microscopy, confocal microscopy, live-cell imaging, endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes, mitochondria, lipid droplets, organelle dynamics, spectral deconvolution
MeSH terms
Animals, Cell Survival, Chlorocebus aethiops, Color, Cytoskeleton, Endoplasmic Reticulum, Golgi Apparatus, Lysosomes, Microtubules, Mitochondria, Organelles, Microscopy, Confocal, COS Cells, Peroxisomes, Systems Biology, Lipid Metabolism, Molecular Imaging, Spatio-Temporal Analysis

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