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  • Expert Recommendation
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Key challenges and recommendations for defining organelle membrane contact sites

Nature Reviews Molecular Cell Biology volume 26, pages 776–796 (2025) Cite this article

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Abstract

Intracellular membrane contact sites (MCSs) between organelles have crucial roles in cellular signalling and homeostasis. These sites, which are often disrupted in pathological conditions, enable the exchange of ions, lipids and metabolites between membrane-bound compartments, helping cells adapt to varying physiological conditions. Specific tether proteins and complexes stabilize these interactions and mediate responses to different intracellular or extracellular stimuli. The study of MCSs has progressed in recent years, owing to the development of new methods such as genetically encoded reporter constructs, advanced imaging techniques, including super-resolution microscopy and electron tomography, and proteomic approaches based on mass spectrometry. These tools have enabled unprecedented visualization and quantification of organelle interactions, as well as identification of the molecular players involved. This Expert Recommendation aims to define and map the ‘organelle contactome’, describing key proteins involved in contact site formation and the roles of MCSs in cellular function. We also explore contact site dynamics and detail advantages and disadvantages of the methodologies for studying them. Importantly, we consolidate open questions in contact site research and discuss challenges and limitations of the current experimental approaches.

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Fig. 1: Biological functions and transported molecules of the organelle contactome.
The alternative text for this image may have been generated using AI.
Fig. 2: Genetically encoded reporters for detection and quantification of organelle contacts.
The alternative text for this image may have been generated using AI.
Fig. 3: Contact site dynamics.
The alternative text for this image may have been generated using AI.

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Acknowledgements

T.C. is grateful to L. Barazzuol for helpful discussions. The work is supported by grants from the Ministry of University and Research (PRIN2017 no. 2017E5L5P3 and PRIN2022 no. 2022XKAAZ7 to T.C. and PRIN2022 no. 20223ABZ82 to M.B.); from the Università degli Studi di Padova (STARS Consolidator Grant 2019 to T.C. and Progetto di Ateneo 2023 no. CALI_BIRD23_01 to T.C.), PNRR — CN3 National Center for Gene Therapy and Drugs based on RNA Technology to M.B., T.C. and R.R. no. CN00000041 (2022–26); from CARIPARO Foundation (Progetto di eccellenza 2023 to M.B.); from the National Agency for Research (Grant ANR-18-CE13-0016 STAYING-TIGHT to E.M.B.); and European Union’s Horizon 2020 research and innovation programme (project 772103-BRIDGING to E.M.B.).

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Authors and Affiliations

  1. Department of Biomedical Sciences (DSB), University of Padova, Padova, Italy

    Tito Calì & Rosario Rizzuto

  2. Padova Neuroscience Center (PNC), University of Padova, Padova, Italy

    Tito Calì

  3. Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy

    Tito Calì & Marisa Brini

  4. Université de Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, Villenave d’Ornon, France

    Emmanuelle M. Bayer

  5. University College London Institute of Ophthalmology, London, UK

    Emily R. Eden

  6. MitoCare Center for Mitochondrial Imaging Research and Diagnostics, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA

    György Hajnóczky

  7. Department of Biochemistry, University of Oxford, Oxford, UK

    Benoit Kornmann

  8. Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA

    Laura Lackner

  9. Department of Physiology, UT Southwestern Medical Center, Dallas, TX, USA

    Jen Liou

  10. Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA

    Karin Reinisch

  11. Department of Chemistry, Seoul National University, Seoul, Republic of Korea

    Hyun-Woo Rhee

  12. Department of Biology, University of Padova, Padova, Italy

    Luca Scorrano

  13. Veneto Institute of Molecular Medicine, Padova, Italy

    Luca Scorrano

  14. Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy

    Marisa Brini

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Contributions

T.C., M.B. and R.R. researched data for the article and contributed substantially to discussion of the content. All authors wrote, reviewed and/or edited the manuscript before submission.

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Correspondence to Tito Calì or Marisa Brini.

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Glossary

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(CMA). A selective form of autophagy in which specific cytosolic proteins are recognized by chaperones and directly translocated into the lysosome for degradation.

Cotyledon

A seed leaf that provides nutrients to the developing plant embryo during germination.

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The direct engulfment of lipid droplets by the lysosome or vacuole for degradation.

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(SOCE). A mechanism in which depletion of intracellular Ca2+ stores triggers the influx of Ca2+ ions from the extracellular space through plasma membrane channels.

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An optical imaging technique that uses evanescent waves to selectively excite fluorophores near the surface of a specimen, allowing high resolution on the z-axis for imaging of cellular processes at or near the membrane.

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Calì, T., Bayer, E.M., Eden, E.R. et al. Key challenges and recommendations for defining organelle membrane contact sites. Nat Rev Mol Cell Biol 26, 776–796 (2025). https://doi.org/10.1038/s41580-025-00864-x

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