Marisa Brini

Membrane contact sites (MCSs) are highly specialized inter-organelle interfaces that coordinate lipid exchange, ion signalling, organelle dynamics, and metabolic adaptation. Their remarkable molecular and temporal heterogeneity makes their visualization particularly challenging, requiring imaging approaches capable of resolving contacts that range from highly transient interactions to long-lived membrane associations. In this Review, we discuss the methodologies currently available to investigate MCSs, with particular emphasis on genetically encoded reporters suitable for live-cell imaging. We examine the biochemical and biophysical principles governing the performance of the main classes of proximity reporters, including split fluorescent proteins systems-, such as split green fluorescent protein (split-GFP) and split Fluorescence-Activating and Absorption-Shifting Tag (split-FAST), dimerization-dependent fluorescent protein (ddFP)-, and Förster resonance energy transfer (FRET)-based reporters, highlighting how thermodynamic stability, association and dissociation kinetics, fluorophore maturation, and environmental factors influence signal generation and the interpretation of contact dynamics. We further integrate current knowledge on the dynamic behaviour of major MCSs —including endoplasmic reticulum–mitochondria, endoplasmic reticulum–plasma membrane, mitochondria–lysosome, and lipid droplet–mitochondria interfaces— to discuss how different reporters capture distinct aspects of organelle communication. Rather than identifying a universally superior probe, we propose a framework in which reporter selection is guided by the biological question, the temporal and spatial resolution required, the experimental model, and the practical constraints of the imaging platform. This perspective emphasizes that complementary imaging approaches are often required to obtain a comprehensive understanding of MCSs organization, remodelling, and function.

Summary: DJ-1 is a redox-sensitive protein implicated in early-onset Parkinson’s disease, and its mitochondrial localization protects against oxidative stress, but the mechanisms regulating its submitochondrial targeting and functional impact on mitochondrial integrity remain poorly understood. We identify voltage-dependent anion channel 1 (VDAC1) as a regulator of the submitochondrial distribution of DJ-1 during stress. Endogenous DJ-1 interacted with VDAC1, and loss of VDAC1 reduced stress-induced DJ-1 accumulation within the mitochondrial matrix. VDAC1-deficient neurons exhibited mitochondrial fragmentation, impaired oxidative phosphorylation, reduced ATP levels, altered reactive oxygen species (ROS) responses, and increased sensitivity to MPP⁺. Matrix-targeted, but not outer-membrane-targeted, DJ-1 rescued basal, ATP-linked, and maximal respiration, improved mitochondrial morphology, and enhanced neuronal survival. ATP synthase inhibition also rapidly increased mitochondrial DJ-1, suggesting bioenergetic stress promotes its mitochondrial accumulation. Our findings identify compartment-specific localization as a key determinant of DJ-1 function and establish VDAC1-dependent matrix targeting as a critical mechanism supporting mitochondrial integrity during stress.

Organelle contact sites are highly dynamic and specialized regions where distinct organelles come into proximity, enabling direct inter-organelle communication. These structures play fundamental roles in cellular homeostasis by coordinating the exchange of lipids, metabolites, and ions, as well as regulating key processes such as organelle dynamics, mitochondrial fission, autophagy, and metabolic integration. Alterations in contact site architecture and function have been increasingly associated with a wide range of human diseases, including neurodegeneration, metabolic disorders, and cancer. Despite their biological relevance, the nanoscale nature and dynamic behaviour of contact sites have historically posed significant challenges for their accurate detection and functional characterization. Here, we provide a comprehensive overview of the methodologies currently available to study organelle contact sites, ranging from classical approaches such as electron microscopy and biochemical fractionation to advanced imaging techniques and genetically encoded reporters. We discuss recent developments in high-resolution and live-cell microscopy that have improved the spatial and temporal resolution of contact site analysis, as well as emerging tools designed to selectively label, quantify, and manipulate these interfaces. Attention is given to the next generation of engineered reporters capable of sensing molecular and ionic exchanges at contact sites, thereby moving beyond structural description toward functional interrogation. By critically evaluating the strengths and limitations of existing approaches, we aim to provide a framework for selecting appropriate tools and to highlight future directions in the field. Ultimately, advancing our ability to monitor and dissect organelle contact sites will be essential for understanding their contribution to cellular physiology and disease.

Mitochondria-nucleus contact sites (also known as nucleus-associated mitochondria, NAMs) are emerging as important platforms for inter-organelle communicat

Ca²⁺ signaling is essential for neuronal development, migration, synaptic activity, spine plasticity, neurotransmitter release, membrane excitability, and long-term synaptic plasticity, as well as for the coupling between membrane depolarization and downstream signaling. Traditionally, Plasma Membrane Ca²⁺ ATPases (PMCAs) were considered high-affinity, low-capacity calcium extruders. However, recent evidence reveals that the PMCA-Neuroplastin complex facilitates ultrafast Ca²⁺ clearance at kilohertz frequencies, reshaping our understanding of calcium regulation, in particular in neurons. For bulk Ca²⁺ clearance, they are overshadowed by more powerful low-affinity/high-capacity systems on the plasma membrane. This raises key questions: what is the specific physiological and pathological role of PMCAs? Why do cells require a high-affinity/low-capacity, ATP-dependent extrusion mechanism? What is the functional meaning of the diversity of isoforms (four) and splice variants (over thirty)? And why do neurons localize distinct PMCA pumps to pre- and postsynaptic sites? The prevailing hypothesis is that PMCAs fine-tune Ca²⁺ microdomains through local regulation and interactions with specific protein partners. Finally, understanding their role in Purkinje cells (PCs) is particularly relevant, as alterations in PMCA function have been implicated in cerebellar pathology and ataxia.

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.

Organelle contact sites are crucial for cellular function, enabling the exchange of lipids, ions, and other molecules between different organelles. The ability to track these contact sites in vivo has been significantly advanced by the development of SPLICS (Split-GFP-based Contact Site Sensors) reporters, which have provided unprecedented insights into the intricate network of organelle communication. This innovative and powerful tool allows the real-time visualization of different organelle interactions in living cells and in vivo thus unraveling the complexity of their dynamic in the context of cellular homeostasis. Recent studies highlighted the dynamic nature of organelle contact sites either in terms of tethering/untethering and of movement of the contact itself in time and space: whether unique temporal behaviors and contact site-specific dynamics of different organelle interactions exist is currently unknown. In this study, we investigated the spatiotemporal distribution of various organelle contact sites using time-lapse in vitro and in vivo imaging and discovered an evolutionarily conserved dynamic pattern among different contact sites, influenced by the specific partner organelles involved. These findings highlight the importance of spatial and temporal regulation at organelle contact sites, which may underlie their diverse physiological functions. The discovery of contact site-specific dynamics opens new avenues for understanding the regulation of organelle interactions in health and disease, with potential implications for developing targeted therapeutic strategies.

IP₃ receptor (IP₃R)-mediated Ca²⁺ transfer at the mitochondria-endoplasmic reticulum (ER) contact sites (MERCS) drives mitochondrial Ca²⁺ uptake and oxidative metabolism and is linked to different pathologies, including Parkinson’s disease (PD). The dependence of Ca²⁺ transfer efficiency on the ER-mitochondria distance remains unexplored. Employing molecular rulers that stabilize ER-mitochondrial distances at 5 nm resolution, and using genetically encoded Ca²⁺ indicators targeting the ER lumen and the sub-mitochondrial compartments, we now show that a distance of ~20 nm is optimal for Ca²⁺ transfer and mitochondrial oxidative metabolism due to enrichment of IP₃R at MERCS. In human iPSC-derived astrocytes from PD patients, 20 nm MERCS were specifically reduced, which correlated with a reduction of mitochondrial Ca²⁺ uptake. Stabilization of the ER-mitochondrial interaction at 20 nm, but not at 10 nm, fully rescued mitochondrial Ca²⁺ uptake in PD astrocytes. Our work determines with precision the optimal distance for Ca²⁺ flux between ER and mitochondria and suggests a new paradigm for fine control over mitochondrial function.

Mitochondrial and lysosomal activities are crucial to maintain cellular homeostasis: optimal coordination is achieved at their membrane contact sites where distinct protein machineries regulate organelle network dynamics, ions and metabolites exchange. Here we describe a genetically encoded SPLICS reporter for short- and long- juxtapositions between mitochondria and lysosomes. We report the existence of narrow and wide lysosome-mitochondria contacts differently modulated by mitophagy, autophagy and genetic manipulation of tethering factors. The overexpression of α-synuclein (α-syn) reduces the apposition of mitochondria/lysosomes membranes and affects their privileged Ca²⁺transfer, impinging on TFEB nuclear translocation. We observe enhanced TFEB nuclear translocation in α-syn-overexpressing cells. We propose that α-syn, by interfering with mitochondria/lysosomes tethering impacts on local Ca²⁺regulated pathways, among which TFEB mediated signaling, and in turn mitochondrial and lysosomal function. Defects in mitochondria and lysosome represent a common hallmark of neurodegenerative diseases: targeting their communication could open therapeutic avenues.

Neurodegenerative diseases (NDs) encompass an assorted array of disorders such as Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis, each characterised by distinct clinical manifestations and underlying pathological mechanisms. While some cases have a genetic basis, many NDs occur sporadically. Despite their differences, these diseases commonly feature chronic neuroinflammation as a hallmark. Consensus has recently been reached on the possibility that mitochondria dysfunction and protein aggregation can mutually contribute to the activation of neuroinflammatory response and thus to the onset and progression of these disorders. In the present review, we discuss the contribution of mitochondria dysfunction and neuroinflammation to the aetiology and progression of NDs, highlighting the possibility that new potential therapeutic targets can be identified to tackle neurodegenerative processes and alleviate the progression of these pathologies.