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Laboratory of Neuropathology of interorganellar contact sites

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RESEARCH

Our research aims to understand how intracellular contact sites control cell fate and to translate this knowledge into new opportunities to counteract neurodegeneration. We study the molecular mechanisms that shape the architecture, function and plasticity of interorganellar contact sites, how these structures adjust to the demands of aging and stress, and how their malfunction contributes to disorders such as neurodegeneration and cancer. Our work also includes drug-discovery efforts to identify molecules that can correct early intracellular defects and help restore the cellular balance that is lost in disease.

A major focus of the lab is the study of mitochondria–endoplasmic reticulum contact sites (MERCS), key hubs coordinating mitochondrial dynamics, metabolism, calcium handling, stress adaptation and regulated cell death. Because MERCS are highly dynamic and heterogeneous, their analysis has long been technically challenging. To overcome this, we develop and apply advanced tools that allow us to monitor, characterize and manipulate these structures in physiologically relevant conditions and across diverse cellular systems.

Among the molecular players we investigate, BCL-2 family proteins are of particular interest—not only as master regulators of apoptosis, but also due to their essential “day-job” roles in shaping MERCS-mediated processes such as mitochondrial dynamics, metabolic control and stress signalling, all of which become disrupted in disease. By integrating these perspectives, we explore how MERCS–BCL-2 crosstalk modulates cellular resilience and contributes to early vulnerability in neurodegenerative disorders.

Our toolkit includes MERLIN, a custom BRET-based biosensor that quantifies mitochondria–ER distance in living cells without perturbing their native organization, proximity-dependent biotinylation coupled to mass spectrometry for MERCS proteomics, and imaging approaches ranging from confocal and STED microscopy to electron microscopy. Together, these technologies enable us to dissect the earliest MERCS alterations that precede mitochondrial dysfunction and contribute to the intracellular vulnerabilities that drive disease.

PROGRAMME

TECHNIQUES

MERCS analysis
We combine cellular, biochemical and biophysical approaches to interrogate MERCS composition, dynamics and function. This includes the MERLIN BRET-based biosensor, which enables quantitative and non-perturbative measurement of mitochondria–ER distance in diverse cellular systems, as well as proximity-dependent biotinylation (APEX2) optimised for MERCS spatial proteomics and interactome reconstruction. We complement these strategies with near-native MERCS extraction workflows that preserve contact-site architecture, allowing biochemical and biophysical profiling of these interfaces under both physiological and pathological conditions.

Advanced imaging
Our work relies heavily on state-of-the-art imaging methodologies. We employ live-cell confocal microscopy to monitor MERCS dynamics, mitochondrial physiology and stress signalling, together with STED nanoscopy for high-resolution mapping of contact-site architecture. Moreover, electron microscopy provides ultrastructural validation and enables the detection of detailed MERCS rearrangements.

Genetic and molecular engineering
We use CRISPR/Cas9-mediated gene editing, and chemically inducible systems to manipulate MERCS components and signalling pathways with high spatial and temporal resolution. These approaches allow us to selectively modulate contact-site architecture, probe causal mechanisms, and engineer cellular models that capture early events driving disease vulnerability.

Functional assays for cell death, inflammation and mitochondrial biology
To mechanistically dissect MERCS-regulated processes, we use a broad portfolio of functional assays covering cell death, inflammation and mitochondrial biology. These include caspase activation, MOMP, mtDNA release, innate immune signalling, mitochondrial membrane potential, Ca²⁺ fluxes and metabolic stress responses. We also employ in vitro reconstitution systems such as model membranes and isolated mitochondria, to characterize the activity of BCL-2 family proteins and other MERCS regulators with molecular precision.

RESOURCES

People

Principal Investigator

Research Assistant

  • Alvaro Larrañaga San Miguel

Latest publications

  1. Modulation of Mitochondria–Endoplasmic Reticulum Contacts (MERCs) by Small Molecules as a New Strategy for Restoring Lipid Metabolism in an Amyotrophic Lateral Sclerosis Model

    Etxebeste-Mitxeltorena, Mikel; Flores-Romero, Hector; Ramos-Inza, Sandra; Masiá, Esther; Nenchova, Maria; Montesinos, Jorge; Martinez-Gonzalez, Loreto; Porras, Gracia; Orzáez, Mar; Vicent, María J.; Gil, Carmen; Area-Gomez, Estela; Garcia-Saez, Ana J.; Martinez, Ana
    Journal of Medicinal Chemistry (Jan, 2025) DOI: 10.1021/acs.jmedchem.4c01368
  2. Crosstalk between mitochondria–ER contact sites and the apoptotic machinery as a novel health meter

    Larrañaga-SanMiguel, Alvaro; Bengoa-Vergniory, Nora; Flores-Romero, Hector
    Trends in Cell Biology (Jan, 2025) DOI: 10.1016/j.tcb.2024.08.007
  3. Targeting mitochondrial metabolism by the mitotoxin bromoxib in leukemia and lymphoma cells

    Schmitt, Laura; Krings, Karina S.; [...] Bhatia, Sanil; Wesselborg, Sebastian
    Cell Communication and Signaling (Nov, 2024) DOI: 10.1186/s12964-024-01913-2
  4. Novel meriolin derivatives activate the mitochondrial apoptosis pathway in the presence of antiapoptotic Bcl-2

    Schmitt, Laura; Lechtenberg, Ilka; [...] Müller, Thomas J. J.; Wesselborg, Sebastian
    Cell Death Discovery (Mar, 2024) DOI: 10.1038/s41420-024-01901-y