Biology subjects

Elortza, F.

Publications and source records attributed to Elortza, F..

16 recordsLinked to original sources

bioRxiv2026

Oncostatin M cytokine promotes breast cancer progression by remodelling the extracellular matrix and activating integrin signalling in cancer cells

Tumours reshape their surrounding extracellular matrix (ECM), creating a microenvironment with altered chemical and mechanical properties. Integrins detect these changes, linking the ECM to the intracellular cytoskeleton and promoting cell survival, motility, invasion and differentiation, and further ECM remodelling. However, the molecular mechanisms by which tumours remodel their ECM are not well understood. Here, we found that the cytokine oncostatin M (OSM) promotes breast cancer progression by activating ECM remodelling and integrin signalling in cancer cells, as shown by combining complementary in vitro, in ovo and in vivo models, and transcriptomic and proteomic analyses. We demonstrated that OSM induces fibrosis, characterized by increased collagen deposition and hydroxylation, together with activation of ECM and ECM-associated proteins and modifiers such as fibronectin, tenascin C, LOX, PLOD2 and collagen prolyl hydroxylases. OSM also promoted the expression of integrins. Integrin alpha 5 (ITGA5) was identified as an important mediator of OSM-effects. ITGA5 blockade, by means of small interference RNA and therapeutic inhibition with a blocking peptide, abrogated OSM-induced cancer cell migration, invasion and in vivo tumour growth. In addition, OSM blockade with a specific inhibitor reduced tumour growth in an immunocompetent mouse model. Our results are clinically relevant as the expression of integrins and matrisome genes strongly correlated with OSM and its receptor OSMR in breast cancer clinical samples; and co-expression of OSMR and ITGA5 associated with decreased survival in basal breast cancer patients. Collectively, our data reinforce the potential of the OSM-ITGA5 axis as a therapeutic target in this breast cancer subtype, which shows the highest mortality rates.

cancer biology↗

bioRxiv2026

Loss of PGC1α drives extracellular matrix remodelling in prostate cancer through CTHRC1

Despite the high curation rate of localized prostate cancer, the fraction of patients that progress to metastasis still accounts for thousands of deaths worldwide, underscoring the need to identify early molecular events that prime tumours for aggressive disease. Here, we demonstrate that loss of the metabolic transcriptional coactivator PGC1 drives early extracellular matrix (ECM) remodelling in PCa, functionally linking epithelial transcriptional programs to tumour-microenvironment interactions. Using genetically engineered mouse models, we show that combined deletion of Pten and Pgc1 induces early activation of ECM-related transcriptional programs, increased collagen deposition, and a transition towards an aligned collagen fibre architecture--hallmarks of aggressive disease--prior to metastatic dissemination. Consistently, human prostate tumours with low PGC1 expression display increased collagen deposition, supporting the clinical relevance of these findings. Restoration of PGC1 expression in prostate cancer cells suppresses cell adhesion to multiple ECM substrates, disrupts collagen organization, and impairs tumour growth in a transcription-dependent manner. Through integrative matrisome proteomics and transcriptomics, we identify the secreted glycoprotein CTHRC1 as a key downstream effector that enhances the prognostic value of PGC1 in PCa patients. Functional loss- and gain-of-function studies establish CTHRC1 expression as both necessary and sufficient to restore ECM adhesion, cytoskeletal organization, collagen architecture, and tumorigenic capacity in PGC1-expressing cells. Importantly, recombinant CTHRC1 rescues adhesion defects, indicating that its extracellular pool mediates this phenotype, whereas deglycosylation abolishes its pro-adhesive function, revealing a mechanistic requirement for glycosylation. Collectively, our findings uncover an early, cell-intrinsic ECM remodelling program driven by PGC1 loss and identify the PGC1-CTHRC1 axis as a mechanistic and clinically relevant regulator of PCa aggressiveness.

cancer biology↗

bioRxiv2025

Stiffness and Viscoelasticity of Adipose Tissue Decellularized Extracellular Matrix Hydrogels Influence Proliferation, Growth Pattern, Migration and Invasion of Breast Cancer Cells

Breast cancer remains the leading cause of cancer-related mortality among women. Cellular behavior is influenced by the physicochemical factors of the extracellular matrix (ECM) surrounding them. In order to model the breast ECM, adipose tissue decellularized extracellular matrix (dECM)-derived hydrogels are generated, which retain the full biochemical complexity of the source tissue, while also exhibiting stiffness and viscoelastic properties comparable to those of breast tissue. By recapitulating the characteristics of their native environment, validated through proteomic analysis and rheology, the poorly metastatic MCF-7 and the highly invasive MDA-MB-231 breast cancer cell lines exhibit their archetypal behaviors within the 3D hydrogels. Moreover, these cells display significantly distinct proliferation, invasion, and growth patterns in hydrogels with different stiffness and viscoelasticity, highlighting the importance of biophysical parameters in modulating cell phenotype. These results illustrate that user-friendly 3D biomaterial models based on adipose tissue dECM can effectively replicate crucial aspects of in vivo cellular behavior. Table of ContentsThis study presents 3D hydrogels derived from porcine adipose tissue dECM that mimic biophysical and biochemical properties of breast tissue. Two breast cancer cell lines mimicking luminal and triple-negative subtypes, exhibited distinct proliferation, migration, and invasion behaviors depending on hydrogel stiffness and viscoelasticity. The results highlight how biophysical cues shape cell phenotype in a user-friendly 3D model. O_FIG O_LINKSMALLFIG WIDTH=179 HEIGHT=200 SRC="FIGDIR/small/693682v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@d0216eorg.highwire.dtl.DTLVardef@42c45borg.highwire.dtl.DTLVardef@1693385org.highwire.dtl.DTLVardef@1b598e1_HPS_FORMAT_FIGEXP M_FIG Created with Biorender.com C_FIG

bioengineering↗

bioRxiv2025

An astrocytic AMPK clock drives circadian behaviour

Circadian clocks coordinate behaviour and physiology with daily cycles of light and nutrient availability, but how metabolic signals influence brain timing remains incompletely understood. Astrocytes integrate metabolic and hormonal cues and exhibit time-of-day-dependent responses, suggesting that they may convey temporal information to hypothalamic circuits. Here, we show that hypothalamic AMP-activated protein kinase (AMPK) exhibits circadian regulation independently of light and feeding cues, is modulated by nutrient availability and astrocytic Ca{superscript 2} signalling, and regulates the temporal organisation of the hypothalamic phosphoproteome. Genetic manipulation of astrocytic AMPK signalling alters PER2 abundance and phosphorylation, including at a conserved residue implicated in circadian period regulation. At the behavioural level, AMPK and PER2 in ventromedial hypothalamic astrocytes contribute to food-anticipatory activity, whereas disruption of astrocytic AMPK signalling alters SCN-dependent circadian locomotor rhythms and energy homeostasis in a sex-dependent manner. Together, these findings identify astrocytic AMPK signalling as a temporally regulated pathway that couples metabolic signals to hypothalamic circadian timing and systemic homeostasis.

neuroscience↗

bioRxiv2025

Loss of UFMylation supports prostate cancer metastasis and rewires cell metabolism towards hexosamine biosynthesis

The acquisition of metastatic features in tumor cells encompasses genetic and non-genetic adaptation, including reprogramming of cellular metabolism. Here we show that loss of UFMylation reroutes glucose metabolism, promotes invasive capacity and supports prostate cancer metastasis. Through transcriptome-based bioinformatics analysis, we identified a reduction in the ubiquitin-like modifier UFM1 and its ligase UFL1 in metastatic prostate cancer. We demonstrate that loss of UFMylation results in enhanced cancer cell dissemination and a switch from cellular proliferation to invasion. Using biotin-based proteomics, we identified phosphofructokinase (PFKAP) as an unprecedented UFMylation substrate. Consistent with UFMylation playing a role in the regulation of phosphofructokinase activity, loss of UFMylation reduced glucose metabolism in favour of hexosamine biosynthesis, which resulted in elevated glycosylation of proteins relevant for cell invasion. These results reveal a role for UFMylation in the regulation of phosphofructokinase and glucose metabolism to support prostate cancer metastasis.

cancer biology↗

bioRxiv2025

Vesicular Rps6 released by astrocytes regulate local translation and enhance synaptic markers in neurons

In neurons, like in any other cell, their function often relies on the fine tuning of their protein levels, which is achieved by the balance between protein synthesis and turnover. Defects in protein homeostasis frequently leads to neuronal dysfunction and neurological disorders. Given their extreme morphological complexity and high compartmentalization, neurons highly depend on the asymmetrical distribution of their proteome. The common belief is that proteins that sustain axonal, dendritic and synaptic functions are synthesized in the soma and then transported to distal neuronal compartments. However, there is a complementary mechanism by which the mRNAs, and not the proteins, are transported to distal subneuronal domains, and once they reach their destination they are locally translated. Although once considered heretical, local translation (or local protein synthesis) is now widely accepted by the scientific community. Nonetheless there is one question that remains largely unexplored in the field and that is whether local translation in dendrites, axons and synapses is fully regulated by the neuron itself or if non-neuronal cells (e.g. glia) can modulate this mechanism in a non-cell-autonomous manner. Here we show that astroglia regulates local protein synthesis and enhances synaptic markers by releasing extracellular vesicles (EVs) containing ribosomal protein Rps6. To our knowledge this is the first report that directly demonstrates glial control of local translation in neurons through EV-mediated glia-to-neuron communication.

neuroscience↗

bioRxiv2025

Cullin-RING ligase BioE3 reveals molecular-glue-induced neosubstrates and rewiring of the endogenous Cereblon ubiquitome

BackgroundThe specificity of the ubiquitination process is mediated by the E3 ligases. Discriminating genuine substrates of E3s from mere interacting proteins is one of the major challenges in the field. We previously developed BioE3, a biotin-based approach that uses BirA-E3 fusions together with ubiquitin fused to a low-affinity AviTag to obtain a site-specific and proximity-dependent biotinylation of the substrates. We proved the suitability of BioE3 to identify targets of RING and HECT-type E3 ligases. MethodsBioE3 experiments were performed in HEK293FT and U2OS stable cell lines expressing TRIPZ-bioGEFUb transiently transfected with BirA-cereblon (CRBN). Cells were seeded using biotin-free media, adding a short-biotin pulse. We evaluated the applicability of the BioE3 system to CRBN and molecular glues by western blot and confocal microscopy, blocking the proteasome with bortezomib, inhibiting NEDDylation with MLN4924 and treating the cells with pomalidomide. For the identification of endogenous substrates and neosubstrates we analyzed the eluates of streptavidin pull-downs of BioE3 experiments by LC-MS/MS. Analysis of targets which ubiquitination changes significantly upon treatment was done using two-sided Students t-test. Orthogonal validations were performed by histidine pull-down, GFP-trap and computational modelling. ResultsHere we demonstrate that BioE3 is suitable for the multi-protein complex Cullin-RING E3s ligases (CRLs), the most utilized by targeted protein degradation strategies. Choosing CRBN as proof of concept, one of the substrate receptors of CRL4 E3 ligase, we identified both endogenous substrates and novel neosubstrates upon pomalidomide treatment, including CSDE1 which contains a G-loop motif potentially involved in the binding to CRBN in presence of pomalidomide. Importantly, we observed a major rearrangement of the endogenous ubiquitination landscape upon treatment with this molecular glue. ConclusionsThe ability of BioE3 to detect and compare both substrates and neosubstrates, as well as how substrates change in response to treatments, will facilitate both target and off-target identifications and offer a broader characterization and validation of targeted protein degradation degraders, like molecular glues and PROTACs.

cell biology↗

bioRxiv2024

Secreted spermidine synthase reveals a paracrine role for PGC1a-induced growth suppression in prostate cancer

Prostate cancer is the fifth cause of death by cancer worldwide, second in incidence in the male population. The definition of the molecular basis of its development and the oncogenic signals driving lethality continue to be important objectives in prostate cancer research. Prior work from others and us has demonstrated that loss of PGC1 expression results in a metabolic, signaling and transcriptional reprogramming that supports the development of metastatic disease. However, we do not fully understand the spectrum of tumor suppressive effects regulated by this co-regulator. Here we show that PGC1 governs non-cell autonomous paracrine tumor suppression in prostate cancer. A systematic analysis of the transcriptional landscapes associated to PGC1 loss of expression revealed that PGC1 alters the expression of genes encoding for secreted proteins. Cell secretome studies corroborated that PGC1-dependent ERR regulation in prostate cancer cells suppresses the growth of tumor cells exposed to their conditioned media. The integration of in vitro and in vivo secretomics data and genetic perturbation assays revealed spermidine synthase as a transcriptional target of PGC1 and mediator of a paracrine metabolic growth suppressive effect. Moreover, the activity of the regulatory axis PGC1-ERR-SRM was reflected in patients and had prognostic value. Altogether, this work provides unprecedented evidence of the non-cell autonomous tumor suppression role of PGC1, which broadens the view of this co-regulator as a multifactorial tumor suppressor in prostate cancer.

cancer biology↗

bioRxiv2024

ANKRD55 interacts with an IFT-B-like complex in microglia

IntroductionSNPs associated with genome-wide risk for multiple sclerosis (MS) modulate expression of ankyrin repeat domain protein 55 (ANKRD55). The function of ANKRD55 is not well understood. A role for ANKRD55 in ciliar transport in multiciliated cells has been reported. To gain deeper insight in how ANKRD55 may modulate neuro-inflammatory parameters, we identified the ANKRD55 interactomes from human neuroblastoma, astrocytic, microglial and monocytic cell lines. MethodsCell lines were transfected with synthetic ANKRD55 RNA in conjunction with nanoparticles. ANKRD55 interactomes were determined by affinity purification coupled to mass spectrometry (AP-MS) and analyzed bioinformatically. Results were validated and interpreted using confocal immunofluorescence microscopy, RNAseq transcriptomics, and a visible immunoprecipitation assay (VIP). ResultsShared among the interactomes were the 14-3-3 isoforms 14-3-3{eta} and 14-3-3{beta}{eta}. Unique to the microglial interactome were eight proteins belonging to the intraflagellar transport complex B (IFT-B). The IFT-B complex is known to mediate anterograde protein trafficking from the base to the tip of cilia. The dimer IFT46-IFT56 was identified as the minimum entity of IFT-B needed to support interaction with ANKRD55. To verify whether ANKRD55 is a ciliar transport protein, we induced ciliogenesis by serum starvation. Primary ARL13B+ cilia could be induced in the astrocytic and neuroblastoma, but not microglial, cell lines. By confocal microscopy, ANKRD55 was not detectable in these cilia but was enriched at the basal body. In the microglial cell line, ANKRD55 and IFT-B components were enriched at the centrosome. In two human primary myeloid cell models, monocyte-derived microglia (MoMG) and monocyte-derived dendritic cells (MoDC), we were able to recapitulate the co-localization of ANKRD55 and IFT81 at the centrosome. DiscussionOur work shows that an ANKRD55 - IFT-B-like complex is assembled in microglial cells. Together with the finding that ANKRD55 was not detected in primary cilia, the results suggest that ANKRD55 is associated with an IFT-B pathway that can operate independent of ciliogenesis.

immunology↗

bioRxiv2024

Trajectory analysis of hepatic stellate cell differentiation reveals metabolic regulation of cell commitment and fibrosis

Defining the trajectory of cells during differentiation and disease offers the possibility to understand the mechanisms driving cell fate and identity. However, trajectories of human cells are largely unexplored. By investigating the proteome trajectory of iPSCs differentiation to hepatic stellate cells (dHSCs), we identified RORA as a key transcription factor governing the metabolic reprogramming of HSCs necessary for HSCs commitment, identity, and activation. Using RORA deficient iPSCs and pharmacologic interventions, we showed that RORA is required for mesoderm differentiation and prevents dHSCs activation by reducing the high energetic state of the cells. While RORA knockout mice had enhanced fibrosis, RORA agonists rescued multi- organ fibrosis in in vivo models. RORA expression was consistently found to be negatively correlated with liver fibrosis and HSCs activation markers in patients with liver disease. This study reveals that RORA regulates cell metabolic plasticity, crucial for mesoderm differentiation, pericyte quiescence, and fibrosis, influencing cell commitment and disease mechanisms. SummaryThis study describes the trajectory of induced pluripotent stem cells (iPSCs) differentiation to hepatic stellate cells (dHSCs). We identify RAR-related orphan receptor alpha (RORA) as a transcription factor essential for mesoderm commitment and dHSCs identity and fibrogenic activation by regulating metabolic plasticity.

cell biology↗

bioRxiv2023

Maintenance of cell wall remodeling and vesicle production are connected in Mycobacterium tuberculosis

Pathogenic and nonpathogenic mycobacteria secrete extracellular vesicles (EVs) under various conditions. EVs produced by Mycobacterium tuberculosis (Mtb) have raised significant interest for their potential in cell communication, nutrient acquisition, and immune evasion. However, the relevance of vesicle secretion during tuberculosis infection remains unknown due to the limited understanding of mycobacterial vesicle biogenesis. We have previously shown that a transposon mutant in the LCP-related gene virR (virRmut) manifested a strong attenuated phenotype during experimental macrophage and murine infections, concomitant to enhanced vesicle release. In this study, we aimed to understand the role of VirR in the vesicle production process in Mtb. We employ genetic, transcriptional, proteomics, ultrastructural and biochemical methods to investigate the underlying processes explaining the enhanced vesiculogenesis phenomenon observed in the virRmut. Our results establish that VirR is critical to sustain proper cell permeability via regulation of cell envelope remodeling possibly through the interaction with similar cell envelope proteins, which control the link between peptidoglycan and arabinogalactan. These findings advance our understanding of mycobacterial extracellular vesicle biogenesis and suggest that these set of proteins could be attractive targets for therapeutic intervention.

microbiology↗

bioRxiv2023

Thermodynamic Stabilization of Human Frataxin

Recombinant proteins and antibodies are routinely used as drugs to treat prevalent diseases such as diabetes or cancer, while enzyme replacement and gene therapies are the main therapeutic intervention lines in rare diseases. In protein-based therapeutics, optimized in vivo stability is key as intrinsic denaturation and intracellular proteostatic degradation will limit potency, particularly in treatments requiring a sustained action, while clearance mechanisms may limit the amount of circulating protein. In vivo stability is ultimately correlated with the intrinsic thermodynamic stability of the biomolecule, but this is difficult to optimize because it often goes at the expense of reducing protein activity. Here, we have used in silico engineering approaches to thermodynamically stabilize human frataxin, a small mitochondrial protein that acts as an allosteric activator for the biosynthesis of Fe-S clusters, whose genetically-driven impairment results in a rare disease known as Friedreich ataxia. Specifically, we developed an efficient thermostability engineering computational approach that combines information on amino acid conservation, the Rosetta energy function, and two recent artificial intelligence tools - AlphaFold and ProteinMPNN - to produce thermodynamically stabilized variants of human frataxin. Such protein variants rescued the large destabilization exerted by well-known pathological mutations, with an increase over 20 {degrees}C in the melting temperature and a thermodynamic stabilization of more than 3 kcal{middle dot}mol-1 at the physiological temperature. This stability surplus is translated into an enhanced resistance to proteolysis, while maintaining the protein fully functional. This case-study highlights the power of our combined computational approach to generate optimized variants, adequate for protein-based therapeutics.

biophysics↗

bioRxiv2023

BioE3 enables the identification of bona fide targets of E3 ligases

The post-translational modification of proteins by ubiquitination is a highly regulated process that involves a dynamic, three-step enzymatic cascade, where more than 600 E3 ligases play a critical role in recognizing specific substrates for modification. Separating bona fide targets of E3s from E3-interacting proteins remains a major challenge in the field. In this study, we present BioE3, a novel approach for identifying substrates of ubiquitin-like (UbL) E3 ligases of interest. Using BirA-E3 ligase fusion proteins and bioUbLs, the method facilitates site-specific biotinylation of UbL-modified substrates of particular E3s for proteomic identification. We demonstrate that the BioE3 system can identify both known and novel targets of two RING-type ubiquitin E3 ligases: RNF4, known to be involved in DNA damage response and the regulation of PML nuclear bodies, and MIB1, implicated in endocytosis, autophagy, and centrosomal protein homeostasis. We further show the versatility of BioE3 by identifying targets of an organelle-specific E3 (MARCH5) and a relatively uncharacterized E3 (RNF214). Furthermore, we show that BioE3 works with HECT-type E3 ligases and identify novel targets of NEDD4 involved in vesicular trafficking. BioE3 is a powerful tool that enables identification of bona fide substrates of UbL E3 ligases and how they change with chemical perturbations. BioE3 may also be applicable for UbLs beyond Ub and SUMO, as well as other E3 ligase classes. The resulting knowledge can shed light on the regulation of cellular processes by the complex UbL network and provide information useful for strategies such as targeted protein degradation (TPD), advancing our understanding of fundamental biological mechanisms and their applications.

cell biology↗

bioRxiv2023

NF-κB c-REL-OTUD4 axis regulates B-cell receptor in B-cell lymphoma

The B-cell receptor (BCR) is essential for B-cell development and a crucial clinical target in immuno-oncology. However, therapeutic success against the BCR and downstream signaling pathways is hampered by enhanced NF-{kappa}B activation as a resistance mechanism. Using a multiomic approach, we discover the c-REL proto-oncogenic subunit of the NF-{kappa}B family as a key transcription factor regulating BCR subunit levels in B-cell lymphoma. Subsequent ChIP- seq, cell biology experiments, and patient data analysis reveal that OTUD4 is a critical deubiquitinase for inhibiting proteasomal degradation of c-REL and for stabilizing a multi-loop positive feedback of NF-{kappa}B to the BCR pathway. Remarkably, OTUD4 downregulation destabilizes c-REL and BCR levels and inhibits cell growth of B cell lymphoma. Thus, we shed light on the malignant potential of c-REL abundance, identify a positive feedback from c-REL to upstream BCR and present OTUD4 as a vulnerability to synergistically target NF-{kappa}B and BCR pathways in B-cell lymphoid malignancies.

cancer biology↗

bioRxiv2020

Identification of proximal SUMO-dependent interactors using SUMO-ID

The fast dynamics and reversibility of posttranslational modifications by the ubiquitin family pose significant challenges for research. Here we present SUMO-ID, a technology that merges proximity biotinylation by TurboID and protein-fragment complementation to find SUMO-dependent interactors of proteins of interest. We developed an optimized split-TurboID version and show SUMO interaction-dependent labelling of proteins proximal to PML and RANGAP1. SUMO-dependent interactors of PML are involved in transcription, DNA damage, stress response and SUMO modification and are highly enriched in SUMO Interacting Motifs, but may only represent a subset of the total PML proximal proteome. Likewise, SUMO-ID also allowed us to identify novel interactors of SUMOylated SALL1, a less characterized SUMO substrate. Thus, SUMO-ID is a powerful tool that allows to study the consequences of SUMO-dependent interactions, and may further unravel the complexity of the ubiquitin code.

biochemistry↗

bioRxiv2019

LUZP1, a novel regulator of primary cilia and the actin cytoskeleton, is altered in Townes-Brocks Syndrome

Primary cilia are sensory organelles that are crucial for cell signaling during development and organ homeostasis. Cilia arise from the centrosome and their formation is governed by numerous regulatory factors. We show that the leucine-zipper protein LUZP1 localizes to the pericentriolar material and actin cytoskeleton. Using TurboID proximity labeling and pulldowns, LUZP1 associates with factors linked to centrosome and actin filaments. Loss of LUZP1 reduces F-actin levels, facilitating ciliogenesis and altering Sonic Hedgehog signaling, pointing to a key role in the cytoskeleton-cilia interdependency. Moreover, we show that LUZP1 interacts with a truncated form of the transcription factor SALL1 that causes Townes-Brocks Syndrome. TBS is characterized by digit, heart and kidney malformations and is linked in part to defective cilia. Truncated SALL1 increases the ubiquitin proteasome-mediated degradation of LUZP1. Alteration of LUZP1 levels may be a contributing factor to TBS, suggesting possible therapies using modulators of cilia and cytoskeletal function.

cell biology↗