Biology subjects

Aransay, A. M.

Publications and source records attributed to Aransay, A. M..

18 recordsLinked to original sources

bioRxiv2026

Noncanonical CD11b on CD8+ T cells promotes cytotoxic effector function

Cancer immunosurveillance largely relies on effector CD8+ T cells, yet surface determinants of cytotoxic competence within tumor-reactive populations remain incompletely defined. Using single-cell surface proteomics in a mouse breast cancer model, we identified a tumor-enriched subset of antigen-experienced CD8+ T cells expressing CD11b, a prototypic myeloid integrin. CD11b CD8 T cells were detected across mouse tumor models and human solid tumors and, within tumor-reactive populations, CD11b marked cells with greater cytotoxic potential. Following activation, naive CD8+ T cells induced ITGAM transcription and CD18-dependent CD11b surface expression. Mechanistically, CD11b localized to the peripheral adhesive ring of the immune synapse and promoted lytic-granule secretion. Accordingly, CD11b+ T cells exhibited enhanced TCR- and CAR-mediated tumor cell killing, whereas CD11b deletion impaired T cell antitumor activity. Together, these findings identify CD11b as an inducible, noncanonical component of the T cell immune synapse that marks cytotoxic competence and promotes antitumor T cell function.

immunology↗

bioRxiv2026

eRREMS expands regulatory CpG coverage in reduced representation methylome sequencing

Profiling the regulatory DNA methylation landscape remains technically challenging. Reduced-representation bisulfite sequencing (RRBS) misses distal enhancers and non-canonical regulatory elements, while whole-genome bisulfite sequencing (WGBS) distributes reads genome-wide, limiting consistent recovery of informative CpGs across sample collections. Here we present eRREMS (enhanced Reduced Representation Enzymatic Methylation Sequencing), addressing both limitations by combining MspI and HaeIII digestion with enzymatic cytosine conversion. eRREMS approximately doubles regulatory CpG recovery relative to standard RRBS, outperforming TaqI-based extended protocols, with gains concentrated in dynamically regulated enhancers, alternative promoters, and splicing-associated regions. HaeIII-specific CpGs capture additional complex trait heritability beyond standard RRBS. At modest, comparable sequencing depths, eRREMS achieves greater cohort-level completeness for regulatory and dynamically variable CpGs than WGBS and requires substantially fewer reads. CpG capture is stable across enzymatic conversion kits and library preparation conditions, supporting broad adoption. eRREMS provides a cost-efficient and reproducible strategy for scalable methylome profiling of regulatory CpGs across cohorts.

genomics↗

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↗

bioRxiv2026

Surface potential as a strong early osteogenic trigger via mechanotransduction and calcium accumulation

Analyzing the differentiation potential of cells in contact with newly developed materials is essential for assessing their ability to integrate into biological tissues and promote functional regeneration. Material properties such as rigidity, topography, and wettability significantly influence stem cell differentiation and are therefore optimized in implants. In this context, surface potential has been repeatedly, albeit inadvertently, shown to enhance osteogenesis. Here, we demonstrate that this surface property modulates cellular mechanosensing by altering the cells perception of substrate rigidity. Specifically, we show that human bone marrow-derived mesenchymal stem cells (hBM-MSCs) on surfaces with a net zero charge, coated with collagen type I, exhibit characteristics typical of cells adhering to compliant substrates. Conversely, mesenchymal stem cells on polarized surfaces activate mechanoresponsive pathways that promote osteogenesis, as evidenced by large spreading areas, enhanced contractility, and Yes-associated protein (YAP) translocation into the nucleus. Furthermore, our data suggest that negative net surface potentials lead to the local accumulation of calcium ions, which further facilitates osteogenic differentiation. Collectively, our findings reveal that biomaterials surface potential, a previously uncharacterized mediator of cellular mechanotransduction, should be considered in the design of next-generation biomaterials for tissue regeneration applications.

cell biology↗

bioRxiv2025

Epigenetic control of microglial developmental milestones from proliferative progenitors to efficient phagocytes

Early immune perturbations increase the risk of neurodegenerative and neurodevelopmental disorders, yet the mechanisms underlying the maturation of microglia, the resident immune cells of the brain parenchyma, remain poorly defined. Specifically, how proliferation, morphological differentiation, and phagocytosis are coordinated among microglia progenitors as they colonize the embryonic brain remains unclear. Here, we combined mathematical modeling with spatiotemporal analyses of the murine hippocampus and cerebellum from postnatal day 2 (P2) to P60 to reconstruct the trajectory of microglial development. We identified a proliferative-to-quiescent (P/Q) switch around P3/P4 that preceded the acquisition of morphological complexity and efficient phagocytosis and was accompanied by coordinated shifts in cell-cycle dynamics and metabolic state. Strikingly, this P/Q switch was recapitulated in repopulation contexts in mice and in the human fetal brain, where later stages displayed enhanced phagocytic function coupled to reduced proliferation. Perturbing the proliferative phase through pharmacological or genetic disruption of CSF1R signaling impaired subsequent microglial complexity and phagocytosis efficiency, revealing an unexpected reliance of phagocytosis on proliferation-driven colonization. Finally, we show that microglia stepwise maturation during development is associated with chromatin remodeling and driven by the epigenetic regulator Ikaros. Together, these findings uncover the sequential milestones of microglial development, revealing a potential period of early vulnerability and establishing an unexpected linkage between proliferation and phagocytosis essential to understanding how these processes are coordinated in neurodegenerative disorders.

neuroscience↗

bioRxiv2025

A dual genetic constraint underlies the conservation of early brains in vertebrates.

As the body plan, the embryonic brain bauplan reflects the shared features of vertebrate brains. Yet, disagreements among sparse histogenetic frameworks have undermined the bauplans power to trace homologies. Here, we generate and integrate five vertebrate single-cell multi-omic atlases of early embryonic brains, revealing a conserved cellular blueprint that defines equivalent progenitor domains across species. Our cellular neuromeric model provides an unified and unbiased framework for the vertebrate brain bauplan and revises the regionalisation of the prosencephalon, refining its molecular boundaries and developmental relationships. Furthermore, cross-species gene-network analyses expose regulatory complexity beyond classical neuromeric patterning, resolving networks into modules aligned with regional cell types or cell class (progenitor/neuron). Evolutionarily, two main developmental constraints emerge: brain bauplan genes, early essential for regional identity, and pleiotropic stemness gene modules, indispensable across all proliferating cells. In turn, later development displays tissue-specific and less essential modules, explaining its rapid divergence into species-specific features. Together, these findings reveal a dual evolutionary constraint--neuromeric identity and pleiotropic stemness--that underlies the conservation of early vertebrate brains. This duality explains how deeply conserved regulatory architectures coexist with evolutionary flexibility to develop into the immense diversity of vertebrate nervous systems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/684766v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@a337a2org.highwire.dtl.DTLVardef@19987adorg.highwire.dtl.DTLVardef@9a9394org.highwire.dtl.DTLVardef@4ef279_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2025

Transcription factor 19 is an androgen responsive gene that modulates vessel homeostasis and sustains metastatic prostate cancer

Prostate cancer is a prevalent tumor type that, despite being highly curable, progresses to metastatic disease in a fraction of patients, thus accounting for more than 350.000 annual deaths worldwide. In turn, uncovering the molecular insights of metastatic disease is instrumental to improve the survival rate of prostate cancer patients. By means of gene expression metanalysis in multiple prostate cancer patient cohorts, we identified a set of genes that are differentially expressed in aggressive prostate cancer. Transcription factor 19 (TCF19) stood out as an unprecedented epithelial gene upregulated in metastatic disease, with prognostic potential and associated with the activity of androgen receptor. By combining computational and empiric approaches, our data revealed that TCF19 is required for full metastatic capacity and its depletion influences core cancer-related processes, such as vascular permeability, supporting the role of this gene in the dissemination of prostate tumor cells.

cancer biology↗

bioRxiv2025

Candida albicans enhances melanoma cell aggressiveness through p38-MAPK and HIF-1α pathways and metabolic reprogramming

Recent studies have increasingly focused on the role of fungi, including Candida albicans, in carcinogenesis. Since C. albicans is a component of the human microbiota, particularly on the skin, we investigated its effect on the phenotype and signalling pathways of melanoma cells. Assays for migration, adhesion, angiogenesis, and hepatic metastasis showed that C. albicans promotes a more malignant phenotype in melanoma cells. At the transcriptomic level, C. albicans increased the expression of VEGF (Vegfa), and genes associated with MAPK and HIF-1 signalling pathways, and with aerobic glycolysis. Further in vitro analysis revealed that TLRs and EphA2 receptors are involved in the recognition of live C. albicans, stimulating VEGF secretion and expression of the AP-1 transcription factor component c-Fos through p38-MAPK and HIF-1. These pathways also regulate the expression of other AP-1 constituents such as Atf3, Jun, and Jund. Moreover, p38-MAPK regulates glycolytic genes like Hk2, Slc2a1, and Eno2. In conclusion, C. albicans activates the p38-MAPK/c-Fos/AP-1 and HIF-1/HIF-1/c-Fos/AP-1 pathways in melanoma cells, promoting a pro-angiogenic environment and metabolic reprogramming. Therefore, this study clarifies the impact of C. albicans on melanoma cells, which can lead to the use of antifungal therapies as complementary to traditional treatments for melanoma.

microbiology↗

bioRxiv2024

Mitochondrial dysfunction: unraveling the elusive biology behind anti-TNF response during ulcerative colitis

BackgroundRecent studies hint at mitochondrial genes influencing UC patient response to anti-TNF treatment. We evaluated this hypothesis by following a targeted strategy to identify gene expression that captures the relationship between mitochondrial dysregulation and response to treatment. Our objective was to initially examine this relationship in colon samples and subsequently assess whether the resulting signal persists in the bloodstream. MethodsWe analyzed the transcriptome of colon samples from an anti-TNF treated murine model characterized by impaired mitochondrial activity and treatment resistance. We then transferred the findings that linked mitochondrial dysfunction and compromised treatment response to an anti-TNF treated UC human cohort. We next matched differential expression in the blood using monocytes from peripheral blood of controls and IBD patients, and we evaluated a classification process at baseline with whole blood samples from UC patients. ResultsIn human colon samples, the derived gene-set from the murine model showed differential expression, primarily enriched metabolic pathways, and exhibited similar classification capacity as genes enriching inflammatory pathways. Moreover, the evaluation of the classification signal using blood samples from UC patients at baseline highlighted the involvement of mitochondrial homeostasis in treatment response. ConclusionOur results highlight the involvement of metabolic pathways and mitochondrial homeostasis in determining treatment response and their ability to provide promising classification signals with detection levels in both colon and bloodstream.

immunology↗

bioRxiv2024

The transcriptional landscape of metastatic hormone-naive prostate cancer

Metastatic hormone-naive prostate cancer (mHNPC) is an infrequent form of this tumour type that is characterized by metastasis at the time of diagnosis and accounts for 50% of prostate cancer-related deaths. Despite the extensive characterization of localized and metastatic castration resistant prostate cancer (mCRPC), the molecular characteristics of mHNPC remain largely unexplored. Here we provide the first extensive transcriptomics characterization of mHNPC. We generated discovery and validation bulk and single-cell RNA-Seq datasets and performed integrative computational analysis in combination with experimental studies. Our results provide unprecedented evidence of the distinctive transcriptional profile of mHNPC and identify stroma remodelling as a predominant feature of these tumours. Importantly, we discover a central role for the transcription factor SOX11 in triggering a heterotypic communication that is associated to the acquisition of metastatic properties. Our study will constitute an invaluable resource for a profound understanding of mHNPC that can influence patient management.

cancer biology↗

bioRxiv2024

Evolutionary convergence of sensory circuits in the pallium of amniotes

The amniote pallium contains sensory circuits structurally and functionally equivalent, yet their evolutionary relationship remains unresolved. Our study employs birthdating analysis, single-cell RNA and spatial transcriptomics, and mathematical modeling to compare the development and evolution of known pallial circuits across birds (chick), lizards (gecko) and mammals (mouse). We reveal that neurons within these circuits stations are generated at varying developmental times and brain regions across species, and found an early developmental divergence in the transcriptomic progression of glutamatergic neurons. Together, we show divergent developmental and evolutionary trajectories in the pallial cell types of sauropsids and mammals. Our research highlights significant differences in circuit construction rules among species and pallial regions. Interestingly, despite these developmental distinctions, the sensory circuits in birds and mammals appear functionally similar, which suggest the convergence of high-order sensory processing across amniote lineages.

developmental biology↗

bioRxiv2024

Beyond Basic Characterization and Omics: Immunomodulatory Roles of Platelet-Derived Extracellular Vesicles Unveiled by Functional Testing

Renowned for their role in hemostasis and thrombosis, platelets are also increasingly recognized for their contribution in innate immunity, immunothrombosis and inflammatory diseases. Platelets express a wide range of receptors, which allows them to reach a variety of activation endpoints and grants them immunomodulatory functions. Activated platelets release extracellular vesicles (PEVs), whose formation and molecular cargo has been shown to depend on receptor-mediated activation and environmental cues. This study compares the immunomodulatory profiles of PEVs generated via activation of platelets by different receptors, glycoprotein VI, C-type lectin-like receptor 2, and combining all thrombin-collagen receptors. Functional assays in vivo in zebrafish and in vitro in human macrophages respectively highlighted distinct homing and secretory responses triggered by the PEVs. In contrast, omics analyses of protein and miRNA cargo combined with physicochemical particle characterization found only subtle differences between the PEV types, which were insufficient to explain their different functional immunomodulatory profiles. Constitutively released PEVs, formed in the absence of an exogenous activator, displayed a disparate activation profile from the receptor induced PEVs. Our findings underscore that PEVs are tunable through receptor-mediated activation. To truly comprehend their role(s) in mediating platelet functions among immune cells, conducting functional assays is imperative. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/570750v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@75a9dborg.highwire.dtl.DTLVardef@e2787corg.highwire.dtl.DTLVardef@543525org.highwire.dtl.DTLVardef@6d1362_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

A synthetic CRISPR-Cas nuclease with expanded enzymatic activities

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonucleases have revolutionized biotechnology for their potential as programmable genome editors. Yet, most natural nucleases and their variants have limitations. Here, we report a fully synthetic CRISPR-associated (Cas) nuclease (-synCas) designed by Ancestral Sequence Reconstruction (ASR) that displays a set of robust and distinct targeting properties, not found in any other known CRISPR-Cas Class 2 system. We show that -synCas is a PAMless nuclease able to catalyse RNA-guided, specific cleavage of dsDNA, ssDNA and ssRNA. The synthetic enzyme is also capable of sequence-nonspecific degradation of dsDNA, ssDNA and ssRNA following activation by complementary dsDNA, ssDNA and ssRNA targets. Furthermore, -synCas exhibits a robust genome editing activity in human cells and bacteria. Cryo-electron microscopy structures of -synCas ternary and quaternary complexes provide a framework to understand the structural basis for its expanded enzymatic activities. The capability for programmable multimodal targeting of virtually any nucleic acid sequence distinguishes -synCas as a promising new tool to extend current CRISPR-based technologies.

molecular biology↗

bioRxiv2023

BirthSeq, a new method to isolate and analyze dated cells from any tissue in vertebrates

Embryonic development is a complex and dynamic process that unfolds over time and involves the production of increasing numbers of cells, as well as the diversification of different cell types. The impact of developmental time on the formation of the central nervous system is well-documented, with evidence showing that time plays a critical role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via FACS, and analysis using high-throughput techniques. We demonstrate the effectiveness of BirthSeq for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in brain development across three vertebrate species (mouse, chick, and gecko). Overall, BirthSeq provides a versatile tool for studying any tissue in any vertebrate organism, helping to fill the necessity in developmental biology research by targeting cells and their temporal cues. SUMMARY STATEMENTBirthSeq allows the isolation and investigation of alive cells according to their birthdate, in any kind of tissue and vertebrate species.

developmental 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↗

bioRxiv2020

USP29 is a novel non-canonical Hypoxia Inducible Factor-α activator

Hypoxia Inducible Factor (HIF) is the master transcriptional regulator that orchestrates cellular adaptation to low oxygen. HIF is tightly regulated via the stability of its -subunit, which is subjected to oxygen-dependent proline hydroxylation by Prolyl-Hydroxylase Domain containing proteins (PHDs/EGLNs), and ultimately targeted for proteasomal degradation through poly-ubiquitination by von-Hippel-Lindau protein (pVHL). However, sustained HIF- signalling is found in many tumours independently of oxygen availability pointing towards the relevance of non-canonical HIF- regulators. In this study, we establish the Ubiquitin Specific Protease 29 (USP29) as direct post-translational activator of HIF- in a variety of cancer cell lines. USP29 binds to HIF-, decreases poly-ubiquitination and thus protects HIF- from proteasomal degradation. Deubiquitinating activity of USP29 is essential to stabilise not only HIF-1 but also HIF-2, via their C-termini in an oxygen/PHD/pVHL-independent manner. Furthermore, in prostate cancer samples the expression of USP29 correlates with the HIF-target gene CA9 (carbonic anhydrase 9) as well as disease progression and severity.

cell biology↗

bioRxiv2018

Integrative analysis of transcriptomic and clinical data uncovers the tumor suppressive activity of MITF in prostate cancer.

The dysregulation of gene expression is an enabling hallmark of cancer. Computational analysis of transcriptomics data from human cancer specimens, complemented with exhaustive clinical annotation, provides an opportunity to identify core regulators of the tumorigenic process. Here we exploit well-annotated clinical datasets of prostate cancer for the discovery of transcriptional regulators relevant to prostate cancer. Following this rationale, we identify Microphthalmia-associated transcription factor (MITF) as a prostate tumor suppressor among a subset of transcription factors. Importantly, we further interrogate transcriptomics and clinical data to refine MITF perturbation-based empirical assays and unveil Crystallin Alpha B (CRYAB) as an unprecedented direct target of the transcription factor that is, at least in part, responsible for its tumor suppressive activity in prostate cancer. This evidence was supported by the enhanced prognostic potential of a signature based on the concomitant alteration of MITF and CRYAB in prostate cancer patients. In sum, our study provides proof-of-concept evidence of the potential of the bioinformatics screen of publicly available cancer patient databases as discovery platforms, and demonstrates that the MITF-CRYAB axis controls prostate cancer biology.

cancer biology↗