Biology subjects

Brito, C.

Publications and source records attributed to Brito, C..

16 recordsLinked to original sources

bioRxiv2026

CRISPR-Cas9 Editing of Myeloid Lectins Reveals Target-Dependent Transcriptional Remodeling in Tumor-Associated Macrophages

Tumor-associated macrophages (TAMs) integrate multiple microenvironmental signals, including lectin-mediated recognition of tumor-associated glycans. Although several myeloid lectins have been implicated in tumor-macrophage interactions, their contributions to immunosuppressive TAM phenotypes remain poorly defined. We implemented a CRISPR-Cas9 ribonucleoprotein (RNP) workflow in primary human monocytes to enable comparative loss-of-function interrogation of five potentially immunosuppressive lectins we previously reported. CRISPR-Cas9 RNP delivery conditions were benchmarked in freshly isolated monocytes using CD14 as a technical target, followed by sgRNA editing efficiency screening for CLEC4E, CLEC6A, CD209, SELL, and SIGLEC9 in HeLa S3 cells. Selected guides were applied to primary monocytes before co-culture in a 3D model with BT474 breast cancer cells. Editing was quantified by Sanger-sequencing deconvolution, while co-culture-derived CD45+ macrophages were isolated by fluorescence-activated cell sorting and characterized by bulk RNA sequencing. All five lectins were successfully perturbed, although gene editing efficiency remained target- and donor-dependent. Transcriptomic analysis revealed target-specific reprogramming and recurrent immunometabolic responses. mTORC1 signaling was consistently enriched, together with the remodeling of cholesterol homeostasis, fatty acid metabolism, and oxidative phosphorylation. CLEC6A deletion achieved attenuation of hypoxia-, angiogenesis-, and TNF/NF-kB-associated programs. CD209 and SIGLEC9 deletion similarly reduced hypoxia- and angiogenesis-associated signatures while promoting lipid and oxidative metabolism. CLEC4E perturbation induced broad remodeling of lipid and oxidative metabolism and stress-response, despite comparatively limited editing efficiency. Comparative lectin perturbation thus identified CLEC6A as the strongest candidate for further mechanistic investigation, while CLEC4E showed broad transcriptional remodeling despite lower editing efficiency, supporting its prioritization for improved genetic interrogation. Responses to CD209 and SIGLEC9 targeting further support tumor glycan-myeloid signaling as a regulator of TAM state. Overall, lectin perturbation redirected TAM transcriptional states through distinct immunometabolic programs rather than a uniform pro-inflammatory polarization, highlighting lectin-dependent immunometabolic regulation as a promising axis for further investigation.

cancer biology↗

bioRxiv2026

Myeloid Lectin Profiling Identifies SYK as a Targetable Signaling Node for Remodeling Immunosuppressive Tumor-Associated Macrophages in Breast Cancer

Immunosuppressive tumor microenvironments (TMEs) are common in breast cancer (BC), where tumor-promoting myeloid-driven inflammation contributes to immune dysfunction and poor immunotherapy response. Lectins expressed by tumor-associated macrophages (TAMs) act as glycan-sensing immunoregulatory receptors driving immunosuppression, but whether specific myeloid lectins define immunosuppressive TAM states, or their signaling is pharmacologically targetable remain unclear. We used an orthogonal prioritization approach combining immunosuppressive stratification of the SCAN-B cohort (3207 patients), differential expression, single-cell myeloid localization, and immune-related upstream-regulator inference. Immunosuppressive tumors were enriched for Basal-like and HER2-enriched subtypes, with worse survival. This identified a 12-lectin panel, which was probed in a human 3D immunosuppressive TME model combining BC spheroids, fibroblasts, and blood-derived macrophages under agitation. Flow cytometry confirmed high expression of eight lectins, with four upregulated in TAMs. Survival analyses associated CLEC4E/Mincle, CLEC6A/Dectin-2, and CD209/DC-SIGN with poorer outcomes. As CLEC4E and CLEC6A converge on FcR{gamma}/SYK signaling, this shared node was selected for pathway-level pharmacological perturbation. R406 reduced SYK phosphorylation and induced transcriptional remodeling in TAMs, with attenuation of immunosuppressive macrophage features, reduced CD204/CD206, increased HLA-DR, and remodeling of the soluble-factor profile. These findings define a myeloid lectin framework associated with BC immunosuppression and identify SYK as a candidate targetable node for remodeling TAMs.

cancer biology↗

bioRxiv2026

Src-dependent tyrosine-phosphorylation of NM2A has a protective role against bacterial pore-forming toxins

Pore-forming toxins (PFTs) are key bacterial virulence factors that disrupt host plasma membrane (PM) integrity, triggering cellular stress and initiating repair mechanisms. The cytolysin Listeriolysin O (LLO), secreted by Listeria monocytogenes, has well established roles in infection, yet the host signaling responses to LLO-induced damage remain poorly understood. Here, we identify a previously unrecognized protective pathway in which LLO triggers rapid activation of the tyrosine kinase Src, leading to phosphorylation of the non-muscle myosin II heavy chain NMHC2A at tyrosine 158. While Src activation and NMHC2A tyrosine phosphorylation have been observed during Listeria infection, we demonstrate here that both responses are directly driven by LLO. This phosphorylation event does not alter NMHC2A motor activity in vitro but is required for cytoskeletal reorganization and efficient responses to PM damage. Using Caenorhabditis elegans, we further show that phosphorylation of the NMHC2A homolog NMY-2 at the conserved tyrosine 163 is required for survival under PFT-induced stress and heat shock, revealing an evolutionarily conserved defense mechanism. Together, our findings establish Src-mediated NMHC2A phosphorylation as a critical link between PFT-induced PM damage sensing and actomyosin remodeling, advancing our understanding of host defense against bacterial toxins. Author SummaryPathogenic bacteria often produce toxins that create pores in the membranes of host cells, compromising cell survival and helping the infection spread. To counter this, host cells must quickly detect and repair the damage. We studied how cells respond to Listeriolysin O (LLO), produced by the human pathogenic bacterium Listeria monocytogenes. We found that LLO activates the host Src kinase, which in turn modifies a key structural protein, non-muscle myosin II (NMII). Although this modification does not affect NMIIs normal motor function, it is crucial for organizing the cellular skeleton and protecting the cells membrane after toxin damage. Importantly, we found that this protective mechanism is conserved in the worm Caenorhabditis elegans, where it also defends against a similar bacterial toxin and even heat stress. Our findings reveal a new way that cells use existing structural proteins to rapidly respond to external threats, providing insight into how organisms protect themselves from harmful microbes and environmental stress.

microbiology↗

bioRxiv2025

Engineering a perfusion bioreactor system for hiPSC-derived progenitor co-culture capturing microglial features in CNS development

Microglia are critical regulators of brain homeostasis and immune responses in the central nervous system (CNS). However, existing human-based models fail to reproduce the early and complex microglia-neural cell interactions. The differentiation of human induced pluripotent stem cells (hiPSCs) into specialized cell types offers promising avenues for understanding human development and disease modeling. Herein, we explore the differentiation of hiPSC-derived erythromyeloid progenitors (iEMPs) and their 3D co-culture with hiPSC-derived neurospheres, utilizing the Ambr(R) 250 Modular system. The aim of this research was to build a complex co-culture model between iEMP and neurospheres in a scalable and controlled environment. Our results demonstrate that the Ambr(R) 250 Modular system effectively supports the co-culture process, with iEMPs integration into the neurospheres, exhibiting cell density, aggregate morphology and concentration similar to the neurosphere monocultures. The co-culture environment induced the upregulation of transcription factors critical for microglial lineage commitment. iEMP-neurospheres displayed a unique secretory profile, releasing proteins involved in extracellular matrix remodeling and neuronal differentiation, essential for microenvironment remodeling. In conclusion, this study underscores the role of iEMPs in CNS development and presents a robust platform for preclinical research.

bioengineering↗

bioRxiv2025

3D co-cultures of primary human hepatocytes and Kupffer-like cells to address innate immune responses to rAAV

Recombinant adeno-associated viruses (rAAVs) are a platform of choice for gene therapy. However, liver-directed transduction has been hindered by immune responses unpredicted in the preclinical models, resulting in therapy failure. Liver immune responses are strictly regulated by the interactions between hepatocytes and non-parenchymal liver cells, such as Kupffer cells (the liver-resident macrophages) but how rAAVs induce such responses remains largely unknown. Therefore, human models recapitulating such interactions are required to address innate immune responses. Here, we developed a human 3D model to characterize the contribution of hepatocytes and Kupffer cells to the innate immune response. We developed a strategy for the differentiation of Kupffer-like cells from circulating monocytes based on cell-cell contact with primary human hepatocytes. We fine-tuned critical co-culture parameters to obtain a Kupffer-like phenotype while retaining hepatocyte viability and identity. Functional assessment of the differentiated 3D co-cultures showed that the model is responsive to classical pathogen-associated molecular pattern molecules, at a gene expression and secretory level. Moreover, we observed increased proinflammatory cytokine expression and secretion when challenged with a rAAV vector. Our data indicate the suitability of the novel model to investigate hepatocyte-Kupffer cell interactions and address innate immune responses within a human liver microenvironment.

immunology↗

bioRxiv2025

Innate immunocompetent iNSpheroids: A hiPSC-derived 3D model to study the central nervous system captures an early CNS response to rAAV

Gene therapies using adeno-associated viruses (AAVs) for central nervous system (CNS) disorders face challenges due to host immune responses not represented in classical preclinical models. Here, we present a human-induced pluripotent stem cell (hiPSC)-derived innate immunocompetent 3D CNS model that recapitulates neuroinflammatory hallmarks, serving as a platform for preclinical gene therapy development. Utilizing various scales of stirred-tank bioreactor systems, we generated (neurospheroids) iNSpheroids composed of neurons, astrocytes, and oligodendrocytes, alongside microglial cells (iMGL) to mimic the neuro-immune axis. These systems enabled large-scale production of iNSpheroids and subsequent miniaturization for co-culture experiments and screening of inflammatory stimuli, while maintaining a highly controlled environment. The iMGL-iNSpheroids demonstrated active neuron-microglia crosstalk and exhibited distinct inflammatory responses to a series of neuroinflammatory factors. iMGL-iNSpheroids mounted a mild and transient response to rAAV9, mediated by the activation of inflammatory pathways (e.g., TNF-via NF-{kappa}B activation) in glial cell populations. This model offers a valuable tool to dissect neuroinflammatory mechanisms, accelerating gene therapy development. TeaserImmune-competent 3D human CNS model recapitulates glial responses to rAAVs, enabling reliable preclinical gene therapy screening.

bioengineering↗

bioRxiv2025

In vitro reconstitution of minimal human centrosomes

CDK5RAP2/CEP215 is a key pericentriolar material (PCM) protein that recruits microtubule-nucleating factors at human centrosomes. Using an in vitro reconstitution system, we show that CDK5RAP2 is sufficient to form micron-scale scaffolds around a nanometer-scale nucleator in a PLK-1-regulated manner. CDK5RAP2 assemblies recruited and activated gamma tubulin ring complexes ({gamma}-TuRCs) which, in the presence of /{beta} tubulin, generated microtubule asters. We found that F75 in CDK5RAP2 is partially needed to recruit {gamma}-TuRC yet is indispensable for {gamma}-TuRC activation. Furthermore, our system recapitulated key features of centrosome-amplified cancer cells. CDK5RAP2 scaffolds selectively recruited the molecular motor KifC1/HSET, which enhanced concentration of /{beta} tubulin, microtubule polymerization, and clustering of the assemblies. Our results highlight the specificity and selectivity of in vitro generated CDK5RAP2 scaffolds and identify a minimal set of components required for human centrosome assembly and function. This minimal centrosome model offers a powerful tool for studying centrosome biology and dysfunction in human health and disease.

cell biology↗

bioRxiv2024

To FID or not to FID: Applying GANs for MRI Image Generation in HPC

With the rapid growth of Deep Learning models and neural networks, the medical data available for training - which is already significantly less than other types of data - is becoming scarce. For that purpose, Generative Adversarial Networks (GANs) have received increased attention due to their ability to synthesize new realistic images. Our preliminary work shows promising results for brain MRI images; however, there is a need to distribute the workload, which can be supported by High-Performance Computing (HPC) environments. In this paper, we generate 256x256 MRI images of the brain in a distributed setting. We obtained an FIDRadImageNet of 10.67 for the DCGAN and 23.54 for the WGAN-GP, which are consistent with results reported in several works published in this scope. This allows us to conclude that distributing the GAN generation process is a viable option to overcome the computational constraints imposed by these models and, therefore, facilitate the generation of new data for training purposes.

bioengineering↗

bioRxiv2024

NuMA is a mitotic adaptor protein that activates dynein and connects it to microtubule minus ends

Nuclear mitotic apparatus protein (NuMA) is indispensable for the mitotic functions of the major microtubule minus-end directed motor cytoplasmic dynein 1. NuMA and dynein are both essential for correct spindle pole organization. How these proteins cooperate to gather microtubule minus ends at spindle poles remains unclear. Here we use microscopy-based in vitro reconstitutions to demonstrate that NuMA is a dynein adaptor, activating processive dynein motility together with dyneins cofactors dynactin and Lissencephaly-1 (Lis1). Additionally, we find that NuMA binds and stabilizes microtubule minus ends, allowing dynein/dynactin/NuMA to transport microtubule minus ends as cargo to other minus ends. We further show that the microtubule-nucleating {gamma}-tubulin ring complex ({gamma}TuRC) hinders NuMA binding. This shows that either {gamma}TuRC needs to be released or microtubules need to be severed to generate free minus ends before they can be incorporated into spindle poles by dynein/dynactin/NuMA. These results provide new mechanistic insight into how dynein, dynactin, NuMA and Lis1 cooperate to organize spindle poles in cells.

biochemistry↗

bioRxiv2024

MAC: An Artifact Correction Framework for Brain MRI based on Deep Neural Networks

The correction of artifacts in Magnetic Resonance Imaging (MRI) is increasingly relevant as voluntary and involuntary artifacts can hinder data acquisition. Reverting from corrupted to artifact-free images is a complex task. Deep Learning (DL) models have been employed to preserve data characteristics and to identify and correct those artifacts. We propose MOANA, a novel DL-based solution to correct artifacts in multi-contrast brain MRI scans. MOANA offers two models: the simulation and the correction models. The simulation model introduces perturbations similar to those occurring in an exam while preserving the original image as ground truth; this is required as publicly available datasets rarely have motion-corrupted images. It allows the addition of three types of artifacts with different degrees of severity. The DL-based correction model adds a fourth contrast to state-of-the-art solutions while im-proving the overall performance of the models. MOANA achieved the highest results in the FLAIR contrast, with a Structural Similarity Index Measure (SSIM) of 0.9803 and a Normalized Mutual Information (NMI) of 0.8030. With this, the MOANA model can correct large volumes of images in less time and adapt to different levels of artifact severity, allowing for better diagnosis.

bioinformatics↗

bioRxiv2024

A Distributed Computing Solution for Privacy-Preserving Genome-Wide Association Studies

Breakthroughs in sequencing technologies led to an exponential growth of genomic data, providing unprecedented biological in-sights and new therapeutic applications. However, analyzing such large amounts of sensitive data raises key concerns regarding data privacy, specifically when the information is outsourced to third-party infrastructures for data storage and processing (e.g., cloud computing). Current solutions for data privacy protection resort to centralized designs or cryptographic primitives that impose considerable computational overheads, limiting their applicability to large-scale genomic analysis. We introduce GO_SCPLOWYOSAC_SCPLOW, a secure and privacy-preserving distributed genomic analysis solution. Unlike in previous work, GO_SCPLOWYOSAC_SCPLOW follows a distributed processing design that enables handling larger amounts of genomic data in a scalable and efficient fashion. Further, by leveraging trusted execution environments (TEEs), namely Intel SGX, GO_SCPLOWYOSAC_SCPLOW allows users to confidentially delegate their GWAS analysis to untrusted third-party infrastructures. To overcome the memory limitations of SGX, we implement a computation partitioning scheme within GO_SCPLOWYOSAC_SCPLOW. This scheme reduces the number of operations done inside the TEEs while safeguarding the users genomic data privacy. By integrating this security scheme in Glow, GO_SCPLOWYOSAC_SCPLOW provides a secure and distributed environment that facilitates diverse GWAS studies. The experimental evaluation validates the applicability and scalability of GO_SCPLOWYOSAC_SCPLOW, reinforcing its ability to provide enhanced security guarantees. Further, the results show that, by distributing GWASes computations, one can achieve a practical and usable privacy-preserving solution.

bioinformatics↗

bioRxiv2023

3D human retinal organoid model for the study of early diabetic retinopathy

Diabetic retinopathy (DR) is a significant complication of diabetes and a primary cause of visual impairment among working-age individuals. DR is a degenerative condition in which hyperglycaemia results in morphological and functional changes in certain retinal cells. Existing treatments mainly address the advanced stages of the disease, which involve vascular defects such as macular edema or neovascularization. However, it is now known that retinal neurodegeneration and inflammation precede these vascular changes. Therefore, there is a pressing need to identify new therapeutic approaches that target the early stages of DR and prevent its progression. In the last decade, the development of reliable in vitro models resembling the complexity of the retinal tissue has significantly improved. Namely, three-dimensional (3D) retinal organoids derived from human induced-pluripotent stem cells (hiPSCs) recapitulate the cellular organization and complexity of the human retina. Here, we used hiPSCs-derived retinal organoids to generate a model of early DR. In this model, we observe well-established molecular and cellular features of early DR: i) loss of retinal ganglion and amacrine cells; ii) glial reactivity and inflammation, with increased expression of the vascular endothelial-derived growth factor (VEGF) and interleukin-1{beta} (IL-1{beta}), and monocyte chemoattractant protein-1 (MCP-1) secretion; iii) increased levels of reactive oxygen species accompanied by activation of key enzymes involved in antioxidative stress response. The data provided highlight the utility of retinal organoid technology in modelling early-stage DR. This offers new avenues for the development of targeted therapeutic interventions on neurodegeneration and inflammation in the initial phase of DR, potentially slowing the diseases progression.

neuroscience↗

bioRxiv2023

The minus end depolymerase KIF2A drives flux-like treadmilling of γTuRC-uncapped microtubules

During mitosis, a functional spindle requires high microtubule turnover. Such turnover is highlighted by the multiple functions of spindle poles, where microtubule minus ends are concentrated, and where microtubule nucleation and depolymerization happen side by side. How these seemingly antagonistic processes are coordinated during poleward microtubule flux is not understood. Here we reconstitute this coordination in vitro combining different pole localized activities. We find that the spindle pole-localized kinesin-13 KIF2A is a microtubule minus-end depolymerase, in contrast to its paralog MCAK. Due to its asymmetric activity, KIF2A still allows microtubule nucleation by plus-end growth from the {gamma}-tubulin ring complex ({gamma}TuRC), which in turn serves as a protective cap that shields the minus end against KIF2A binding. Efficient {gamma}TuRC-uncapping requires the combined action of KIF2A and a microtubule severing enzyme, then leading to treadmilling of the uncapped microtubule driven by KIF2A. Together these results provide insight into the molecular mechanisms by which a minimal protein module coordinates microtubule nucleation and depolymerization at spindle poles consistent with their role in poleward microtubule flux.

biochemistry↗

bioRxiv2020

Src-dependent NM2A tyrosine-phosphorylation regulates actomyosin dynamics

Non-muscle myosin 2A (NM2A) is a key cytoskeletal enzyme that along with actin assembles into actomyosin filaments inside cells. NM2A is fundamental in cellular processes requiring force generation such as cell adhesion, motility and cell division, and plays important functions in different stages of development and during the progression of viral and bacterial infections. We previously identified a novel tyrosine phosphorylation on residue 158 (pTyr158) in the motor domain of NM2A. This phosphorylation is dependent on Src kinase and is promoted by Listeria monocytogenes infection of epithelial cells, however its role is unknown. Here we show that Listeriolysin O (LLO), the pore-forming toxin (PFT) secreted by L. monocytogenes, is sufficient to trigger NM2A pTyr158 by activating Src, an upstream regulator of actomyosin remodeling. We further address the role of NM2A pTyr158 on the organization and dynamics of the actomyosin cytoskeleton and find that, by controlling the activation of the NM2A, the status of the pTyr158 alters cytoskeletal organization, dynamics of focal adhesions and cell motility. In vitro, we observe that non-phosphorylatable and phospho-mimetic versions of NM2A at Tyr158 display motor and ATPase activities similar to the wild-type NM2A, which indicates that the phenotype of these mutants in cells is independent of their ability to translocate actin filaments. Importantly, we find the regulation of this phosphorylation site to be of physiological relevance in Caenorhabditis elegans, in particular in response to intoxication by a PFT and to heat shock. We conclude that the control of the phosphorylation status at NM2A Tyr158 is a conserved trait that contributes to the regulation of actomyosin dynamics and the ability of cells to respond to bacterial infection. We propose Src-dependent NM2A pTyr158 as a novel layer of regulation of the actomyosin cytoskeleton.

cell biology↗

bioRxiv2019

Mechanics of allostery: contrasting the induced fit and population shift scenarios

In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed number of stable configurations, explain such cooperative binding from a thermodynamic viewpoint. Yet, understanding what mechanical principles constrain these models remains a challenge. Here we provide an empirical study on 34 proteins supporting the idea that allosteric conformational change generally occurs along a soft elastic mode presenting extended regions of high shear. We argue, based on a detailed analysis of how the energy profile along such a mode depends on binding, that in the induced fit scenario there is an optimal stiffness [Formula] for cooperative binding, where N is the number of residues involved in the allosteric response. We find that the population shift scenario is more robust to mutation affecting stiffness, as binding becomes more and more cooperative with stiffness up to the same characteristic value [Formula], beyond which cooperativity saturates instead of decaying. We confirm numerically these findings in a non-linear mechanical model. Dynamical considerations suggest that a stiffness of order [Formula] is favorable in that scenario as well, supporting that for proper function proteins must evolve a functional elastic mode that is softer as their size increases. In consistency with this view, we find a significant anticorrelation between the stiffness of the allosteric response and protein size in our data set.

biophysics↗

bioRxiv2019

Characterizing and inferring epistasis via direct evolutionary couplings in models of allostery

In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such al-losteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data. Currently, different methods lead to conflicting results, in particular on the existence of long-range evolutionary couplings between distant amino-acids mediating allostery. Here we propose a resolution of this conundrum, by studying epistasis and its inference in models where an allosteric material is evolved in silico to perform a mechanical task. We find four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range and have a simple mechanical interpretation. We perform a Direct Coupling Analysis (DCA) and find that DCA predicts well mutation costs but is a rather poor generative model. Strikingly, it can predict short-range epistasis but fails to capture long-range epistasis, in agreement with empirical findings. We propose that such failure is generic when function requires subparts to work in concert. We illustrate this idea with a simple model, which suggests that other methods may be better suited to capture long-range effects.\n\nAuthor summaryAllostery in proteins is the property of highly specific responses to ligand binding at a distant site. To inform protocols of de novo drug design, it is fundamental to understand the impact of mutations on allosteric regulation and whether it can be predicted from evolutionary correlations. In this work we consider allosteric architectures artificially evolved to optimize the cooperativity of binding at allosteric and active site. We first characterize the emergent pattern of epistasis as well as the underlying mechanical phenomena, finding four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range. The numerical evolution of these allosteric architectures allows us to benchmark Direct Coupling Analysis, a method which relies on co-evolution in sequence data to infer direct evolutionary couplings, in connection to allostery. We show that Direct Coupling Analysis predicts quantitatively mutation costs but underestimates strong long-range epistasis. We provide an argument, based on a simplified model, illustrating the reasons for this discrepancy and we propose neural networks as more promising tool to measure epistasis.

biophysics↗