Biology subjects

Carvalho, E.

Publications and source records attributed to Carvalho, E..

10 recordsLinked to original sources

bioRxiv2026

From mice to humans: A multi-omic predictive framework for translational immunology

Mice are key preclinical animal models in vaccine and immunological research, yet their predictive value for human immunity remains contested. Here, we evaluated the translatability of murine models across inactivated and subunit vaccination (influenza, hepatitis B), acute infection (S. aureus, E. coli), and injury (burns and trauma), integrating transcriptomic profiles with sequence evolution, cis-regulatory architecture, and functional annotation. Functional modules were more conserved between species than individual orthologous genes. Translational accuracy depended on stimulus intensity, as infections and injuries engaged conserved signatures, while single-dose vaccination diverged. We then built multilayer models to predict human expression rank and direction of change, and to classify shared leading-edge genes. Adding evolutionary and regulatory layers improved these predictions. We provide a step-by-step R Markdown notebook to apply the models to user data. The study code and datasets are available at https://github.com/wapsyed/mousetohuman_multilayer

bioinformatics↗

bioRxiv2026

Closed-loop control of in vitro neuronal activity using reinforcement learning after in silico pre-training

Controlling specific neuronal dynamics with electrical stimulation is critical for therapeutic neuromodulation, yet deriving optimal control policies remains challenging due to the complex and non-stationary nature of biological neuronal networks. While reinforcement learning (RL) offers a powerful closed-loop control framework, its reliance on prolonged stimulus-driven exploration is difficult to reconcile with the physiological limits of living tissue. Here, we demonstrate an in silico-to-in vitro transfer strategy that achieves efficient state-dependent control of network bursting in cultured neurons. The transferred policy outperforms heuristic controls, while maintaining constrained stimulation usage. Concurrent calcium imaging reveals the mechanistic basis of the learned policy: the agent optimizes stimulation spatially and temporally, exploiting local network topology and intrinsic physiological temporal dynamics. These results establish in vitro brain-on-chip cultures as a tractable stepping stone for RL-based neuromodulation and demonstrate that effective control policies can be derived in biophysically calibrated digital twins and transferred directly to living networks.

neuroscience↗

bioRxiv2024

Rac1 inhibition prevents axonal cytoskeleton dysfunction in Transthyretin Amyloid Polyneuropathy

Hereditary transthyretin amyloidosis with polyneuropathy (ATTRv-PN) is characterized by the deposition of amyloidogenic TTR, particularly in dorsal root ganglia (DRG) and peripheral nerve axons, resulting in sensorimotor axonopathy with autonomic dysfunction. Here, we investigated cytoskeleton alterations in peripheral axons from an ATTRv-PN mouse model, the hTTRA97S knock-in mice. Proteomics of hTTRA97S sural nerves revealed dysregulation of actin-related proteins. hTTRA97S DRG neurons presented a defective actin distribution in growth cones along with a reduction in axonal actin trails, and an associated impairment in the pool of pre-synaptic vesicles. Microtubule dynamics and axonal transport abnormalities were also observed in mutant axons. Importantly, cytoskeletal defects in hTTRA97S neurons preceded axonal degeneration and were mediated by Rac1 hyperactivation in DRG neurites and sciatic nerves of pre-symptomatic mice. Rac1 inhibition rescued cytoskeleton alterations, preventing degeneration. Remarkably, in ATTRv-PN patients with late-onset disease, a variant in RACGAP1, encoding a Rac1 inactivator, supported the neuroprotective role of Rac1 inhibition. Our findings demonstrate that cytoskeletal defects precede axonal degeneration in ATTRv-PN and highlight Rac1 as a promising therapeutic target.

neuroscience↗

bioRxiv2024

Circulating microRNAs as biomarkers of chronic kidney disease and its association with renal and cardiovascular outcomes in non-dialysis patients

Chronic kidney disease (CKD) affects over 10% of the population worldwide and entails a significant risk for cardiovascular disease (CVD), leading to a 500-fold increase in cardiovascular mortality in advanced stages. Still, the pathophysiological mechanisms underlying kidney-heart intercommunication remain largely unknown. In recent years, microRNAs (miRNAs) emerged as important key regulators of gene expression that may serve as biomarkers for several diseases, however, their role in kidney-heart crosstalk in CKD remains underexplored. In this study, we evaluated the expression of a miRNA panel in plasma samples from non-dialysis CKD patients and explored their association with main comorbidities and significant outcomes in a 5-year follow-up. Results show that miR-30c-5p and miR-132-3p were downregulated in CKD patients presenting a significant power to discriminate the disease state. Importantly, only miR-30c-5p was downregulated in early glomerular filtration rate (GFR) categories, being able to discriminate these CKD patients from non-diseased individuals. Concerning cardiovascular outcomes, miR-199a-5p was found to be associated with an increased frequency of CVD. When analyzing the major disease outcomes in a 5-year time, miR-199a-5p upregulation at baseline was associated with increased mortality, while miR-324-3p was downregulated in patients who progressed to more advanced stages of the disease. These findings highlight the involvement of novel circulating miRNAs in CKD onset and progression, and identify, for the first time, the enrollment of miR-199a-5p in kidney-heart pathophysiological crosstalk, paving the way for the establishment of new biomarkers and therapeutic targets for CKD and its outcomes.

molecular biology↗

bioRxiv2024

Rab5 Overcomes CAR T Cell Dysfunction Induced by Tumor-Mediated CAR Capture

Continuous interaction between chimeric antigen receptor (CAR) T cell (CART) and tumors often result in CART dysfunction and tumor escape. We observed that tumors can take up CAR molecules, leaving CARTs without surface-expressed CARs and thus unable to kill tumors after prolonged exposure. Overexpression of Rab5 resulted in augmented clathrin-independent endocytosis, preventing loss of surface-expressed CARs, and enhanced CART activity. Interestingly, we observed membrane protrusions on the CART cell surface which disappeared after multiple tumor challenges. Rab5 maintained these protrusions after repeated tumor engagements and their presence correlated with effective tumor clearance, suggesting a link between endocytosis, membrane protrusions, and cytolytic activity. In vivo, Rab5-expressing CARTs demonstrated improved activity and were able to clear an otherwise refractory mesothelin-expressing solid cancer in humanized mice by maintaining CAR surface expression within the tumor. Thus, pairing Rab5 with CAR expression could improve the clinical efficacy of CART therapy. Highlights O_LI"CAR-jacking" occurs when surface CAR is internalized by target tumor cells. C_LIO_LIRab5 overexpression prevents "CAR-jacking" and enhances CART function. C_LIO_LIRab5 promotes CAR endocytic recycling and maintains membrane protrusions. C_LIO_LIRab5-expressing CARTs exhibit enhanced therapeutic efficacy against solid tumors. C_LI

immunology↗

bioRxiv2024

Comprehensive Molecular Epidemiology of Influenza Viruses in Brazil: Insights from a Nationwide Analysis

Influenza A and B viruses pose significant global health threats, with substantial impacts on morbidity and mortality. Understanding their molecular epidemiology in Brazil, a key hub for the circulation and dissemination of these viruses in South America, remains limited. This study, part of the Center for Viral Surveillance and Serological Assessment (CeVIVAS) project, addresses this by analyzing data and samples from all Brazilian macroregions, along with publicly available sequences from 2021-2023. Phylogenetic analysis of the Hemagglutinin (HA) segment of Influenza A/H1N1pdm09, A/H3N2, and Influenza B/Victoria-lineage revealed the predominance of A/H3N2 2a.3 strain in 2021 and early 2022. This was succeeded by A/H3N2 2b until October 2022, after which A/H1N1pdm09 5a.2a and 5a.2a.1 lineages became prevalent, maintaining this status throughout 2023. B/Victoria circulated at low levels between December 2021 and September 2022, becoming co-prevalent with A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. Comparing the vaccine strain A/Darwin/9/2021 with circulating A/H3N2 viruses from 2021-2023 revealed shared mutations to aspartic acid at residues 186 and 225, altering the RBD domains charge. For A/H1N1pdm09, the 2022 consensus of 5a.2a.1 and the vaccine strain A/Victoria/2570/2019 had 14 amino acid substitutions. Key residues such as H180, D187, K219, R223, E224, and T133 are involved in hydrogen interactions with sialic acids, while N130, K142, and D222 may influence distance interactions based on docking analyses. Distinct Influenza A lineage frequency patterns across Brazils macroregions underscore regional variations in virus circulation. This study characterizes the dynamics of Influenza A and B viruses in Brazil, offering valuable insights into their circulation patterns. These findings have significant public health implications, informing strategies to mitigate transmission risks, optimize vaccination efforts, and enhance outbreak control measures. Author summaryThis study investigates the molecular epidemiology of Influenza A and B viruses in Brazil from 2021 to 2023. Utilizing data from the Center for Viral Surveillance and Serological Assessment (CeVIVAS) and public databases, we performed a comprehensive phylogenetic analysis of the Hemagglutinin segments of Influenza A/H1N1pdm09, A/H3N2, and B/Victoria-lineage viruses across all Brazilian macroregions. Key findings reveal that the A/H3N2 2a.3 strain was predominant in 2021 and early 2022, followed by A/H3N2 2b, and later by A/H1N1pdm09 5a.2a and 5a.2a.1 lineages in late 2022 and throughout 2023. The B/Victoria strain circulated at low levels initially and later co-prevailed with A/H1N1pdm09 lineages. Comparing the vaccine strain A/Darwin/9/2021 with circulating A/H3N2 viruses from 2021-2023 and A/Victoria/2570/2019 with 5a.2a.1 of A/H1N1pdm09 circulating in 2022 revealed significant mutations which could affect the interaction of the viruses with sialic acids and potentially impact vaccine efficacy. Notably, we identified a substitution pattern among the predominant Influenza subtypes and observed distinct regional variations in Influenza A lineage frequencies across Brazil. These findings are critical for optimizing vaccination strategies and provide valuable data to inform public health policy and improve health outcomes.

evolutionary biology↗

bioRxiv2020

A genome-wide association study highlights a regulatory role for IFNG-AS1 contributing to cutaneous leishmaniasis in Brazil

BackgroundCutaneous leishmaniasis (CL) caused by Leishmania braziliensis remains an important public health problem in Brazil. The goal of this study was to identify genetic risk factors for CL. MethodsGenome-wide analysis was undertaken using DNAs from 956 CL cases and 868 controls (phase 1) and 1110 CL cases and 1178 controls (phase 2) genotyped using Illumina HumanCoreExome BeadChips. Imputation against 1000G data provided 4,498,586 quality-controlled single nucleotide variants (SNVs) common across phase 1 and phase 2 samples. Linear mixed models in FastLMM were used to take account of genetic diversity/ethnicity/admixture. Cellular cytokines were measured using flow cytometry. ResultsCombined analysis across cohorts found no associations that achieved genome-wide significance, commonly accepted as P<5x10-8. Support for variants at wound-healing genes previously studied as candidate genes for CL included SMAD2 (rs115582038/rs75753347; Pimputed_1000G=1.47x10-4). Top novel GWAS hits at P<5x10-5 in plausible candidate genes for CL included SERPINB10 (rs62097497;Pimputed_1000G=2.67x10-6), CRLF3 (rs75270613; Pimputed_1000G=5.12x10-6), STX7 (rs144488134;Pimputed_1000G=6.06x10-6), KRT80 (rs10783496 Pimputed_1000G=6.58x10-6), LAMP3 (rs74285558;Pimputed_1000G=6.54x10-6) and IFNG-AS1 (rs4913269;Pimputed_1000G=1.32x10-5). Of these, LAMP3 (Padjusted=9.25x10-12; +6-fold), STX7 (Padjusted=7.62x10-3; +1.3-fold) and CRLF3 (Padjusted=9.19x10-9; +1.97-fold) were all expressed more highly in CL biopsies compared to normal skin, whereas expression of KRT80 (Padjusted=3.07x10-8; -3-fold) was lower. Notably, the percent peripheral blood CD3+ T cells making interferon-{gamma} in response to Leishmania antigen differed significantly by IFNG-AS1 genotype. ConclusionsIn addition to supporting variants in wound-healing genes as genetic risk factors for CL, our GWAS results provide important novel leads to understanding pathogenesis of CL including through the regulation of interferon-{gamma} responses.

genetics↗

bioRxiv2019

Virulence potential of a multidrug-resistant Escherichia coli belonging to the emerging clonal group ST101-B1 isolated from bloodstream infection

Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from bloodstream infection of an inpatient with persistent gastroenteritis and Zone T lymphoma, that died due to septic shock. Despite causing an extraintestinal infection, it harbors few known virulence factors and was assigned into phylogenetic group B1. To evaluate if the EC121 was pathogenic or opportunistic, its genome was sequenced, and an in vitro characterization of some pathogenicity-associated properties was performed. The data retrieved from genome analysis showed that E. coli strain EC121 belongs to the O154:H25 serotype, and to ST101-B1, which was epidemiologically linked to extraintestinal infections and antimicrobial resistance spread as well. Moreover, it was closely related to Shiga-toxin producing E. coli (STEC). Besides, strain EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2, and more than 50 complete virulence genetic clusters, which are reported to be associated either with DEC or ExPEC. The strain also displays the capacity to adhere to a variety of cell lineages, and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, it is virulent in the Galleria mellonella model. Altogether, E. coli EC121 unveiled to be a pathogen powered by its multi-drug resistance characteristic. Carry out studies providing accurate information about the virulence potential of all kinds of MDR strains are essential because these studies will help in the development of alternative therapies of infection management and spread control of MDR strains. Authors summaryThe phylogenetic origin of extraintestinal pathogenic Escherichia coli is mostly associated with phylogroup B2, and the majority of the studies regarding extraintestinal infection focus on the most virulent strains, which might also present multidrug-resistant (MDR) phenotype. Strains belonging to phylogroup B1 and isolated from extraintestinal infections are considered as opportunist pathogens and have their virulence neglected. We focus our study in one MDR strain isolated from bloodstream infection that belongs to phylogenetic group B1 to enlarge the knowledge about the virulence of this kind of strain. We demonstrated that the EC121 is capable of adheres to intestinal and bladder human cells, and invades the latter one; it survives to human serum bactericidal effects and produces biofilm. Additionally, the in vivo assay confirmed the EC121 virulence, showing that it should be considered a pathogenic strain. The genetic analyzes highlighted important aspects of EC121 which are typical from strains of sequence type 101, like its involvement in the spread of antimicrobial resistance genes and its relationship with extraintestinal infection from diverse sources. Information concerning the virulence of MDR strains is important for the development of global actions treating the spread of antimicrobial resistance, as well as to elucidate the pathogenesis of strains that were considered as an opportunist.

microbiology↗

bioRxiv2018

MORPhA Scale: behavioral and electroencephalographic validation of a rodent anesthesia scale

Degree of anesthesia in laboratory rodents is normally evaluated by testing loss of reflexes. While these are useful endpoint assessments, they are of limited application to study induction/reversal kinetics or factors affecting individual susceptibility (e.g. sex or age). We developed and validated a grading system for a temporal follow up of anesthesia. The Minho Objective Rodent Phenotypical Anesthesia (MORPhA) scale was tested in mice and rats anaesthetized with a mixture of ketamine/dexmedetomidine (ket/dex - 3 doses). The scale comprises 12 behavioral readouts organized in 5 stages - (i) normal/(ii) hindered voluntary movement, elicited response to (iii) non-noxious/(iv) noxious stimuli and (v) absence of response - evaluated at regular time points. Progression across stages was monitored by electroencephalography (EEG) in rats during anesthesia induction and reversal (atipamezole) and during induction with a second anesthetic drug (pentobarbital). Higher anesthetic doses decreased the time to reach higher levels of anesthesia during progression, while increasing the time to regain waking behavior during reversal, in mice and in rats. A regular decrease in high frequencies (low and high gamma) power was observed as the MORPhA score increased during anesthesia induction, while the opposite pattern was observed during emergence from anesthesia through reversion of dex effect. The devised anesthetic scale is of simple application and provides a semi-quantifiable readout of anesthesia induction/reversal.

neuroscience↗

bioRxiv2018

Expansion, retention and loss in the Acyl-CoA Synthetase \"Bubblegum\" (Acsbg) gene family in vertebrate history

AO_SCPLOWBSTRACTC_SCPLOWFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

genetics↗