Biology subjects

Silva, J. M.

Publications and source records attributed to Silva, J. M..

10 recordsLinked to original sources

bioRxiv2026

The loss of Tau in the adult brain triggers neuroplastic, epigenetic and behavioral deficits

INTRODUCTIONAccumulation of pathological Tau precipitates neuronal malfunction in Alzheimers disease (AD). However, the impact of loss of normal Tau function in the adult brain, independently of Tau aggregates, remains unclarified. METHODSWe used a mouse model with conditional mapt knocking-down in forebrain of 5-7 months old animals (cTau-KO), a virus-driven selective Tau knockdown in wild-types (WT) and Tau re-expression approaches, accompanied by neurostructural, epigenetic, proteomic, electrophysiological, neurochemical and behavioral analyses. RESULTSLoss of Tau in the adult brain of cTau-KOs triggers neuronal atrophy and malfunction, epigenetic as well cognitive and mood deficits. Importantly, these perturbations were confirmed by selective Tau loss in WT adult brain and reverted by Tau re-expression or pharmacologically-induced epigenetic correction in cTau-KOs. DISCUSSIONOur findings highlight the contribution of loss of normal Tau function in the adult brain malfunction that could be relevant in diverse brain pathologies beyond AD, associated to Tau and its dysfunction.

neuroscience↗

bioRxiv2025

miR-424(322)~503 impairs colon cancer progression driven by PTEN deficiency.

Colorectal cancer (CRC) is a leading cause of cancer-related morbidity and mortality worldwide, with molecular subtypes and signaling pathways playing critical roles in its progression. The miR-424(322)[~]503 cluster, comprising miR-424 and miR-503, has been implicated in various malignancies, exhibiting dual roles as tumor suppressors or oncogenes depending on the context. However, its function in CRC remains poorly understood. This study investigates the role of the miR-424(322)[~]503 cluster in CRC driven by PTEN deficiency using genetically modified mouse models. Our findings reveal that the loss of miR-424(322)[~]503 significantly exacerbates CRC progression in PTEN-deficient mice. Double knockout (dKO) mice lacking both PTEN and miR-424(322)[~]503 exhibited a higher number and larger size of colorectal lesions compared to PTEN-deficient counterparts. Histological analysis demonstrated increased severity of dysplasia and adenocarcinoma development in dKO mice. Mechanistically, while Wnt/{beta}-catenin signaling remained unaltered, transcriptomic analyses highlighted dysregulation of MAPK and TGF{beta} pathways, alongside epithelial-to-mesenchymal transition (EMT)-related gene signatures. Protein-level validation confirmed hyperactivation of MAPK (ERK1/2 and p38) and TGF{beta} signaling, as well as elevated cyclin D1 expression in dKO colonic tissues. These results underscore the tumor-suppressive role of the miR-424(322)[~]503 cluster in CRC by modulating key oncogenic pathways such as MAPK and TGF{beta}. Our study provides novel insights into the interplay between PTEN loss and miRNA regulation in CRC pathogenesis.

cancer biology↗

bioRxiv2025

Endometrial cancer progression driven by PTEN-deficiency requires miR-424(322)~503.

Endometrial cancer is the most frequent type of cancer in the female reproductive tract. Loss-of-function alterations in PTEN, leading to enhanced PI3K/AKT activation, are among the most frequent molecular alterations in endometrial cancer. Increased PI3K/AKT signaling resulting from PTEN loss promotes cellular proliferation and confers resistance to TGF{beta}-mediated apoptosis, a key regulator of endometrial homeostasis. In this study, we have analyzed the role of miRNAs in driving these altered cellular responses. A comprehensive transcriptomic analysis of miRNA expression revealed the upregulation of several miRNAs caused by PTEN deficiency and/or TGF{beta} stimulation. The miR-424(322)[~]503 cluster drew our attention due to its involvement in regulating apoptosis and proliferation. However, miR-424(322)[~]503 cluster has a paradoxical role in cancer, exhibiting either oncogenic and tumor suppressive functions depending on cell type or context. To ascertain the function of miR-424(322)[~]503 in endometrial carcinogenesis caused by PTEN deficiency, we generated a double Pten/miR-424(322)[~]503 knock-out mice. We demonstrate that loss of miR-424(322)[~]503 impairs proliferation of both wild type or Pten deficient endometrial organoids by interfering with growth factor and PI3K/AKT signaling. Furthermore, the absence of miR-424(322)[~]503 restores TGF{beta}-induced apoptosis, which is otherwise compromised by PTEN deficiency. In vivo, Pten/miR-424(322)[~]503 knock-out mice exhibit reduced endometrial cancer progression compared to Pten deficient mice through a cell-autonomous mechanism.

cancer biology↗

bioRxiv2025

Identification of astrocytomas through serum protein fingerprint using MALDI-TOF MS and machine learning

Gliomas account for most brain malignancies, with astrocytomas being the most common subtype. Among these, glioblastoma (GBM) stands out as the most aggressive form, exhibiting a median survival time of just 15 months despite intensive therapy. Current diagnostic practices rely on magnetic resonance imaging (MRI) and histopathological analysis, which often necessitate invasive surgical sampling. This underscores the need for minimally invasive diagnostic tools capable of characterizing glioma progression and guiding treatment strategies. Advances in glioma classification have integrated histological and molecular markers, notably IDH1 mutations, which are prognostically significant, particularly in low-grade gliomas and in the previously defined "secondary GBM" (IDH-mutant astrocytoma grade 4). This study aimed to explore the potential of serum proteomics as a non-invasive diagnostic tool using MALDI-TOF mass spectrometry (MS) combined with machine learning techniques. We analyzed serum samples from 269 patients, employing machine learning models to differentiate between healthy individuals and astrocytoma patients. The MALDI-TOF MS approach achieved a balanced accuracy of 94.5% in distinguishing GBM patients from healthy controls. However, it showed limited efficacy in classifying tumor grades or determining IDH1 mutational status. Further investigation using bottom-up proteomics by GeLC-MS/MS identified potential biomarkers, such as transthyretin, previously associated with high-grade gliomas. These findings highlight the promise of MALDI-TOF MS in identifying serum-based biomarkers for astrocytoma diagnosis. While the results are promising, further validation in independent cohorts is essential to assess the clinical utility of these biomarkers for non-invasive glioma diagnostics and patient monitoring.

systems biology↗

bioRxiv2024

TIA1 Mediates Divergent Inflammatory Responses to Tauopathy in Microglia and Macrophages

The RNA binding protein TIA1 is known to regulate stress responses. Here we show that TIA1 plays a much broader role in inflammatory cells, being required for the microglial sensome. We crossed TIA1 cKO mice (using a CX3CR1 driven cre element) to PS19 MAPT P301S tauopathy mice. The peripheral macrophages of TIA1 cKO mice exhibited a hyper-inflammatory phenotype with increased cytokine signaling, as expected. Surprisingly, the brains of these mice showed striking reductions in inflammation, including decreases in microglial inflammatory cytokines (TNF and IL-1{beta}) and sensome markers (CLEC7A, TREM2, ITGAX); these reductions were accompanied by corresponding decreases in tau pathology. Analysis of the brain TIA1 protein interactome identified brain selective TIA1 protein mediated pathways, including strong interactions with the microglial protein C1q, which directs pruning of dystrophic neurons. These results uncover a previously unknown regulatory role for TIA1 in microglial activation in the context of neurodegenerative disease and highlights the divergent regulation of two mononuclear phagocytic lineages: microglia and macrophages.

neuroscience↗

bioRxiv2023

AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data

Low-complexity data analysis is the area that addresses the search and quantification of regions in sequences of elements that contain low-complexity or repetitive elements. For example, these can be tandem repeats, inverted repeats, homopolymer tails, GC biased regions, similar genes, and hairpins, among many others. Identifying these regions is crucial because of their association with regulatory and structural characteristics. Moreover, their identification provides positional and quantity information where standard assembly methodologies face significant difficulties because of substantial higher depth coverage (mountains), ambiguous read mapping, or where sequencing or reconstruction defects may occur. However, the capability to distinguish low-complexity regions (LCRs) in genomic and proteomic sequences is a challenge that depends on the models ability to find them automatically. Low-complexity patterns can be implicit through specific or combined sources, such as algorithmic or probabilistic, and recurring to different spatial distances, namely local, medium, or distant associations.This paper addresses the challenge of automatically modeling and distinguishing LCRs, providing a new method and tool (AlcoR) for efficient and accurate segmentation and visualization of these regions in genomic and proteomic sequences. The method enables the use of models with different memories, providing the ability to distinguish local from distant low-complexity patterns. The method is reference- and alignment-free, providing additional methodologies for testing, including a highly-flexible simulation method for generating biological sequences (DNA or protein) with different complexity levels, sequence masking, and a visualization tool for automatic computation of the LCR maps into an ideogram style. We provide illustrative demonstrations using synthetic, nearly synthetic, and natural sequences showing the high efficiency and accuracy of AlcoR. As large-scale results, we use AlcoR to unprecedentedly provide a whole-chromosome low-complexity map of a recent complete human genome and the haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar.The AlcoR method provides the ability of fast sequence characterization through data complexity analysis, ideally for scenarios entangling the presence of new or unknown sequences. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence in FASTA format. The source code is freely provided at https://github.com/cobilab/alcor.

bioinformatics↗

bioRxiv2022

New broad-spectrum anti-Flavivirus human antibodies with Zika virus-neutralizing potential

Flavivirus infections show recurrent outbreaks and can be responsible for disease complications such as Hemorrhagic Dengue Fever and Congenital Zika Virus Syndrome. Effective therapeutic interventions are still a challenge. Antibodies can provide significant protection, although antibody response may fail due to ADE (Antibody-Dependent Enhancement) reactions or immune escape mutations. To generate effective neutralizing antibodies, the choice of the target antigen is a crucial part of the process. Human anti-Flavivirus antibodies were selected from a combinatorial library displayed on a phage surface. The antibodies were selected against a mimetic peptide based on the fusion loop region in Domain II of the protein E, which is highly conserved among different Flavivirus. Four rounds of selection were performed using the synthetic peptide in two strategies: the first was using acidic elution of bound phages, and the second was applying a competing procedure. After panning, the selected VH and VL domains were determined by combining NGS and bioinformatic approaches. Three different human monoclonal antibodies were expressed as scFvs and further characterized. All showed binding capacity to Zika (ZIKV), Yellow Fever (YFV), and Dengue (DENV) viruses. Two of these antibodies, AZ1p and AZ6m, could neutralize the ZIKV infection in a PRNT assay. These new antibodies have the potential to be used in therapeutic intervention against different Flavivirus illnesses and, due to the conservation of the fusion loop region, they may be resistant to scape mutations. Author summaryThe central idea of this work is to present a possible unique therapeutic approach to combat different diseases that cause health problems annually, such as Dengue and yellow fever infections and Zika congenital syndromes. The viruses that cause these diseases, of the Flavivirus genus, typically have disease amplification reactions and evasion mechanisms of the immune response that hinder the success of specific therapies and vaccines and require new forms of effective and safe treatments. We have developed new neutralizing human antibodies so that they bind to a highly conserved region of Flavivirus, called the fusion loop, and in such a way as to avoid adverse effects associated with anti-Flavivirus antibodies. We showed that the antibodies have high cross-reactivity against different Flaviviruses and we exemplified their neutralizing capacity for Zika virus infection in an ex vivo assay. New monoclonal antibodies such as those presented here may contribute to the control of important tropical diseases in a safer and more efficient way.

immunology↗

bioRxiv2021

Rab35 and glucocorticoids regulate APP and BACE1 trafficking to modulate Aβ production

Chronic stress and elevated glucocorticoids (GCs), the major stress hormones, are risk factors for Alzheimers disease (AD) and promote AD pathomechanisms, including overproduction of toxic amyloid-{beta} (A{beta}) peptides and intraneuronal accumulation of hyperphosphorylated Tau protein. The latter is linked to downregulation of the small GTPase Rab35, which mediates Tau degradation via the endolysosomal pathway. Whether Rab35 is also involved in A{beta} overproduction remains an open question. Here, we find that hippocampal Rab35 levels are decreased not only by stress/GC but also by aging, another AD risk factor. Moreover, Rab35 negatively regulates A{beta} production by sorting amyloid precursor protein (APP) and {beta}-secretase (BACE1) out of the endosomal network, where they interact to produce A{beta}. Interestingly, Rab35 coordinates distinct intracellular trafficking events for BACE1 and APP, mediated by its effectors OCRL and ACAP2, respectively. Finally, we show that Rab35 overexpression prevents the amyloidogenic trafficking of APP and BACE1 induced by high GC levels. These studies identify Rab35 as a key regulator of APP processing and suggest that its downregulation may contribute to stress- and AD-related amyloidogenesis.

neuroscience↗

bioRxiv2020

Oncogenic mutant RAS activity is rescaled by the ERK/MAPK pathway

Activating mutations in RAS are present in [~]30% of human tumors, and the resulting aberrations in ERK/MAPK signaling play a central role in oncogenesis. However, the form of these signaling changes is uncertain, with activating RAS mutants linked to both increased and decreased ERK activation in vivo. Rationally targeting the kinase activity of this pathway requires clarification of the quantitative effects of RAS mutations. Here, we use live-cell imaging in cell lines expressing only one RAS isoform to quantify ERK activity with a new level of accuracy. We find that despite large differences in their biochemical activity, mutant KRAS isoforms within cells have similar ranges of ERK output. We identify roles for pathway-level effects, including variation in feedback strength and feedforward modulation of phosphatase activity, that act to rescale pathway sensitivity independent of expression level, ultimately resisting changes in the dynamic range of ERK activity while preserving responsiveness to growth factor stimuli. Our results reconcile seemingly inconsistent reports within the literature and imply that the initial signaling changes induced by RAS mutations in oncogenesis are subtle.

systems biology↗

bioRxiv2018

Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients

Rheumatoid arthritis (RA) is an autoimmune disorder associated with increased periodontal destruction. It is thought that RA increases the risk of periodontal disease; it is not known how it influences the oral microbiota. Our aim was to analyze the impact of RA on subgingival microbiota and its association with periodontal inflammation and RA activity. Forty-two patients with RA were compared to 47 control subjects without RA. Patients were screened for probing depth, clinical attachment level, bleeding on probing and classified as with or without periodontitis. Subgingival plaque was examined by Illumina MiSeq Sequencing of 16S rRNA gene V4 region and inflammatory cytokines were measured in saliva. RA was associated to severe periodontal disease. In addition, the severity of RA, reflected by the number of tender and swollen joints, was significantly correlated with the presence of pathogenic oral bacteria (i.e. Fusobacterium nucleatum and Treponema socransky). Non-periodontitis RA patients compared to healthy controls had increased microbial diversity and bacterial load, higher levels of pathogenic species (Prevotella, Selenomonas, Anaeroglobus geminatus, Parvimonas micra, Aggregatibacter actinomycetemcomitans) and reduction of health-related species (Streptococcus, Rothia aeria, Kingela oralis). Genes involved with bacterial virulence (i.e. lipopolysaccharide biosynthesis, peptidases) were more prevalent in the subgingival metagenome of subjects with RA. In addition, the degree of oral inflammation reflected by IL-2, IL-6, TNF-, IFN-{gamma} salivary levels was increased in non-periodontitis RA patients in comparison with controls. Our findings support the hypothesis that RA triggers dysbiosis of subgingival microbiota, which may contribute to worsening periodontal status.\n\nAuthor SummaryRheumatoid arthritis (RA) is an autoimmune disease characterized by joints inflammation, swelling, pain and stiffness. Exactly what starts this disease is still unclear. Some recent studies have suggested mucosal surfaces in the body, like those in the gums, could affect the disease process. It has been observed that people with RA have higher risk of periodontitis (a bacterial inflammatory disease of the gums), compared with the general population, and this may be the start of the autoimmune process. Also, periodontitis increases the severity of RA while interventions by treating periodontitis can improve the symptoms of RA. One of the possible mechanisms that link the higher prevalence of periodontitis in RA patients is the dysbiosis of the oral microbiota triggered by the chronic inflammation in RA. Increased levels of molecules of inflammation may affect the oral environment and change the type of bacteria that live there. Here, we examined RA patients and healthy subjects, screening their oral health and inflammatory markers. We collected their saliva and the dental plaque from the space between the teeth and the gum. We found that RA patients exhibited severe periodontitis, increased levels of inflammatory mediators on their saliva and distinct bacterial communities, with higher proportions of bacteria species linked to periodontal disease, even in patients without periodontitis. We also found that the presence of these bacteria species was linked to worse RA conditions. Our study provides new insights to understand the bi-directional mechanisms linking periodontal disease to the development of RA, showing that we need to pay attention to the oral cavity in patients with RA and refer people for dental evaluation. This practice might have a positive impact in the course of RA.

microbiology↗