Biology subjects

Silva, T.

Publications and source records attributed to Silva, T..

11 recordsLinked to original sources

bioRxiv2026

Post-outbreak surveillance reveals contrasting circulation dynamics of West Nile, Usutu and Bagaza viruses in southern Portugal, 2021 - 2023

Mosquito-borne orthoflaviviruses pose a significant threat to human and animal health worldwide. In Europe, West Nile (WNV), Usutu (USUV) and Bagaza (BAGV) viruses have expanded their geographic distribution and are detected with increasing frequency. Following the emergence of BAGV in 2021, we investigated the circulation dynamics and genomic diversity of orthoflaviviruses in southern Portugal, where their epidemiology remains poorly understood. Active Orthoflavivirus surveillance was conducted in birds and mosquitoes during 2021-2023 using serological and molecular assays, complemented by viral genome sequencing and phylogenomic analyses. Viral RNA was detected in 3.5% (41/1,171) of birds, while seroneutralization assays identified an overall seroprevalence of 55.3% (503/910). WNV RNA (lineage-1, strains WMed-1.2 and WMed-1.3) was detected annually in resident birds, including Alectoris rufa, Cyanopica cooki and Garrulus glandarius (1.5%, 18/1,171), and in Culex univittatus mosquitoes (0.8%, 2/255). Together with a WNV-specific seroprevalence of 28.5% (259/910) in birds, these findings support sustained local circulation. USUV RNA (Africa 3.1 sub-lineage) was detected in A. rufa in 2021 and 2023 (0.2%, 2/1,171), but seroprevalence was low (1.3%, 8/623), consistent with intermittent circulation. BAGV RNA (genotype-2) was detected only during the 2021 outbreak in A. rufa and Emberiza calandra (1.8%, 21/1,171), although BAGV-specific antibodies (6.6%, 60/910) were detected for up to two years after the outbreak, suggesting continued exposure or low-level circulation. Overall, our findings reveal contrasting circulation dynamics of orthoflaviviruses in southern Portugal. Sustained WNV circulation implies the need to strengthen avian and human surveillance in Portugal to better assess its public health risk, while the sporadic detection of USUV and BAGV underscores the value of long-term, integrated One Health surveillance for improving early warning and preparedness for emerging mosquito-borne diseases.

genetics↗

bioRxiv2026

A tumor-cell MHC-II program is associated with checkpoint-blockade outcomes across stages of bladder cancer

Purpose: A minority of patients with bladder cancer derive lasting benefit from immunotherapy, and current biomarkers capture only part of the biology. We evaluated whether tumor-cell MHC class II defines an immune state associated with outcome across disease stages and after PD-1/PD-L1 blockade. Experimental Design: We localized differential MHC-II activity to malignant epithelial cells by single-nucleus and single-cell RNA sequencing and confirmed HLA-DR expression by immunohistochemistry in 122 specimens. Chromatin profiling and IFN-{gamma} stimulation of cell lines and primary tumors supported derivation of an 11-gene tumor-cell program. Associations were tested in 434 patients with non-muscle-invasive disease, 82 receiving neoadjuvant pembrolizumab, and 288 receiving atezolizumab for metastatic disease. Results: Tumor-cell MHC-II was present in approximately one third of bladder cancers, and malignant cells accounted for the differential signal between MHC-II-high and MHC-II-low tumors. The program was inducible by IFN-{gamma} through JAK/STAT signaling. Within luminal non-muscle-invasive disease, MHC-II-low status was associated with progression (HR 3.31, 95% CI 1.37 to 7.99). In PURE-01, the 11-gene program was associated with pathological complete response (52% versus 24%, p = 0.018) and recurrence-free survival (p = 0.0054), retaining an independent association in models including tumor mutational burden and PD-L1. In bladder-primary metastatic disease, program-high status was associated with overall survival in unadjusted analysis (HR 0.62, 95% CI 0.44 to 0.89); the association did not extend to upper tract tumors (interaction p = 0.0018). Conclusions: Tumor-cell MHC-II defines an inducible state associated with outcomes across bladder cancer stages and after checkpoint blockade, supporting prospective evaluation by RNA and immunohistochemistry.

cancer biology↗

bioRxiv2026

Extracellular matrix defects destabilise apical cytoarchitecture and mechanical properties during early Down syndrome neurodevelopment

Down syndrome (DS) is associated with altered brain development, especially in the cerebellum. However, how trisomy 21 (TS21) is linked to cerebellar defects remains poorly understood. Cerebellar organoids reveal that TS21 leads to extracellular matrix (ECM) alterations, perturbing downstream pathways linked to reduction of apical RAB11+ endosomes. These changes lead to impaired apical maintenance and altered progenitor composition. Significantly, ECM-enriched culture rescues apical defects in TS21 organoids, supporting a functional role for ECM in preserving apical organisation and progenitor niche integrity. In the developing human DS cerebellum and 2D neural cultures, where exogenous ECM is present, severe epithelial disorganisation is attenuated. Nevertheless, ECM organisation and mechanical properties remain altered in 2D cultures. Our findings identify TS21-driven ECM abnormalities as a mechanism impairing apical integrity, progenitor composition and mechanical proprieties in neural stem cell models of DS. Altogether, we established apical maintenance instability as an early developmental defect contributing for DS neuropathology.

Developmental Biology↗

bioRxiv2026

Identification of Malignant Peripheral Nerve Sheath Tumor subtypes with distinct genomic identities

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft-tissue sarcomas arising sporadically or in people with neurofibromatosis type 1 (NF1). Their marked heterogeneity challenges diagnosis and has hampered an integrative view of MPNST molecular pathogenesis. Here, a thorough whole-genome and transcriptome analysis of MPNSTs and the re-analysis of a large independent cohort allowed us to identify three molecular subtypes of MPNSTs (G1-G3) with distinct genomic identities and clinicopathological features. Furthermore, it provided a simple and unifying model of MPNST development, defining a distinct progression path for each group. This work uncovers new genomic aspects of MPNSTs, including the identification of recurrent copy-neutral loss of heterozygosity regions, distinct copy-number profiles among G1-G3, and CDKN2A-inactivating translocations in pre-malignant lesions (ANNUBPs). Altogether, these analyses overcome the dominant influence of PRC2 status in MPNST classification and provide a framework for their differential diagnosis and potential precision oncology treatment. SIGNIFICANCEMPNST is a highly heterogeneous soft-tissue sarcoma with difficult clinical management and no effective systemic therapies. This work defines three molecular subtypes of MPNSTs with distinct development paths and histological and clinical characteristics with potential impact on translational studies and subtype-tailored treatments.

cancer biology↗

bioRxiv2024

Harmonising digitised herbarium data to enhance biodiversity knowledge: creating an updated checklist for the flora of Greenland.

International efforts to digitise herbarium specimens provide the building blocks for a global digital herbarium. However, taxonomic changes and errors can result in inconsistencies when amalgamating specimen metadata, that compromise the assignment of occurrence records to correct taxa, and the subsequent interpretation of patterns in biodiversity. We present a novel workflow to mass-curate digital specimens. By employing existing digital taxonomic backbones, we aggregate specimen names by their accepted name and flag remaining cases for manual review. We then validate names using site-specific floras, balancing automation with taxonomic expert-based curation. Applying our workflow to the vascular plants of Greenland, we harmonised 175,266 digitised herbarium specimens and observations from 92 data providers from the Global Biodiversity Information Facility (GBIF). The harmonised metacollection for the Greenland flora contains 780 plant species. Our workflow increases the number of species known from Greenland compared to other currently available species checklists and increases the mean number of occurrences per species by 42.6. Our workflow illustrates the integration required in order to create a global, universally accessible digital herbarium, and shows how previous obstacles to database curation can be overcome through a combination of automation and expert curation. From the specific perspective of the Greenland flora, our approach arrives at a new checklist of taxa, a new curated metacollection of occurrence data, and revised estimates of plant richness. The list of taxa and their prevalence allow a new basis for biodiversity assessment and conservation planning. Societal Impact StatementDigitising plant collections has allowed for data to be aggregated across multiple collections, forming a single harmonised resource of unprecedented scale. This resource is only accurate once the database names are assigned to one accepted name per species. We established a semi-automated workflow for processing plant name data, leveraging taxonomic backbones and employing taxonomic expertise at key stages. Applying our workflow to the flora of Greenland, we developed a curated checklist of 780 species, capturing greater species richness than previously published, while also curating 175,266 plant records. Our findings redefine our knowledge of Greenlandic plant diversity, while harmonising a vast digital collection for further research.

ecology↗

bioRxiv2024

Usutu virus African 3.1 lineage, Portugal, 2021-2023

BackgroundUsutu virus (Orthoflavivirus usutuense, USUV), a neurotropic arthropod-borne RNA virus of the family Flaviviridae, is a zoonotic virus that has spread throughout the European continent over the last three decades, since its emergence in Italy in 1996. However, no cases of USUV have been reported in Portugal so far. Material and methodsIn the scope of an active surveillance program for Orthoflavivirus, we collected growing feather samples from 249 red-legged partridges (Alectoris rufa) hunted in southern Portugal during the 2021-2023 hunting seasons. Samples positive for USUV were subjected to whole genome sequencing and strain characterization. ResultsTwo partridges tested positive for USUV. Phylogenetic analyses of whole and partial genomes assigned the USUV strains to the African 3 lineage, specifically the African 3.1 sub-lineage. ConclusionsOur study confirms, for the first time, the circulation of USUV in wild birds in Portugal. Active surveillance of hunted partridges proved to be a useful, accessible, and cost-effective method for USUV monitoring, further supporting their value as effective sentinels for Orthoflavivirus surveillance. Given the ongoing circulation of USUV and the increasing risk of its spillover to other domestic and wild animals, and humans, additional efforts are needed to improve virus surveillance in Portugal from a One Health perspective.

microbiology↗

bioRxiv2022

Serum Amyloid A proteins reduce bone mass during mycobacterial infections

Osteopenia has been associated to several inflammatory conditions, including mycobacterial infections. How mycobacteria cause bone loss remains elusive, but direct bone infection may not be required. Using genetically engineered mice and morphometric, transcriptomic and functional analyses, we found that infection with Mycobacterium avium impacts bone turnover by decreasing bone formation and increasing bone resorption, in a IFNg- and TNFa-dependent manner. IFNg produced during infection enhanced macrophage TNFa secretion, which in turn increased the production of serum amyloid A (SAA) 3. Saa3 expression was upregulated in the bone of both M. avium- and Mycobacterium tuberculosis-infected mice and SAA proteins were increased in the serum of patients with active tuberculosis. Furthermore, the increased SAA levels seen in active tuberculosis patients correlated with altered serum bone turnover markers. Additionally, human SAA proteins impaired bone matrix deposition and increased osteoclastogenesis in vitro. Overall, we report a novel crosstalk between the cytokine network operating in macrophages and bone homeostasis and disclose SAA proteins as potential biomarkers of bone loss during infection by mycobacteria.

immunology↗

bioRxiv2022

Single cell atlas of the neonatal small intestine with necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a gastrointestinal complication of premature infants with high rates of morbidity and mortality. A comprehensive view of the cellular changes and aberrant interactions that underlie this disease is lacking. Here, we combine single cell RNA sequencing, T Cell Receptor beta (TCR{beta}) analysis, bulk transcriptomics, and imaging to characterize cell identities, interactions and zonal changes in NEC. We find that inflammatory macrophages are abundant in NEC and that T cells exhibit increased expression of inflammatory genes and cytokines accompanied by an increase in TCR{beta} clonal expansion. Fibroblasts and endothelial cells increase in proportion and exhibit a switch to an activated pro-inflammatory state. Villus tip epithelial cell identity is substantially reduced in NEC and the remaining epithelial cells up-regulate pro-inflammatory genes. We establish a detailed map of aberrant epithelial-mesenchymal-immune interactions that may be driving inflammation in NEC mucosa. Our analyses highlight the cellular changes underlying NEC disease pathogenesis and identify potential targets for biomarker discovery and therapeutics.

immunology↗

bioRxiv2021

CCR5 closes the temporal window for memory linking

Real world memories are formed in a particular context and are not acquired or recalled in isolation 1-5. Time is a key variable in the organization of memories, since events experienced close in time are more likely to be meaningfully associated, while those experienced with a longer interval are not1-4. How does the brain segregate events that are temporally distinct? Here, we report that a delayed (12-24h) increase in the expression of the C-C chemokine receptor type 5 (CCR5), an immune receptor well known as a co-receptor for HIV infection6,7, following the formation of a contextual memory, determines the duration of the temporal window for associating or linking that memory with subsequent memories. This delayed CCR5 expression in mouse dorsal CA1 (dCA1) neurons results in a decrease in neuronal excitability, which in turn negatively regulates neuronal memory allocation, thus reducing the overlap between dCA1 memory ensembles. Lowering this overlap affects the ability of one memory to trigger the recall of the other, thus closing the temporal window for memory linking. Remarkably, our findings also show that an age-related increase in CCL5/CCR5 expression leads to impairments in memory linking in aged mice, which could be reversed with a CCR5 knockout and an FDA approved drug that inhibits this receptor, a result with significant clinical implications. All together the findings reported here provide the first insights into the molecular and cellular mechanisms that shape the temporal window for memory linking.

neuroscience↗

bioRxiv2021

MethReg: estimating the regulatory potential of DNA methylation in gene transcription

Epigenome-wide association studies (EWAS) often detect a large number of differentially methylated sites or regions, many are located in distal regulatory regions. To further prioritize these significant sites, there is a critical need to better understand the functional impact of CpG methylation. Recent studies demonstrated CpG methylation-dependent transcriptional regulation is a widespread phenomenon. Here we present MethReg, an R/Bioconductor package that analyzes matched DNA-methylation and gene-expression data, along with external transcription factor (TF) binding information, to evaluate, prioritize, and annotate CpG sites with high regulatory potential. By simultaneous modeling three key elements that contribute to gene transcription (CpG methylation, target gene expression and TF activity), MethReg identifies TF-target gene associations that are present only in a subset of samples with high (or low) methylation levels at the CpG that influences TF activities, which can be missed in analyses that use all samples. Using real colorectal cancer and Alzheimers disease datasets, we show MethReg significantly enhances our understanding of the regulatory roles of DNA methylation in complex diseases.

bioinformatics↗

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↗