Biology subjects

Teixeira, A.

Publications and source records attributed to Teixeira, A..

11 recordsLinked to original sources

bioRxiv2026

Microfluidic Extraction of Extracellular Vesicle-Associated Nucleic Acids for Downstream Molecular Analysis

Aim: To develop a microfluidic workflow for extracting extracellular vesicle (EV)-associated nucleic acids (NAs) from biofluids, such as blood plasma and serum, for downstream molecular analysis. Methods: Healthy serum and plasma samples were spiked with EVs obtained from Hec-1-A cells carrying defined mutations and characterized in accordance with MISEV guidelines. The spiked samples were then processed using either the standard centrifugation-based ExoGAG protocol or a microfluidic workflow. The latter combines ExoGAG mediated aggregation of EVs with mechanical entrapment of the resulting EV aggregates in a microfluidic filtration device (EVNA-chip). The retained material was washed and on-chip lysed to release its NA cargo. NAs were subsequently purified using a commercial silica column, producing an output suitable for molecular analysis through droplet digital PCR (ddPCR). Results: The EVNA-chip recovery yield was 42.0 +/- 4.28% and 38.1 +/- 1.46% for double-stranded DNA (dsDNA) and microRNA respectively. The recovered dsDNA remained compatible with ddPCR detection of the KRAS p.G12D variant (c.35G>A) and with the assessment of MSI-associated alterations using BAT25, BAT26, NR21, NR24, and MONO27. The method was demonstrated for pilot cohort of patients with endometrial cancer. The RNA workflow supported reverse transcription and was demonstrated for the quantification of miR-X, a potential marker of Fabry disease, using patient samples and healthy controls. Conclusion: Although recovery was lower than with the standard protocol (~45% for DNA and for RNA), the centrifugation-free EVNA-chip workflow demonstrates the compatibility of the method with downstream NA molecular analyses and is advantageous for the development of an integrated, automated platform for EV-based liquid biopsy applications.

bioengineering↗

bioRxiv2026

Dual Ligand Cooperation at the Plasma Membrane Drives Transport of Engineered Small Extracellular Vesicles Across Brain Endothelial Cells

The natural delivery properties of small extracellular vesicles (sEVs) can be harnessed and enhanced through engineering to create a new class of biotherapeutics, particularly for central nervous system (CNS) disorders. While evidence supports the ability of sEVs to cross biological barriers and deliver functional cargo to target cells, a limited understanding of their uptake and transport across the brain hinders their translational potential. In this study, we investigated either native and engineered sEVs, developed by us, using a novel modular engineering platform that employs a dual-targeting strategy to facilitate uptake and transport through human brain endothelial cells (BECs). By utilizing super-resolution microscopy, we provided direct insights into the mechanisms of docking, intracellular sorting, and transport of engineered sEVs. The engineered sEVs formulation demonstrated significantly enhanced uptake, intracellular trafficking across BECs, and the ability to bypass degradative pathways. In vivo, the engineered sEVs exhibited preferential accumulation in the brain choroid plexus, a structure located within the lateral and fourth ventricles, thereby effectively targeting the blood-cerebrospinal fluid (CSF) barrier. These findings highlight the potential of combining advanced targeting strategies with high-resolution imaging to study sEV interactions with the brain biological barriers and develop more effective CNS therapies.

bioengineering↗

bioRxiv2025

Single cell-derived spheroids for real-time growth and metabolomic studies in breast cancer

Breast cancer remains a leading cause of cancer-related mortality, with disease progression and metastasis posing significant challenges in treatment. Three-dimensional (3D) cancer models have emerged as valuable tools for studying cancer cell biology in a physiologically relevant microenvironment. Studying the tumour heterogeneity and metabolic adaptations at the single-cell level can be crucial to identify factors driving metastatic progression. Here, we present a novel approach to generate single cell-derived breast cancer spheroids using cell lines (MCF-7 and MCF-10A) within a decellularised adipose tissue extracellular matrix (adECM). Spheroid culture conditions were optimised with integrated plasmonic nanosensors (gold nanostars - GNSs), to enable real-time surface-enhanced Raman scattering (SERS)-based measurements. Our results demonstrated that spheroid growth kinetics and viability in adECM were comparable to commonly used animal-derived matrices, validating its use as a reproducible ECM hydrogel. We further show that the concentration of plasmonic nanosensors used was compatible with cell culture and enabled SERS detection of a model reporter, paving the way for label-free, non-destructive analysis of cancer cell metabolism. This platform offers a promising approach to study cancer progression, including metabolic adaptations, with potential applications in biomarker discovery and preclinical research.

cancer biology↗

bioRxiv2023

Effects of orally administered crofelemer on the incidence and severity of neratinib-induced diarrhea in female dogs

Management guidelines for cancer therapy-related diarrhea (CTD) should be revised because newer targeted therapies have increased CTD burden, with high incidence and/or severity of diarrhea for some agents that inhibit epidermal growth factor receptor and receptor tyrosine kinases. Neratinib, a pan-HER tyrosine kinase inhibitor, approved for breast cancer treatment, causes severe diarrhea in >95% of patients. Crofelemer, a novel intestinal chloride ion channel modulator, is an approved antidiarrheal for patients with HIV receiving antiretroviral therapy. The objective of this study was to evaluate the effectiveness of crofelemer prophylaxis in reducing the incidence and severity of neratinib-induced diarrhea without loperamide in dogs. Female dogs received neratinib orally daily concomitantly with either matching placebo tablets (CTR) or crofelemer 125 mg delayed-release tablet two or four times/day (BID or QID) for 28 consecutive days. At the end of treatment, 37.5%, 75%, and 87.5% of the CTR, BID, and QID dogs were responders defined as [≤]7 loose/watery stools/week for at least 2 of 4 weeks (p<0.05). The average number of watery stools per week was 9, 6, and 6 in the CTR, BID, and QID groups, respectively (p<0.05). The average number of weeks with no loose/watery stools was 1.3, 2.1, and 2.3 for the CTR, BID, and QID groups, respectively (p<0.05). The weekly mean fecal scores and stool consistency were 5.1, 3.9, and 4.1 for the CTR, BID, and QID groups (p<0.05). In this 28-day preclinical study, crofelemer prophylaxis without loperamide reduced the incidence and severity of neratinib-associated diarrhea in female dogs by 30%. Ethical ComplianceAll procedures performed in studies involving canine participants were in accordance with the ethical standards of the institutional and/or national research committee and applicable Institutional Animal Care and Use Committee (IACUC).

pharmacology and toxicology↗

bioRxiv2023

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Contiguous assemblies are fundamental to decipher the exact composition of extant genomes. In molluscs, this task is considerably challenging owing to their large size, heterozygosity, and widespread content of repetitive content. Consequently, the usage of long-read sequencing technologies is fundamental to achieve high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, has been produced recently. However, the current genome is highly fragmented since the assembly relied solely on short-read approaches. To overcome this caveat, here, a new improved reference genome assembly is produced using a combination of PacBio CLR long reads and Illumina paired-end short reads. This novel genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4Mbp. The ab initio gene prediction resulted in a total of 48,314 protein-coding genes. This new assembly represents a substantial improvement and is an essential resource for studying this species unique biological and evolutionary features that ultimately will help to promote its conservation.

genomics↗

bioRxiv2023

PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793

Mussels of order Unionida are a group of strictly freshwater bivalves with nearly 1,000 described species widely dispersed across world freshwater ecosystems. They are highly threatened showing the highest record of extinction events within faunal taxa. Conservation is particularly concerning in species occurring in the Mediterranean biodiversity hotspot that are exposed to multiple anthropogenic threats, possibly acting in synergy. That is the case of the dolphin freshwater mussel Unio delphinus Spengler, 1793, endemic to the western Iberian Peninsula with recently strong population declines. To date, only four genome assemblies are available for the order Unionida and only one European species. We present the first genome assembly of Unio delphinus. We used the PacBio HiFi to generate a highly contiguous genome assembly. The assembly is 2.5 Gb long, possessing 1254 contigs with a contig N50 length of 10 Mbp. This is the most contiguous freshwater mussel genome assembly to date and is an essential resource for investigating the species biology and evolutionary history that ultimately will help to support conservation strategies.

bioinformatics↗

bioRxiv2022

The impact of the ABO/Rh blood group on susceptibility and severity among COVID-19 patients in Luanda, Angola

SARS-CoV-2 is a public health concern worldwide. Identification of biological factors that could influence transmission and worsen the disease has been the subject of extensive investigation. Herein, we investigate the impact of the ABO/Rh blood group on susceptibility and severity among COVID-19 patients in Luanda, Angola. This was a multicentric cohort study conducted with 101 COVID-19 patients. Chi-square and logistic regression were calculated to check factors related to the worsening of the disease and deemed significant when p<0.05. Blood type O (51.5%) and Rh-positive (93.1%) were the most frequent. Patients from blood type O had a high risk to severe disease [OR: 1.33 (95% CI: 0.42 - 4.18), p=0.630] and hospitalization [OR: 2.59 (95% CI: 0.84 - 8.00), p=0.099]. Also, Rh-positive blood type presented a high risk for severe disease (OR: 10.6, p=0.007) and hospitalization (OR: 6.04, p=0.026). We find a high susceptibility, severity, hospitalization, and mortality, respectively, among blood group O and Rh-positive patients, while blood group AB presented a low susceptibility, severity, hospitalization, and mortality, respectively. Our findings add to the body of evidence suggesting that ABO/Rh blood groups play an important role in the course of SARS-CoV-2 infection.

genetics↗

bioRxiv2021

Identification of leptospiral protein antigens recognized by WC1+ γδ T cell subsets as target for development of recombinant vaccines

Pathogenic Leptospira species cause leptospirosis, a neglected zoonotic disease recognized as a global public health problem. It is also the cause of the most common cattle infection that results in major economic losses due to reproductive problems. {gamma}{delta} T cells play a role in the protective immune response in livestock species against Leptospira while human {gamma}{delta} T cells also respond to Leptospira. Thus, activation of {gamma}{delta} T cells has emerged as a potential component for optimization of vaccine strategies. Bovine {gamma}{delta} T cells proliferate and produce IFN-{gamma} in response to vaccination with inactivated leptospires and this response is mediated by a specific subpopulation of the WC1-bearing {gamma}{delta} T cells. WC1 molecules are members of the group B scavenger receptor cysteine rich (SRCR) superfamily and are composed of multiple SRCR domains, of which particular extracellular domains act as ligands for Leptospira. Since WC1 molecules function as both pattern recognition receptors and {gamma}{delta} TCR coreceptors, the WC1 system has been proposed as a novel target to engage {gamma}{delta} T cells. Here, we demonstrate the involvement of leptospiral protein antigens in the activation of WC1+ {gamma}{delta} T cells and identified two leptospiral outer membrane proteins able to interact directly with them. Interestingly, we show that the protein-specific {gamma}{delta} T cell response is composed of WC1.1+ and WC1.2+ subsets, although a greater number of WC1.1+{gamma}{delta} T cells respond. Identification of protein antigens will enhance our understanding of the role {gamma}{delta} T cells play in the leptospiral immune response and in recombinant vaccine development.

immunology↗

bioRxiv2020

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2,4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

genomics↗

bioRxiv2019

The role of 3’UTR-protein complexes in the regulation of protein multifunctionality and subcellular localization

Multifunctional proteins often perform their different functions when localized in different subcellular compartments. However, the mechanisms leading to their localization are largely unknown. Recently, 3UTRs were found to regulate the cellular localization of newly synthesized proteins through the co-translational formation of 3UTR-protein complexes. Here, we investigate the formation of 3UTR-protein complexes involving multifunctional proteins by exploiting large-scale protein-protein and protein-RNA interaction networks. Focusing on 238 human extreme multifunctional (EMF) proteins, we predicted 1411 3UTR-protein complexes involving 128 EMF proteins and evaluated their role in regulating protein cellular localization and multifunctionality. Notably, we find that EMF proteins lacking localization addressing signals, yet present at both the nucleus and cell surface, often form 3UTR-protein complexes. In addition, they provide EMF proteins with the diversity of interaction partners necessary to their multifunctionality. Archetypal moonlighting proteins are also predicted to form 3UTR-protein complexes thereby reinforcing our findings. Finally, our results indicate that the formation of 3UTR-protein complex may be a common phenomenon in human cells, affecting up to 20% of the proteins in the human interactome.

systems biology↗

bioRxiv2019

Degree and site of chromosomal instability define its oncogenic potential

Most human cancers are aneuploid, due to a chromosomal instability (CIN) phenotype. Despite being hallmarks of cancer, however, the roles of CIN and aneuploidy in tumor formation have not unequivocally emerged from animal studies and are thus still unclear. CIN can both promote and suppress tumorigenesis, but variances in mechanisms and timings of CIN induction in different oncogenic backgrounds and associated tissues limit interpretation of the contributions of CIN. Using a novel conditional mouse model for diverse degrees of CIN, we find that a particular range is sufficient to drive very early onset spontaneous adenoma formation in the intestine, showing that CIN can act as a much more potent oncogenic driver than was previously reported. In mice predisposed to intestinal cancer (ApcMin/+), moderate but not low CIN causes a remarkable increase in adenoma burden in the entire intestinal tract, especially in the distal colon, more closely modelling human disease. Strikingly, high levels of CIN promote adenoma formation in the distal colon even more than moderate CIN does, but have no effect in the small intestine. Our results thus show that CIN can be potently oncogenic, but that certain levels of CIN can have contrasting effects in distinct tissues.

cancer biology↗