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Lopes, S.

Publications and source records attributed to Lopes, S..

7 recordsLinked to original sources

Same-section spatial metabolo-transcriptomics using Stereo-meta-seq reveals DHA-driven kidney maturation

A central unresolved question in developmental biology is whether local metabolites merely accompany, or actively instruct, tissue maturation. Addressing this question requires direct spatial coupling of metabolic states with genome-wide transcriptional programs in situ at high spatial resolution, which existing approaches do not readily achieve. Here, we introduce Stereo-meta-seq, a workflow that integrates quantitative MALDI-MSI with Stereo-seq spatial transcriptomics within a single tissue section. A conductive adapter was designed to overcome the electrical incompatibility of non-conductive Stereo-seq chips with vacuum MALDI platforms, improving efficiency of MSI detection that preserves RNA integrity. MALDI laser-ablation marks are retained in downstream Stereo-seq data and serve as intrinsic fiducials for direct co-registration at 10 m or 20 m resolution, enabling fine grained spatial metabolite-transcript integration. Applying Stereo-meta-seq to human kidney development, we uncover selective enrichment of docosahexaenoic acid (DHA) in maturing proximal tubules. Functional studies in human kidney organoids demonstrate that DHA activates PPAR-and HNF4-driven transcriptional programs and promotes proximal tubule maturation in vitro and after transplantation in vivo. These findings identify lipid metabolism as an instructive regulator of human nephrogenesis and establish Stereo-meta-seq as a practical platform for dissecting metabolite-gene coupling and tissue heterogeneity in situ.

Cell Biology↗

An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies

Single cell transcriptomics has transformed our knowledge of reproductive tissues, yet studies remain largely organ-specific and temporally limited, leaving an incomplete picture of how cell types are distributed across the reproductive system over a lifetime. Gynaecological conditions affect more than one in four females and frequently span multiple organs and life stages. To advance our understanding and treatment of these conditions, an integrated cellular reference is essential. Here we present the Human Female Reproductive System Cell Atlas v1: a single-cell transcriptomic resource integrating more than 2M cells across the ovary, fallopian tube, uterus, cervix and vagina over the lifespan and menstrual cycle, further integrated with spatial transcriptomics and chromatin accessibility profiling to define 210 cell types through community-based annotation. Cross-organ integration resolves shared and organ-specific cellular states, identifying uterine-specific perivascular populations lining uterine spiral arteries, hypoxia-sensing type 3 innate lymphoid cells (ILC3s) enriched in the uterus, and lipid-associated macrophages with distinct subsets in each reproductive organ, including a previously undescribed population shared between the uterus and fallopian tube. Cross-organ integration enables detection of ectopic epithelial populations in otherwise healthy donors, including endometrial-like cells within a paediatric ovary consistent with early endometriosis. Integration with genome-wide association studies (GWAS) reveals that risk variants for major gynecological conditions act in mesenchymal cell states defined by specific transcriptional programmes and spatial or temporal context - for instance, heavy menstrual bleeding risk is enriched in basal fibroblasts (SFRP5) of the regenerative endometrial compartment. An integrated chromatin accessibility atlas provides peak-to-gene maps across reproductive cell types, enabling nomination of disease effector genes and providing the first regulatory evidence linking a Polyendocrine Metabolic Ovarian Syndrome (PMOS) risk locus to INHBB in granulosa cells. Together, this resource establishes a cellular and molecular framework for reproductive biology and the pathogenesis of neglected gynaecological conditions.

Cell Biology↗

Mesenchymal Stromal Cell Therapeutic Potential to RestoreNeurovascular Integrity in Machado-Joseph Disease

BackgroundMachado-Joseph disease (MJD), or Spinocerebellar Ataxia type 3 (SCA3), is a neurodegenerative disorder caused by an expansion of the CAG repeat in the MJD1/ATXN3 gene, which encodes for a polyglutamine-expansion in Ataxin-3. Similar to what occurs in other neurodegenerative disorders, the cerebrovascular system, particularly the blood-brain barrier (BBB), is impaired in MJD. BBB is an important cellular barrier that controls homeostasis of the central nervous system, and its disruption compromises neuronal function. To date, there is no disease-modifying therapy for MJD. Our group previously demonstrated that MSC administration can ameliorate the phenotype of MJD transgenic mice. However, the effect of MSC on the neurovascular unit and BBB integrity remains unexplored in the context of MJD. In the present work, we aimed to evaluate the therapeutic potential of MSC in mitigating vascular abnormalities and BBB disruption in MJD. MethodsEight-month-old MJD transgenic mice were treated with two consecutive bone marrow-MSC intravenous injections (1 week apart). Behavioral tests to assess motor coordination were conducted before and after treatment. Vascular structure, function, and BBB disruption were evaluated by immunohistochemistry and western blot. ResultsMSC administration partially restored vascular impairment in MJD transgenic mice. Treated mice exhibited improved gait and motor performance footprint and beam walking tests) and concurrently attenuated vascular dysfunction. Specifically, MSC-treated mice exhibited a decrease in collagen IV surface area and stabilized cerebellar blood supply. Additionally, MSC treatment diminished BBB permeability to the Evans blue (EB) dye in MJD mice and restored the levels of important adherent and tight junction-associated proteins in the cellular membrane, including vascular endothelial cadherin (VE-cadherin), claudin-5, and occludin, in a sex-specific manner. Conclusionsour results highlight significant cerebrovascular dysregulations in MJD, which are sex-dependent and progress with the disease stage. Moreover, our findings suggest that MSC administration partially reverted vascular impairments, providing valuable insights into the mechanisms underlying the therapeutic potential of MSC in MJD. Graphical AbstractMSC treatment partially reverts neurovascular dysregulation in MJD. MJD mice exhibit increased vessel coverage, increased BBB permeability, and altered TJ and AJ expression and subcellular localization. MSC administration modulates vessel coverage, reduces BBB leakage, and partially normalizes TJ/AJ subcellular localization. List of abbreviations: AJ - Adherent junction; BBB - Blood-Brain barrier; MJD- Machado-Joseph disease; MSC - mesenchymal stromal cell; TJ - thigh junction. Created with BioRender.com O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/703043v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@8fa0a2org.highwire.dtl.DTLVardef@17b13f9org.highwire.dtl.DTLVardef@15c5ce3org.highwire.dtl.DTLVardef@d67539_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Antigenic and genetic diversity of H1 and H3 influenza A viruses in swine in Brazil

BackgroundInfluenza A virus (IAV) circulates within human and swine populations, and pigs are considered intermediate hosts for the generation of IAV with pandemic potential. Surveillance and characterization of IAVs circulating in pig populations are crucial to strain match vaccines to control IAV transmission in pigs and quantify pandemic potential to humans. MethodsHere, we characterized the genetic and antigenic diversity of IAVs circulating in Brazilian swine between 2010-2018. Phylogenetic maximum-likelihood trees were generated for 84 Brazilian hemagglutinin (HA) gene segments. Hemagglutination inhibition (HI) assay data was used with antigenic cartography to quantify the antigenic differences among representative H1 and H3 swine viruses and relative cross-reactivity between these viruses and human seasonal vaccine strains. ResultsWe identified two genetic lineages of H1 viruses derived from separate human-to-swine transmission events (H1 1B lineage, clades 1B.2.3 and 1B.2.4), an H3 lineage that has diversified into two genetic clades (H3 1990.5.1 and 1990.5.2), and HA genes associated with the 2009 H1N1 pandemic. There was limited cross-reactivity between circulating swine lineages and significant antigenic variation within lineage. ConclusionsThe antigenic diversity among endemic IAV in swine indicates a need for regional strain-specific vaccination strategies in Brazil. Our data supports the need for systematic genomic surveillance and characterization in Brazil to improve the efficacy of swine vaccines and quantify the pandemic potential of endemic swine influenza A viruses.

microbiology↗

Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine

The first pandemic of the 21st century was caused by an H1N1 influenza A virus (IAV) introduced from pigs into humans, highlighting the importance of swine as reservoirs for pandemic viruses. Two major lineages of swine H1 circulate in North America: the 1A classical swine lineage (including the 2009 pandemic H1N1) and 1B human seasonal-like lineage. Here, we investigated the evolution of these H1 IAV lineages in North American swine and their potential pandemic risk. We assessed the antigenic distance between the HA of representative swine H1 and human seasonal vaccine strains (1978-2015) in hemagglutination inhibition (HI) assays using a panel of monovalent anti-sera raised in pigs. Antigenic cross-reactivity varied by strain but was associated with genetic distance. Generally, swine 1A lineage viruses that seeded the 2009 H1 pandemic were antigenically most similar to H1 pandemic vaccine strains, with the exception of viruses in the genetic clade 1A.1.1.3 that had a two-amino acid deletion mutation near the receptor-binding site, dramatically reducing antibody recognition. The swine 1B lineage strains, which arose from previously circulating (pre-2009 pandemic) human seasonal viruses, were more antigenically similar to pre-2009 human seasonal H1 vaccine viruses than post-2009 strains. Human population immunity was measured by cross-reactivity in HI assays to representative swine H1 strains. There was a broad range of titers against each swine strain that was not associated with age, sex, or location. However, there was almost no cross-reactivity in human sera to the 1A.1.1.3 and 1B.2.1 genetic clades of swine viruses, and the 1A.1.1.3 and 1B.2.1 clades were also the most antigenically distant from all human vaccine strains. Our data demonstrate that antigenic distances of representative swine strains from human vaccine strains represent a rational assessment of swine IAV for zoonotic risk research and pandemic preparedness prioritization. ImportanceHuman H1 influenza A viruses (IAV) spread to pigs in North America, resulting in sustained circulation of two major groups of H1 viruses in swine. We quantified the genetic diversity of H1 in swine and measured antigenic phenotypes. We demonstrated that swine H1 lineages were significantly different from human vaccine strains and this antigenic dissimilarity increased over time as the viruses evolved in swine. Pandemic preparedness vaccine strains for human vaccines also demonstrated a loss in similarity with contemporary swine strains. Human sera revealed a range of responses to swine IAV, including two groups of viruses with little to no immunity. Surveillance and risk assessment of IAV diversity in pig populations are essential to detect strains with reduced immunity in humans, providing critical information for pandemic preparedness.

microbiology↗

Field efficacy of guppies and pyriproxyfen (Sumilarv(R) 2MR) combined with community engagement on dengue vectors in Cambodia: a randomized controlled trial

Evidence on the effectiveness of low-cost, sustainable biological vector control tools for Aedes mosquitoes is limited. Therefore, the purpose of this trial is to estimate the impact of guppy fish, in combination with the use of the larvicide Pyriproxyfen (Sumilarv(R) 2MR), and Communication for Behavioral Impact (COMBI) activities to reduce entomological indices in Cambodia. In this cluster randomized, controlled superiority trial, 30 clusters comprising of one or more villages each (with approximately 170 households) will be allocated, in a 1:1:1 ratio, to receive either a) three interventions (guppies, Sumilarv(R) 2MR, and COMBI activities), b) two interventions (guppies and COMBI activities), or c) control (standard vector control). Households were invited to participate, and entomology surveys among 40 randomly selected households per cluster were carried out quarterly. The primary outcome was the population density of adult female Aedes mosquitoes (i.e. number per house) trapped using adult resting collections. Secondary outcome measures include the House index, Container index, Breteau index, Pupae Per House, Pupae Per Person, mosquito infection rate, guppy fish coverage, Sumilarv(R) 2MR coverage, and percentage of respondents with knowledge about Aedes mosquitoes causing dengue. In the primary analysis, adult female Aedes density and mosquito infection rates was aggregated over follow-up time points to give a single rate per cluster. This was analyzed by negative binomial regression, yielding density ratios. The number of Aedes females was reduced by roughly half compared to the control in both the guppy and PPF arm (Density Ratio (DR)=0.54 [95% CI 0.34-0.85], p=0.0073), and guppy arm (DR=0.49 [95% CI 0.31-0.77], p=0.0021). The extremely low cost of including guppy rearing in community-based health structures along with the effectiveness demonstrated suggest guppies should be considered as a vector control tool as long as the benefits outweigh any potential environmental concerns. PPF was also highly accepted and preferred over current vector control tools used in Cambodia, however product costs and availability are still unknown. Author SummaryDengue is one of the most rapidly spreading mosquito-borne viral diseases in the world, is caused by bites of infected Aedes mosquitoes, and can sometimes lead to death. Cambodia has one of the highest per-capita incidence rates in Asia. Without a cure or routinely available efficacious vaccine, dengue control relies largely on reduction and avoidance of mosquitoes. In Cambodia, dengue mosquito control activities are focused on larviciding with temephos and pyrethroid based adulticide sprays to which Aedes have been shown to be increasingly resistant. This study was designed to evaluate novel biological vector control tools (guppy fish and a controlled release larvicidal matrix) utilizing an integrated vector management approach with community-based methods tailored to the local context. The results indicate that the tools resulted in a statistically significant reduction in immature and adult Aedes mosquito density. The interventions were accepted by and communities were willing to pay for them. The results suggest guppies are an ideal vector control tool as long as the benefits outweigh any potential environmental concerns. PPF was also highly accepted and preferred over current vector control tools used in Cambodia, however product costs and availability are still unknown.

ecology↗

PathoFact: A pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

BackgroundPathogenic microorganisms cause disease by invading, colonizing and damaging their host. Virulence factors including bacterial toxins contribute to their pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is therefore essential to identify virulence factors and antimicrobial resistance genes in metagenomic datasets. At present, there is a clear lack of computational approaches to simultaneously identifying these factors. Here we present PathoFact, a tool for the contextualized prediction of virulence factors and antimicrobial resistance genes in metagenomic data. ResultsPathoFact predicts virulence factors, bacterial toxins and antimicrobial resistance genes with high accuracy (0.92, 0.83 and 0.99) and specificity (0.96, 0.99 and 0.98), respectively. The performance of PathoFact was furthermore demonstrated on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins were predicted to play a role. With PathoFact, we identified virulence factors (including toxins) and antimicrobial resistance genes, and identified signature genes which differentiated between the disease and control groups. ConclusionPathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, toxins and antimicrobial resistance genes in metagenomic data. Additionally, PathoFact combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, each module (virulence factors, toxin and antimicrobial resistance genes) of PathoFact is also a standalone component, making it a flexible and versatile tool. PathoFact is freely available online at https://git-r3lab.uni.lu/laura.denies/PathoFact.

microbiology↗