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Setubal, J. C.

Publications and source records attributed to Setubal, J. C..

13 recordsLinked to original sources
bioRxiv2026

Multi-scale Transcriptional Characterization of HPV16 and HPV18 in Cervical Cancer: Host Pathway Alterations and Links With Viral Gene Expression Programs

High-risk HPV is central to cervical carcinogenesis, but whether individual genotypes drive distinct tumor biology or converge on a shared oncogenic state remains unclear. Profiling viral and host gene expression across two independent cohorts (n = 93; 76 HPV16, 17 HPV18), we show that HPV16- and HPV18-associated cervical cancers differ in host transcriptional programs. A 55-gene signature discriminated the two genotypes, and 293 genes were concordantly differentially expressed across cohorts. Pathway and transcription-factor activity inference organized these differences along genotype-specific axes: HPV16 tumors were enriched for epithelial polarity and RTK-RAS-MAPK signatures, with elevated inferred CDX2 regulon activity, a transcription factor not normally active in cervical epithelium, suggesting an aberrant lineage-identity program not previously linked to this genotype. HPV18 tumors instead showed metabolic reprogramming and inflammatory signaling (STAT3, HIF1A), alongside reduced CASP8 and increased FDX1 expression, a pattern consistent with sensitization to immunogenic cell death. Both genotypes also organized along a continuum of early-to-late viral gene expression correlating with distinct host pathways: extracellular-matrix and translation-related in HPV16, interferon/antiviral and cell-cycle/mitochondrial in HPV18, indicating that viral transcriptional state associates with host biology beyond genotype alone. These results point to candidate genotype-specific vulnerabilities that merit functional validation.

cancer biology↗
bioRxiv2026

PARG activity is required for cell death by parthanatos

Cell death by a non-apoptotic pathway termed parthanatos is induced by hyperactivation of the DNA damage sensor PARP1, which uses NAD+ as a substrate to catalyse the poly-ADP-ribosylation (PARylation) of proteins. Parthanatos has been implicated in several pathological conditions such as ischaemia-reperfusion injury and neurodegenerative processes, including Alzheime[r]s and Parkinso[n]s diseases, as well as rare genetic disorders characterized by PARP1 hyperactivation. However, the precise sequence of molecular events by which excessive PARP1 activity causes cell death is currently unclear. Here we show that, in addition to PARP1-dependent PARylation, the execution of parthanatos also requires the hydrolysis of poly-ADP-ribose (PAR) chains by the glycohydrolase PARG. While complete inhibition of PARG activity prevents parthanatos, low levels of residual PARG activity are sufficient to support cell death by this pathway. Due to a phenotypic discrepancy between CRISPR/Cas9-generated PARG KO cells and PARG inhibitor-treated cells, we uncovered a new PARG splice variant predicted to encode an isoform of 53 kDa, termed PARG53, and provide evidence for the incorrect annotation of the previously reported isoforms PARG55 and PARG60. PARP1 hyperactivation during parthanatos leads to rapid and profound depletion of NAD+ and ATP pools, but full PARG inhibition only prevents the depletion of ATP, indicating that the depletion of these core metabolites can be uncoupled, and that ATP depletion is more closely correlated with cell death. This work sheds light on the initial steps of parthanatos induction, demonstrating that PAR formation and PAR hydrolysis are both required for this type of cell death.

biochemistry↗
bioRxiv2026

Cryo-EM structure analysis of phage {Phi}Xacm4-11 that infects the phytopathogen Xanthomonas citri

Very few bacteriophages that infect Xanthomonas species have been characterized genetically and only one 3D structure, the capsid of a siphovirus that infects the phytopathogen Xanthomonas citri, has been determined at high resolution. This study presents the annotated DNA sequence and detailed structural analysis of {Phi}Xacm4-11, a podovirus that infects Xanthomonas citri, shedding light on its unique architecture and functional attributes, providing insights into the molecular mechanisms underlying host recognition and infection. Annotation of the genome revealed conserved features among related phages, but also distinct genetic elements that may contribute to {Phi}Xacm4-11s specificity toward X. citri. Genes associated with host recognition and infection were identified, including the genes potentially coding for the receptor-binding proteins (RBPs) at the tail fibre tip, offering insights into their role in bacterial attachment. Using high-resolution cryo-electron microscopy, we resolved the architecture of the mature, pre-released virion, revealing a T7-like head-tail assembly with a well-defined portal-tail complex embedded at a unique fivefold vertex. Our findings provide a detailed view of the structural and functional components of {Phi}Xacm4-11, furthering our understanding of its molecular interactions with X. citri and its potential application in phage therapy against phytopathogens. SIGNIFICANCE STATEMENTBacteriophages are increasingly recognized as powerful tools to control bacterial pathogens in medicine and agriculture, yet the structural basis of host recognition and genome delivery remains poorly understood for most phages. Here, we present a comprehensive structural and functional analysis of {Phi}Xacm4-11, a podovirus that infects the plant pathogen Xanthomonas citri. By combining genome annotation, proteomics, and high-resolution cryo-electron microscopy, we reveal the complete architecture of the mature virion and its specialized portal-tail machinery. Our results show how this short-tailed phage deploys an internal injection device to penetrate the bacterial cell envelope and highlight structural features linked to type IV pilus-dependent infection. These findings provide insights into phage entry mechanisms and establish {Phi}Xacm4-11 as a model for engineering biocontrol strategies.

biochemistry↗
bioRxiv2025

Pathological angiogenesis RNA network analysis reveals a VEGF-independent gene signature with prognostic power for HER2+ breast cancer

Cancer and many ophthalmic diseases share angiogenesis as a common element for disease progression. Using a well-accepted animal model, we performed network coexpression analysis of mRNA and regulatory RNA to investigate the molecular landscape of pathological angiogenesis in the mouse retina. We assessed the relevance of the RNA coexpression analysis by building gene signatures for breast cancer (METABRIC cohort). Most of the gene signatures were prognostic, and one was prognostic for HER2+ breast cancer, outperforming previously reported HER2+ signatures. Interestingly, it did not include VEGF as variable, and multivariate Cox analysis further highlighted ANGPT2 as a key gene, suggesting that VEGF-independent neovascularization plays an important role in breast cancer. Next, we constructed a network linking mRNAs and regulatory RNAs involved in pathological angiogenesis; this analysis revealed three novel lncRNAs that may play a role in angiogenesis and tumor development. The novel prognostic gene signature and a comprehensive RNA-based regulatory network advance the understanding of angiogenic pathways and provide clinically relevant tools for HER2+ breast cancer stratification. Author SummaryThe formation of new blood vessels by angiogenesis is central in the origin and growth of cancer. Gene signatures are lists of genes that have strong correlation with a disease and/or its development. This study presents a novel angiogenesis gene signature with strong prognostic value for HER2+ breast cancer, an aggressive subtype of this disease. We also discovered novel long noncoding RNA genes that may have important roles in angiogenesis and in tumor development. These findings enhance our understanding of angiogenic mechanisms and offer clinically relevant tools for HER2+ breast cancer diagnosis, potentially guiding more precise therapeutic interventions.

cancer biology↗
bioRxiv2025

Microbial diversity of Atlantic Rainforest ponds assessed by nanopore sequencing

Despite their limited size, ponds are ecologically important habitats that harbor rich microbial communities and play key roles in global biodiversity and biogeochemical cycling. In this study, we conducted a metagenomic survey of microbial diversity in three ponds - Vermelha, Grande, and Furnas - situated within the Atlantic Rainforest biome in Brazil. Vermelha and Grande are natural, remote, and minimally impacted by human activity, whereas Furnas is an artificial pond with greater human accessibility. Using a long-read nanopore shotgun metagenomics approach, we sequenced DNA extracted from pond water, assembled metagenomes, and performed taxonomic classification and functional annotation. Furthermore, 21 metagenome-assembled genomes (MAGs) were recovered. Our results reveal striking biodiversity contained within ponds, with pond-specific microbial community structures and functional profiles. In addition to bacterial communities, some dsDNA bacteriophages and eukaryotic viruses were also detected. Functional annotation identified putative antimicrobial resistance genes (ARGs), most of them in Furnas, potentially reflecting human impact. Cyanotoxin biosynthesis genes were detected as well, predominantly in Vermelha. Our findings underscore the ecological distinctiveness of each pond and demonstrate the utility of nanopore-based metagenomics for investigating microbial biodiversity in understudied freshwater ecosystems, with implications for conservation and biotechnological exploration. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/660208v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1941bd9org.highwire.dtl.DTLVardef@b06d66org.highwire.dtl.DTLVardef@de6df3org.highwire.dtl.DTLVardef@1048bbd_HPS_FORMAT_FIGEXP M_FIG Through nanopore metagenomic sequencing, this work uncovered the microbiome of the 3 analysed freshwater ponds of the Brazilian Atlantic Forest. Results include the taxonomic profile present in each sample, countless genes identified and 21 MAGs recovered. C_FIG

bioinformatics↗
bioRxiv2021

Isolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide- degrading enzyme CynD

Cyanide is widely used in industry as a potent lixiviant due to its capacity to tightly bind metals. This property imparts cyanide enormous toxicity to all known organisms. Thus, industries that utilize this compound must reduce its concentration in recycled or waste waters. Physical, chemical, and biological treatments have been used for cyanide remediation; however, none of them meet all the desired characteristics: efficiency, low cost and low environmental impact. A better understanding of metabolic pathways and biochemistry of enzymes involved in cyanide degradation is a necessary step to improve cyanide bioremediation efficacy to satisfy the industry requirements. Here, we used several approaches to explore this topic. We have isolated three cyanide-degrading Bacillus strains from water in contact with mine tailings from Lima, Peru, and classified them as Bacillus safensis PER-URP-08, Bacillus licheniformis PER-URP-12, and Bacillus subtilis PER-URP-17 based on 16S rRNA gene sequencing and core genome analyses. Additionally, core genome analyses of 132 publicly available genomes of Bacillus pumilus group including B. safensis and B. altitudinis allowed us to reclassify some strains and identify two strains that did not match with any known species of the Bacillus pumilus group. We searched for possible routes of cyanide-degradation in the genomes of these three strains and identified putative B. licheniformis PER-URP-12 and B. subtilis PER-URP-17 rhodaneses and B. safensis PER-URP-08 cyanide dihydratase (CynD) sequences possibly involved cyanide degradation. We identified characteristic C-terminal residues that differentiate CynD from B. pumilus and B. safensis, and showed that, differently from CynD from B. pumilus C1, recombinant CynD from the Bacillus safensis PER-URP-08 strain remains active up to pH 9 and presents a distinct oligomerization pattern at pH 8 and 9. Moreover, transcripts of B. safensis PER-URP-08 CynD (CynDPER-URP-08) are strongly induced in the presence of cyanide. Our results warrant further investigation of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tools for cyanide-bioremediation.

microbiology↗
bioRxiv2021

Comparative genomics of Xylella fastidiosa suggests determinants of host-specificity and expands its mobile genetic elements repertoire

The Gram-negative bacterium Xylella fastidiosa colonizes plant xylem vessels and is obligately vectored by xylem sap-feeding hemipteran insects. X. fastidiosa causes diseases in many plant species but in a variety of its plant hosts this bacterium behaves as a commensal endophyte. Originally confined to the Americas, infecting mainly grapevine, citrus and coffee plants, X. fastidiosa has spread to several plant species in Europe, causing devastating crop diseases. Although many pathogenicity and virulence factors have been identified in X. fastidiosa which enable the bacterium to successfully establish in the xylem tissue, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in specific plant hosts have not been fully elucidated. Here we present comparative analyses of 94 publicly available whole-genome sequences of X. fastidiosa strains with the goal of providing insights into plant host specificity determinants for this phytopathogen as well as of expanding the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results revealed a pangenome of 4,549 protein coding sequences (CDSs) which is still open. The core- and accessory genomes comprise 954 and 2,219 CDSs, respectively. Phylogenetic tree construction using all core genome CDSs grouped the strains in three major clades of subspecies fastidiosa, multiplex and pauca, with subclades related to the strains sequence type (ST) obtained from multi-locus sequence typing (MLST). The geographic region where the strains were collected showed stronger association with the clades of X. fastidiosa strains rather than the plant species from which they were isolated. Among the CDS related to virulence and pathogenicity found in the core genome, those related to lipopolysaccharide (LPS) synthesis and trimeric autotransporter adhesins (TAA) are somewhat related with the plant host of a given strain according to phylogenetic inference. The X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, which includes a diversity of prophage regions. In summary, the genome comparisons reported here will enable a better understanding of the diversity of phylogenetically close genomes and warrant further investigation of LPS and TAAs as potential X. fastidiosa host-specificity determinants. Impact statementThe bacterium Xylella fastidiosa is a pathogen that infects many plant species and has caused devastating diseases in grapevine, citrus, coffee, and olive plants. This phytopathogen X. fastidiosa is original from the Americas and has emerged in Europe where it is causing severe economic losses for olive producers, mainly in Italy. Although many pathogenicity and virulence factors have been identified in X. fastidiosa, which enable this bacterium to successfully establish in the xylem vessels network, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in the different plant host species have not been fully elucidated. The comparative analyses of 94 whole-genome sequences from X. fastidiosa strains from diverse hosts and geographic regions provide insights into host specificity determinants for this phytopathogen as well as expand the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results contribute for a better understanding of the diversity of phylogenetically close genomes and warrant further experimental investigation of lipopolysaccharide and trimeric autotransporter adhesins as potential host-specificity determinants for X. fastidiosa. Data summaryAll genomic sequences were accessed from publicly available GenBank RefSeq database at NCBI (National Center for Biotechnology Information). A full listing of NCBI accession numbers for X. fastidiosa strains described in this paper is available in Table S1 (available in the online version of this article).

genomics↗
bioRxiv2021

Plasmodium falciparum Acetyl-CoA Synthetase is essential for parasite intraerythrocytic development and chromatin modification

The malaria parasite Plasmodium falciparum possesses a unique Acetyl-CoA Synthetase (PfACS) which provides acetyl moieties for different metabolic and regulatory cellular pathways. We characterized PfACS and studied its role focusing on epigenetic modifications using the var gene family as reporter genes. For this, mutant lines to modulate plasmodial ACS expression by degron-mediated protein degradation or ribozyme induced transcript decay were created. Additionally, an ACS inhibitor was tested for its effectiveness and specificity in interfering with PfACS. The knockdown of PfACS or its inhibition led to impaired parasite growth. Decreased levels of PfACS also led to differential histone acetylation patterns, altered variant gene expression and concomitantly decreased cytoadherence of infected red blood cells containing knocked-down parasites. Further, ChIP analysis revealed the presence of PfACS in many loci in ring stage parasites, underscoring its involvement in the regulation of chromatin. Due to its significant differences to human ACS, PfACS seems an interesting target for drug development.

microbiology↗
bioRxiv2020

vHULK, a new tool for bacteriophage host prediction based on annotated genomic features and deep neural networks

The experimental determination of a bacteriophage host is a laborious procedure. For this reason, there is a pressing need for reliable computational predictions of bacteriophage hosts in phage research in general and in phage therapy in particular. Here, we present a new program called vHULK for phage host prediction based on 9,504 phage genome features. These features take into account alignment significance scores between predicted-protein sequences in the phage genomes and a curated database of viral protein families. The features were fed to a deep neural network, and four distinct models were trained to predict 61 different host genera and 52 host species. In random controlled test sets, the program obtained 99% and 98% accuracy values at the genus and species levels, respectively. On a validation dataset with 2,178 phage genomes, mean accuracies were 82% and 52% at the genus and species levels, respectively. When compared against other phage host prediction programs on the same validation dataset, vHULK achieved substantially better performance, therefore demonstrating that the program is an advance on the state-of-art in phage host prediction. vHULK is freely available at https://github.com/LaboratorioBioinformatica/vHULK.

bioinformatics↗
bioRxiv2020

Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life

Assessing the phylogenetic compatibility between individual gene families is a crucial and often computationally demanding step in many phylogenomics analyses. Here we describe the Evolutionary Similarity Index (IES) to assess shared evolution between gene families using a weighted Orthogonal Distance Regression applied to sequence distances. This approach allows for straightforward pairing of paralogs between co-evolving gene families without resorting to multiple tests, or a priori assumptions of molecular interactions between protein products from assessed genes. The utilization of pairwise distance matrices, while less informative than phylogenetic trees, circumvents error-prone comparisons between trees whose topologies are inherently uncertain. Analyses of simulated gene family evolution datasets showed that IES was more accurate and less susceptible to noise than popular tree-based methods (Robinson-Foulds and geodesic distance) for assessing evolutionary signal compatibility, since it bypasses phylogenetic reconstruction and its inherent uncertainty. Applying IES to a real dataset of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends. Four of these clusters included genes with a taxonomic distribution across all archaeal phyla, while other clusters included a subset of taxa that do not map to generally accepted archaeal clades, indicating possible shared horizontal transfers by clustered gene families. We identify one strongly connected set of 62 genes from the same cluster, occurring as both single-copy and multiple homologs per genome, with compatible phylogenetic reconstructions closely matching previously published species trees for Archaea. An IES implementation is available at https://github.com/lthiberiol/evolSimIndex.

evolutionary biology↗
bioRxiv2019

Global distribution and evolution of Mycobacterium bovis lineages

Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. Previous studies suggested the existence of genetic groups of M. bovis strains based on limited DNA markers (a.k.a. clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced two wildlife M. bovis strains, gathering 823 genomes from 21 countries and 21 host-species, including humans, to complete a phylogenomic analyses. We propose the existence of four distinct global lineages of M. bovis (Lb1, Lb2, Lb3 and Lb4) underlying the current disease distribution. These lineages are not fully represented by clonal complexes and are dispersed based on geographic location rather than host species. Our data divergence analysis agreed with previous studies reporting independent archeological data of ancient M. bovis [(South Siberian infected skeletons at [~]2,000 years BP (before present)] and indicates that extant M. bovis originated during the Roman period, subsequently dispersing across the world with the discovery and settlement of the New World and Oceania, directly influenced by trades among countries.

genetics↗
bioRxiv2019

Identification and characterization of putative Aeromonas spp. T3SS effectors

The genetic determinants of bacterial pathogenicity are highly variable between species and strains. However, a factor that is commonly associated with virulent Gram-negative bacteria, including many Aeromonas spp., is the type 3 secretion system (T3SS), which is used to inject effector proteins into target eukaryotic cells. In this study, we developed a bioinformatics pipeline to identify T3SS effector proteins, applied this approach to the genomes of 105 Aeromonas strains isolated from environmental, mutualistic, or pathogenic contexts and evaluated the cytotoxicity of the identified effectors through their heterologous expression in yeast. The developed pipeline uses a two-step approach, where candidate families are initially selected using HMM profiles with minimal similarity scores against the Virulence Factors DataBase (VFDB), followed by strict comparisons against positive and negative control datasets, greatly reducing the number of false positives. Using our approach, we identified 21 Aeromonas T3SS likely effector groups, of which 8 represented known or characterized effectors, while the remaining 13 had not previously been described in Aeromonas. We experimentally validated our in silico findings by assessing the cytotoxicity of representative effectors in Saccharomyces cerevisiae BY4741, with 15 out of 21 assayed proteins eliciting a cytotoxic effect in yeast. The results of this study demonstrate the utility of our approach, combining a novel in silico search method with in vivo experimental validation, and will be useful in future research aimed at identifying and authenticating bacterial effector proteins from other genera.

microbiology↗
bioRxiv2017

Panaconda: Application of pan-synteny graph models to genome content analysis

MotivationWhole-genome alignment and pan-genome analysis are useful tools in understanding the similarities and differences of many genomes in an evolutionary context. Here we introduce the concept of pan-synteny graphs, an analysis method that combines elements of both to represent conservation and change of multiple prokaryotic genomes at an architectural level. Pan-synteny graphs represent a reference free approach for the comparison of many genomes and allows for the identification of synteny, insertion, deletion, replacement, inversion, recombination, missed assembly joins, evolutionary hotspots, and reference based scaffolding.\n\nResultsWe present an algorithm for creating whole genome multiple sequence comparisons and a model for representing the similarities and differences among sequences as a graph of syntenic gene families. As part of the pan-synteny graph creation, we first create a de Bruijn graph. Instead of the alphabet of nucleotides commonly used in genome assembly, we use an alphabet of gene families. This de Bruijn graph is then processed to create the pan-synteny graph. Our approach is novel in that it explicitly controls how regions from the same sequence and genome are aligned and generates a graph in which all sequences are fully represented as paths. This method harnesses previous computation involved in protein family calculation to speed up the creation of whole genome alignment for many genomes. We provide the software suite Panaconda, for the calculation of pan-synteny graphs given annotation input, and an implementation of methods for their layout and visualization.\n\nAvailabilityPanaconda is available at https://github.com/aswarren/pangenome_graphs and datasets used in examples are available at https://github.com/aswarren/pangenome_examples\n\nContactAndrew Warren anwarren@vt.edu

bioinformatics↗