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- AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicryPublication . Baptista, Delora; Gomez-Lucas, Lídia; Jänes, Jürgen; Krogan, Nevan J.; Amorim, Maria João; Ivarsson, Ylva; Beltrão, PedroPathogens exploit host cellular machinery through protein-protein interactions (PPIs), often using molecular mimicry to hijack host cellular processes. While there have been thousands of host-pathogen PPIs determined to date, the lack of structural information for these impedes the study of the prevalence of molecular mimicry and convergent evolution of protein interaction interfaces. To address this, we benchmarked AlphaFold2 and 3 for prediction of structures of host-pathogen interactions observing that accurate models can be retrieved when ranking by modelling confidence, despite an overall low performance. We predicted structures for 6,782 pathogen-human PPIs yielding 803 models of higher confidence. Most pathogen proteins interacting with a common human protein are predicted to do so via the same interface, suggesting a high degree of convergent evolution of protein interaction interfaces. When comparing structural models from host-pathogen and host-host interactions, we observe that a majority of pathogen proteins are predicted to target existing human PPI interfaces. We categorized instances of mimicry into different modes, occurring at different frequencies: 1) via the same domain family (least common); 2) via a similar structural motif; and 3) via a similar linear motif (most common). We selected examples of linear motif interactions for binding assay testing, confirming 8 out of 12 predicted interfaces, including 3 viral linear motif interactions. This validates AlphaFolds ability to model some host-pathogen interactions and the mechanisms underlying molecular mimicry. This work showcases the value of large-scale structural modelling to study convergent evolution of host-pathogen interactions and how molecular mimicry may contribute to infection or host defense.
- Climate-driven spatiotemporal dynamics of Aedes infestation and dengue transmission in Porto Alegre, Southern Brazil.Publication . Silva, Adryan Aparecido da; Ferreira, Álvaro Gil Araujo; Lourenco, José; Freitas, Amanda Cupertino deDengue transmission is strongly influenced by climatic conditions that affect mosquito population dynamics and virus circulation. In Southern Brazil, where dengue historically occurred at low levels, recent climatic anomalies may be contributing to the expansion of Aedes vectors and an increase in local dengue incidence. This study investigated the spatiotemporal association between climatic variables, Aedes mosquito infestation and dengue cases in Porto Alegre (Southern Brazil, 2018 to 2025). Entomological, surveillance and climatic data were analyzed using Morans I and LISA for spatial association, Kendall correlation, polynomial regression and LASSO to identify relevant drivers and develop predictive models of mosquito infestation and dengue incidence. A strong spatial association between Aedes aegypti and Aedes albopictus was observed, with persistent local clusters detected across all years. Annual climatic variables were associated with mosquito abundance in several districts. Overall, rainfall frequency had a stronger effect on Aedes aegypti abundance than accumulated rainfall. Temperature and lagged infestation indices showed strong association with both species and dengue incidence, with effects observed up to four weeks prior. Predictive models demonstrated good agreement between observed and predicted values, particularly within low to moderate infestation levels. Lagged variables were consistently retained in both mosquito infestation abundance and dengue incidence models, highlighting the importance of temporal predictors for anticipating vector dynamics and dengue risk. This approach is generally applicable for predicting Aedes infestation and disease incidence and emphasizes the importance of integrating entomological and climatic surveillance data to improve anticipation and detection of dengue risk periods and support more effective public health interventions. Author summaryDengue is a viral disease transmitted by mosquitos that affects millions of people worldwide. Its spread is strongly influenced by climatic conditions that modulate mosquito life cycles. In Southern Brazil, where dengue historically occurred at low levels, recent climate variability and extreme weather events may be creating favorable conditions for the expansion of Aedes mosquitos and local dengue activity. In this study, we analyzed mosquito, dengue, and climatic surveil in Porto Alegre, Brazil, from 2018 to 2025 to understand how climate influences mosquito infestation and dengue incidence. We found that mosquito infestation and dengue cases show clear spatial patterns across the city and are strongly influenced by temperature and rainfall. Interestingly, the number of rainy days had a stronger effect on mosquito abundance than the total amount of rainfall. We also observed that higher mosquito infestation was associated with an increase in dengue cases up to four weeks later. These findings show that combining climatic and mosquito surveillance data can help anticipate periods of higher dengue risk and support more effective mosquito control and public health actions.
- Direct suppression of host gluconeogenesis by Trypanosoma bruceiPublication . Figueiredo, Luísa M.; Amin, Abdulbasit; Colaço, João; Machado, Henrique; Nunes-Cabaço, Helena; Trindade, Sandra; Scherer, Philipp; Pereira, Sara SilvaThe cause of hypoglycaemia in African trypanosomiasis remains unresolved. We found that infected mice show normal carbohydrate digestion, intestinal glucose absorption, and tissue glucose uptake, but a profound reduction of host glucose production via gluconeogenesis. Liver transcriptomics uncovered coordinated repression of gluconeogenic pathways alongside inflammatory activation. Infection of Rag2⁻/⁻ mice showed that adaptive immunity contributes only minimally to suppression of host gluconeogenesis. In contrast, therapeutic parasite clearance completely restored host glycaemia and gluconeogenesis despite persistent immune activation. These results demonstrate that live parasites directly repress gluconeogenesis in vivo. Using a co-culture assay, we showed that T. brucei is sufficient to directly repress gluconeogenic gene expression in primary hepatocytes in vitro. Finally, we found that providing glycerol in drinking water to infected animals stimulated gluconeogenesis, elevated glycaemia, and improved survival without impacting parasitaemia. This study reveals a previously unrecognised pathogenic strategy in which a eukaryotic parasite directly suppresses host gluconeogenesis.
- A 3D tumor-on-a-chip platform to identify drugs that block breast cancer cell intravasationPublication . Perera, Narmada; Coutinho, Diogo; Morais, Carolina; Faria, Maria; Neto, Raquel; Roman, William; Gomes, E. R.; Franco, Cláudio A.; Costa, Luís; Barata, David; Serre, Karine; Dias, Sérgio; Magalhães, AnaMetastasis is the leading cause of death in breast cancer patients, yet there are no drugs specifically designed to block cancer cell intravasation, an early step of the metastatic cascade that originates circulating tumour cells (CTCs). A major challenge in developing anti-intravasation drugs is the scarcity of relevant in vitro platforms suitable for predictable drug discovery. Intravasation is a fundamental step of metastasis and involves the crossing of cancer cells through an endothelial barrier to enter the blood circulation. Here we developed an intravasation-on-a-chip model with controlled extracellular matrix composition, fluid flow and shear stress, which mimics the dynamic tumour-endothelium interface. The systems allows real-time imaging of intravasation and the isolation and quantification of intravasated cancer cells. As a proof-of-concept for drug testing, we show that perfusion with the PI3K/mTOR inhibitor Dactolisib, significantly reduced intravasation without compromising endothelial cell viability. The system also provides the capability to evaluate inhibitor on-target activity via imaging analysis. This intravasation-on-a-chip model offers a powerful, scalable, and imaging-compatible platform for discovering and evaluating anti-intravasation compounds.
- The biological clock of multimorbidity: temporal dynamics of disease co-occurrence in primary carePublication . Sánchez-Valle, Jon; Zambrana, Carme; Navarro-Martínez, Alejandro; Costa, Felipe Xavier; Rocha, Luís; Cirillo, Davide; Violán, Concepción; Valencia, AlfonsoMultimorbidity is the dominant clinical reality of primary care, yet the temporal dynamics governing when and how persistent comorbidity associations emerge remain poorly characterised. Most large-scale comorbidity studies adopt a single observation window after an index diagnosis, implicitly assuming that associations detectable at one year are equally detectable at five. Using 11 years of electronic health records from 5,821,197 individuals in Catalan primary care, we applied a matched cohort design across nine complementary follow-up windows – five cumulative (0-1 to 0-5 years) and four conditional (1-2 to 4-5 years) – to 1,315 index diseases, identifying 144,030 significant directed comorbidity associations in the five-year network. We found that 60.1% of these associations required at least three years of follow-up and were undetectable in shorter-window analyses, demonstrating that observation window length is a primary determinant of which comorbidities can be observed. To organise this temporal heterogeneity, we introduce the biological clock of multimorbidity: a twodimensional framework that positions ICD-10 disease categories according to their rates of cumulative signal attenuation and the persistence of conditional risk. This framework identifies four reproducible temporal patterns (episodic, chronic stable, chronic progressive, and transient-persistent) that are robust under bootstrap resampling, leave-one-disease-out sensitivity analysis, and alternative clustering approaches. The biological clock is systematically modulated by sex, with Blood/Immune and Musculoskeletal disorders showing the largest sex differences in temporal dynamics. Network analysis identified 19 disease "initiators" that generate broad downstream comorbidity burdens and 21 "sinks" representing convergent endpoints of multiple disease trajectories. Comparison with hospital-based Danish data from 6,909,676 individuals showed that shared associations were 2.7-fold enriched over chance expectation (hypergeometric test, p<10-300) and showed moderate concordance of effect sizes (Spearman ρ=0.460), confirming that the comorbidity structure identified here reflects genuine, generalisable signal; nonetheless, only 3.6% of primary care associations were replicated in the hospital network, indicating that the two settings capture largely complementary segments of the disease co-occurrence landscape. Together, these findings establish the observation window length as a principal design parameter in EHR-based multimorbidity research and the biological clock as a framework for understanding how and over what timescale disease associations emerge, persist, and resolve.
- TTF2 prevents premature rRNA synthesis during mitotic exitPublication . Pedro, Catarina; Tovini, Laura; Peneda, Catarina; Krapinec, Mia Maesano; Oliveira, Raquel A.Mitosis poses major challenges to cellular transcription. As cells enter mitosis, transcription is globally silenced and must be precisely restored upon mitotic exit. These processes are primarily regulated by Cdk1-dependent phosphorylation. In parallel, additional mechanisms, including Transcription Termination Factor 2 (TTF2)-mediated removal of nascent transcripts, reinforce transcriptional shutdown. How these layers of regulation control individual RNA polymerases and influence transcriptional reactivation at mitotic exit remains poorly understood. Here, we probed how TTF2 differentially controls transcription of distinct RNA classes, using polymerase-specific perturbations and nascent RNA labelling across mitosis. Loss of TTF2 led to accumulation of chromatin-associated transcripts during metaphase, predominantly RNA Polymerase II–derived, consistent with its established role in transcriptional clearance. More unexpectedly, TTF2 depletion caused premature RNA Polymerase I reactivation during anaphase, resulting in unscheduled rRNA synthesis and early recruitment of nucleolar proteins. These findings place TTF2 as a novel regulator of RNA Polymerase I reactivation at mitotic exit. Disruption of this control persists beyond mitosis, resulting in increased nucleolar fragmentation in interphase. Together, these findings reveal TTF2 as a conserved regulator that interfaces with multiple RNA polymerases through functionally distinct modes of control, coordinating both transcriptional shutdown and timely reactivation across mitosis.
- Distance backbones optimize spreading dynamics and centrality ranks in the sparsification of complex networksPublication . Pereira, Bernardo; Costa, Felipe Xavier; Rocha, Luís M.Detailed network models of social, biological and other complex systems are often dense, which increases their computational complexity in simulations and analysis. To address this challenge, graph sparsification is used to remove edges while preserving desired network properties. Distance backbones of weighted graphs, which remove edges that break a generalized triangle inequality for any given path-length measure, preserve all shortest paths of weighted graphs. They have been shown to typically sparsify graphs more, as well as preserve community structure and spreading dynamics better than alternative state-of-the-art methods. Here, We show that they significantly best preserve node centrality ranks, as well as local and global dynamics in spreading phenomena. This is done by introducing the distance backbone synthesis (DBS) to progressively sparsify weighted graphs according to a general family of nested distance backbones, whereby each edge is associated with the smallest distance backbone in which it appears. DBS provides a principled and natural method to sweep all degrees of sparsification possible while preserving connectivity, allowing us to precisely study (directed and undirected) weighted graph sparsification under multi-objective criteria. It provides an algebraically-principled explanation of edge importance by revealing the precise topological space associated with each edge. The theory is demonstrated with a battery of social contact networks obtained from real-world social activity in different scenarios. Our study also shows that the optimal preservation of node centrality and spreading dynamics happens for the distance backbone obeying the generalized triangle inequality for the path-length measure g(x, y) = (?3 x + ?3 y) 3 , which removes more than half of the edges from the empirical networks studied.
- Removal of nascent transcripts by TTF2 is required for efficient sister chromatid resolution in human cellsPublication . Tovini, Laura; Milagre, Inês; Peneda, Catarina; Oliveira, Raquel A.During mitosis, chromosome assembly is accompanied by a global shutdown of transcriptional activity. However, the contribution of mitotic transcriptional silencing to mitotic fidelity and genome stability remains poorly understood. Here, we used depletion of the Transcription Termination Factor 2 (TTF2) – a key factor in mitotic transcriptional inactivation – to investigate the impact of pervasive transcription on mitotic fidelity. TTF2 depletion leads to the accumulation of elongating transcripts on mitotic chromatin and triggers a spectrum of mitotic defects, including abnormal chromosome alignment, delayed progression, and impaired chromosome compaction. Among these, defects in sister chromatid resolution are particularly prominent, with DNA bridges emerging as the major segregation error and resulting in increased micronuclei formation. We further show that these defects are linked to changes in chromatin organisation, including R-loops accumulation. Importantly, most anaphase defects are significantly suppressed when transcription is chemically inhibited, establishing a causal link between transcriptional engagement during mitosis and the observed mitotic defects. Our findings reveal how abnormal retention of transcriptional activity on mitotic chromatin disrupts multiple mitotic processes, with impaired sister chromatid resolution representing a key pathway linking transcriptional dysregulation to genome instability.
- Pervasive relaxed selection on spermatogenesis genes coincident with the evolution of polygyny in gorillasPublication . Bowman, Jacob D.; Silva, Neide; Schüftan, Erik; Almeida, Joana M.; Brattig-Correia, Rion; Oliveira, Raquel A.; Tüttelmann, Frank; Enard, David; Navarro-Costa, Paulo; Lynch, VincentGorillas have a polygynous social system in which the highest-ranking male has almost exclusive access to females and sires most of the offspring in the troop. Such behavior results in a dramatic reduction of sperm competition, which is ultimately associated with numerous traits that cause low efficacy of gorilla spermatogenesis. However, the molecular basis behind the remarkable erosion of the gorilla male reproductive system remains unknown. Here, we explored the genetic consequences of the polygynous social system in gorillas by testing for altered selection intensity across 13,310 orthologous protein-coding genes from 261 Eutherian mammals. We identified 578 genes with relaxed purifying selection in the gorilla lineage, compared with only 96 that were positively selected. Genes under relaxed purifying selection in gorillas have accumulated numerous deleterious amino acid substitutions, their expression is biased towards male germ cells, and are enriched in functions related to meiosis and sperm biology. We tested the function of gorilla relaxed genes previously not implicated in sperm biology using the Drosophila model system and identified 41 novel spermatogenesis genes required for normal fertility. Furthermore, by exploring exome/genome sequencing data of infertile men with severe spermatogenic impairment, we found that the human orthologs of the gorilla relaxed genes are enriched for loss-of-function variants in infertile men. These data provide compelling evidence that reduced sperm competition in gorillas is associated with relaxed purifying selection on genes related to male reproductive function. The accumulation of deleterious mutations in these genes likely provides the mechanistic basis behind the low efficacy of gorilla spermatogenesis and uncovers new candidate genes for human male infertility.
- Sex-specific transcriptome similarity networks elucidate comorbidity relationshipsPublication . Sánchez-Valle, Jon; Flores-Rodero, María; Costa, Felipe Xavier; Carbonell-Caballero, Jose; Núñez-Carpintero, Iker; Tabarés-Seisdedos, Rafael; Rocha, Luis Mateus; Cirillo, Davide; Valencia, AlfonsoHumans present sex-driven biological differences. Consequently, the prevalence of analyzing specific diseases and comorbidities differs between the sexes, directly impacting patients’ management and treatment. Despite its relevance and the growing evidence of said differences across numerous diseases (with 4,370 PubMed results published within the past year), knowledge at the comorbidity level remains limited. In fact, to date, no study has attempted to identify the biological processes altered differently in women and men, promoting differences in comorbidities. To shed light on this problem, we analyze expression data for more than 100 diseases from public repositories, analyzing each sex independently. We calculate similarities between differential expression profiles by disease pairs and find that 13-16% of transcriptomically similar disease pairs are sex-specific. By comparing these results with epidemiological evidence, we recapitulate 53-60% of known comorbidities distinctly described for men and women, finding sex-specific transcriptomic similarities between sex-specific comorbid diseases. The analysis of shared underlying pathways shows that diseases can co-occur in men and women by altering alternative biological processes. Finally, we identify different drugs differentially associated with comorbid diseases depending on patients’ sex, highlighting the need to consider this relevant variable in the administration of drugs due to their possible influence on comorbidities.