Abstract

Abstract
Background: Aberrant or loss of cell adhesion drives invasion and metastasis, key hallmarks of cancer progression. In this work, we hypothesized that a gene signature related to cell adhesion could predict breast cancer prognosis. Methods: Highly variant genes were tested for association with overall survival using Cox regression. Adhesion-related genes were identified through gene ontology analysis and multivariate Cox regression, with AIC selection, defined the prognostic signature. The AdhesionScore was then calculated as a weighted sum of gene expression, with risk stratification assessed by Kaplan-Meier and log-rank tests. Results: We found that the AdhesionScore was a significant independent predictor of poor survival in three large independent datasets, as it provided a robust stratification of patient prognosis in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (HR: 2.65; 95% CI: 2.33-3.0, p = 2.34 x 10-51), The Cancer Genome Atlas (TCGA) (HR: 3.46; 95% CI: 2.35-5.09, p = 3.50 x 10-10), and the GSE96058 (HR: 2.83; 95% CI: 2.20-3.65, p = 6.29 x 10-16) datasets. The 5-year risk of death in the high-risk group was 32.41% for METABRIC, 27.8% for TCGA, and 17.54% for GSE96058 datasets. Consistently, HER2-enriched and triple-negative breast carcinomas (TNBC) cases showed higher AdhesionScores than luminal subtypes, indicating an association with aggressive tumor biology. Conclusions: We have developed, for the first time, a molecular signature based on cell adhesion, as well as an associated AdhesionScore that can predict patient prognosis in invasive breast cancer, with potential clinical application. We developed a novel adhesion-based molecular signature, the AdhesionScore, that robustly predicts prognosis in breast cancer across independent cohorts, highlighting its potential clinical utility for patient risk stratification.

Abstract
Breakthroughs in sequencing technologies led to an exponential growth of genomic data, providing novel biological insights and therapeutic applications. However, analyzing large amounts of sensitive data raises key data privacy concerns, specifically when the information is outsourced to untrusted third-party infrastructures for data storage and processing (e.g., cloud computing). We introduce Gyosa, a secure and privacy-preserving distributed genomic analysis solution. By leveraging trusted execution environments (TEEs), Gyosa allows users to confidentially delegate their GWAS analysis to untrusted infrastructures. Gyosa implements a computation partitioning scheme that reduces the computation done inside the TEEs while safeguarding the users' genomic data privacy. By integrating this security scheme in Glow, Gyosa provides a secure and distributed environment that facilitates diverse GWAS studies. The experimental evaluation validates the applicability and scalability of Gyosa, reinforcing its ability to provide enhanced security guarantees.

Abstract
BackgroundTobacco smoke is the main cause of preventable mortality worldwide. Smoking increases the risk of developing many diseases and has been proposed as an aging accelerator. Yet, the molecular mechanisms driving smoking-related health decline and aging acceleration in most tissues remain unexplored.MethodsHere, we use data from the Genotype-Tissue Expression Project (GTEx) to perform a characterization of the effect of cigarette smoking across human tissues. We perform a multi-tissue analysis across 46 human tissues. Our multi-omics characterization includes analysis of gene expression, alternative splicing, DNA methylation, and histological alterations. We further analyze ex-smoker samples to assess the reversibility of these molecular alterations upon smoking cessation.ResultsWe show that smoking impacts tissue architecture and triggers systemic inflammation. We find that in many tissues, the effects of smoking significantly overlap those of aging. Specifically, both age and smoking upregulate inflammatory genes and drive hypomethylation at enhancers (odds ratio (OR) = 2). In addition, we observe widespread smoking-driven hypermethylation at target regions of the Polycomb repressive complex (OR = 2), which is a well-known aging effect. Smoking-induced epigenetic changes overlap causal aging CpGs, suggesting that these methylation changes may directly mediate the aging acceleration observed in smokers. Finally, we find that smoking effects that are shared with aging are more persistent over time.ConclusionOverall, our multi-tissue and multi-omic analysis of the effects of cigarette smoking provides an extensive characterization of the impact of tobacco smoke across tissues and unravels the molecular mechanisms driving smoking-induced tissue homeostasis decline and aging acceleration.

Abstract
APAtizer is a tool designed to analyze alternative polyadenylation events on RNA-sequencing data. The tool handles different file formats, including BAM, htseq, and DaPars bedGraph files. It provides a user-friendly interface that allows users to generate informative visualizations, including Volcano plots, heatmaps, and gene lists. These outputs allow the user to retrieve useful biological insights such as the occurrence of polyadenylation events when comparing two biological conditions. In addition, it can perform differential gene expression, gene ontology analysis, visualization of Venn diagram intersections, and correlation analysis.