Biology subjects

Ramos, S. A. A.

Publications and source records attributed to Ramos, S. A. A..

3 recordsLinked to original sources

bioRxiv2025

FERROPTOSIS GENE SIGNATURES REVEAL DISTINCT REGULATORY LANDSCAPES IN GASTRIC ADENOCARCINOMA AND OTHER TISSUES

BackgroundGastric adenocarcinoma (GAC) remains one of the most lethal malignancies worldwide, with late-stage diagnosis and limited therapeutic options. Ferroptosis, a regulated form of cell death driven by iron-dependent lipid peroxidation, has emerged as a promising target for overcoming tumor resistance mechanisms. This study aimed to characterize the transcriptional landscape of ferroptosis-related genes in GAC, comparing tumor, peritumoral, metaplastic, and normal gastric tissues. MethodsRNA-Seq was performed on 385 biopsied samples from patients treated at the Joao de Barros Barreto University Hospital. Differential expression analysis was conducted using DESeq2, and genes related to ferroptosis were identified based on FerrDb V2 annotations. Visualization included volcano plots, DAPC clustering, heatmaps, and gene dominance scoring. ResultsGAC samples showed a distinct ferroptotic expression signature, with simultaneous upregulation of key promoters (e.g., CDKN2A, NOX4, EGFR, IL6) and suppressors (e.g., HSPB1, SCD, NUPR1, GDF15). Notably, the tumor tissue exhibited a net dominance of ferroptosis-inhibitory genes, suggesting an adaptive response to oxidative stress. Adjacent tissues showed partial overlap with tumor profiles, while metaplastic tissue displayed a hybrid signature with selective suppression of ferroptosis. Normal mucosa exhibited dominant expression of promoters, contrasting with the tumors anti-ferroptotic phenotype. ConclusionThe transcriptional heterogeneity and regulatory imbalance of ferroptosis-related genes in GAC support its role as a potential therapeutic axis. These findings provide molecular insights for biomarker discovery and ferroptosis-targeted strategies in gastric cancer.

cancer biology↗

bioRxiv2025

Viral Landscape of Gastric Adenocarcinoma Reveals Clinically Relevant Viruses

BackgroundGastric cancer (GC) ranks among the most common and lethal cancers worldwide, with poor prognosis mainly due to late diagnosis. Accumulating evidence highlights the role of the gastric microbiome in carcinogenesis through inflammation, genomic instability, and immune modulation. Unlike the bacterial component, the gastric virome remains largely unexplored despite its potential contribution to tumor development. The present study aimed to characterize the virome present in tumor and peritumoral tissues from patients with GC. Materials and Methods105 tumor and 85 peritumoral gastric tissues were analyzed. RNA was extracted, libraries were prepared, and sequencing was performed on the Illumina NextSeq 500. Viral reads were classified with Kraken2. Taxonomic profiles, viral abundance and diversity metrics were computed in R, with group differences assessed by Wilcoxon tests and PERMANOVA (p < 0.05). ResultsIn this study, 38 viral orders and 329 viral genera were identified in gastric tumor and peritumoral tissues. Tumor tissues harbored 210 viral genera, including 109 exclusive to this microenvironment, with bacteriophages comprising the majority, alongside human-infecting and other eukaryotic viruses. Lymphocryptovirus, Cytomegalovirus, and Alphapapillomavirus were enriched in tumors. Alpha and beta diversity analyses revealed no significant differences between tumor and peritumoral tissues, indicating comparable viral richness and composition. ConclusionThese findings underscore the complexity of the gastric virome and provide a foundation for future investigations into the interactions and mechanisms through which the viral community could influence the development of gastric cancer, highlighting its potential role in gastric health and disease.

genetics↗

bioRxiv2025

Characterization of Human Endogenous Retroviruses in Gastric Cancer with Helicobacter pylori: A Study from Northern Brazil

Human endogenous retroviruses (HERVs) are retroelements that have integrated their genetic material into the human genome, accumulating mutations over time and accounting for approximately 8% of the genome. Under abnormal deregulation conditions, these elements can be expressed and contribute to the development of diseases, such as gastric cancer. This malignancy may be associated with infections, including those caused by Helicobacter pylori. However, the scientific literature does not yet provide clear evidence regarding the relationship between HERVs and H. pylori in the context of gastric cancer. Thus, HERVs may represent potential biomarkers for this neoplasm, as well as possible therapeutic targets. This study aimed to characterize HERV expression in gastric cancer using next-generation sequencing (NGS). We analyzed 46 tumor tissue samples and 42 peritumoral tissue samples from patients diagnosed with gastric adenocarcinoma, collected at HUJBB and Ophir Loyola hospitals. Among the tumor samples, 38 tested positive for H. pylori infection. For library preparation, 1 g of total RNA per sample was used, with integrity assessed via TapeStation ([~]260 bp band). cDNA libraries were sequenced using the Illumina NextSeq 500 platform (paired-end), following the ID Output V2 kit protocol. Alignment was performed with STAR software, and HERVs were identified and quantified using Telescope. Differential expression analysis of HERVs was performed on transcript data using DESeq2. A total of 183 HERVs were found to be differentially expressed in tumor tissues compared to adjacent tissues. In tumor samples associated with H. pylori infection, 44 HERVs showed differential expression. Overall, tumor tissues exhibited higher HERV transcription compared to adjacent tissues.

genetics↗