Biology subjects

da Silva, J. M. C.

Publications and source records attributed to da Silva, J. M. C..

12 recordsLinked to original sources

bioRxiv2025

Transcriptional Signatures of Field Cancerization in Gastric Cancer

The high rate of local recurrence in gastric adenocarcinoma (GA) suggests that carcinogenesis is not a focal event but a field-wide process. This phenomenon, known as "field cancerization," posits that histologically normal peritumoral tissue is, in fact, a pre-neoplastic field harboring incipient molecular alterations that confound genomic studies using it as a normal control. To overcome this limitation, we performed a three-way comparative transcriptomic analysis of tumor, peritumoral, and true-normal gastric tissues using a deep learning framework. We identified a stable 138-gene signature established within the peritumoral field and conserved in the tumor, which was absent in healthy controls. Within this signature, three key COSMIC-listed driver genes were highlighted: the Hippo pathway component FAT4 and the p53-inhibitor MDM4 were upregulated, while the EMT-suppressor NDRG1 was repressed. Co-expression analysis revealed a dynamic rewiring of these drivers, with a significant positive correlation between FAT4 and MDM4 emerging exclusively in the peritumoral field. In contrast, a negative correlation between FAT4 and NDRG1 was observed specifically in the tumor context. In public cohorts, high expression of FAT4 and MDM4 was significantly associated with poor patient prognosis, whereas NDRG1 showed no prognostic association. Critically, the prognostic power of MDM4 was validated in our local patient cohort. Our findings demonstrate that the peritumoral field is a molecularly distinct state in gastric carcinogenesis, characterized by a metabolic shift, and identify FAT4 and MDM4 as key drivers of this early transition, with significant potential as prognostic biomarkers.

genetics↗

bioRxiv2025

Dietary Patterns and Gene Expression Profiles in Gastric Adenocarcinoma Patients from the Northern Region of Brazil

BackgroundGastric adenocarcinoma (GA) remains a major public health concern worldwide, with incidence influenced by demographic, socioeconomic, and lifestyle factors. Diet is a modifiable risk factor that can shape tumor biology, potentially affecting gene expression and the tumor microenvironment. Understanding how dietary patterns correlate with molecular signatures in GA may provide insights for preventive and therapeutic strategies. MethodsThis retrospective, cross-sectional, analytical study included 60 patients diagnosed with gastric adenocarcinoma and treated at the Joao de Barros Barreto University Hospital, Para, Brazil. Structured questionnaires collected sociodemographic, lifestyle (smoking and alcohol), clinical, and dietary data. Dietary patterns were analyzed according to the Brazilian Ministry of Health guidelines. A subset of 16 patients was selected for gene expression profiling to evaluate correlations between dietary exposure and molecular alterations. ResultsThe patient cohort exhibited a predominance of males (56.7%) and older adults (>60 years), often from socioeconomically disadvantaged backgrounds. Dietary analysis revealed insufficient intake of fruits, vegetables, and legumes, alongside high consumption of ultraprocessed foods, especially sugar-sweetened beverages. Gene expression analysis identified 48 differentially expressed genes between patients with lower (LEDRF) and higher (HEDRF) dietary risk exposure. Six genes with potential biological relevance were highlighted: MAGEA3, IL6, HCAR2, NLRP4, PGA3, and CTCFL. MEFDR patients showed overexpression of MAGEA3, IL6, and HCAR2, associated with cell proliferation, inflammation, and tumor microenvironment remodeling. DiscussionThe results suggest that dietary patterns may modulate gene expression and influence the tumor microenvironment in gastric adenocarcinoma. Diets rich in ultraprocessed foods and sugar may promote a pro-inflammatory and pro-oxidant microenvironment, while consumption of fruits, vegetables, and bioactive compounds appears protective, potentially regulating epigenetic, metabolic, and immunological pathways. The study underscores the importance of integrated approaches combining nutritional intervention and molecular profiling to better understand GA progression and identify potential therapeutic targets.

cancer biology↗

bioRxiv2025

Cancer-Testis Antigens as Clinical and Prognostic Biomarkers in Gastric Adenocarcinoma: Integration of Differential Expression, Clinical Associations, Survival, and Co-Expression Networks

Gastric adenocarcinoma (GAC) remains one of the leading causes of cancer-related mortality, characterized by marked molecular and clinical heterogeneity, which underscores the need for robust biomarkers. In this study, we aimed to evaluate the role of cancer-testis antigens (CTAs) in GAC through integrated analyses of differential expression, clinical associations, survival impact, and gene co-expression networks. The cohort included 156 patients with complete clinical data, comprising a total of 362 tissue samples (tumor, peritumoral, and metaplastic). We identified 541 differentially expressed genes, of which 49 corresponded to previously described CTAs. Between GAC and peritumoral tissues, 14 CTAs exhibited significant differential expression, with MAGEA3, MAGEA6, GOLGA6L1, and MAGEA2 among the most highly expressed in tumors. Relevant associations were observed between the expression of MAGEA3, MAGEA6, POTEF, and CTCFL with TNM staging, as well as IGF2BP1, DAZ1/3/4, YBX2, and PCDHA4 in relation to variables such as tumor depth, metastasis, and TCGA subtypes. Survival analysis demonstrated that high expression of IGF2BP1, CTCFL, CT45A5, and LIN28B was strongly associated with worse prognosis (HR > 2.7), whereas SYCE1L, PIK3R3, and ZNF683 showed a protective effect. The co-expression network revealed five main clusters, highlighting germline-related modules (MAGEA, DAZ, CSAG), adhesion and transcriptional regulation (YBX2, POTEF, PCDHA, TAF1L), and immune-related genes (IRAK3, CXCR1, PIK3R3), evidencing functional integration between proliferation, adhesion, and immune microenvironment modulation. Collectively, these findings reinforce CTAs as potential clinical and prognostic biomarkers in GAC, with direct implications for risk stratification and the development of personalized therapeutic strategies.

cancer biology↗

bioRxiv2025

Transcriptomic Mutational Profiling of Gastric Adenocarcinoma in Northern Brazil

Gastric cancer (GC) remains among the neoplasms with the worst prognosis, partly due to its biological heterogeneity and the scarcity of robust biomarkers. The characterization of mutational profiles from transcripts can reveal specific tumor signatures and point to therapeutic targets. This study investigated the landscape of mutations expressed in 102 samples of gastric adenocarcinoma from northern Brazil, which were sequenced using NGS. Readings were aligned to the reference genome using STAR (two-pass mode), and variants were called with GATK and VarDict. Annotations and impact predictions were generated using VEP, SIFT, and PolyPhen. We identified >90,000 variants; among the most frequently mutated genes, FTH1 stood out. The mutational profile was described using maftools, and signatures were inferred with MutationalPatterns. We observed a predominant distribution of SNVs, with C>T transitions as the most common event, in addition to patterns compatible with signatures related to replication damage and DNA repair. To mitigate biases inherent to RNA-seq, we applied filters for coverage, strand bias, and RNA editing hotspots. Together, the data outline a regional landscape of mutations expressed in GC and reinforce the usefulness of the transcriptome for prioritizing biomarkers and functional hypotheses that may guide genomic validations and subsequent clinical studies.

bioinformatics↗

bioRxiv2025

Interspecies Functional Divergence: The Microbiome's Role in FLOT Response e Across Gastric Cancer Subtypes

BackgroundGastric adenocarcinoma exhibits marked molecular and histological heterogeneity, which is reflected in distinct patterns of progression, therapeutic response, and prognosis. Although the FLOT regimen (5-fluorouracil, leucovorin, oxaliplatin, and docetaxel) represents the current standard for perioperative chemotherapy, its systemic effects on the tumor microenvironment, including the associated bacterial microbiome and host gene expression, remain poorly understood. MethodsThis study investigated the effects of FLOT on the functional and ecological structure of intestinal and diffuse subtype gastric tumors by assessing its simultaneous influence on the human transcriptome, the bacterial transcriptome, and inter-kingdom interactions. We analyzed 55 tumor samples (37 intestinal subtype; 18 diffuse subtype) and explored potential genetic-functional interactions between the bacterial microbiome and the human genome. ResultsThe results reveal a highly specific functional pattern in the diffuse subtype, absent in the intestinal subtype, demonstrating a unique ecological-transcriptional plasticity mediated by the microbiota under chemotherapeutic pressure. The interaction network was dominated by high-magnitude positive correlations. Notably, the bacterial gene leuS showed a robust association with the human gene HCN1 and processes such as potassium ion transmembrane transport, membrane depolarization, and regulation of postsynaptic membrane potential, indicating a coordinated activation of ion channels and neuroepithelial circuits. Bacterial species including Bacteroides uniformis, Faecalibacterium prausnitzii, Butyrivibrio crossotus, Prevotella copri, and Simiaoa sunii also converged functionally on HCN1. Additionally, bacterial genes mfd, nifJ, secY, rplF, and tet(Q) were associated with pathways related to cell adhesion, epithelial proliferation, membrane potential control, and synaptic transduction. DiscussionIntegrative analysis reveals that the FLOT regimen acts as a systemic remodeler of the gastric tumor microenvironment, exerting distinct effects according to the histological subtype. While the intestinal subtype responds more aligned with the cytotoxic goals of chemotherapy, the diffuse subtype exhibits a functional plasticity that favors the emergence of adaptive and possibly pro-tumoral phenotypes. We propose a mechanistic model where in chemotherapy selectively reshapes the microbial ecosystem, which in turn modulates host functional circuits, directly influencing tumor behavior. These findings open perspectives for combined therapeutic strategies that include targeted modulation of the microbiome as an adjuvant to chemotherapy.

cancer biology↗

bioRxiv2025

MOLECULAR STRATIFICATION OF INTESTINAL AND DIFFUSE SUBTYPES OF GASTRIC ADENOCARCINOMA AND ITS PROGNOSTIC IMPACT

Gastric adenocarcinoma is routinely classified by Lauren histology into Intestinal and Diffuse types; however, its prognostic use is limited by molecular heterogeneity within each subtype. We tested whether transcriptomic features refine risk beyond histology and whether biomarker signals generalize across populations. The premise is that when underlying programs diverge across tumors and cohorts, a single biomarker is unlikely to be universally informative; accordingly, integrating molecular signatures with histology may improve risk stratification. We analyzed TCGA-STAD and GTEx gene expression data for discovery and validated the findings in ACRG. Cell-program markers guided unsupervised clustering, and a predictive signature was learned using recursive feature elimination with a random forest and cross-validation. Pathway context was assessed with GSEA, and clinical relevance was evaluated within each Lauren subtype. Clustering of canonical gastric and intestinal programs yielded two molecular clusters that did not explain survival. However, Diffuse tumors with stronger intestinal-like programs tended to experience better outcomes. Consistently, the derived signature was associated closely with Lauren categories and defined two molecular groups. Nevertheless, neither histology nor the signature alone stratified overall survival at conventional thresholds. Moreover, gene-level survival analyses indicated subtype specificity rather than universality. In TCGA, 28 signature genes were associated with overall survival (P < 0.05; HR, 0.79-1.63). ROC analyses for Lauren typing were heterogeneous, with CRLF1 achieving an AUC of 0.92, followed by CYP1B1 and MMRN2. ACRG gene expression revealed an inversion of the TCGA pattern, with prognostic risk shifting toward the Diffuse subtype. Specifically, CRLF1, ERG, and FRZB shifted from Intestinal risk to Diffuse risk, while CDX1 shifted from Intestinal to Diffuse protection. Taken together, these findings suggest that the utility of biomarkers in gastric cancer depends on histology and the population context. Consequently, a contextual strategy that integrates molecular signatures with the Lauren classification has the potential to improve risk stratification beyond either source alone.

genomics↗

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

Integrated Expression Analysis of C-MYC Oncogene-Associated Pathways in Gastric Adenocarcinoma and its Correlation with Clinicopathological Factors

BackgroundThe C-MYC oncogene is a well-established driver of gastric carcinogenesis, yet the integrated expression pattern of its complex regulatory network and its clinical implications in gastric adenocarcinoma (GAC) remain to be fully elucidated. This study aimed to perform an integrated bioinformatic analysis of C-MYC and its associated pathways in a cohort of GAC patients to delineate its expression profile, assess its potential as a biomarker, and correlate its patterns with clinicopathological factors such as Lauren classification and neoadjuvant treatment status. MethodsThe study included transcriptome data from 74 GAC tumor samples and 68 normal gastric tissue samples. Following RNA sequencing, a comprehensive bioinformatic analysis was conducted on a curated list of 21 C-MYC-associated genes. The methodology included differential expression analysis (DESeq2), unsupervised hierarchical clustering, Principal Component Analysis (PCA), and Receiver Operating Characteristic (ROC) curve analysis to evaluate diagnostic performance. Gene expression levels were also statistically correlated with Lauren histological subtypes and neoadjuvant therapy status using the Wilcoxon rank-sum test. ResultsThe analysis revealed a profound dysregulation of the C-MYC network in GAC. While MYC itself was significantly upregulated, its transcriptional antagonists, particularly MXD4 and MXD3, were the most significantly downregulated genes. This gene signature robustly separated tumor from normal tissues in both hierarchical clustering and PCA. ROC analysis demonstrated the outstanding diagnostic potential of several genes, with MXD4 achieving a perfect Area Under the Curve (AUC) of 1.00, surpassing the diagnostic value of MYC (AUC=0.86). Stratification by Lauren classification showed that MYC and its stability regulator PTBP1 were significantly more expressed in the intestinal subtype, whereas the repressors MXD3 and MXI1 were higher in the diffuse subtype. No significant expression differences were observed based on neoadjuvant treatment status. ConclusionGastric adenocarcinoma is characterized by a coordinated dysregulation of the C-MYC network, marked by both oncogene activation and a concurrent loss of its key transcriptional repressors. The profound downregulation of antagonists like MXD4 serves as an exceptionally accurate molecular signature for GAC, suggesting its potential as a diagnostic biomarker superior to MYC alone. The divergent expression patterns between Lauren subtypes highlight distinct molecular pathobiology and may have implications for targeted therapies

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↗

bioRxiv2025

Molecular Insights into ANPEP in Gastric Adenocarcinoma

Alanyl aminopeptidase (ANPEP) has been implicated in various cancers, but its specific role in gastric adenocarcinoma (GC) remains incompletely understood. This study analyzed ANPEP gene expression in gastric cancer (GC), peritumoral tissue (PTT), metaplasia (M), and normal tissue (N). Total RNA was extracted, libraries were prepared and sequenced on the Illumina NextSeq 500. Data was processed using the nf-core/rnaseq pipeline. Transcript quantifications were imported with tximport and normalized using DESeq2. Differential expression (|log2FC| >2; adj. p < 0.05) and Kruskal-Wallis tests identified key genes. ANPEP was significantly upregulated in GC, PTT, and M compared to normal tissue (p < 0.01), suggesting its involvement in early mucosal transformation and malignant progression. Heatmap analysis revealed upregulation of genes related to immune function and oxidative stress, indicating an immunosuppressive and apoptosis-resistant tumor microenvironment. Correlation analyses identified strong positive associations between ANPEP and genes involved in cytoskeletal remodeling, immune modulation, and metabolic regulation, suggesting that ANPEP supports both the invasive potential of tumor cells and the establishment of an immunosuppressive niche. These findings position ANPEP as a promising biomarker for early detection and a candidate for targeted therapies.

cancer biology↗

bioRxiv2025

EXPRESSION INSIGHTS INTO GASTRIC ADENOCARCINOMA: NETWORK ANALYSIS REVEALS KEY HUB GENES AND FUNCTIONAL MODULES

Gastric cancer remains a leading cause of cancer-related mortality worldwide, with poor survival rates. To uncover its molecular basis, we performed weighted gene coexpression network analysis on RNA-seq data from 119 gastric adenocarcinoma (GAC) and peritumoral tissue (PTT) samples. We identified six key coexpression modules: MEmagenta, MEbrown, MEgreen, and MEturquoise showed strong positive correlations with GAC, whereas MEblack and MEblue were negatively correlated. Hub genes such as COL3A1, PGAM1, and CFL1 were among the most highly expressed in GAC samples compared to PTT. ROC analyses of selected hub genes yielded AUC values exceeding 0.80 for distinguishing GAC from PTT, underscoring their diagnostic potential. Integrating cellular deconvolution with module expression revealed that MEblack hub genes (TFF1, TFF2, GKN1, GKN2 and MUCL3) correlated positively with B-cell abundance and negatively with resting mast cells and neutrophils. Conversely, MEturquoise hub genes (COL1A2, COL3A1, TAGLN and SPARC) correlated strongly with Cance Associated Fibroblasts and inversely with B-cells, reflecting a collagen-rich stroma. We also observed overlapping expression profiles between GAC and PTT, indicating tumor heterogeneity and a molecular continuum between normal and neoplastic tissues. These integrated insights highlight candidate biomarkers and in GAC.

genomics↗

bioRxiv2025

Immune Remodeling and Dysbiosis May Distinguish the Microenvironments of Gastric Adenocarcinoma and Peritumoral Tissue

The gastric tumor microenvironment is dynamically shaped by the interactions between the local microbiota and the host immune system, although the functional integration of these elements remains incompletely understood. In this study, we characterized microbial diversity, immune cell composition, and immune-related gene expression profiles in samples of gastric adenocarcinoma (GAC) and adjacent peritumoral tissue (PTT), aiming to elucidate their functional organization. A total of 106 samples of 75 patients were analyzed using bulk RNA-Seq expression profiling, immune deconvolution, and bacterial taxonomic reconstruction. While alpha diversity remained preserved between GAC and PTT, distinct compositional differences emerged: GAC was enriched with Pseudomonadota, Enterobacteriaceae, and Escherichia, whereas PTT exhibited a predominance of Helicobacteraceae and Helicobacter. Immune deconvolution revealed an expansion of cancer-associated fibroblasts (CAFs) and mast cells in GAC, correlated with higher expression levels of TGFB1 and FOXP3, while neutrophils and B cells predominated in PTT. Integrated analysis demonstrated that GAC formed dense and cohesive networks connecting pro-inflammatory bacteria, activated immune cells, and inflammatory genes such as IL1B, CXCL8, and IFNG. In contrast, PTT exhibited dispersed networks and negative correlations, suggesting a less structured, tolerogenic environment. Our findings indicate that gastric cancer progression involves not only compositional shifts in microbiota and immune cells but also the active construction of functionally integrated inflammatory networks, providing new insights into potential therapeutic targets at the microbiome-immune interface.

genetics↗