Explore the vast range of titles available.

Background Recent studies have highlighted the importance of the cell-free DNA (cfDNA) methylation profile in detecting breast cancer (BC) and its different subtypes. We investigated whether plasma cfDNA methylation, using cell-free Methylated DNA Immunoprecipitation and High-Throughput Sequencing (cfMeDIP-seq), may be informative in characterizing breast cancer in patients with BRCA1/2 germline mutations for early cancer detection and response to therapy. Methods We enrolled 23 BC patients with germline mutation of BRCA1 and BRCA2 genes, 19 healthy controls without BRCA1/2 mutation, and two healthy individuals who carried BRCA1/2 mutations. Blood samples were collected for all study subjects at the diagnosis, and plasma was isolated by centrifugation. Cell-free DNA was extracted from 1 mL of plasma, and cfMeDIP-seq was performed for each sample. Shallow whole genome sequencing was performed on the immuno-precipitated samples. Then, the differentially methylated 300-bp regions (DMRs) between 25 BRCA germline mutation carriers and 19 non-carriers were identified. DMRs were compared with tumor-specific regions from public datasets to perform an unbiased analysis. Finally, two statistical classifiers were trained based on the GLMnet and random forest model to evaluate if the identified DMRs could discriminate BRCA-positive from healthy samples. Results We identified 7,095 hypermethylated and 212 hypomethylated regions in 25 BRCA germline mutation carriers compared to 19 controls. These regions discriminate tumors from healthy samples with high accuracy and sensitivity. We show that the circulating tumor DNA of BRCA1/2 mutant breast cancers is characterized by the hypomethylation of genes involved in DNA repair and cell cycle. We uncovered the TFs associated with these DRMs and identified that proteins of the Erythroblast Transformation Specific (ETS) family are particularly active in the hypermethylated regions. Finally, we assessed that these regions could discriminate between BRCA positives from healthy samples with an AUC of 0.95, a sensitivity of 88%, and a specificity of 94.74%. Conclusions Our study emphasizes the importance of tumor cell-derived DNA methylation in BC, reporting a different methylation profile between patients carrying mutations in BRCA1, BRCA2, and wild-type controls. Our minimally invasive approach could allow early cancer diagnosis, assessment of minimal residual disease, and monitoring of response to therapy.

Background Microsatellite instability (MSI) is a well-established predictive biomarker for immune checkpoint inhibitor (ICI) response in metastatic colon cancer. Both high MSI and tumor mutational burden (TMB) are markers of genomic instability. However, the prognostic and predictive value of TMB in patients with microsatellite stable (MSS) tumors remains unclear. Methods We evaluated the prognostic significance of TMB levels in MSS metastatic colon cancer patients undergoing standard treatments. Tumor responses were assessed using RECIST v1.1 criteria. Comprehensive clinical and molecular profiling was conducted, including next-generation sequencing (NGS) for TMB evaluation with the TruSight Oncology® kit. Overall survival (OS) was the primary endpoint. Multivariate Cox regression analysis was utilized to assess the relationship among potential prognostic factors. Results Among 102 MSS metastatic colon cancer patients, high TMB (> 10 mut/mb) was associated with a significantly longer median OS compared to low TMB (70.0 vs 45.0 months, respectively; HR: 0.45; 95% CIs 0.21 to 0.96; P = 0.0396). Multivariate analysis, adjusting for age, gender, number of metastatic sites, response to first-line chemotherapy, RAS mutational status, and liver involvement, identified TMB as an independent prognostic factor, along with response to first-line chemotherapy. Conclusions Our results highlight the prognostic significance of TMB in MSS metastatic colon cancer patients, suggesting its potential role in patient stratification and treatment decision-making.

Background DNA mutations are the fundamental engines of cancer, driving its initiation and progression. The forces that fuel malignancy are also the architects of evolution, shaping life through genetic variations. Mutations, in fact, can emerge naturally from endogenous processes, such as oxidative DNA damage or errors in replication, as well as induced by external factors, including cosmic radiation and chemical carcinogens. Main body A key question in cancer research is whether tumor evolution is primarily governed by selective bottlenecks, neutral evolution, or dynamic genetic plasticity. In this work, we examine cancer as a disease driven by evolutionary processes rooted in fundamental biological requirements, including sustained proliferation and nutrient utilization. We hypothesize that the accumulation of mutations activates an evolutionary switch, enabling tumor cells to acquire an enhanced capacity for survival, adaptation, and growth at rates far exceeding typical evolutionary timescales. We propose the “evolutionary cascade hypothesis,” a unifying framework that integrates these models into a coherent sequence. At its core lies the failure of DNA repair mechanisms, representing a critical transition in cancer progression. This shift marks the transition from an initial non-Darwinian, neutral phase to a Darwinian, more deterministic phase. Conclusions As predictive models of tumor evolution advance through genomic big data and artificial intelligence-driven analysis, the future of cancer treatment may extend beyond targeting individual mutations to disrupting the underlying evolutionary mechanisms that sustain malignancy. This paradigm shift could redefine therapeutic strategies and ultimately improve patient outcomes.

Background Glioblastoma (GBM) is the most common, aggressive and poor prognosis malignant brain tumor in adults, that is still orphan of effective medical treatments. The formyl peptide receptor 2 (FPR2), a G protein– coupled receptor implicated in inflammation and cancer biology, has emerged as a potential therapeutic target, yet its role in GBM remains poorly defined. Methods We investigated the effects of MR-39, a novel selective FPR2 agonist, in three human GBM cell lines (U87MG, U138-MG, U251-MG). Antiproliferative effects were assessed via CCK-8 assays, cell counts, Ki67 immunostaining, and cell cycle analysis. The specificity of MR-39 was tested using the FPR2 antagonist WRW4 and siRNA-mediated knockdown. Whole-transcriptome analysis, RT-qPCR, Western Blot, woundhealing assays, in vitro tube formation assay, and hypoxia models were used to explore its impact on invasion, angiogenesis, and hypoxia-driven pathways. Results MR-39 significantly reduced proliferation in all GBM cell lines and induced a non-canonical, p53dependent S-phase arrest associated with the inhibition of both MAPK/ERK and AKT pathways. These effects were reversed by the FPR2 antagonist WRW4 or by FPR2 silencing. Transcriptomic and functional assays revealed downregulation of epithelial-to-mesenchymal transition (EMT) drivers, including Neuralcadherin (N-cadherin), Snail Family Transcriptional Repressor 2 (Slug), Snail Family Transcriptional Repressor 1 (Snail), matrix metalloproteinase-2 (MMP2), fibronectin 1 (FN1), and increased Epithelialcadherin (E-cadherin) expression, resulting in impaired migration. MR-39 displays anti-angiogenic and anti-hypoxia related activities, indeed it is able to inhibit Vascular Endothelial Growth Factor (VEGF) and Vascular Endothelial-cadherin (VE-cadherin) expression, to disrupt endothelial network formation, and to attenuate Hypoxia Inducible Factor 1 Subunit Alpha (HIF-1α) stabilization under hypoxic conditions. Notably, MR-39 exhibited significant anti-inflammatory effects, as evidenced by the downregulation of pro-inflammatory genes, including Cyclooxygenase 2 (COX-2), Chemokine (C-X-C Motif) Ligand 7. (CXCL-7), Nuclear Factor Kappa B Subunit 1 (NFKB1), Interleukin 1 Beta (IL-1β), and Interleukin 6 (IL6), and the inhibition of NF-κB protein levels. Conclusion This study identifies MR-39 as a potent modulator of FPR2, and identifies its mechanisms of action in GBM, such as anti-tumor activity, including S-phase arrest, inhibition of EMT, and suppression of both angiogenesis and hypoxic adaptation. By directing FPR2 signaling toward an anti-tumor profile, MR-39 represents a promising therapeutic candidate for GBM.

Background TAS-102 (Lonsurf ® ) is an oral fluoropyrimidine consisting of a combination of trifluridine (a thymidine analog) and tipiracil (a thymidine phosphorylation inhibitor). The drug is effective in metastatic colorectal cancer (mCRC) patients refractory to fluorouracil, irinotecan and oxaliplatin. This study is a real-world analysis, investigating the interplay of genotype/phenotype in relation to TAS-102 sensitivity. Methods Forty-seven consecutive mCRC patients were treated with TAS-102 at the National Cancer Institute of Naples from March 2019 to March 2021, at a dosage of 35 mg/m 2 , twice a day, in cycles of 28 days (from day 1 to 5 and from day 8 to 12). Clinical-pathological parameters were described. Activity was evaluated with RECIST criteria (v1.1) and toxicity with NCI-CTC (v5.0). Survival was depicted through the Kaplan-Meyer curves. Genetic features of patients were evaluated with Next Generation Sequencing (NGS) through the Illumina NovaSeq 6000 platform and TruSigt™Oncology 500 kit. Results Median age of patients was 65 years (range: 46–77). Forty-one patients had 2 or more metastatic sites and 38 patients underwent to more than 2 previous lines of therapies. ECOG (Eastern Cooperative Oncology Group) Performance Status (PS) was 2 in 19 patients. The median number of TAS-102 cycles was 4 (range: 2–12). The most frequent toxic event was neutropenia (G3/G4 in 16 patients). There were no severe (> 3) non-haematological toxicities or treatment-related deaths. Twenty-six patients experienced progressive disease (PD), 21 stable disease (SD). Three patients with long-lasting disease control (DC: complete, partial responses or stable disease) shared an FGFR4 (p.Gly388Arg) mutation. Patients experiencing DC had more frequently a low tumour growth rate ( P  = 0.0306) and an FGFR4 p.G388R variant ( P  < 0.0001). The FGFR4 Arg388 genotype was associated with better survival (median: 6.4 months) compared to the Gly388 genotype (median: 4 months); the HR was 0.25 (95% CI 0.12- 0.51; P = 0.0001 at Log-Rank test). Conclusions This phenotype/genotype investigation suggests that the FGFR4 p.G388R variant may serve as a new marker for identifying patients who are responsive to TAS-102. A mechanistic hypothesis is proposed to interpret these findings. Graphical Abstract

Background Exosomes are nanosized vesicles released from all cells into surrounding biofluids, including cancer cells, and represent a very promising direction in terms of minimally invasive approaches to early disease detection. They carry tumor-specific biological contents such as DNA, RNA, proteins, lipids, and sugars, as well as surface molecules that are able to pinpoint the cellular source. By the above criteria, exosomes may be stratified according to the presence of tissue and disease-specific signatures and, due to their stability in such biofluids as plasma and serum, they represent an indispensable source of vital clinical insights from liquid biopsies, even at the earliest stages of cancer. Therefore, our work aimed to isolate and characterize LCa patients’ derived exosomes from serum by Flow Cytometry in order to define a specific epitope signature exploitable for early diagnosis. Methods Circulating exosomes were collected from serum collected from 30 LCa patients and 20 healthy volunteers by the use of antibody affinity method exploiting CD63 specific surface marker. Membrane epitopes were then characterized by Flow cytometry multiplex analysis and compared between LCa Patients and Healthy donors. Clinical data were also matched to obtain statistical correlation. Results A distinct overexpression of CD1c, CD2, CD3, CD4, CD11c, CD14, CD20, CD44, CD56, CD105, CD146, and CD209 was identified in LCa patients compared to healthy controls, correlating positively with tumor presence. Conversely, CD24, CD31, and CD40, though not overexpressed in tumor samples, showed a significant correlation with nodal involvement in LCa patients (p < 0.01). Conclusion This approach could allow us to set up a cost-effective and less invasive liquid biopsy protocol from a simple blood collection in order to early diagnose LCa and improve patients’ outcomes and quality of life. Graphical Abstract

Background RAS mutations, present in 40–50% of metastatic colorectal cancer (mCRC) cases, drive oncogenic signaling and confer resistance to anti-EGFR therapies. Tumor mutational burden (TMB), a marker of genomic instability, has recently emerged as a predictive biomarker of response to immunotherapy. However, the prognostic interaction between RAS status and TMB in mCRC remains poorly defined. Patients and methods We analyzed 108 patients with microsatellite-stable metastatic colon cancer (mCC). Tumor samples were profiled using the TruSight Oncology ® platform. Eligible patients had an ECOG Performance Status < 2, a cachexia risk score < 1, and no peritoneal carcinomatosis. TMB and RAS mutation status were assessed, and the prognostic significance of the different RAS /TMB combinations was evaluated for overall survival (OS) using Kaplan–Meier and Cox proportional hazards models. Biological differences across selected subgroups were explored using Gene Ontology (GO) enrichment and Phenolyzer network analyses. Results RAS mutations were associated with reduced OS (46.4 vs. 67.9 months for mutant vs. wild-type; HR 1.76; P  = 0.0495). Stratified analysis showed that the adverse effect of RAS mutations was restricted to patients with low TMB (< 10 mutations/Mb). The subgroup with both RAS mutations and low TMB had the poorest OS (28.0 months; HR 2.34; P  = 0.0058), whereas patients with either RAS wild-type or high TMB showed comparable survival. GO analysis revealed enrichment of receptor-mediated signaling pathways in RAS -mutant/TMB-low tumors. Phenolyzer highlighted distinct molecular networks, with APC , TP53 , and ERBB2 as central hubs in RAS -mutant/TMB-low tumors, and APC , TP53 , and BRCA1 in RAS -wild-type/TMB-high tumors. Conclusions This study demonstrates a prognostic interaction between RAS mutations and TMB in mCC, identifying the RAS -mutant/TMB-low subgroup as having the poorest outcomes. Integrative bioinformatic analyses suggest distinct biological mechanisms underlying these differences. These findings support the development of tailored therapeutic and monitoring strategies for specific molecular subgroups. Graphical Abstract

The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus   bromii , associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches. A large, publicly available dataset integrating RNA, whole-exome, T cell receptor and 16S rRNA sequencing from patients with colon cancer enables the discovery of a prognostic score consisting of tumor, immune and microbial features.

TAS-102 (Lonsurf.sup.[R]) is an oral fluoropyrimidine consisting of a combination of trifluridine (a thymidine analog) and tipiracil (a thymidine phosphorylation inhibitor). The drug is effective in metastatic colorectal cancer (mCRC) patients refractory to fluorouracil, irinotecan and oxaliplatin. This study is a real-world analysis, investigating the interplay of genotype/phenotype in relation to TAS-102 sensitivity. Forty-seven consecutive mCRC patients were treated with TAS-102 at the National Cancer Institute of Naples from March 2019 to March 2021, at a dosage of 35 mg/m.sup.2, twice a day, in cycles of 28 days (from day 1 to 5 and from day 8 to 12). Clinical-pathological parameters were described. Activity was evaluated with RECIST criteria (v1.1) and toxicity with NCI-CTC (v5.0). Survival was depicted through the Kaplan-Meyer curves. Genetic features of patients were evaluated with Next Generation Sequencing (NGS) through the Illumina NovaSeq 6000 platform and TruSigt[TM]Oncology 500 kit. Median age of patients was 65 years (range: 46-77). Forty-one patients had 2 or more metastatic sites and 38 patients underwent to more than 2 previous lines of therapies. ECOG (Eastern Cooperative Oncology Group) Performance Status (PS) was 2 in 19 patients. The median number of TAS-102 cycles was 4 (range: 2-12). The most frequent toxic event was neutropenia (G3/G4 in 16 patients). There were no severe (> 3) non-haematological toxicities or treatment-related deaths. Twenty-six patients experienced progressive disease (PD), 21 stable disease (SD). Three patients with long-lasting disease control (DC: complete, partial responses or stable disease) shared an FGFR4 (p.Gly388Arg) mutation. Patients experiencing DC had more frequently a low tumour growth rate (P = 0.0306) and an FGFR4 p.G388R variant (P < 0.0001). The FGFR4 Arg388 genotype was associated with better survival (median: 6.4 months) compared to the Gly388 genotype (median: 4 months); the HR was 0.25 (95% CI 0.12- 0.51; P = 0.0001 at Log-Rank test). This phenotype/genotype investigation suggests that the FGFR4 p.G388R variant may serve as a new marker for identifying patients who are responsive to TAS-102. A mechanistic hypothesis is proposed to interpret these findings.