Molecular Oncology最新文献

Gene expression is tightly controlled by DNA elements called enhancers by associating with lineage-specific transcription factors. These enhancers transcribe noncoding RNAs (called enhancer RNAs or eRNAs). eRNA expression is an early indicator of transcription factor activity and is associated with treatment response and survival in cancer patients. By analysing ~ 300 000 eRNA loci profiled using RNA-sequencing data sets from 975 breast cancer patients using machine learning approaches, we categorised eRNAs specific to breast cancer molecular subtypes and survival. We associated these eRNAs with subtype-specific mRNAs to define proximal co-expressed regulatory eRNAs (ProxCReAm), which are enriched in pathways characteristic of their respective subtypes. Interestingly, cistrome and transcription factor motif analyses on these eRNAs highlighted involvement of diverse nuclear receptors (GR/AHR for luminal and GR/RAR for basal) and FOX factors in luminal regions. Moreover, luminal eRNAs were associated with better outcomes and Her2 eRNAs with worse outcomes in patients. Overall, we demonstrate that machine learning approaches performed on RNA-seq data sets can classify functionally relevant subtype-specific and prognostic eRNAs, which can identify critical gene pathways and transcription factor networks in breast cancer.

The c-Myc protein is a well-known oncoprotein that plays a crucial role in regulating cell growth, proliferation, and differentiation. The overexpression or dysregulation of c-Myc is commonly associated with tumorigenesis in several cancers, including colorectal cancer (CRC). c-Myc forms a heterodimer with its partner MAX to activate the expression of various genes. Here, we synthesized a novel c-Myc-targeting small molecule, 2,2'-((cyclohexylazanedyl)bis(methylene))bis(4-ethylphenol), or ECD, and demonstrate ECD's anticancer activity via interference with the c-Myc/MAX dimer to promote c-Myc degradation in CRC cells in vitro, in silico, and in vivo. This study revealed the activity of ECD toward CRC cells as a c-Myc inhibitor. Computer-aided analysis revealed that the effect of ECD was mediated through disturbance of the c-Myc/MAX complex. Moreover, ECD exhibited cytotoxic activity by inducing DNA damage, leading to apoptotic cell death. This DNA damage-inducing property was also confirmed by whole-proteome profiling of HT29 cells after ECD treatment. In the chick embryo chorioallantoic membrane (CAM) xenograft assay, we demonstrated a remarkable inhibition of the tumorigenic activity upon ECD exposure. In summary, we identified ECD as a novel potent compound targeting the oncoprotein c-Myc that may offer new opportunities for CRC treatment.

Liquid biopsies containing circulating tumor DNA (ctDNA) are important biomarkers across several forms of cancer. The detection of mutations in cell-free DNA (cfDNA) indicates the presence of ctDNA. However, unsatisfactory ctDNA mutation sensitivities, issues with sequencing errors, and clonal hematopoiesis variants have limited the clinical utility of mutation-based ctDNA assays. Recently, a new avenue of cfDNA assays has been developed, focusing on cfDNA epigenetics. Here, we outline the recent advancements in cfDNA epigenetics, focusing on cfDNA methylation, fragmentomics, and post-translational modifications (PTMs) of circulating nucleosomes. We present various methylation strategies concerning ctDNA detection and tissue of origin (TOO) analyses. cfDNA fragmentomics focuses on cfDNA fragment lengths, fragment end motifs, and nucleosome positioning to infer gene expression and estimate the ctDNA fraction. Lastly, we discuss the development of cell-free chromatin immunoprecipitation of circulating nucleosomes with PTMs. This method has been implemented to detect tumor gene expression, TOO, and treatment resistance. Combining the epigenetic features of cfDNA will expand the utility of liquid biopsies to give a more comprehensive insight into tumor biology, treatment response, and resistance.

Bladder cancer incidence has recently risen, making it the ninth most diagnosed cancer, highlighting an urgent need for novel and effective diagnostic and therapeutic strategies to improve patient outcomes. Here, we report on a secreted glycoprotein, Galectin-3-binding protein (LGALS3BP), as a potential biomarker and therapeutic target for bladder cancer. We found a significantly elevated LGALS3BP expression in bladder cancer tissues, correlating with disease progression. Moreover, urinary and serum levels of LGALS3BP were significantly higher in patients compared to healthy individuals, with a strong correlation observed between elevated urinary protein levels and tumor grade. Of note, LGALS3BP produced by tumor cells treated with a mannosidase I inhibitor, Kifunensine, exhibited increased reactivity to a therapeutic antibody (denoted as "1959"), suggesting that glycosylation of LGALS3BP may influence antibody recognition and protein function. Furthermore, administration of 1959-sss/DM4 antibody-drug conjugate in two xenograft mouse models of human bladder cancer resulted in complete inhibition of tumor growth. In summary, findings presented here highlight LGALS3BP as a promising candidate for further investigation into its potential as a urinary biomarker and a therapeutic target for bladder cancer.

Epigenetic plasticity and large-scale chromatin remodeling characterize tumor evolution and the emergence of subclones resistant to conventional therapies. Catalytically inactive class IIa HDACs (HDAC4, HDAC5, HDAC7, HDAC9) control the targeted recruitment of chromatin remodeling complexes, making them attractive therapeutic targets in oncology. In this study, we found that HDAC4 is degraded by the proteasome in cancer cells with impaired DNA repair by homologous recombination and after oxaliplatin (OXPT) treatment. Genetic screening identified FBXW7 as the E3 ligase responsible for HDAC4 degradation. FBXW7 loss-of-function mutations are frequently found in patients with colorectal cancer (CRC) and were found associated with the development of resistance to OXPT. Forced degradation of Class IIa HDACs using a PROTAC-based compound restored OXPT sensitivity in FBXW7-mutated CRC cells, patient-derived organoids (PDOs), and mice. Mechanistically, removal of HDAC4 in FBXW7-mutated CRC treated with OXPT recreated an epigenetic state comparable to OXPT-sensitive cells. Furthermore, patient profiling based on the epigenetic state of the super-enhancers controlled by HDAC4 successfully identified a priori CRC patients resistant to platinum. This study supports HDAC4 as a key mediator of oxaliplatin resistance in FBXW7-mutated CRC and highlights the remodeling of a well-defined super-enhancer repertoire as part of the process of OXPT resensitization.

Transcriptional heterogeneity in pancreatic ductal adenocarcinoma (PDAC) arises not only from changes in gene expression but also from dynamic rewiring of gene-gene coordination. Using a divergent-edge framework applied to 77 155 malignant cells from 42 tumors, we identified four reproducible adaptive modules-integrated growth-energy (IGE), stress-adaptive transcription (SAT), IL-2-linked immune evasion (IL2), and multi-pathway collective invasion (MPC)-that cut across canonical PDAC states and reflect distinct regulatory programs. Integrating these modules with CRISPR-Cas9 dependency profiles and PRISM drug-response data revealed that adaptive behaviors collapse into two higher-order axes: a biosynthetic-metabolic IGE axis enriched for translational and DNA-repair dependencies, and a broader SAT-IL2-MPC stress-immune-invasion axis characterized by proteostasis, cytokine-linked, and cytoskeletal vulnerabilities. This architecture emerges only when divergent-edge modules are mapped into functional genomics space. Module activity also carried clinical relevance in PDAC. SAT-high tumors showed poorer survival, while MPC-high tumors exhibited a similar adverse trend; together, these modules defined a stress-immune-invasion poor-prognosis axis. In contrast, IGE activity showed no overall risk association, although an optimal-cut point-defined IGE-high subgroup displayed modestly improved survival.

The detection of actionable mutations in liquid biopsies is a crucial tool for precision oncology in patients with non-small-cell lung cancer (NSCLC). We evaluated actionable alterations using a multigene panel in circulating tumor DNA (ctDNA) from Brazilian NSCLC patients. We analyzed 32 samples from 30 patients with NSCLC, including four samples from a lung cancer screening program. ctDNA isolation and library preparation were performed using the Oncomine Lung cfDNA Assay, which covers 11 actionable genes, and sequenced on an Ion S5 Sequencer. The IonReporter 5.20 software was used for variant calling. Median read coverage reached 80 967, with a detection limit of 0.1%. TP53 (40.6%), KRAS (28.1%), and EGFR (12.5%) were the most frequently mutated genes, particularly in patients who had previously received treatment. BRAF, MAP2K1, PIK3CA, and ALK mutations were observed at lower frequencies (6.2%, 3.1%, 3.1%, and 3.1%, respectively). The EGFR p.T790M mutations related to resistance were identified in a patient who had been previously treated, and the TP53 p.R248Q mutation was discovered in an asymptomatic patient before diagnosis. No variants were observed in NRAS, ROS1, and MET genes. Our data showed that this commercial NGS panel could detect actionable mutations, enabling early detection, treatment monitoring, and disease surveillance.

Genetic testing in epithelial ovarian cancer (EOC) in Ontario includes germline next-generation sequencing (NGS) for 19 genes. Additionally, tumor tissue undergoes reflex NGS testing for BRCA1/2 to assess eligibility for PARPi. Although parallel testing confers advantages, this model duplicates healthcare resources. Here, we prospectively assessed the feasibility of tumor-first multigene testing by comparing tumor tissue with germline testing of peripheral blood. An 18-gene NGS panel was used to test tumor and germline DNA (n = 106 patients). In 26 patients, 27 tumor Tier I or II variants were identified, with 16/27 (59%) being germline pathogenic variants (PV) (13 BRCA1/2; 3 other genes) and 11/27 (41%) somatic variants (9 BRCA1/2; 2 other). In 51/106 patients, there were no tumor variants (excluding TP53), of which one patient had a germline BRCA1 copy number variant deletion in exon 12. Tumor-first testing detected variant-positive and variant-negative germline cases in 105/106 patients (99.1%). Among 50 BRCA-negative patients, 14/50 (28%) were homologous recombination deficiency (HRD)-positive. Therefore, we demonstrate that multigene NGS tumor-testing is effective in identifying germline variants in EOC with a < 1% false-negative rate.

The vasculature and the immune system both play roles in breast cancer progression and metastasis. In an experimental mouse model of Shb-gene deficiency in endothelial cells, breast cancer lung metastasis correlated with immune suppression rather than with vascular leakage. The present study aimed to assess underlying gene expression changes in endothelial and immune cells responsible for this phenotype and to explore their relationship to human disease. Mouse endothelial cell Shb-gene deficiency, leading to 'vessel normalization', resulted in altered expression of chemo/cytokine genes and upregulation of immune checkpoint genes in immune cells. Endothelial cells under these conditions exhibited gene expression patterns compatible with reduced angiogenesis and vascular leakage. Additionally, genes whose products relate to immune cell vascular transmigration and function were affected. In a human triple-negative breast cancer cohort, tumors with reduced vascular leakage exhibited a higher relative proportion of regulatory T cells and larger tumor size. However, these changes were not associated with increased metastasis. In conclusion, a low leakage vascular phenotype reduces tumor cell intravasation/metastasis and modifies the immune response, which in the current context becomes pro-tumoral.

Hepatic fibrogenesis is characterized by the excessive accumulation of extracellular matrix proteins, ultimately predisposing to hepatocarcinogenesis. The lack of reliable models that faithfully recapitulate early stage fibrogenesis is one of the main limitations in identifying translationally relevant therapeutics. Here, we establish a model using CRISPR/Cas9-mediated TP53 knockout iPSC (endoderm)-derived human hepatic organoids (eHEPOs) to mimic human liver fibrosis. Transcriptomic profiling of TP53KO-eHEPOs revealed enrichment of pathways associated with inflammation, ECM remodeling, and fibrosis, with notable alterations in pivotal fibrotic regulators. We also find increased expression of myofibroblasts and fibrosis markers (PDGFRB, COL1A1, COL3A1, COL11A1) and early liver cancer markers (GPC3 and MUC1). Histological analysis confirmed advanced fibrotic hallmarks and exposure to an exogenous profibrotic environment (pf-ME) further enhanced these fibrotic phenotypes. This model provides a valuable platform for exploring the role of key driver genes, such as TP53, in the initiation and progression of fibrosis, enabling the study of hepatic progenitor cell transformation across diverse microenvironmental contexts. As such, it holds the potential for advancing early stage drug discovery and the identification of novel therapeutic targets for the treatment of liver fibrosis.