The intestinal epithelium is a highly regenerative tissue organized along the crypt-villus axis, where spatially compartmentalized gene expression governs stem cell renewal, proliferation, and differentiation. Super-enhancers (SEs) are large clusters of regulatory elements densely bound by transcription factors (TFs) and cofactors that drive high-level expression of genes controlling cell identity and fate, yet their roles in intestinal epithelial identity and differentiation remain unclear. Here, we generate a spatiotemporal map of SEs in the small intestine, identifying compartment-specific SEs that define crypt and villus programs. Using mouse genetic models, we identify CDX2, HNF4, and SMAD4 as core TFs orchestrating SE-driven transcriptional networks essential for epithelial differentiation. CDX2 is required for SE integrity, and its loss causes widespread SE collapse and silencing of intestinal identity genes. We further demonstrate SE remodeling during colorectal cancer, in which HNF4 and SMAD4 function as SE-associated tumor suppressors that restrain oncogenic enhancer programs. Together, our findings establish SEs as central regulators of intestinal architecture, epithelial fidelity, and tumor progression.
The continuous expression of HPV oncogenes E6 and E7 contributes to the maintenance of the cervical cancer (CC) phenotype by altering gene expression programs involved in tumor progression and aggressiveness. MicroRNAs (miRNAs) have emerged as critical regulators of gene expression in CC, including miR-218-5p, which has been described as a tumor suppressor. In this study, we investigated the impact of HPV-16 oncoproteins E6 and E7 on the regulation of miR-218-5p expression and its target gene PIK3C2A, as well as their functional and clinical relevance in CC. We found that miR-218-5p expression is significantly reduced in HPV-16-positive CC cell lines, while PIK3C2A expression is increased. Silencing the expression of the E6/E7 oncogenes in Ca Ski cells restored miR-218-5p levels and reduced PIK3C2A expression. Conversely, overexpression of the E6 and E7 oncogenes in C-33 A cells significantly decreased miR-218-5p expression and increased PIK3C2A expression. Functional assays performed on C-33 A cells expressing E6 and E7 revealed that ectopic expression of miR-218-5p suppresses cell proliferation and migration, effects that are partially mediated by PIK3C2A. Bioinformatics analysis showed that low miR-218-5p expression and high PIK3C2A expression are associated with reduced overall survival in patients with cervical cancer. Our findings identify the miR-218-5p/PIK3C2A axis as a novel regulatory pathway modulated by HPV-16 oncoproteins E6 and E7 that contributes to CC cell proliferation and migration. Furthermore, miR-218-5p and PIK3C2A emerge as potential prognostic biomarkers in CC.
Even though epigenetic factors contribute to oncogenesis, most human cancer models still assume that disease originates from driver DNA mutations. Thus, it is still unclear if non-genetic mechanisms are sufficient to trigger malignant transformation. Special AT-rich binding protein 2 (SATB2) is a chromatin organizer that brings distal DNA elements into close proximity, thus remodeling chromatin structures to reprogram cell-specific and/or developmentally sensitive gene networks. Here, we chronically exposed human bronchial lung epithelial cells to ≤ 2 µM inorganic arsenic, and then used biochemical, molecular, and phenotypic assays to understand how changes in SATB2 expression and chromatin structure relate to oncogenic transformation. We discovered that SATB2 generates a co-expressed circ3915 RNA that can be translated into a peptide that co-localizes with SATB2 in and around the nuclear membrane. Ectopic SATB2 or circ3915 expression rearranged global chromatin accessibility, generated KRAS- and NFE2L2-like oncogenic gene expression patterns, and induced oncogenic phenotypes and KRAS-like transcriptional programs in lung epithelial cells without iAs exposure or engineered driver mutations. SATB2 and circ3915 transcripts persisted through the epithelial-to-mesenchymal transition and were co-regulated in human LUAD and LUSC tumors and adjacent normal tissue. This study shows that transcriptional programs associated with oncogenic pathways can be activated in differentiated mammalian cells without predisposing mutations in oncogenes or epigenetic regulators.
Despite technological advances in radiation therapy (RT), improvements in locoregional control of locally advanced disease remain limited, indicating a plateau in RT effectiveness. It is becoming increasingly clear that RT occurs within a dynamic metabolic microenvironment that merges oncogenic activity with metabolic and immune interactions. This includes responses to oxidative stress, regulation of cell death and survival signals, energy metabolism, protein synthesis, autophagy of molecules and organelles, and ultimately, the anti-tumor immune response. Each tumor, regardless of its histology, maintains a unique molecular and microenvironmental identity that influences its response to RT. Furthermore, RT acts as a cellular stressor that activates responses in cancer and stromal cells, impacting clinical outcomes. The concept of Metabolism and Immunity Adaptive Radiotherapy (M.I.A.R) recognizes that RT success depends not only on radiation dose and distribution but mainly on key interventions that alter and influence the biological environment before, during, and after therapy. It highlights the importance of an initial diagnostic workup, which is achievable with current tools, to identify tumor-specific oncogenes, metabolic, and immune profiles. Within the context of M.I.A.R., effective RT requires tumor preconditioning combined with concurrent use of drugs, including metabolism-targeting agents, to increase tumor sensitivity to radiation. Post-RT metabolic and immune interventions are essential for complete tumor eradication. This involves combining existing oncogene-targeting therapies with available immune treatments, supported by low-toxicity modulating drugs/agents with demonstrated preclinical activity against specific molecular and microenvironmental features. Overall, while MIAR remains a theoretical approach, existing preclinical and recent clinical data, e.g., those exploiting tumor hypoxia and re-oxygenation status, or post-RT immunotherapy, strongly support further dedicated investigation.
Extrachromosomal DNAs (ecDNAs) attach to chromosomes during mitosis for random segregation and promote cancer heterogeneity. However, the mechanism governing ecDNA-chromosome mitotic interactions remains poorly understood. Here we show that ecDNAs tether to histone H3 lysine 27 acetylation (H3K27ac)-marked chromatin during mitosis. Depleting H3K27ac disrupts this interaction. Diverse bromodomain proteins, as H3K27ac readers, stabilize ecDNA-chromosome binding in a context-dependent and complementary manner. Although disrupting the Mediator complex in asynchronous cells detaches ecDNAs from mitotic chromosomes, Mediator and active Pol II are absent from ecDNAs during mitosis, suggesting that ecDNAs are transcriptionally silent during mitosis. Instead, inactive Pol II mediates ecDNA attachment. Furthermore, CRISPR interference targeting transcriptional regulatory elements on ecDNA impairs ecDNA segregation. Mis-segregated ecDNAs were expelled into the cytosol, leading to diminished oncogene expression and a reversal of therapy resistance. Our research provides universal cis and trans regulatory mechanisms of ecDNA segregation, offering deeper insight into ecDNA-driven oncogenesis.
Pregnancy induces adaptations in the maternal immune system, including the liver and spleen, in a gestation-dependent manner. The Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway participates in immune tolerance at the maternal-fetal interface. Nevertheless, whether pregnancy affects the JAK/STAT signaling pathway in the liver and spleen of ewes has remained unclear. In this study, samples of ovine liver and spleen were collected at day 16 of the estrous cycle and at days 13, 16, 25, and 70 of gestation (n = 6 for each group). The expression of JAK/STAT members, including interferon α/β receptor 1 (IFNAR1), JAK1, tyrosine kinase 2 (TYK2), STAT3, interferon regulatory factor 9 (IRF9), B-cell lymphoma-extra large (BCL-XL), BCL-2, myelocytomatosis viral oncogene homolog (c-Myc), and P21 (a protein with a molecular weight of 21 kDa), was analyzed using RT-qPCR, western blotting, and immunohistochemistry. The results revealed that pregnancy enhanced the expression of IFNAR1, JAK1, TYK2, BCL-2, and P21 in the liver and IFNAR1 and P21 in the spleen, but inhibited the expression of STAT3 and BCL-XL in the liver, and JAK1, TYK2, STAT3, IRF9, and BCL-XL in the spleen. In addition, the expression of c-Myc and IRF9 in the liver, and c-Myc and BCL-2 in the spleen was modulated in a pregnancy-stage-specific manner. In summary, pregnancy modulated the expression of JAK/STAT members in maternal liver and spleen in a pregnancy-stage- and tissue-specific manner, which may contribute to the maternal immunotolerance and increases of spleen and liver sizes during gestation.
To analyze the clinicopathological features and long-term outcomes of papillary thyroid carcinoma (PTC) patients with rearranged during transfection (RET) proto-oncogene fusion positive and to explore their genotype-phenotype associations and prognostic significance. A retrospective study was conducted on 828 PTC patients treated at Sun Yat-sen University Cancer Center between January 2018 and December 2020. RET fusions, as well as BRAF and TERT promoter mutations, were primarily detected by quantitative real-time polymerase chain reaction. Demographic, clinicopathological, and follow-up data were obtained and analyzed to identify genotype-specific disease patterns. RET fusions were identified in 64 patients (7.7%). RET fusion-positive patients had a significantly greater proportion of pediatric and adolescent onset (12.5% vs. 0.7%; p < 0.001) and had larger tumors (34.4% vs. 10.1%, p < 0.001), higher rates of lateral cervical lymph node metastasis (64.1% vs. 24.6%, p < 0.001), distant metastasis (14.1% vs. 1.0%, p < 0.001), extrathyroidal extension (23.4% vs. 13.9%, p = 0.037), vascular invasion (17.2% vs. 3.9%, p < 0.001), perineural invasion (17.2% vs. 4.6%, p < 0.001), and extranodal extension (34.4% vs. 4.8%, p < 0.001) than their RET fusion-negative counterparts. The follow-up data indicated a higher rate of disease progression and poorer clinical outcomes in RET fusion-positive patients than in RET fusion-negative patients (21.9% vs. 2.6%, p < 0.001). RET fusion-positive PTC is associated with aggressive clinicopathological behavior and poor prognosis. This study highlights the importance of RET fusion testing in PTC for more accurate risk stratification and personalized therapeutic approaches, particularly for high-risk patients.
Dysregulation of the c-Myc oncogene is a pivotal event in leukemia pathogenesis and therapy resistance. This review synthesizes current evidence, illustrating that c-Myc drives leukemogenesis by enhancing proliferation, inhibiting apoptosis, and upregulating immune checkpoints like PD-L1. Its overexpression is linked to poor treatment outcomes across various leukemia subtypes. Directly targeting c-Myc remains challenging; however, indirect epigenetic modifiers (BET inhibitors), transcriptional disruption (CDK9 inhibitors), and combination therapies emerge as promising strategies to suppress its oncogenic activity and overcome resistance, paving the way for improved clinical management.
Growing evidence suggests that esculetin, a 5-lipoxygenase inhibitor, has pharmacotherapeutic potential due to its various pharmacological properties, such as potent anti-inflammatory, anti-nociceptive, and γ-aminobutyric acid type A (GABAA) receptor partial agonist activities. However, the effects of this promising agent on migraine remain unexplored. This study therefore examined the impact of esculetin on relevant mechanisms in migraine-like conditions in rats. The systemic effects of esculetin at three distinct doses (5, 10, and 20 mg/kg) were tested in a nitroglycerin (NTG)-induced migraine model using in vivo experimental sets. The direct action of esculetin on the release of calcitonin gene-related peptide (CGRP) from critical structures of the trigeminovascular system (trigeminal ganglion, trigeminal nucleus, and meningeal afferents) was also tested in ex vivo experimental sets. Sumatriptan was used as a positive control in both sets of experiments. The in vivo results showed that esculetin reduced NTG-induced mechanical hyperalgesia and decreased trigeminal CGRP and cellular Fos proto-oncogene (c-Fos) levels. It also decreased degranulation and meningeal mast cell numbers. The ex vivo results revealed that esculetin reduced NTG-stimulated CGRP release from trigeminovascular explants, with the exception of meningeal explants. Sumatriptan reversed the NTG-induced changes in both experimental sets. Our findings suggest that esculetin exhibits anti-nociceptive activities in experimental migraine conditions, alleviating trigeminovascular CGRP concentrations and the degranulation of meningeal mast cells. Esculetin may thus represent a therapeutic option for relieving migraine headaches, although further research is needed to confirm this. 越来越多的证据表明，秦皮乙素作为一种5-脂氧合酶抑制剂，因其具有强效抗炎、抗伤害感受及γ-氨基丁酸A型（GABAA）受体部分激动活性等多种药理学特性，而显示出药物治疗潜力。然而，其对偏头痛的治疗效果仍有待探索。因此，本研究探讨了秦皮乙素在大鼠偏头痛样状态下相关机制的影响。通过体内实验测试了三种不同剂量（5、10和20 mg/kg）的秦皮乙素在硝酸甘油（NTG）诱导的偏头痛模型中的全身性效应;同时，通过体外实验检测了其对三叉神经血管系统关键结构（三叉神经节、三叉神经核以及脑膜传入神经）释放降钙素基因相关肽（CGRP）的直接作用。两组实验均以舒马普坦为阳性对照。体内实验结果显示，秦皮乙素减轻了NTG诱导的机械性痛觉过敏，降低了三叉神经CGRP和c-Fos表达水平，并减少了脑膜肥大细胞脱颗粒和数量;体外实验表明，秦皮乙素能抑制NTG刺激下的三叉神经血管组织块（脑膜组织块除外）的CGRP释放。舒马普坦可逆转两组实验中NTG诱发的变化。综上所述，秦皮乙素能抗伤害感受活性，降低三叉神经血管的CGRP浓度，并减轻脑膜肥大细胞的脱颗粒，因此可作为一种缓解偏头痛的治疗选择，但仍需进一步研究来加以证实。.
Emerging evidence indicates that cancer is associated with widespread splicing alterations that generate tumour-specific isoforms. One example is NUMB, an evolutionarily conserved adaptor protein, which produces four isoforms (p72, p71, p66, and p65) through alternative splicing of exons 3 and 9. Although traditionally considered as a tumour suppressor, NUMB has also been reported as an oncogene. We propose that this dual role reflects isoform-specific expression. Using public databases, we identify a tumour-associated switch in NUMB isoform expression: p72 and p71 are upregulated in tumours, whereas p66 and p65 are more highly expressed in non-tumour tissues. These isoforms show distinct associations with key cellular processes. NUMBL, a NUMB homolog, displays expression patterns similar to p65. We further identify two transcriptional clusters: one characterised by high expression of p72 and p71, and the other by enhanced p66/p65/NUMBL expression. These clusters exhibit differential associations with Notch, WNT/β-catenin, Hedgehog, and Hippo signalling pathways, suggesting isoform-specific regulatory roles. In breast cancer cell lines, we develop a NUMB-score based on isoform expression, which classifies cell lines into biologically distinct groups. The p72/p71-enriched group shows distinct signatures, pathway activity, and drug sensitivity. Application of this score to TCGA-BRCA samples reveals a significant link between high NUMB-score and poor survival, as confirmed by Kaplan-Meier analysis. We find that NUMB emerges as a potential oncogenic contributor and biomarker in the context of splicing-based precision oncology, highlighting Isoform-specific expression as a clinical determinant of tumour behaviour, pathway activity, and therapeutic response.
Linear polycarbonyl motifs constitute flexible chemical frameworks with relevance to conformational analysis, molecular stability, and interaction modeling. Here, we report a combined density functional theory (DFT) and molecular docking study of the structural stability, conformational preferences, and interaction behavior of linear C₆ triketo and diketo scaffolds. Equilibrium geometries, intramolecular hydrogen-bonding patterns, and relative Gibbs free energies were evaluated at the B3LYP/6-311 +  + G(d,p) level. Symmetric diketone isomers were identified as the most stable conformers, whereas arrangements containing adjacent carbonyl groups exhibited pronounced conformational flexibility accompanied by energetic destabilization of up to ~ 18 kcal mol⁻1. Across the scaffold series, a consistent instability window of ~ 12-16 kcal mol⁻1 was observed, associated with characteristic geometric distortions. To qualitatively probe interaction behavior, representative conformers spanning the stability range were subjected to molecular docking. Docking simulations were carried out against three key non-small cell lung cancer (NSCLC)-related targets, epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), and Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS), to evaluate the biological relevance of the studied conformers and to relate conformational stability to binding behavior in a disease-relevant context. Energetically favorable conformers displayed well-defined and reproducible interaction poses, while less stable structures showed increased orientational variability consistent with their flexible potential energy surfaces.
Extrachromosomal DNA (ecDNA) amplification represents a distinct mechanism of genomic instability in cancer, increasingly recognized for its role in aggressive disease progression. This review examines how ecDNA drives tumour evolution and assesses its potential as both a prognostic marker and therapeutic target. The authors integrate findings from multiple detection platforms-including FISH, whole-genome sequencing, and specialized reconstruction algorithms-and present data across diverse cancer types; no preregistration is noted, and no animal studies are included. ecDNA consists of circular, acentric DNA elements carrying high-copy oncogene amplifications (such as EGFR, MYC, MDM2, and CDK4). Unlike chromosomal DNA, ecDNA segregates unevenly during cell division, generating intratumoral heterogeneity, accelerating adaptation to selective pressures, and promoting resistance to therapy. Pan-cancer surveys summarized here reveal ecDNA in a significant subset of tumours, with particularly high frequencies in liposarcoma, glioblastoma, and HER2-positive breast cancer, and consistent associations with worse clinical outcomes. The authors conclude that ecDNA amplification serves as a credible adverse prognostic indicator and holds promise for refining risk stratification and guiding treatment strategies. However, they stress that clinical adoption remains constrained by the absence of standardized, scalable, and reproducible detection.
Hepatocellular carcinoma (HCC) is undergoing a profound global epidemiological shift, transitioning from viral-driven etiologies to metabolic dysfunction-associated steatotic liver disease (MASLD). This transition challenges traditional cirrhosis-centric surveillance, as a significant proportion of MASLD-HCC develops in non-cirrhotic livers. Parallel to these metabolic shifts, the gut-liver axis has emerged as a central orchestrator of hepatocarcinogenesis. This review decodes the complex gut-driven pathways fueling HCC, highlighting the oncogenic consequences of structural and functional dysbiosis. Dietary patterns and etiology-specific microbial shifts compromise the intestinal and gut-vascular barriers, precipitating a structural "leaky gut". This disruption facilitates the robust translocation of pathogen-associated molecular patterns (PAMPs), particularly lipopolysaccharide (LPS), and toxic microbial metabolites like secondary bile acids, specifically deoxycholic acid, into the portal circulation. Consequently, hepatic innate immunity is chronically activated via Toll-like receptor 4 (TLR4) signaling on Kupffer and hepatic stellate cells, fostering metainflammation, cellular senescence, genomic instability, and a highly immunosuppressive, pro-tumorigenic microenvironment. Furthermore, the depletion of keystone commensals diminishes the protective reservoir of short-chain fatty acids (SCFAs), exacerbating oncogene activation. Translating these mechanistic insights into the clinic, we explore the utility of distinct microbial signatures and metabolomic profiles as non-invasive diagnostic biomarkers. Such tools are urgently needed to bridge the early-detection gap in the expanding MASLD demographic. Finally, we discuss the pivotal role of the microbiome in modulating responses to immune checkpoint inhibitors (ICIs), notably through immune-stimulating taxa like Akkermansia muciniphila, and outline emerging gut-targeted therapies, including next-generation probiotics and fecal microbiota transplantation, aimed at restoring host-microbiome homeostasis to prevent and manage HCC. By decoding these gut-driven pathways, this review provides a comprehensive framework for integrating the microbiome-onco axis into precision oncology, offering novel avenues to combat the rising global burden of hepatocellular carcinoma.
MYBL2 is an oncogene that has been found to be upregulated in diverse cancers. However, the role of MYBL2 in multiple myeloma (MM) remains unclear. Here we used bioinformatic analysis to identify the differentially expressed genes in MM. In this study, western blot was conducted to detect protein levels. Ferroptosis was evaluated by detecting reactive oxygen species (ROS), ferrous iron (Fe2+), lipid peroxidation, and glutathione (GSH) levels. Cell viability and apoptosis were detected by the cell counting kit-8 assay and flow cytometry, respectively. Luciferase reporter assay was performed to confirm the binding between MYBL2 and CDKN3. We found that MYBL2 upregulation was observed in MM. Further in vitro studies showed that knockdown of MYBL2 promoted ferroptosis with increased ROS production, Fe2+ content, lipid peroxidation level, and reduced GSH content. MYBL2 knockdown also enhanced the bortezomib (BTZ) sensitivity of MM cells. In addition, CDKN3 was identified as a downstream target of MYBL2. CDKN3 overexpression prevented the effects of si-MYBL2 on ferroptosis and BTZ sensitivity in MM cells by interacting with the PI3K/Akt signaling pathway. In conclusion, knockdown of MYBL2 promoted ferroptosis and enhanced the BTZ sensitivity of MM cells through transcriptional regulation of CDKN3 and inactivation of the PI3K/Akt signaling pathway.
Breast cancer (BC) is one of the most common malignant tumors in women worldwide, with metastasis and recurrence constituting major therapeutic challenges. F-Box Protein 5(FBXO5), a core component of the E3 ubiquitin ligase complex, is overexpressed in multiple cancers, but its specific role and underlying mechanism in BC remain unclear and require further investigation. We screened E3 ubiquitin ligase-related cancer dependency genes by integrating data from the DepMap and UniProt databases, and further analyzed transcriptomic data from TCGA and GEO to identify the candidate gene FBXO5. We then validated its expression at the mRNA and protein levels in BC tissues from two independent centers and in cell lines, employing qRT-PCR, Western blot, and immunohistochemistry.The effects of FBXO5 on the proliferation, migration, and invasion abilities of BC cells were evaluated in vitro and in vivo through colony formation, CCK8, Transwell assays, wound healing assays, IHC, and subcutaneous tumor formation in nude mice. The interactions between FBXO5 and proteins, as well as its main functions and pathways, were investigated using Co-IP, mass spectrometry, immunofluorescence confocal microscopy, molecular docking and bioinformatics analysis, with results validated by rescue experiments. The mRNA and protein expression levels of FBXO5 were significantly upregulated in BC tissues from two centers, high expression of FBXO5 was significantly correlated with adverse clinicopathological features, including larger tumor size, positive nodal status, and elevated Ki-67, and was associated with poor overall survival (OS) and disease-free survival (DFS).In vitro and in vivo experiments confirmed that FBXO5 significantly affected the proliferation, invasion, and migration abilities of BC cells. Mechanistically, Co-IP, mass spectrometry, molecular docking and immunofluorescence confocal microscopy experiments confirmed that FBXO5 directly interacts with ribosomal protein L23a (RPL23A) and promotes its polyubiquitination at the K48 chain, thereby regulating its degradation. Further experiments showed that the ubiquitination-mediated degradation of RPL23A led to a decrease in the stability of Tumor Protein p53(p53) and facilitated its degradation by Proto-Oncogene MDM2 (MDM2). Our study establishes the existence of a novel FBXO5/RPL23A/MDM2/p53 oncogenic axis in BC. These findings thereby nominate FBXO5 as a promising therapeutic target for BC intervention.
Cancer is increasingly recognized as a disease of the dysregulated epigenome; however, current epi-drugs are blunt, systemically toxic instruments. Catalytically dead CRISPR nucleases (dCas9) linked to chromatin effectors have now made it possible not only to write and erase epigenetic marks at specified loci without double-strand breaks but also to add an element of optogenetics, or reversible and light-encoded control over the timing and localization of the editors. In this review, the technological underpinnings of light-controlled CRISPR-dCas9 epigenome editing, which include architectures of dCas9 scaffold and guide, blue-to-near-infrared photoswitches, and high-gain epigenetic effector designs, is synthesized, and viral, non-viral, and stimuli-responsive delivery platforms, which have to be co-optimized with clinical light interfaces, is discussed. We then outline four functional routes by which opto-epigenome editors may be used therapeutically in cancer: tumor suppressor reactivation; oncogene and super-enhancer repression with metabolic rewiring; control of cancer stem cell differentiation; and immunomodulation of the tumor microenvironment. Lastly, a translational roadmap is defined in terms of preclinical model tiers, biomarker strategies, regulatory and manufacturing factors, and future directions, including NIR and bioluminescent actuation, implantable μLED devices, and AI-guided closed-loop illumination. Together, these aspects constitute design principles for advancing light-addressable epigenome editors toward first-in-human studies and for integrating them into combination regimens as a new class of precision cancer therapeutics.
Canine oral melanoma is a highly aggressive tumor with limited therapeutic options and a poor prognosis. To elucidate the molecular mechanisms underlying its progression and response to radiation therapy (RT), we performed a longitudinal multi-omics analysis incorporating whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) on tumor and blood samples from a single neutered male mixed-breed canine case. WGS of pre-treatment tumor tissue revealed a predominance of endogenous mutational processes, with frequent mutations in cancer-associated genes such as NTRK3, EGFR, and ADAM17, and structural variants affecting oncogenes like MDM2 and BCL2. In contrast, mutational signatures observed in the post-RT blood sample were associated with homologous recombination and mismatch repair deficiencies, with minimal structural alterations. Transcriptomic profiling demonstrated dynamic, time-dependent gene expression changes following RT. Acute responses involved immune modulation and cytoskeletal remodeling, whereas later stages were associated with oxidative stress response, epithelial regeneration, and immune resolution pathways. Shared differentially expressed genes between tumor and blood post-RT samples suggest that peripheral blood may partially capture systemic molecular responses after RT. These findings offer preliminary insights into the molecular landscape of canine oral melanoma and provide a hypothesis-generating basis for future validation of candidate molecular markers associated with RT response.
Lung adenocarcinoma is a common type of lung cancer with high incidence and mortality rates. TMEM33, a tumor-associated protein, has not been fully elucidated in lung adenocarcinoma. To explore the expression of TMEM33 in lung adenocarcinoma, its impact on tumor progression, and its role in the PI3K/AKT/mTOR signaling pathway. Key genes associated with lung adenocarcinoma were screened using the Gene Expression Omnibus (GEO) dataset GSE140797 in combination with a weighted correlation network analysis (WGCNA). Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on these key genes. TMEM33 expression in Lung adenocarcinoma patients was validated using data from the TCGA database. The directly interactive molecules were screened through a bioinformatics method. Cellular assays (Western Blot, CCK8, colony formation, scratch assay, Trans well assay) and a nude mouse model were used to investigate the effects of TMEM33 on cell proliferation, migration, and tumor growth. TMEM33 is highly expressed in lung adenocarcinoma tissues (P < 0.05) and associated with poor prognosis. Overexpression of TMEM33 promotes cell proliferation and migration, and activates the PI3K/AKT/mTOR signaling pathway (P < 0.01). In the nude mouse model, TMEM33 overexpression increases tumor volume (P < 0.001), and PI3K/AKT pathway inhibition suppresses these effects (P < 0.05, P < 0.01). TMEM33 acts as an oncogene in lung adenocarcinoma by activating the PI3K/AKT/mTOR pathway, providing new therapeutic targets.
Gene fusions play a pivotal role in the pathogenesis and classification of hematologic malignancies. RNA sequencing (RNA-seq) has emerged as a powerful tool for detecting gene fusions; however, many clinical studies have focused on targeted RNA-seq, and optimal parameters for whole transcriptome RNA-seq remain uncertain. We retrospectively analyzed whole RNA-seq data from 301 patients diagnosed with acute leukemia between October 2022 and May 2025 to characterize the landscape of pathogenic gene fusions. Fusions were identified using the Arriba algorithm, and subsampling analyses were performed on cases with recurrent fusions to determine the minimum sequencing output required for reliable detection. Pathogenic gene fusions were identified in 113 of 301 patients (37.5%). Whole RNA-seq detected fusions that were not identifiable by conventional assays, including UBTF::ATXN7L3, and highlighted frequent fusion events, such as ZNF384 rearrangements. Subsampling analysis demonstrated that a sequencing output ≥ 100 million reads (moderate confidence) or ≥300 million reads (high confidence) was sufficient for 100% detection of recurrent fusions. Whole RNA-seq reliably detects clinically relevant gene fusions in acute leukemia, aligns well with conventional karyotyping results, and surpasses targeted RNA-seq in comprehensiveness. A sequencing output of at least 100 million reads is recommended for clinical fusion detection.
Non-small cell lung cancer (NSCLC) is a leading cause of cancer-related mortality, driven by invasive behavior and frequent resistance to systemic therapies. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) benefit patients with EGFR-mutant NSCLC, but their efficacy is often limited by tumor-intrinsic and environmental resistance mechanisms. Benzo[a]pyrene (BaP), a ubiquitous polycyclic aromatic hydrocarbon from tobacco smoke, combustion, and dietary sources, is a known carcinogen; however, its role in modulating therapeutic responses is poorly understood. Studies, including ours, implicate the platelet-activating factor-receptor (PAFR) pathway in mediating environmental pollutant and therapy-induced effects on tumor growth and microvesicle particle (MVP) release. We hypothesized that PAFR activation mediates BaP-induced NSCLC progression and influences EGFR-TKI responses. We assessed the effects of BaP, PAFR agonist CPAF, EGFR-TKIs, and their combinations on cell viability, proliferation, migration, anchorage-independent growth, and MVP secretion. BaP did not alter cell survival but significantly increased migration, growth, colony formation, and MVP release, similar to CPAF, and these effects were blocked by a PAFR antagonist or acid sphingomyelinase inhibitor. Notably, BaP did not significantly reduce EGFR-TKI efficacy at tested concentrations. These results show that environmental carcinogens modulate NSCLC behavior through PAFR signaling without compromising EGFR-TKI responsiveness, highlighting PAFR as a potential therapeutic target.