Bulk RNA sequencing (bulk RNA-seq) and single-cell RNA sequencing (scRNA-seq) are two important high-throughput sequencing platforms that have wide applications in biomedical research. Bulk RNA-seq reflects the average gene expression of all cells in the sample at a low experimental cost, whereas scRNA-seq enables transcriptomics profiling at a single-cell level, although with higher experimental costs. To integrate the strengths of both sequencing approaches and capitalize on the wealth of existing bulk RNA-seq datasets, we developed a U-Net-based deep learning algorithm, BLUE, to deconvolve bulk RNA-seq samples into cell-type proportions and cell-type-specific gene expression profiles. Built upon a U-Net backbone, BLUE leverages its powerful feature extraction and representation learning capabilities to achieve accurate predictions for cell-type-specific gene expression profiles, which significantly outperform existing deconvolution algorithms. Given the accurate prediction from BLUE, we developed an integrative framework for subtyping cancer patients and identifying cell-type-specific gene signatures that can function as prognostic biomarkers for cancer.

Cancer progression involves coordinated regulation of oncogenes and tumor suppressors. This study explores the interplay of ENOX2 (ecto-NADH oxidase disulfide-thiol exchanger 2), MMP2 (matrix metalloproteinase-2), and regulatory genes Ras Association Domain Family Member 1, Isoform A (RASSF1A), WAP Four-Disulfide Core Domain Protein 10A (WFDC10A), and Methyltransferase-Like Protein 7A (METTL7A) across multiple cancer cell lines, and evaluates the anticancer potential of repurposed mebendazole.

Pancreatic ductal adenocarcinoma (PDAC) is highly treatment resistant and characterized by a hypoxic microenvironment. Here, we investigated the role of hypoxia-inducible factor 1α (HIF1α) in regulating resistance to radiation and KRAS-inhibitor. We employed CRISPR/Cas9 to knock out (KO) HIF1α from the murine KRASG12D/+; p53R172H/+ KPC and the KRASG12D/+; p53R273H; CDK2NA-/- Panc-1 human pancreatic cell lines. Compared to WT, the HIF1α KO cell lines demonstrated a shift toward an epithelial phenotype and had decreased proliferation and migration under hypoxia. HIF1α KO cell lines were less likely to survive after radiotherapy, and neutral comet assays demonstrated DNA damage four hours after treatment, suggesting that HIF1α promotes radioresistance through non-homologous end joining. When treated with a KRASG12D inhibitor, HIF1α KO cells exhibited significantly increased apoptosis due to decreased p53 degradation, likely mediated through Mdm2. Confirming this, enrichment of hypoxic signaling was associated with KRAS inhibitor resistance in a cohort of 31 KRASG12D cell lines. Our results thus suggest that inhibiting HIF1α may sensitize PDAC to radiation and KRAS inhibitors. To explore this, we conducted a drug repurposing screen and identified three HIF1α inhibitors (bakuchiol, BAY-87-2243, 2-methoxyestradiol) whose sensitivities were correlated with sensitivity to Deltarasin, a KRAS inhibitor. Our findings suggest that HIF1α inhibitors could be used to sensitize PDAC to radiotherapy and KRAS inhibitors.

Drug chemoresistance remains a major reason of treatment failure in cancer patients. In head and neck squamous cell carcinoma (HNSCC), the seventh most common cancer worldwide, cisplatin chemotherapy remains the gold standard for advanced tumors but often faces loss of responsiveness and the drawback of relapse. We previously showed that the metabolic and angiogenic factor angiopoietin-like 4 (ANGPTL4) is a molecular biomarker of oral dysplasia and HNSCC. We also found that through interaction with Neuropilin 1 (NRP1), ANGPTL4 activates proliferative and migratory pathways that contribute to HNSCC development. Using HNSCC xenografts, patient tumor-derived organoids, tumor spheroids, and HNSCC cell lines, CAL27, HN13, and HN4, here we provide evidence of the role of ANGPTL4 in the development of platinum-based chemoresistance in HNSCC through the promotion of DNA damage response (DDR) and homologous recombination (HR). ANGPTL4 enhanced these mechanisms by promoting phosphorylation of RAD51 recombinase in Tyr315/54 through an NRP1/ABL1-dependent mechanism. Pharmacologic inhibition of NRP1 or ABL1 reversed ANGPTL4-mediated DDR and HR, and increased HNSCC cell death in combination with cisplatin, in vitro and in vivo. Our results reveal a role for ANGPTL4 in RAD51-dependent DNA repair and suggest that ANGPTL4/NRP1/ABL1/RAD51 may serve as an alternative therapeutic target for HNSCC.

The World Health Organization introduced substantial revisions in the 2020 fifth edition of the classification system for bone and soft-tissue tumors, reorganizing what were previously called the Ewing sarcoma family of tumors or Ewing-like sarcomas into a new category of "undifferentiated small round cell sarcomas" based on molecular genetic characteristics. This reclassification established four distinct entities: Ewing sarcoma (ES), CIC-rearranged sarcoma, sarcoma with BCOR genetic alterations, and sarcoma with EWSR1-non-ETS fusion genes. Each subtype may demonstrate specific clinical, pathologic, and imaging features, with different treatment responses and prognoses. ES primarily affects children and young adults, with characteristic "moth-eaten" lytic bone destruction, aggressive periosteal reactions, and extensive surrounding soft-tissue masses. CIC-rearranged sarcomas typically manifest as well-circumscribed lobulated soft-tissue masses with extensive internal necrosis and hemorrhage but no calcification. Sarcomas with BCOR genetic alterations commonly occur in adolescent boys as osteolytic or sclerotic lesions in the long bones or the pelvis, often with calcification in the extraosseous component. Sarcomas with EWSR1-non-ETS fusion genes may manifest as osteolytic lesions with cortical expansion and saucer-like surface erosion in long bone diaphyses. Radiologic recognition of CIC-rearranged sarcomas enables oncologists to anticipate their aggressive nature and poor response to standard ES treatments, which may necessitate more intensive initial surgical interventions. In comparison, identifying BCOR-CCNB3 sarcomas through imaging allows clinicians to inform patients of their potentially more favorable outcomes compared with those of ES while still applying appropriate comprehensive treatment approaches. The authors provide an overview of the clinical features, pathologic findings, imaging characteristics, differential diagnosis, and treatment outcomes of each entity. ©RSNA, 2026.

Neocentromeres are newly formed chromosomal regions that can replace the function of traditional centromeres and are well documented in human clinical studies. However, their occurrence in neoplasia, including acute leukemia, appears to be rare. We analyzed complex karyotypes in bone marrow cells from 113 patients with acute myeloid leukemia and one patient with acute lymphoblastic leukemia using centromeric/multicentromeric fluorescence in situ hybridization and identified four cases (3.5%) with derivative chromosomes exhibiting newly formed constrictions. Three of these patients had secondary leukemia following preexisting hematological disorders, suggesting a potential role for neocentromeres in disease progression. In all four cases, neocentromeres were detected on derivative chromosome 11. To our knowledge, this is the first report of neocentromeres derived from this chromosome in acute leukemia. All four patients in our study died; however, all exhibited complex karyotypes, which are independently associated with poor prognosis and an aggressive disease course. Neocentromeres are a rare but potentially important source of genomic instability in malignant diseases. Generally, the formation of a new constriction allows mitotic rescue of acentric chromosomes, preventing their loss. An increase in genomic alterations in tumor cells predicts a more aggressive disease course and adverse outcomes. Due to limited data, the prognostic significance of neocentromeres remains unclear. Further rigorous investigation is required to deepen our understanding of the mechanisms underlying neocentromere formation and their implications in cancer.

Constitutional mismatch repair deficiency (CMMRD) is a rare hereditary cancer predisposition syndrome that frequently manifests with pediatric high-grade gliomas. However, recognition remains challenging, particularly in the absence of a clear family history. We report a pediatric high-grade glioma with PMS2 deficiency and complex molecular alterations to highlight key diagnostic clues and the importance of routine mismatch repair assessment.

The extracellular matrix (ECM) is a highly organised and dynamic regulator of tissue structural integrity and biochemical signalling, and its dysregulation is a hallmark of fibrosis and cancer. Recent evidence highlights the critical role of epigenetic mechanisms in controlling ECM-related gene expression and remodelling activity. This review integrates recent advances in understanding how epigenetic mechanisms govern ECM composition, remodelling, and mechanotransduction, and how reciprocal ECM-derived signals reshape the epigenetic landscape. Growing evidence links DNA methylation, histone modifications, and non-coding RNAs to the regulation of key ECM components, matrix-modifying enzymes, and stiffness-associated signalling pathways, including TGF-β, Wnt, and PI3K/Akt are summarised in this review. The bidirectional feedback between altered ECM mechanics and epigenetic enzyme activity is emphasised, showing how matrix stiffening and aberrant epigenetic programming cooperatively drive pathological tissue remodelling and tumour progression. This review summarises findings from in vitro systems, animal models, and human disease studies that illustrate the functional consequences of ECM-epigenetic crosstalk. The emerging therapeutic approaches targeting the ECM-epigenetic axis, including epigenetic modulators and ECM-directed interventions, outline current challenges and future directions for restoring matrix homeostasis in disease. Together, this review provides an integrated framework for understanding the bidirectional ECM-epigenetic interactions and their translational relevance in molecular biomedicine.

Leptomeningeal disease (LMD) is a devastating complication of advanced solid tumors with limited prognostic and response-assessment tools. Because LMD molecular evolution is frequently compartmentalized behind CNS barriers, cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) may provide CNS-specific molecular readouts of disease activity. We evaluated whether baseline CSF ctDNA profiles and longitudinal ctDNA kinetics associate with survival in LMD.

Triple-negative breast cancer (TNBC) is an aggressive subtype lacking estrogen and progesterone receptors and HER2 amplification. Representing 10-15% of breast cancer cases, TNBC disproportionately affects Black and pre-menopausal women and is associated with poorer outcomes. With chemotherapy as the primary systemic treatment option, achieving a pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) is a key prognostic factor. However, TNBC biological heterogeneity complicates treatment response prediction. This study aimed to identify transcriptomic biomarkers predictive of NAC response in TNBC patients and evaluate machine-learning models for response classification.

Anti-PD-1 treatment has shown clinical benefit in malignant cancers. However, EGFR-mutant (EGFR-MT) lung adenocarcinoma, an immune-cold tumor, shows poor response to this immunotherapy. This scenario is associated with elevated levels of B7-H4, an immune checkpoint demonstrating CD8+ T cell inhibition activity. Our previous study has revealed that deubiquitinase USP2a could stabilize B7-H4 protein. Therefore, we further explore whether USP2a inhibition could remodel immune-cold microenvironment in this study. First, we confirmed that USP2a inhibitors effectively promoted proteasomal degradation of B7-H4 through blocking its deubiquitination process. To rule out the possiblity that USP2a might directly inhibit EGFR MT endocytosis so as to inhibit B7-H4 expression,we investigated the effect of USP2a inhibitor ML364 on EGFR mutants protein levels. It showed that ML364 did not inhibit EGFR mutant protein levels. ML364 could directly inhibit tumor cell proliferation in vitro. In immune-deficient nude mice ML364 inhibited tumor growth through inhibiting USP2a substrates Cyclin D1 and MDM2. In immune-competent C57BL/6 mouse model, ML364 could downregulate B7-H4 level thereby repress tumor growth through remodeling immune-cold microenvironment. Finally, we proved that ML364 could sensitize tumor to anti-PD-1 therapy in immune-competent mice. Immunohistochemical staining analysis showed that ML364 could inhibit B7-H4 expression, thereby enhanced Qa-1b (homolog of HLA-E in mouse) expression and CD8+ T cell infiltration. This study proved that inhibition USP2a could suppress tumor growth through two mechanisms: directly inhibiting tumor cell proliferation and remodel immune-cold microenvironment. Therefore, inhibiting USP2a could sensitize tumor to anti-PD-1 therapy.

Bladder cancer (BCa) holds a critical position among urological malignancies worldwide, characterized by its significant impact on public health. Current detection methods are often constrained by invasiveness, high costs, or limited sensitivity, impeding early and rapid diagnosis and prediction of reoccurrence. Here, we present a detection method combining loop-mediated isothermal amplification (LAMP) with lateral flow dipsticks (LFD) for the identification of methylated TWIST1 and PENK genes in urine samples. This approach aims to provide a rapid, convenient, and point-of-care (POC) tool for BCa detection, particularly in resource-limited settings. Featuring an optimized sample preprocessing protocol, a robust LAMP system, and intuitive visual readout via LFD, the LAMP-LFD method achieved 100% accuracy in both diagnostic (25/25) and prognostic (3/3) cohorts, which demonstrates significant potential for DNA methylation-based diagnostics and prognosis monitor. With further refinement, we anticipate that this method will play a crucial role in improving diagnosis and prognostic recurrence surveillance for BCa, facilitating earlier intervention and improved patient outcomes.

Gliomas are primary brain tumors that develop from glial cells within the central nervous system and are among the deadliest human cancers. Glioblastoma (GBM) is the most malignant form of glioma. NLRX1 is an innate immune pattern recognition receptor that exhibits tumor-suppressive or tumor-promoting effects that may be cancer type- and context-dependent, aided by differences in the microenvironment. Here, we report that NLRX1 is differentially expressed in microglia, astrocytes, GBM cell lines, and glioma patient tissues. siRNA-mediated silencing of NLRX1 induces metabolic stress in GBM cells, as observed by an increased number of tunneling nanotubes (TNTs) formation between GBM cells and decreased expression of autophagy markers. Moreover, silencing of NLRX1 decreases the ability of the GBM cell lines, LN-229 and LN-18, to proliferate and migrate. si-NLRX1 GBM cells exhibit attenuated ability to generate 3D spheroids. In summary, our findings indicate that NLRX1 positively regulates GBM pathophysiology by supporting GBM cell metabolism, proliferation, migration, and anchorage-independent growth. We believe our understanding of NLRX1 in GBM pathophysiology paves the way for potential development of GBM-targeting therapeutics that may delay disease progression and/or improve survival.

Genetic testing for gene variants associated with hereditary cancers can help with cancer prevention, early detection, and treatment. However, testing has not been well integrated into primary care settings where its preventative impact can be realized. To explore patient-level barriers and facilitators throughout the genetic testing process in primary care settings, we conducted a thematic analysis of semi-structured interviews with 31 patients within the Early Detection of Genetic Risk (EDGE) study who had not completed the risk assessment (n = 2), had completed the risk assessment but were ineligible (n = 8), had declined testing (n = 10), and had completed testing (n = 11). Interviewees were broadly interested in genetic testing. Those who did not complete the risk assessment cited limited access to technology, exacerbated by health and financial struggles. Several interviewees who completed the risk assessment but were deemed ineligible for testing indicated that their lack of knowledge about biological relatives prevented complete responses to the risk assessment. Those who opted out of testing cited concerns over privacy, insurance discrimination, and potential psychological burden. Notably, the majority who declined testing were unsure if they would refuse again in the future, and three went on to request genetic testing after being invited to complete an interview. Those who changed their minds about testing stated changes in life circumstances (such as obtaining life insurance) that facilitated openness to testing. Patients who completed testing shared similar concerns to those who declined but were motivated by their familial cancer history and believed genetic testing could lead to preventative options. A key finding of this study was that patient readiness for testing changed over relatively brief follow-up times. These results highlight the need for practicable approaches to re-offering genetic testing to individuals over time.

Malignant and non-malignant cells within the tumor microenvironment (TME) actively secrete extracellular vesicles (EVs) that may mediate intercellular communication or enter the blood stream. Circulating EVs in Diffuse Large B-Cell Lymphoma (DLBCL) patients are a promising source of liquid biopsy biomarkers; however, whether different cellular components of the TME preferentially secrete small (S-) and/or large (L-) EVs is still unknown. With an established density-gradient separation protocol and tunable resistive pulse sensing analysis, we demonstrate that DLBCL cells in culture produce 100-1000-fold higher numbers of S-EVs (50-200 nm) compared with L-EVs (200-1000 nm) and very large EVs (>1000 nm). In contrast, the plasma from DLBCL patients contains comparable concentrations of S- and L-EVs, consistent with various cellular origins. Small RNA sequencing showed minor differences in miRNA content between plasma S- and L-EVs; however, messenger RNA sequencing revealed stark differences in cargo between EV-size subtypes and between healthy donors and patients. Deconvolution analysis with single-cell sequencing data from 17 DLBCL tumor tissues as reference using the Statescope algorithm indicated that circulating S-EVs from malignant cells outnumber the L-EVs. In contrast, TME macrophage-, T cell-, and natural killer-derived L-EVs outnumber S-EVs. Together, these findings suggest that circulating S- and L-EVs can originate from distinct cellular compartments within the DLBCL TME, representing complementary biological information. These observations have important implications for the development of EV-based liquid biopsy strategies.

Acute lymphoblastic leukemia (ALL) mainly affects children, though it also occurs in adults. About 25% of adults with ALL have the more aggressive Philadelphia chromosome-positive (Ph+) subtype. Standard treatment includes tyrosine kinase inhibitors (TKIs) in combination with chemotherapy or corticosteroids, which have greatly enhanced survival rates over the past 2 decades. Ponatinib, a third-generation TKI demonstrated greater efficacy compared with imatinib, a first-generation TKI, in the PhALLCON trial.

BackgroundLung cancer remains one of the leading causes of cancer-related mortality worldwide. Holocytochrome c synthase (HCCS), a mitochondrial enzyme involved in apoptosis and energy metabolism, has been implicated in tumorigenesis; however, its role in lung cancer is not well defined.AimThis study aimed to elucidate the prognostic and therapeutic potential of HCCS in lung cancer through integrative bioinformatics analyses.MethodsTranscriptomic, methylation, and clinical data from TCGA were analyzed using TNMplot, UALCAN, and TIMER2.0 to evaluate HCCS expression, promoter methylation, immune infiltration, and prognostic relevance in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Meta-analysis of 18 independent cohorts from LUNG CANCER EXPLORER and four GEO datasets validated expression patterns, while Kaplan-Meier analysis assessed survival outcomes.ResultsHCCS was significantly upregulated in LUAD and LUSC and showed promoter hypermethylation in LUAD. Meta-analysis and external validation confirmed its overexpression. Patients with low HCCS expression exhibited poorer overall survival, suggesting a potential tumor-suppressive effect. HCCS expression positively correlated with immune cell infiltration and co-expressed genes enriched in mitochondrial and apoptotic pathways.ConclusionHCCS may serve as a prognostic and therapeutic biomarker in lung cancer, linking mitochondrial regulation, epigenetic modification, and immune interactions.

A Japanese phase 2 trial of encorafenib plus binimetinib met the primary endpoint of the centrally assessed objective response rate in patients with unresectable BRAF V600E-mutated thyroid cancer. Consequently, encorafenib plus binimetinib has been approved in Japan. We present the health-related quality of life (HR-QoL) outcomes from the trial.

ObjectiveTo evaluate the efficacy and safety of radiotherapy plus immune checkpoint inhibitors versus radiotherapy plus chemotherapy in driver gene-negative patients with non-small cell lung cancer and brain metastases.MethodsThis single-center retrospective cohort study (Strengthening the Reporting of Observational Studies in Epidemiology-compliant) enrolled 60 consecutive driver gene-negative patients with non-small cell lung cancer and brain metastases (29 radiotherapy plus immune checkpoint inhibitors, 31 radiotherapy plus chemotherapy) treated between June 2018 and December 2023, with follow-up until July 2025. Survival, tumor response, and immune-related adverse events were analyzed using Kaplan-Meier methods, Cox models, and chi-square tests. The study was approved by the Institutional Review Board and used deidentified data.ResultsRadiotherapy plus immune checkpoint inhibitors significantly prolonged median overall survival (586 vs. 509 days, p = 0.0208) and progression-free survival (494 vs. 383 days, p = 0.0127) as well as improved objective response rate (34.48% vs. 19.35%, p = 0.0394) and disease control rate (75.86% vs. 51.61%, p = 0.0265) compared with radiotherapy plus chemotherapy. Favorable prognostic factors included age <60 years, Eastern Cooperative Oncology Group Performance Status <2, programmed death-ligand 1 tumor proportion score ≥50%, and absence of extracranial metastasis. Radiotherapy plus immune checkpoint inhibitors-related immune-related adverse events (24.14%) were mostly grades 1-2, with no grade ≥4 events.ConclusionsRadiotherapy plus immune checkpoint inhibitors may confer survival benefits and favorable safety in driver gene-negative patients with non-small cell lung cancer and brain metastases. However, caution is warranted in interpreting these findings, which require validation in large-scale prospective studies.

Bisphenol A (BPA), an endocrine-disrupting chemical with estrogenic activity, has been implicated in cancer development, although its role remains controversial. This study investigated the effects of BPA on ovarian cancer and its underlying mechanisms. BPA treatment dose-dependently (0-10 μM) increased cell viability and invasion. Kyoto Encyclopedia of Genes and Genomes analysis revealed the enrichment of the central carbon metabolism pathway following BPA exposure. Consistent with this, BPA upregulated glycolytic enzymes HK2 and LDHA. In addition, BPA activated ERα, which enhanced HK2 transcription and promoted glycolysis. The resulting lactate accumulation increased histone H3 lysine 18 lactylation (H3K18la), enriched at the IGF2BP3 promoter, to upregulate its expression. IGF2BP3 then stabilized HK2 mRNA via m6A recognition, amplifying the glycolysis. Our findings suggest that BPA promotes ovarian cancer progression through the HK2/H3K18la/IGF2BP3 sequential regulatory axis, providing insights for epigenetic-targeted therapies.