Correlation between ACTA2, TAGLN, and TPM2 expression and drug sensitivity of selected compounds of drug screening

Evaluation of dasatinib sensitivity in tB-TNBC models in vitro and in vivo. A, Dose–response curves showing cell viability of indicated cell lines treated with increasing concentrations of dasatinib for 72 hours. Solid lines represent the mean of three biological replicates performed in technical replicates normalized to untreated controls, and IC50 values are indicated. B, Representative IHC images of tB-TNBC PDXs (PDX_01 and PDX_02) showing expression of SMA, TAGL, and TPM2. Scale bars, 100 μm. C, Quantification of positive tumor cells for each tB-marker in PDX_01 and PDX_02. Data are shown as mean ± SEM of different tumor areas. D, Schematic representation of the dasatinib treatment protocol. E, Tumor growth curves of the tB-TNBC PDXs treated with vehicle (black) or dasatinib (red). Error bars, ± SEM. P values calculated by Wilcoxon test. F, Bar plot showing tumor weight at the end point. Data are shown as mean ± SEM. P values calculated by two-tailed Student t test. **, P < 0.01. D, Created in BioRender. Rodilla, V. (2026) https://BioRender.com/qpb7bux.

Abstract Antigen density critically influences CAR T-cell efficacy. We show that ibrutinib induces CD19 upregulation in B-cell lymphoma models, enhancing CAR T-cell cytotoxicity. Pharmacologic modulation of target antigen expression represents a promising strategy to overcome resistance.

Distribution of clinical and pathological features in the validation cohort of Hospital Universitario Santa Lucía, Cartagena

The MAPRE3 gene is aberrantly expressed in several cancers. We profiled DNA methylation in tumor tissues from early‐stage non‐small cell lung cancer (NSCLC) patients and assessed associations with overall survival (OS). Significant CpG probes were validated in The Cancer Genome Atlas (TCGA). The methylation level of cg12821679 MAPRE3 showed significant associations with OS in lung squamous cell carcinoma (LUSC) (HR = 0.32, P = 6.55 × 10 −7 ), but it was not observed in lung adenocarcinoma (LUAD). In LUSC, MAPRE3 expression was significantly correlated with cg12821679 MAPRE3 ( r = 0.17, P = 2.96 × 10 −3 ) and potential trans ‐regulated genes were enriched in the Nicotine addiction pathway. Additionally, MAPRE3 expression showed significant associations with OS in both LUAD and LUSC (LUAD: HR low vs high = 2.28, P = 2.40 × 10 −3 ; LUSC: HR low vs high = 1.61, P = 0.0244). The association between smoking cessation and overall survival was significantly modified by MAPRE3 expression (HR interaction = 0.69, P = 0.0282). Smoking cessation improved OS only in patients with high MAPRE3 expression (HR = 0.56, P = 2.82 × 10 −3 ). We conclude MAPRE3 may predict NSCLC prognosis and influence the prognostic benefit of smoking cessation.

Expression and prognostic impact of tB-markers in TNBC. A, Unsupervised hierarchical clustering of the percentage of positive cells/sample in the discovery and validation cohorts of TNBC (n = 243). Color code denotes percentage of expression (blue, 0%; red, 100%). B, Scatter plots representing the percentage of tumor cells positive for SMA, TAGL, and TPM2 in two independent TNBC cohorts: the commercial TMA BR1301a (left) and the Cartagena cohort (right). Each dot represents one patient sample; horizontal lines indicate mean ± SEM. Statistical significance was determined using two-way ANOVA. ****, P < 0.0001. C, Heatmap showing the expression levels of the tB-markers across breast cancer samples. Expression values are row-normalized, ranging from low (blue) to high (red). The top annotations indicate relevant clinical and molecular characteristics of each sample, including histologic type, disease stage, intrinsic PAM50 subtype, and Lehmann classification (TNBC type_4). NA, not available; NOS, not otherwise specified. D, KM plot depicting RFS of patients with TNBC stratified by tB-marker expression. E, KM plot showing RFS in patients with TNBC treated exclusively with chemotherapy, based on tB-marker expression. F, KM plot illustrates OS of patients with TNBC based on tB-marker expression. In panels D–F, patient subgroups were defined through trichotomization, in which the lower quartile represents the “low expression” group (black), and the upper quartile represents the “high expression” group (red). Patients with intermediate expression levels were excluded to ensure a robust comparison between high and low expressers.

Immune checkpoint blockade (ICB) is a standard treatment for several types of human cancer, yet we still lack a deep understanding of the mechanisms underlying primary resistance. Tumor-intrinsic defects in immune recognition and interferon-gamma (IFNγ) signaling pathways facilitate immune evasion and may limit the efficacy of ICB. Here, we delineate the mutational landscape and functional consequences of amino acid substitutions in key immune-related genes, B2M, CALR, IFNGR1, IFNGR2, JAK1, and JAK2, across more than 12,000 primary tumors and cancer cell lines. Genomic alterations affecting the coding regions of at least one of these genes were identified in approximately 11% of cancers, with missense variants accounting for 55% of these events. B2M, encoding the invariant light chain of the heavy chain-I (HLA-I) complex, exhibited the highest mutation frequency per base pair, the mutations predominantly involving truncating variants. A curated set of 2156 missense mutations in B2M and in components of the IFNγ-signaling pathway (IFNGR1, IFNGR2, and JAK2) was analyzed using SIFT, PolyPhen-2, and AlphaMissense, yielding predicted pathogenicity rates of 52%, 35%, and 27%, respectively. The functional assays, performed in lung cancer cells, revealed JAK2 and IFNGR1 variants that impaired IFNγ-mediated transcriptional activation and growth suppression, and B2M variants that disrupted HLA class I complex formation. Notably, AlphaMissense predictions showed the highest concordance with experimental data. These findings provide a detailed mutational map of antigen presentation and IFNγ-response components in cancer. Overall, our results provide a resource of specific mutations in genes involved in immune pathways that compromise tumor immunogenicity and will serve for support in patient selection for response to ICB.

Wilms Tumour (WT), the most common kidney cancer in children, presents features of altered kidney development and frequently exhibits molecular alterations at the 11p15.5 imprinted locus, affecting the IGF2 and H19 genes, which contribute to tumour growth and predisposition. The epigenetic landscape beyond 11p15.5 suggests diagnostic and prognostic potential, but its link to transcriptomic changes is largely unexplored. We integrated methylomic and transcriptomic datasets of 27 primary tumours and matched non-neoplastic kidneys. DNA methylation profiling identified around 9000 differentially methylated CpG sites distinguishing neoplastic from non-neoplastic tissue and other paediatric cancers, thus representing a novel WT-specific epigenetic signature. We found that cases with Imprinting Centre 1 (IC1) gain of methylation exhibited the most extensive epigenetic alterations; cases with 11p15.5 loss of heterozygosity showed intermediate changes, whereas regressive tumours with largely normal 11p15.5 status were less affected. Three methylation clusters corresponding to transcriptomic subtypes were identified, characterised by distinct tumour microenvironment and chemosensitivity predictions: a regressive-enriched, immune-infiltrated group predicted to respond to paclitaxel, a proliferative group sensitive to doxorubicin, and a stromal-like intermediate group. Combined analysis of methylation and expression data revealed more than 900 genes under epigenetic control, which contributed to defining the WT subtypes. Analysis of the IGF2/H19 locus uncovered multiple regulatory mechanisms underlying IGF2 activation, including imprinting defects at IC1, methylation changes at DMR0, differential promoter usage and transcriptional modulation by PLAG1 and BAHD1. These findings define the epigenetic alterations underlying WT heterogeneity and support improved molecular stratification and therapeutic approaches.

Cancer develops inside organized tissue environments wherein cellular behavior is heavily influenced by local interactions and spatially restricted regulatory programs. While bulk and single-cell sequencing technologies have fundamentally revolutionized our understanding of tumor biology, these techniques often disrupt tissue architecture and therefore fail to capture the spatial context in which molecular processes occur. Spatial transcriptomics has provided important insights into tumor heterogeneity, microenvironmental organization, and cell-to-cell communication. However, gene expression alone offers only an indirect view of the regulatory mechanisms governing cellular states. The emergence of spatial epigenomic technologies now enables the investigation of chromatin accessibility, histone modifications, and DNA methylation while preserving tissue structure. Here, we discuss the current landscape of spatial epigenomics, including spatial ATAC-seq, spatial CUT&Tag, emerging spatial CUT&RUN approaches, spatial DNA methylation profiling, and multimodal strategies integrating epigenetic, transcriptional, and proteomic information within the same tissue context. Despite remaining technical and computational challenges, continued advances are expected to establish spatial epigenomics as a powerful tool for studying cancer pathways and their regulation within intact tissues.

Myeloid sarcoma, an aggressive extramedullary subtype of acute myeloid leukemia (AML), occurs in approximately 20% of patients and remains strikingly understudied in large-scale genomic and multiomic investigations. The key drivers of its tumor evolution are largely unknown; timely detection in asymptomatic patients poses a clinical challenge, and effective treatment options are limited, as patients are often excluded from clinical trials, rendering it a largely neglected disease entity. In this study, we demonstrate that myeloid sarcoma evolves from medullary AML but exhibits distinct site-specific clonal evolution. This is supported by unique transcriptional signatures of myeloid sarcoma, reflecting adaptation to the extramedullary microenvironment. We establish a proof of concept that circulating tumor DNA (ctDNA) sequencing captures the molecular composition of myeloid sarcoma, offering a potential noninvasive approach for molecular profiling of extramedullary AML. Our findings highlight marked differences between medullary AML and myeloid sarcoma, including universal molecular evolution and RAS pathway activation as disease hallmarks. SIGNIFICANCE:We provide a comprehensive multiomic characterization of myeloid sarcoma, identifying key molecular pathways that contribute to its development, and suggest ctDNA as a noninvasive method of detection. We identify RAS pathway activation and transcriptional adaptation to the solid tissue microenvironment as cardinal features of myeloid sarcoma, suggesting novel therapeutic avenues.

Aberrant DNA methylation is a hallmark of cancer. Beyond its established diagnostic applications, growing evidence supports the utility of DNA methylation in predicting therapeutic response. By modulating gene expression patterns, particularly in pathways related to drug metabolism, DNA repair, and immune response, methylation profiles can directly influence how tumors respond to specific treatments. Although clinical implementation remains limited to a few examples, ongoing efforts to standardize assays, enhance sensitivity in liquid biopsy, and validate predictive markers in prospective trials will enable its full recognition as a dynamic, actionable decision-support tool for therapy selection and adaptive management of cancer treatment.

Identification of candidate compounds selectively targeting tB-TNBC cells. A, Heatmap showing the transcriptomic expression of tB-markers in a panel of breast cancer cell lines. B, Schematic representation of the FDA-approved drug library screening workflow. Cell viability heatmap shows the response of each cell line to the 3,200 tested compounds. ***, P < 0.001. C, Dot plot of average cell viability (%) in tB-TNBC (x-axis) and nB-TNBC (y-axis) cell lines after treatment. Dotted red and blue lines indicate the viability thresholds used for compound selection (<20% viability in tB-TNBC and >20% in nB-TNBC). Colored dots highlight the selective compounds. D, Heatmap showing the viability percentages of the selected compounds across the four TNBC cell lines used in the screen. E, Correlation plots showing the association between ACTA2, TAGLN, and TPM2 expression (log2 TPM + 1) and dasatinib sensitivity (AUC) in breast cancer cell lines. Red lines, regression fit; shaded areas show 95% confidence intervals. P values calculated by Pearson correlation. B, Created in BioRender. Rodilla, V. (2026) https://BioRender.com/qpb7bux.

Primary antibodies used for immunohistochemistry

Expression of LC-associated genes in murine mammary epithelial subpopulations

We show how the loss of activity of the translation initiation factor EIF5A2-either through gene hypermethylation or pharmacologic inhibition of its highly specific hypusine post-translational modification-induces venetoclax sensitivity in acute myeloid leukaemia (AML) cells.

Alzheimer’s disease (AD) is a progressive neurodegenerative condition in which genetic predisposition plays a key role, yet the sex-specific mechanisms linking genetic risk to early cognitive changes remain unclear. This study examined the impact of polygenic risk scores (PRS) on early cognitive changes in 318 cognitively unimpaired participants from the ALFA+ cohort, a nested longitudinal cohort from the ALFA study (see details in Study Participants Section, Methods). Participants were followed for three years, with assessments across five cognitive domains and a preclinical composite (PACC). Global AD PRS, including and excluding the apolipoprotein E (APOE) gene, alongside five biologically informed pathway-specific PRS (amyloid, immune, external stimuli signaling, cholesterol efflux, lipoprotein metabolism) were computed. Generalized linear models including interaction by sex and stratified by sex and amyloid status (CSF Aβ42/40 < 0.071) assessed associations between PRS and cognitive change. In women, APOE-independent AD genetic risk predicted worse executive function, particularly via cholesterol efflux and external stimuli signaling pathways. Among Aβ + women, PRS also predicted lower memory performance, partially modulated by reproductive span. In Aβ − women, worse executive functioning performance was linked to amyloid, immune, and signaling pathways. In contrast, men showed associations between AD PRS and worse visual (Aβ−) and attentional (Aβ+) performance, independent of pathway-specific mechanisms. These findings reveal distinct, domain-specific cognitive vulnerabilities to AD genetic risk by sex and amyloid status, highlighting APOE-independent and mechanistic contributions to early and subtle cognitive changes. Results support the need for sex-aware, biologically informed genetic models in preclinical AD for risk stratification and early intervention. Alzheimer’s disease (AD) is a condition that slowly damages the brain, affecting memory, thinking, and behavior over time. Some people are more likely to develop Alzheimer’s because of their genetic profile. One well-known gene, the APOE gene, increases AD genetic risk. Nonetheless, many other genes also play a role, and we still do not fully understand how these genes affect brain health, especially in the very early stages of the disease, before any symptoms appear. In this study, we looked at 318 healthy adults who may be at higher genetic risk of AD. We followed their cognitive abilities over three years. We used genetic scores to estimate each person’s overall risk of developing AD and focused on specific genetic pathways related to processes like inflammation, cholesterol, and how brain cells communicate. We found that women and men showed different patterns. In women, genetic risk (even without APOE) was linked to lower performance in specific cognitive abilities, such as memory and executive function. In women displaying AD-specific pathological burden in the brain, lower cognitive performance was stronger. In men, the genetic risk was tied to changes in visual and attention skills, but through different biological routes. Our findings suggest that AD risk genes affect men and women differently, even before symptoms appear. Understanding these early, sex-specific patterns could help doctors predict who is at higher risk and lead to more personalized prevention strategies. This study highlights the importance of considering both sex and biology when studying AD. In Aβ− women, higher global AD genetic predisposition is associated with worse follow-up performance in episodic memory. The association is attenuated when APOE is included in the PRS and models are adjusted for reproductive span. Across women, genetic predisposition to AD is associated with worse follow-up executive functioning performance, independently of APOE-ε4, amyloid status, and other confounders. Effects are primarily driven by cellular response to external stimuli. In Aβ+ men, the association between genetic predisposition to AD and worse follow-up performance on attention is not independent of cardiovascular risk for dementia, and appears to be mainly driven by signaling pathways to external stimuli. In Aβ− men, genetic predisposition to AD is associated with worse follow-up performance in visual processing independently of APOE-ε4 carriership, cardiovascular risk and neurodegeneration, although these associations are not attributable to any specific AD pathway.

Supplementary Table 1 from Epigenetic Inactivation of the Groucho Homologue Gene TLE1 in Hematologic Malignancies

TAGL as a predictive marker for dasatinib sensitivity. A, Western blot of control and TAGLN-KO cells in Hs578T (top) and BT-549 (bottom) cells. B, Representative immunofluorescence of Hs578T and BT549 control and TAGLN-KO cells, stained with αTAGL (green) and DAPI (blue). Scale bar, 50 μm. C, Cell proliferation in control (black) and TAGLN-KO (purple) cells measured by MTT assays over 72 hours. D, Relative percentage of migrated cells in control and TAGLN-KO cells, assessed by transwell assays. In C and D, values represent the mean ± SEM of at least three experimental replicates, and statistical significance was determined using one-way ANOVA. E, Drug–response curves for cell viability of control and TAGLN-KO cells treated with dasatinib at increasing concentrations. F, Western blot of known dasatinib targets in control and TAGLN-KO cells. G, Data from the DepMap portal showing the correlation between TAGLN and PDGFRB in breast cancer cell lines. H, Western blot of PDGFRβ in TAGLN-KO and cells and clones constitutively expressing PDGFRB. I, Drug–response curves for cell viability of TAGLN-KO and TAGLN-KO/PBGFRB cells treated with dasatinib at increasing concentrations. In E and I, solid lines represent the mean of three biological replicates performed in technical replicates. The dashed line indicates their IC50 value. **, P < 0.01; ****, P < 0.0001; ns, not significant.

High-fat diet (HFD) and obesity are increasingly recognized as risk factors of pancreatic ductal adenocarcinoma (PDAC), yet the mechanisms by which dietary fat contribute to oncogenic transformation remain elusive. Using an inducible acinar-specific KrasG12V / Trp53 -loss genetically-engineered mouse model of PDAC, we established early- and late-onset protocols to assess age-dependent susceptibility to HFD. Specifically, HFD accelerated tumorigenesis with poorer prognosis in early-onset mice and, strikingly, enabled full PDAC development in late-onset adult mice otherwise resistant to oncogenic transformation. Tumors arising under HFD activated a distinct transcriptional and epigenetic state enriched in pathways or genes related to stemness, plasticity, and metastatic competence, which was maintained even in tumor-derived cell lines. Mechanistically, fatty acid-educated macrophages secreted the cathelicidin antimicrobial peptide (CAMP), activating P2X purinoceptor 7 (P2RX7) signaling in tumor cells to drive a highly plastic, immune-evasive phenotype reinforced by the expression of the peptidoglycan recognition protein 1 (PGLYRP1), further shielding tumor cells from macrophage phagocytosis. Functionally, HFD-induced tumors displayed enhanced metastatic potential independent of host context. Analysis of 164 human PDAC samples revealed that elevated body-mass index (BMI) was associated to a conserved CAMP-P2RX7-CXCR4 signature, maintained despite weight loss during disease progression. Together, these findings uncover a diet-imprinted macrophage-tumor cell circuit that promotes transformation and accelerates PDAC progression, positioning it as a therapeutic vulnerability in obesity-associated pancreatic cancer. ### Competing Interest Statement The authors have declared no competing interest. Asociación Española Contra el Cáncer, https://ror.org/00gxct719, PRDMA246123GALV, POSTD258037LÓPE, LABAE223389SANC Asociación Cancer de Pancreas, IX Carmen Delgado/Miguel Pérez-Mateo grant European Research Council, ERC-AG/695566-THERACAN Centro de Investigación Biomédica en Red de Cáncer, CB21/12/00121 AIRC, IG 26201, IG 32351 PNRR Program, PNRR-MCNT2-2023-12377229 NEXTGENERATION-EU, CN00000013 European Regional Development Fund, PID2024-159192OB-I00 Pancreatic Cancer UK, 06/Q0512/106 Instituto de Salud Carlos III, PT20/0045, PT23/00098