Head and neck squamous cell carcinoma (HNSCC) is associated with high locoregional recurrence and poor survival despite multimodal treatment. Reliable biomarkers to guide personalized therapy remain lacking. Circulating...Head and neck squamous cell carcinoma (HNSCC) is associated with high locoregional recurrence and poor survival despite multimodal treatment. Reliable biomarkers to guide personalized therapy remain lacking. Circulating tumor cells (CTCs) represent a promising tool, but their clinical utility in HNSCC is insufficiently defined. In this cohort study, 30 stage I-IVb HNSCC patients undergoing curative-intent surgery were enrolled. Preoperative blood samples were analyzed using the FDA-approved CellSearch™ system for CTC count and Programmed death-ligand 1 (PD-L1) expression. Prognostic associations were assessed using Kaplan-Meier analysis and Cox regression. Combined risk models integrating CTC status with radiological features were explored. CTCs were detected in 37.9% (11/29) of patients. CTC positivity was significantly associated with reduced overall survival (P = 0.031). Univariate and bootstrap-adjusted Cox regression identified CTC presence and tumor volume as factors associated with overall survival. Integrating CTC status with tumor volume or nodal stage improved patient stratification, identifying a high-risk group with shorter recurrence-free and overall survival. Preoperative CTC detection may serve as a prognostic biomarker in HNSCC and enhances risk stratification when combined with imaging-derived tumor characteristics, supporting liquid biopsy integration into pre-surgical evaluation.
Brain tumors remain among the most lethal cancers, largely due to their remarkable heterogeneity, plasticity, and resistance to therapy. The second Brain Tumor Meeting by the Sea (Saint-Malo, France, 2026) brought togeth...Brain tumors remain among the most lethal cancers, largely due to their remarkable heterogeneity, plasticity, and resistance to therapy. The second Brain Tumor Meeting by the Sea (Saint-Malo, France, 2026) brought together researchers, clinicians, and patient representatives to discuss emerging concepts shaping the future of neuro-oncology. A recurring theme was the shift from a tumor-centric perspective toward an ecosystem-based view that integrates tumor cells, microenvironmental cues, developmental context, and patient-centered dimensions. Advances in patient-derived models, multi-omics approaches, spatial technologies, and artificial intelligence are refining tumor classification and revealing novel therapeutic vulnerabilities. Discussions highlighted cellular plasticity and stress-adaptation mechanisms as key drivers of tumor evolution and treatment resistance. They also emphasized the need for identifying dynamic biomarkers and developing more physiologically relevant disease models. Beyond biological discoveries, the meeting underscored the importance of strengthening interactions among research, clinical care, and patient communities. Together, these advances support a more integrated framework for understanding brain tumors and developing future therapeutic strategies.
Cyclin-dependent kinase (CDK) 12 and its paralog, CDK13, phosphorylate RNA polymerase II, enabling transcriptional elongation. In solid tumors, CDK12 loss promotes progression by inducing replication-transcription confli...Cyclin-dependent kinase (CDK) 12 and its paralog, CDK13, phosphorylate RNA polymerase II, enabling transcriptional elongation. In solid tumors, CDK12 loss promotes progression by inducing replication-transcription conflict and fueling genomic instability. However, we have uncovered upregulation of CDK12 and CDK13 in ~5% of colorectal cancer (CRC) specimens, suggesting a role in cancer cell survival. Based on this, we postulated that CDK12/13 inhibition in CRC may represent a useful therapeutic strategy. To test this, we screened CDK12 and CDK12/13 inhibitors across multiple cancer cell lines and patient-derived organoids (PDO) from a range of solid tumors, demonstrating potent activity in CRC PDO. Using siRNA-mediated knockdown, we identified CDK13 as a potential mechanism of resistance to CDK12-specific inhibition. Mechanistically, CDK12/13 inhibition led to a decreased abundance of BRCA1 long transcripts, rendering cells susceptible to combination therapy with PARP inhibitors. To further assess the clinical utility of CDK12/13 inhibition, we focused on CRC, for which there is an urgent need for additional therapies. We tested the efficacy of CT7439, a novel CDK12/13 inhibitor and cyclin K degrader, which showed cytotoxicity in the low nanomolar range, reduced BRCA1 expression, and concomitant DNA damage. Together, our data support further clinical development of CDK12/13 inhibition in CRC.
The emergence of drug resistance in ROS1-rearranged non-small cell lung cancer (NSCLC) represents a major therapeutic challenge. Although several resistance mutations have been described in patients, preclinical models d...The emergence of drug resistance in ROS1-rearranged non-small cell lung cancer (NSCLC) represents a major therapeutic challenge. Although several resistance mutations have been described in patients, preclinical models derived from patient material remain limited, thereby hindering mechanistic insight into this malignancy. In this study, we investigated three clinically relevant ROS1 variants (G2032R, L2026M, and S1986Y) using CRISPR/Cas9-edited patient-derived cell lines and complemented these analyses with molecular docking and molecular dynamics simulations. The efficacy of tyrosine kinase inhibitors (TKIs) crizotinib, ceritinib, lorlatinib, entrectinib, and repotrectinib was systematically evaluated. Dose-response assays with CUTO-28 (TPM3-ROS1) and CUTO-37 (CD74-ROS1) lines reproduced clinical drug responses, revealing fusion-dependent differences in resistance. The G2032R mutation led to reduced sensitivity to entrectinib and lorlatinib, with lower area-over-the-curve values compared with ROS1 wild-type (WT) cells. Similar reductions were observed for L2026M and S1986Y, while complete resistance was only seen in CUTO-37 G2032R. Immunoblotting confirmed impaired inhibition of p-ROS1 (Tyr2274) in resistant models. Structural modelling revealed alterations in kinase active site pocket volume, activation helix rotation, and activation loop dynamics in ROS1 mutants, providing a mechanistic basis for the observed drug responses. Molecular dynamics simulations validated the type I inhibitor binding mode across ROS1 WT and mutant complexes, while highlighting conformational effects extending beyond direct ligand interactions. Our findings underscore that although G2032R and L2026M mutations reside within the kinase active site, their impact extends far beyond steric hindrance, altering overall kinase domain dynamics. Collectively, these data establish a robust panel of patient-derived ROS1 cell lines that recapitulate clinical resistance patterns and, together with complementary computational modeling, provide a valuable framework to dissect ROS1 tumor biology and support rational design of next-generation inhibitors.
The BRAF p.V600E mutation activates the RAS/BRAF/MEK/ERK pathway, leading to cancer cell dedifferentiation and uncontrolled growth. In radioiodine-refractory thyroid cancers, MEK and/or BRAF inhibitors can induce rediffe...The BRAF p.V600E mutation activates the RAS/BRAF/MEK/ERK pathway, leading to cancer cell dedifferentiation and uncontrolled growth. In radioiodine-refractory thyroid cancers, MEK and/or BRAF inhibitors can induce redifferentiation, resensitizing tumors to radioiodine. However, compensatory mechanisms limit this efficacy. We used the SWitchMiner software to identify a small pool of regulatory genes, called switch genes, critically associated with drastic changes in cell phenotypes, using TCGA transcriptomic data from BRAF-mutant papillary thyroid carcinoma and normal thyroid tissues, which highlighted miR-335-5p. Restoring miR-335-5p in thyroid cancer cell lines harboring the BRAF mutation increased expression of thyroid-specific genes and proteins, especially in well-differentiated cell lines, with enhanced sodium-iodide symporter localization and iodine uptake confirmed in organoids. Due to the connection between thyroid-specific and EMT-related genes in the protein-protein interaction network, we examined how miR-335-5p overexpression affects EMT pathway genes that modulate thyroid-specific genes and Kinase Inhibitor (KI) resistance. miR-335-5p inhibited the expression of nearly all analyzed genes in less-differentiated thyroid cell lines. Thus, miR-335-5p may be a viable therapeutic target to restore radioiodine avidity in BRAF-mutant metastatic thyroid cancer and enhance KI treatment redifferentiation.
Bladder cancer is the most prevalent malignancy of the urinary tract; nevertheless, its progression and treatment continue to pose substantial challenges. While the molecular mechanisms underlying bladder cancer progress...Bladder cancer is the most prevalent malignancy of the urinary tract; nevertheless, its progression and treatment continue to pose substantial challenges. While the molecular mechanisms underlying bladder cancer progression remain unknown, the Wnt/β-catenin signaling pathway has established roles in cancer progression. In this study, we investigated the contribution of BCL9(L) (coactivators of β-catenin) to bladder cancer progression and evaluated the therapeutic potential of disrupting the β-catenin/BCL9(L) complex. We demonstrate that BCL9L exerts oncogenic effects on the proliferation and invasion of bladder cancer cells and the knockdown of BCL9 also reduced the proliferation, migration, and invasion of bladder cancer cells, suggesting similar oncogenic roles. Pharmacological inhibition of the β-catenin/BCL9(L) complex using ZW4864 suppresses a subset of Wnt/β-catenin targets in bladder cancer cells, indicating the inhibition of canonical Wnt signaling. We show ZW4864 has an inhibitory effect on the proliferation, migration, and invasion of bladder cancer cells and impedes the growth and formation of multicellular bladder cancer organoids. These findings demonstrate the crucial role of BCL9 and BCL9L in bladder cancer progression and highlight the β-catenin/BCL9(L) axis as a promising therapeutic target.
Ovarian cancer is a heterogeneous gynaecological malignancy characterised by high mortality and an absence of reliable biomarkers for detection. In this study, a CpG-specific, ARMS-PCR approach was employed to evaluate t...Ovarian cancer is a heterogeneous gynaecological malignancy characterised by high mortality and an absence of reliable biomarkers for detection. In this study, a CpG-specific, ARMS-PCR approach was employed to evaluate the methylation status of six diagnostically relevant CpG sites in 65 epithelial ovarian cancer tissues and 35 healthy controls. Based on methylation frequency, the top three CpG sites were selected and evaluated in two diagnostic panels. A TaqMan-based MethyLight assay incorporating cg02957270, cg00480298 and Col2A1 (as endogenous control) was developed for tissue and serum cell-free DNA cohort analysis. ARMS-PCR demonstrated diagnostic sensitivities of 80%, 73.3% and 82.3% for singleplex and multiplex panels, respectively. However, the multiplex MethyLight assay achieved 86% sensitivity and 90% specificity, with an AUC of 0.97 in the serum cohort. Furthermore, while ARMS-PCR panels displayed limited clinicopathological correlations, MethyLight showed significant correlations (P < 0.05). Overall, this pilot study highlights the promise of liquid biopsy-based diagnostics using independent hypermethylated and hypomethylated CpG biomarkers for ovarian cancer detection.
Salhi Y, Makrodimitris S, van Wilpe S
… +12 more, Te Paske I, de Weerd V, Beaufort CM, Westgeest HM, Voortman J, Aarts MJB, Rijnders M, van der Veldt AAM, de Wit R, Mehra N, Wilting SM, Robbrecht DGJ
Accurate prediction of lack of benefit from pembrolizumab in patients with metastatic urothelial cancer (mUC) is an unmet need. We investigated the dynamics of circulating tumor DNA (ctDNA) load, estimated using the modi...Accurate prediction of lack of benefit from pembrolizumab in patients with metastatic urothelial cancer (mUC) is an unmet need. We investigated the dynamics of circulating tumor DNA (ctDNA) load, estimated using the modified fast aneuploidy screening test-sequencing system (mFast-SeqS), as a potential biomarker for early on-treatment identification of treatment response. A total of 104 patients with mUC treated with pembrolizumab from two prospective biomarker discovery trials were included and mFast-SeqS was performed on paired blood samples collected at baseline and on-treatment. Patients with a high on-treatment aneuploidy score (≥ 5, n = 26) had a shorter median OS than patients with a low (< 5) score (n = 76) (3 vs 17 months: P-value< 0.001). Patients with an increased (n = 10), stable (n = 66), or decreased (n = 28) on-treatment score relative to their baseline score had a median PFS of 1.5, 4.0, and 8.3 months, respectively. Median OS was 3.0, 11.1, and 18.7 months, respectively. In patients with mUC treated with pembrolizumab, the on-treatment mFast-SeqS-based ctDNA level and its dynamics relative to baseline are independent prognostic markers that can be used to identify patients that are unlikely to benefit from pembrolizumab.
Microphthalmia-associated transcription factor (MITF) is crucial for development and survival of melanocytes and serves as a lineage-specific oncogene that is amplified in 10-20% of melanomas. The role of MITF in pathway...Microphthalmia-associated transcription factor (MITF) is crucial for development and survival of melanocytes and serves as a lineage-specific oncogene that is amplified in 10-20% of melanomas. The role of MITF in pathways maintaining genome integrity, such as DNA replication, DNA repair, and mitosis has been extensively studied in melanocytes. In addition to its pro-survival role in melanoma, recent studies have shown that MITF expression has important implications for cancer progression and treatment in other cancer types. Nevertheless, studies on the role of MITF in other tissues are scarce. Here, we show that depletion of MITF causes genome instability in nonmelanocytic cell lineages, which results in activation of P53, cell cycle arrest, and apoptosis. Moreover, we show that P53 activation in MITF-depleted cells is dependent on LATS2, a kinase with an established role in the Hippo pathway. Finally, we show that LATS2 mediated upregulation of P53 is ATR-dependent. Collectively, this study highlights the role of MITF as a genome maintenance factor beyond the melanocyte lineage, which might contribute to the tumor suppressive function of MITF.
T-cell death-associated gene 8 (TDAG8) is a proton-sensing G-protein-coupled receptor that is activated by neutral to acidic extracellular pH. TDAG8 is primarily expressed in leukocytes and leukocyte-rich tissues, includ...T-cell death-associated gene 8 (TDAG8) is a proton-sensing G-protein-coupled receptor that is activated by neutral to acidic extracellular pH. TDAG8 is primarily expressed in leukocytes and leukocyte-rich tissues, including the spleen, lymph nodes, and thymus. Genome-wide association studies have identified TDAG8 as a risk gene for inflammatory bowel disease (IBD). Patients with IBD have an increased risk of developing colorectal cancer (CRC), and TDAG8 has been implicated in regulating anti-tumor immunity. We used the MC38 and azoxymethane/dextran sodium sulfate (AOM/DSS) mouse models of CRC to evaluate the effect of TDAG8 deficiency on tumor growth. Tumor development was assessed by measuring size and weight, and tumor tissue was analyzed by immunohistochemistry (IHC), real-time quantitative polymerase chain reaction (qPCR), flow cytometry, and apurinic/apyrimidinic (AP) site quantification. In the MC38 model, Tdag8-deficient mice presented a significantly increased tumor burden together with significantly increased numbers of neutrophils and monocytes in tumor tissue compared with wild-type (WT) mice. In the AOM/DSS model of CRC, Tdag8-deficient mice exhibited significantly increased tumor size, weight, and number of AP sites compared with WT mice. Additionally, Tdag8-deficient mice showed a significantly increased number of macrophages in tumor tissue and an elevated CD4/CD8 ratio, as confirmed by IHC and flow cytometry. In conclusion, loss of Tdag8 significantly worsened colon cancer progression in mice and correlated with increased infiltration of tumor-associated phagocytes. These findings suggest that positive allosteric TDAG8 modulators could represent a promising therapeutic strategy for CRC treatment.
S. Gopinath, K. Alapati, R. R. Malla, C. S. Gondi, S. Mohanam, D. H. Dinh, and J. S. Rao, "Mechanism of p27 Upregulation Induced by Downregulation of Cathepsin B and Upar in Glioma," Molecular Oncology 5, no. 5 (2011): 4...S. Gopinath, K. Alapati, R. R. Malla, C. S. Gondi, S. Mohanam, D. H. Dinh, and J. S. Rao, "Mechanism of p27 Upregulation Induced by Downregulation of Cathepsin B and Upar in Glioma," Molecular Oncology 5, no. 5 (2011): 426-437, https://doi.org/10.1016/j.molonc.2011.07.004. The above article, published online on 26 July 2011 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor in Chief, Kevin Ryan; the Federation of European Biochemical Societies; and John Wiley and Sons Ltd. Following publication, concerns were raised by a third party regarding the duplications of image elements Figure 7, as well as duplicated western blot bands between Figures 4C and 6B, between Figures 1C and 4C, within Figure 3A and within Figure 6A. Internal investigation confirmed the duplications in these figures and additionally identified undeclared splice marks within Figures 2D and 4C, duplicated western blot bands between Figure 3A and Figure 4A of a previous publication with shared authors (DOI: 10.1371/journal.pone.0011668) where the same bands were presented in a different scientific context. The retraction has been agreed because the concerns were determined to affect the authenticity and reliability of the data and results presented. The authors have been informed of the retraction decision where possible; however, current contact details could not be verified.
Nuclear envelope fragility has been identified as a hallmark of the metastatic process. Indeed, cancer cells undertake a challenging journey through diverse environments during metastasis, notably squeezing through narro...Nuclear envelope fragility has been identified as a hallmark of the metastatic process. Indeed, cancer cells undertake a challenging journey through diverse environments during metastasis, notably squeezing through narrow spaces and dense collagen matrices. In their report, Baird et al. identify a key player in nuclear fragility in confined cancer cell migration: the Lamin B receptor. Its overexpression and clustering in specific regions of the nuclear envelope increase nuclear distortion and fragility, rendering nuclei more susceptible to rupture with consequent chromatin extrusion and genomic instability. Elucidating the mechanisms underlying this process, particularly the receptor's sterol reductase activity, represents a promising step towards the identification of novel therapeutic targets.
Breast cancer is the most frequent malignancy and the second leading cause of cancer-related mortality in women. Estrogen receptor-positive (ER+) tumors are treated with endocrine therapies such as tamoxifen or aromatase...Breast cancer is the most frequent malignancy and the second leading cause of cancer-related mortality in women. Estrogen receptor-positive (ER+) tumors are treated with endocrine therapies such as tamoxifen or aromatase inhibitors (AI), aimed at disrupting estrogen signaling. While these therapies are initially effective, resident tumor cells can develop resistance, leading to relapse. The p21-activated kinase 1 (PAK1), a regulator of oncogenic signaling pathways, has been implicated in tamoxifen resistance. However, it remains unclear whether PAK1 also affects the response to other endocrine therapies. Here we show PAK1 activity was elevated in tamoxifen-resistant and long-term estrogen-deprived MCF7 cell lines and showed enhanced responsiveness to EGF stimulation. Inhibition of PAK1 effectively reduced cell proliferation in both models, with distinct effects on PAK1 downstream substrates. In the tamoxifen resistance context, PAK1 inhibition induced activation of the pro-apoptotic protein BAD and triggered apoptosis while proliferation-related kinases were suppressed in the estrogen-deprived model. Our findings position PAK1 as a mediator of resistance to endocrine therapies suggesting that targeting PAK1 may present a novel strategy to overcome endocrine therapy resistance in ER+ breast cancer.
Grochowski M, Dolinchuk L, Jerzak M
… +10 more, Gandurski A, Grochowski T, Wojtyś W, Zadrożny M, Kaźmierczak W, Lenarcik M, Matejak-Górska M, Samsel R, Olesiński T, Walerych D
Patient-derived organoids (PDOs) are becoming established as preclinical models for predicting therapeutic responses in cancer, yet their clinical accuracy remains limited by the insufficient representation of the tumor...Patient-derived organoids (PDOs) are becoming established as preclinical models for predicting therapeutic responses in cancer, yet their clinical accuracy remains limited by the insufficient representation of the tumor microenvironment and a reliance on static viability readouts. Here, we utilized a living biobank of 30 histopathologically and genetically characterized PDOs, alongside a microenvironment-derived from pancreatic, colon, and gastric cancers, to systematically evaluate their ability to respond to standard-of-care or experimental therapies and model patient outcomes. We assessed the impact of incorporating tissue-matched cancer-associated fibroblasts (CAFs) on treatment responses, finding that their presence not only increased chemoresistance in viability assays but significantly improved patient outcome prediction. To further enhance this predictive accuracy, we developed the Organoid Convolution Assay (OCA), a live-cell imaging-based approach that quantitatively captures dynamics of cell migration, clustering, and assembly during organoid formation. Mathematical modeling of these parameters enabled the significant stratification of donor tumors by stage (T0-T2 vs. T3-T4) and the prediction of patient clinical outcomes. Together, our findings demonstrate that incorporating either tumor microenvironment components or dynamic organoid assembly metrics improves the clinical relevance of PDO-based models.
Therapeutic resistance and disease recurrence remain major unresolved challenges in oncology, primarily driven by tumor heterogeneity and the inherent plasticity of cancer cells. Although multiple biological mechanisms c...Therapeutic resistance and disease recurrence remain major unresolved challenges in oncology, primarily driven by tumor heterogeneity and the inherent plasticity of cancer cells. Although multiple biological mechanisms contribute to these processes, epigenetic mechanisms are the key regulators of clonal diversification and adaptive transcriptional reprogramming under treatment pressure. This regulatory layer operates through reversible transcriptional changes that are independent of DNA sequence alterations, enabling cancer cells to respond to a selective environment. Recent advances in analytical methodologies, particularly single-cell multi-omics approaches, have markedly improved our capacity to dissect these regulatory processes at a single-cell resolution. This review explores how diverse therapeutics, including chemotherapy, targeted agents, immunotherapy, hormonal interventions, and epigenetic drugs, induce the widespread remodeling of DNA methylation patterns, histone modifications, and chromatin accessibility. These therapy-induced molecular changes drive transitions to distinct cellular states that confer survival advantages such as drug-tolerant persister (DTP) phenotypes, senescence-like populations, epithelial-mesenchymal transition (EMT) states, and immune-evasive cell populations. We further evaluated the current single-cell multi-omics platforms for profiling chromatin-based plasticity and identifying biomarkers with direct clinical relevance. Finally, we discuss how integrative multi-layer analyses enable comprehensive characterization of tumor-state evolution, providing a conceptual framework for precision oncology strategies aimed at overcoming resistance.
Platinum chemotherapy is a standard therapeutic choice for advanced urothelial cancer, but biomarkers demonstrating its benefits are limited. We tested whether the tumor microenvironment, particularly B-cell infiltration...Platinum chemotherapy is a standard therapeutic choice for advanced urothelial cancer, but biomarkers demonstrating its benefits are limited. We tested whether the tumor microenvironment, particularly B-cell infiltration, could predict overall survival after platinum chemotherapy. Pretreatment tumors from 189 patients in three cohorts treated with cisplatin- or carboplatin-based regimens underwent bulk transcriptome profiling. Immune cell infiltration and multicellular communities were inferred from gene expression and associated with overall survival using cohort-specific multivariable models and meta-analysis. Higher lymphocyte infiltration was associated with longer overall survival (hazard ratio 0.34, 95% confidence interval 0.16-0.72), driven by B cells and memory B cells (hazard ratio 0.19, 95% confidence interval 0.05-0.75). These associations were confined to cisplatin-treated patients and were strongest in tumors with a pro-inflammatory B-cell-rich community and concordant B-cell gene expression signatures. In contrast, higher myeloid infiltration was associated with shorter overall survival. Pretreatment B-cell enrichment in the tumor microenvironment identified a subset associated with improved overall survival among patients receiving platinum chemotherapy, particularly cisplatin, supporting B-cell-focused biomarker development and spatial characterization of tertiary lymphoid structures in urothelial cancer.
After years of hard work, publishing your manuscript is a critical part of the scientific process to tell others about your findings, to allow scrutiny of your results and in addition, to show your capabilities as a scie...After years of hard work, publishing your manuscript is a critical part of the scientific process to tell others about your findings, to allow scrutiny of your results and in addition, to show your capabilities as a scientist, helping forward your career. Often, however, the process is fraught with rejection, frustration and upset. Within this short editorial, we highlight a few suggestions and initiatives that we hope will make the process of publishing easier and more efficient.