Various environmental and endogenous stressors, including ultraviolet (UV) radiation, cytotoxins, and dysregulated translation, can induce ribosome stalling and collisions, disrupting protein homeostasis. The ribotoxic stress response (RSR) is a cellular surveillance mechanism that senses translational stress and activates stress signaling via the MAP3 kinase ZAKα and the stress-activated protein kinases (SAPKs) p38 and JNK. This review outlines the molecular mechanisms behind RSR, distinguishes RSR from other translational stress response pathways, such as the well-studied integrated stress response (ISR), discusses the role of RSR in key cellular processes, and presents new evidence linking RSR to cancer biology. We explore how ribotoxic stress is exploited by chemotherapeutic agents and other compounds to induce cancer cell death, and the potential limitations of such therapeutic strategy. Finally, we highlight future considerations for inducing the RSR pathway in cancer, highlighting both therapeutic potential and the challenges in this emerging field.
Cyclin-dependent kinases (CDK) drive the progression through the cell cycle and thereby form classical targets for cancer therapy. Targeting androgen receptor (AR) is effective against prostate cancer (PC), but frequently leads to development of incurable castration-resistant PC (CRPC). We show that emergence of CRPC is associated with significant upregulation of CDK2 cyclins and downregulation of CDK4/6 cyclins. This rewiring renders CRPC cells dependent on the high CDK2 activity, and CDK2-specific inhibitors efficiently decrease proliferation of PC and CRPC cells. We develop a CDK2 inhibitor-resistant CRPC model and perform a rational compound screen to assess which of the currently used anti-CRPC treatments could augment CDK2 therapy-response. This dual approach revealed that when our CRPC model acquired resistance to CDK2 inhibition, it increased AR signaling, and the combination of CDK2 inhibition with anti-androgens induces synergistic antiproliferative effects on CRPC cells. Importantly, CDK2 inhibitors also show synergistic interaction with cell cycle poisons such as Docetaxel and Cisplatin, and combinatorial effects are also seen with radiotherapy, thereby offering multiple combinations against CRPC. In brief, we propose that CDK2 inhibition provides a rational basis for combinatorial therapy against CRPC.
Sixty percent of papillary thyroid cancers (PTCs) are driven by BRAFV600E, a mutation associated with high inter- and intra-tumoral heterogeneity. PTCs may become highly aggressive anaplastic thyroid cancers (ATCs). While single-cell transcriptomics may resolve this heterogeneity, it is potentially confounded by technical effects whose correction may dampen inter-tumor variations. Here we profiled ATCs and BRAFV600E PTCs with single-nuclei RNA-seq and spatial transcriptomics, and an experimental design disentangling biological and technical variations. It reveals that much transcriptional variation in cancer cells and several immune cell types is idiosyncratic, that is, tumor-specific, a phenomenon obscured by batch integration in a number of single-cell studies. Idiosyncrasies are associated in some cases with genomic aberrations and global tissue states like hypoxia. Beyond idiosyncrasies, differentiation markers SLC5A5 (NIS), TPO, TG, and TSHR are lost in a sequence mirrored by their gain during human thyroid organoids maturation, suggesting a new classification of cancer cell states. PTC cells retain TSHR expression and show features of partial epithelial-mesenchymal transition (EMT) with a massive expression of FN1, which promotes proliferation via an autocrine loop. In contrast, ATCs undergo full-scale EMT, with expression of mesenchymal extracellular components and loss of TSHR. Finally, we show that the microenvironment of cancer cells is driven by inflammation. These findings may help future stratifications of BRAFV600E PTCs.
ADP-ribosylation (ADPRylation) is a post-translational modification best known for its roles in DNA damage responses and cytoplasmic signaling, but it also serves important functions in epigenome regulation. In the nucleus, ADPRylation modulates chromatin structure and gene expression through the coordinated modification of histones and chromatin-associated proteins. Although poly(ADP-ribosyl)ation (PARylation) has dominated the field, particularly as therapeutic targets in DNA repair deficient malignancies, a gap remains in our understanding of how mono(ADP-ribosyl)ation (MARylation)-mediated by mono(ADP-ribosyl) transferases (MARTs)-functions as a discrete, site-specific epigenomic mark. Nuclear MART-mediated ADPRylation modulates the activity, localization, and complex assembly of epigenomic enzymes, and directly modifies histones to influence chromatin accessibility and transcriptional dynamics. These reversible modifications intersect with canonical epigenomic marks, enabling rapid, context-dependent control of gene expression. Emerging studies further implicate dysregulated nuclear ADPRylation in cancer, where altered MARylation of chromatin regulators and transcription factors contributes to aberrant gene expression programs and may represent a novel class of therapeutic vulnerabilities. In this review, we synthesize emerging insights into nuclear ADPRylation, with a focus on MART-mediated regulation of histones and chromatin enzymes, and discuss how this regulatory layer expands current models of epigenomic control in physiology and how its alterations drive oncogenesis, offering novel, nonsynthetically lethal avenues for targeted cancer therapy.
The mutational landscape of head & neck and cutaneous squamous cell carcinomas (HNSCC, cSCC) has major gene alterations involving PIK3CA, NOTCH1, and TP53 among others that contribute to tumorigenesis. In this study, we focused on somatostatin receptor 4 (SSTR4), which was identified in a recent in vivo HNSCC CRISPR screen. Mutations in the SSTR protein family are more commonly implicated in neuroendocrine tumors, and to date, no studies have shown a link between SSTR4 and cSCC/HNSCC. To understand the role of Sstr4 in skin keratinocytes, we employed transcriptomic profiling and proteomic methods and identified enriched pathways and protein-protein interactions (PPIs) networks. Sstr4 activation by J-2156 agonist regulated MAPK-ERK signaling pathway, which simultaneously limited G1 to S phase cell cycle progression. To validate Sstr4 as a driver of cSCC/HNSCC tumorigenesis, we performed a localized and clonal Sstr4 knockout in basal keratinocytes of the Pik3caH1047R oncogenic mouse model using ultrasound-guided in-utero lentivirus injection technology. Tumor formation in mice following Sstr4 knockout occurred rapidly around 12 weeks. Our study is the first to uncover Sstr4 role in cSCC/HNSCC through in-vivo models.
Genetic tumour heterogeneity, driven by clonal evolution, contributes to therapy resistance in many cancers. Most salivary gland cancers, including adenoid cystic carcinoma (AdCC) and myoepithelial carcinoma (MECA), lack effective systemic treatments, highlighting the need to characterise their evolutionary profiles. In this autopsy study, we reconstructed genetic heterogeneity and clonal evolution in two patients with metastatic AdCC and one patient with metastatic MECA. Radiology-guided autopsy was performed between 12 and 56 h after out-of-hospital death. One hundred forty-nine tumour samples were snap-frozen, of which 17 (4-7 per patient) were selected for whole-genome sequencing. Phylogenetic reconstruction was performed using CONIPHER. Autopsy revealed multiple metastatic sites not visible on antemortem or postmortem imaging. MYB-NFIB gene fusions were present across all tumour sites from the two AdCC patients, while a LIFR-PLAG1 fusion was detected in all samples from the MECA patient. All three cases showed extensive genetic tumour heterogeneity and branched phylogenies, suggestive of parallel evolution. Histologic growth patterns were consistent across metastatic sites. Overall, this study demonstrated marked genetic heterogeneity and branched evolution in these AdCC and MECA patients.
Myelodysplastic syndromes (MDS) are a heterogeneous group of pre-leukemic diseases marked by ineffective bone marrow (BM) hematopoiesis, peripheral cytopenia, morphologic dysplasia, and an increased risk of leukemic transformation. Increased programmed cell death (PCD) of hematopoietic stem/progenitor cells (HSPCs) and its associated inflammatory BM microenvironment have been speculated to be one of the major causes of ineffective hematopoiesis. PANoptosis is a collective term for three types of PCD: pyroptosis, apoptosis, and necroptosis. All three are mediated by a very large protein complex called a PANoptosome, composed of the key mediators of the three types of PCD. We reported that the diseased cells in MDS with genetic abnormalities, especially spliceosome mutations, show aberrant hypersensitivity to PANoptotic stimuli. Our study suggests that increased PANoptosis of BM HSPCs is one of the reasons for the ineffective hematopoiesis in MDS patients, and targeting PANoptosis may be a novel treatment strategy for MDS. Here we summarize recent advances in research into PANoptosis and discuss the potential role of PANoptosis in the pathogenesis of MDS. We discuss the potential mechanisms for targeting PANoptotic pathways to treat MDS.
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.
Cachexia, a severe muscle-wasting syndrome, lacks objective biomarkers for early detection. This study aimed to identify circulating microRNA signatures for cachexia and cancer in senior dogs, a comparative oncology model for human disease. Serum microRNA expression was quantified in a cohort of 25 dogs, clinically classified by cachexia and cancer status. We identified a distinct signature for cachexia, with significant downregulation of miR-15a, miR-15b, miR-16, and miR-140. Circulating miR-16 emerged as the most robust individual biomarker for cachexia (AUC = 0.899). Furthermore, a sex-specific analysis revealed that miR-140 was significantly lower in female dogs with cancer compared to noncancer controls (P = 0.045), consistent with a sex- and disease-specific dual suppression mechanism involving estrogen receptor signaling and cachexia-driven systemic inflammation (corrected AUC = 0.667). These findings suggest circulating microRNAs as promising, noninvasive biomarkers for canine cachexia and highlight miR-140 as a candidate sex-specific biomarker for female cancers, warranting validation in larger cohorts. This work reinforces the value of the domestic dog as a spontaneous model for translational biomarker discovery.
Estrogen therapy elicits clinical benefit in ~ 30% of patients with endocrine-resistant estrogen receptor (ER)-positive breast cancer, but its mechanism of action and strategies to increase efficacy remain unclear. Estrogen therapy can induce ER transcriptional hyperactivation and DNA damage; we postulated that such damage could be exacerbated by epigenetic dysregulation via inhibition of histone deacetylases (HDACi). We evaluated the effects of 17b-estradiol and HDACi in three types of ER+ breast cancer models: Cells adapted to growth following long-term estrogen deprivation; cells engineered to overexpress exogenous ER that confers endocrine resistance; mice bearing endocrine-resistant patient-derived xenografts. Assay endpoints included apoptosis, growth, DNA damage, histone post-translational modification, levels of ER-regulated transcripts and encoded proteins, cell cycle and replication status, and genome-wide chromatin accessibility, ER binding, and transcriptional profiles. Entinostat treatment increased histone acetylation and chromatin accessibility. Combination treatment with E2 and entinostat inhibited cell growth and induced apoptosis in ER-overexpressing models. E2 and entinostat induced DNA damage as single agents and in combination. These agents synergized against tumor models, offering HDACi as a strategy to enhance efficacy of estrogen therapy.
Sickle cell disease and cancer represent fundamentally distinct classes of human disease-one is driven by a defined mutation in β-globin, whereas the other arises through complex genetic and epigenetic alterations that reshape cellular identity and behavior. Despite these differences, both contexts illustrate how transcription factors, chromatin regulators, and cis-regulatory elements can impose disease-relevant gene expression states. In β-hemoglobinopathies, therapeutic reactivation of fetal hemoglobin through modulation of γ-globin (HBG1/2) regulatory pathways, most notably disruption of the erythroid-specific BCL11A enhancer, has emerged as a clinically validated strategy. These advances have been facilitated in part by the HUDEP-2 erythroid progenitor cell line, which provides a tractable adult erythroid model for identifying fetal hemoglobin regulators, validating their function, and evaluating relevant gene editing and gene-regulatory therapies. Many of the regulators implicated in γ-globin silencing, including BCL11A, ZBTB7A, NuRD-associated proteins, DNMT1, KDM1A/LSD1, MYB, and ATF4, also function in cancer-associated transcriptional or epigenetic networks. In cancer, these factors can support oncogenic transcription, tumor suppressor repression, impaired differentiation, stress adaptation, invasion, or therapy resistance. This review summarizes discoveries enabled by HUDEP-2 cells in fetal hemoglobin regulation and hemoglobinopathy therapeutic development, then discusses how these mechanisms provide conceptual parallels for understanding and targeting regulatory dependencies in cancer.
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.
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.
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 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 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.
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.
