Cancer Gene Therapy

Nucleolar alterations are characteristic features of cancer cells; however, how changes in the overall morphology relate to internal subcompartment organization and ribosomal RNA (rRNA) dynamics remains unclear. In this study, the nucleolar organization of non-transformed MCF-10A mammary epithelial cells and MDA-MB-231 breast cancer cells was quantitatively compared. MDA-MB-231 cells exhibited differences in nucleolar morphology, accompanied by altered spatial organization of the dense fibrillar component and granular component, and accelerated intranucleolar trafficking of nascent rRNA. Pharmacological perturbation with SU056 shifted multiple structural and dynamic parameters toward an MCF-10A-like profile. Conversely, transient physicochemical perturbation with 1,6-hexanediol induced several MDA-MB-231-like nucleolar features in MCF-10A cells, which returned to their untreated profile after washout. These findings support the view that cancer-associated nucleolar alterations are an integrated reorganization across morphological, spatial, and dynamic dimensions. The observed reversibility further indicates that cancer-associated nucleolar organization can be remodeled in response to perturbations. By linking the morphology, subcompartment organization, and nascent rRNA dynamics within a common framework, this study provides a basis for exploring the establishment, maintenance, and remodeling of distinct nucleolar profiles in cancer.

BackgroundCancer-associated fibroblasts (CAF) are major regulators of the tumor microenvironment (TME), yet the pathways governing CAF function remain incompletely understood. Type 2 deiodinase (DIO2, D2), which converts thyroxine (T4) to the active thyroid hormone triiodothyronine (T3), has not been systematically investigated in CAF across different solid tumors. MethodsWe analyzed DIO2 expression using single-cell RNA sequencing (scRNA-seq) from primary thyroid tumors, a large integrated scRNASeq thyroid cancer atlas, and publicly available scRNA-seq datasets representing six additional solid tumor types. Bulk RNA sequencing data from the Oncology Research Information Exchange Network (ORIEN) database were used to examine correlations among DIO2, CAF subtype markers, and overall survival (OS). A genetically engineered TPO-CreERT2/BrafV600E/Trp53-deficient (TBP) mouse model was evaluated for CAF-specific Dio2 expression and pharmacologic inhibition of D2 activity. TBP mice were crossed with Dio2-/- (Dio2 KO) mice to investigate the role of Dio2 in cancer development and progression. ResultsDIO2 expression was highly restricted to CAF and was largely absent from epithelial-derived cancer, immune, and endothelial cells. Across thyroid cancer and six additional malignancies, DIO2 was consistently detected in CAF, demonstrating that CAF-specific DIO2 expression is a conserved feature of multiple tumor types. Within thyroid cancer, DIO2 was enriched in myofibroblastic CAF (myCAF) compared with inflammatory CAF (iCAF), and bulk transcriptomic analyses demonstrated stronger correlations between DIO2 expression and canonical myCAF markers than iCAF markers across numerous cancers. Elevated DIO2 expression was associated with worse OS in pancreatic and bladder cancers, paralleling the adverse prognostic impact of increased myCAF abundance. In contrast, thyroid cancer demonstrated an inverse association attributable to loss of epithelial DIO2 expression during tumor dedifferentiation. The TBP mouse model recapitulated human disease, with Dio2 expression restricted to CAF, robust stromal fibrosis, and measurable D2 enzymatic activity that was suppressed by cefuroxime and lenvatinib. Genetic loss of Dio2 in the TME resulted in significantly reduced tumor growth. Conclusions DIO2 is a conserved marker of CAF, and myCAF, across multiple solid tumors and is associated with adverse clinical outcomes in some cancers. The TBP mouse provides a robust preclinical model to define the mechanistic role of DIO2 in CAF biology and to evaluate DIO2-directed therapeutic strategies targeting the tumor microenvironment.

Breast cancer progression is driven by dynamic changes in epithelial plasticity, membrane organization, and intracellular signaling, yet the effects of sustained low-dose chemotherapy on these processes remain poorly understood. Here, we investigated the impact of prolonged low-dose doxorubicin on membrane remodeling, epithelial phenotype, membrane-associated Ras lipid-anchor localization, and autophagy in mesenchymal-like MDA-MB-231 breast cancer cells. Low-dose doxorubicin significantly increased Caveolin-1 expression and enhanced E-cadherin protein levels, accompanied by a transition toward a more compact epithelial-like morphology with increased cell-cell contacts. Live-cell imaging demonstrated a significant reduction in the membrane-to-cytoplasm fluorescence ratio of the lipid-anchored GFP-tH probe, indicating redistribution from the plasma membrane to the cytoplasm following treatment. Analysis of autophagy-related proteins revealed decreased LC3-I together with increased LC3-II, ATG5, and p62 expression, consistent with autophagosome accumulation and impaired autophagic flux. Collectively, our findings demonstrate that low-dose doxorubicin promotes extensive remodeling of plasma membrane organization, epithelial plasticity, membrane-associated lipid-anchor localization, and autophagy. This integrated response reveals previously unrecognized links between membrane architecture, Ras membrane association, and autophagy during phenotypic reprogramming of breast cancer cells, providing mechanistic insight into cellular adaptations elicited by sub-cytotoxic doxorubicin exposure.

Abstract Background: Experimental models that retain endogenous tumor immune complexity are needed to investigate heterogeneous responses to immune checkpoint inhibitors (ICIs) in melanoma. We established patient-derived melanoma organoids (PDMOs) to examine retention of parental tumor cellular components and investigate patient-specific and context-dependent responses to checkpoint blockade. Methods: Fresh melanoma specimens (n=50), including primary tumors, neoadjuvant-treated tumors and tumor-infiltrating lymphocyte (TIL) associated samples were processed for Matrigel-embedded culture of patient-derived melanoma organoids (PDMOs). Characterization and functional studies were performed in subsets of established cultures. Immunofluorescence assessed tumor, stromal, immune, and checkpoint-marker expression in PDMOs and matched parental tissues. NGFR expression was evaluated in relation to organoid establishment and growth. Responses to anti PD1 alone or combined with anti-LAG3 or anti-CTLA4 therapies were evaluated using viability and morphological analyses, with selected models undergoing immune phenotyping and multiplex cytokine profiling. Available clinical outcomes were used for exploratory comparison. PDMOs and matched two-dimensional cultures were evaluated under 21% and 5% oxygen conditions. Results: PDMOs were established from 30 of 50 specimens (60%) and retained melanoma, stromal, lymphoid, and myeloid components identified in matched parental tissues during early culture, together with immune checkpoint expression. Higher NGFR (CD271) expression was associated with greater organoid-forming capacity in an exploratory subset. Responses to checkpoint blockade varied across patient-derived models and regimens, with combination blockade not uniformly producing lower viability than PD1 monotherapy. Ex vivo responses showed parallels with available clinical outcomes, with discordant cases also observed. In three selected PDMOs, divergent PD-1 responses were accompanied by differences in T-cell and myeloid representation, MHCII and AXL expression, and inflammatory versus immunoregulatory cytokine profiles. Under normoxic conditions, PDMOs and matched two-dimensional cultures exhibited divergent treatment sensitivities, including clinically responding cases in which sensitivity was retained in PDMOs but attenuated in monolayers. Changing oxygen tension further altered checkpoint sensitivity within individual PDMOs, with the direction and magnitude of the observed shifts varying by model and regimen. Conclusions: Early passage PDMOs retain key endogenous tumor, immune, and stromal components and support functional investigation of patient-derived melanoma biology. Their heterogenous responses across checkpoint regimens and oxygen conditions provide a platform for investigating how tumor-immune composition and environmental context influence treatment sensitivity.

Background: Relapsed and refractory osteosarcoma (OS) remains a major therapeutic challenge, with fewer than 20% of patients surviving beyond 3 years. Increasing evidence indicates that MYC amplification/overexpression is associated with inferior survival. Small molecule inhibitors and immunotherapies have limited single-agent efficacy in pediatric solid tumors. Using syngeneic cell lines derived from p53-driven and MYC-hyperactivated genetically engineered mouse models (GEMMs) of OS, we tested cabozantinib, a multi-tyrosine kinase inhibitor with immunomodulatory properties, with TIGIT immune checkpoint blockade and investigated mechanisms underlying therapeutic response and resistance. Methods: In vitro cabozantinib sensitivity was established in GEMM-derived cell lines. Mice bearing tibial tumors were randomized to vehicle control, cabozantinib, anti-TIGIT antibody, or combination therapy, and tumor growth and survival assessed after a 3-week treatment period. Temporal RNA sequencing was performed at early (8-15 days) and late (18-24 days) time points to characterize transcriptomic changes associated with efficacy. Results: MYC-hyperactivated cell lines were more resistant to cabozantinib in vitro than p53-driven lines (mean IC50 5.51 vs 0.65 mciroM, p=0.0016). In p53-driven orthotopic models, combination therapy significantly decreased tumor growth and improved survival compared to solvent and cabozantinib alone, while in MYC-hyperactivated models cabozantinib-containing regimens delayed tumor progression relative to control or anti-TIGIT monotherapy, however the addition of anti-TIGIT did not significantly improve survival over cabozantinib alone. Temporal transcriptomics revealed upregulated anti-tumor immune-response pathways and decreased M2 macrophages only with combination treatment in the p53-driven model. In contrast, combination-treated MYC-hyperactivated models demonstrated increased TNF signaling and elevated Cxcl5 and Ccr2 expression, indicative of increased myeloid cell recruitment, and upregulation of extracellular matrix (ECM) remodeling pathways suggest a therapy-induced stress adapted state that propagates treatment resistance over time. Conclusion: New therapies are needed for patients with relapse or refractory OS. By targeting tumor-intrinsic resistance mechanisms and modulating the tumor microenvironment using cabozantinib and anti-TIGIT therapy, improved tumor control and survival was achieved in p53-driven orthotopic OS models. MYC-hyperactivated models were able to overcome therapeutic pressure and employ myeloid recruitment and ECM remodeling programs to achieve treatment resistance. Targeting of these programs should be considered in future studies investigating therapeutic strategies in relapsed and refractory OS.

Purpose: How sarcoma subtypes engage telomerase versus alternative lengthening of telomeres (ALT), and with what consequence, is incompletely defined. Methods: We analyzed 11,792 patients with sarcoma sequenced across 19 centers in AACR Project GENIE v20.0. Telomerase activation was defined as TERT promoter mutation, amplification, or rearrangement, and ATRX/DAXX inactivation served as the ALT proxy, each assessed only where the assay interrogated the locus. Findings were tested for TERT expression in The Cancer Genome Atlas (TCGA), for overall survival (OS) in MSK-IMPACT 50K, and for replication in an independent Foundation Medicine cohort. Mendelian randomization (MR) in FinnGen tested germline telomere length. Results: Telomerase activation (8.8%) and ATRX/DAXX loss (8.0%) were mutually exclusive across subtypes (odds ratio [OR], 0.52; 95% CI, 0.29 to 0.92) and segregated by histology. In MDM2-amplified dedifferentiated liposarcoma (DDLPS), telomerase was activated through TERT amplification (17.2%) or rearrangement (2.7%), never promoter mutation (0/261), and never with ATRX/DAXX loss (0/49; P = .011). TERT-amplified tumors expressed TERT (TCGA; P = .002), and amplification was largely focal. Telomere maintenance alterations were present in 28.0% of DDLPS versus 8.7% of well-differentiated liposarcoma (P < .001) and predicted shorter OS in DDLPS (hazard ratio, 2.04; 95% CI, 1.23 to 3.39; P = .005). ATRX/DAXX loss was more frequent in uterine than extrauterine leiomyosarcoma in GENIE (adjusted OR, 1.96) and in the independent cohort (OR, 1.95; both P < .001). Genetically longer telomeres were associated with liposarcoma (OR per SD, 4.10; 95% CI, 2.15 to 7.81). Conclusion: Sarcoma telomere maintenance is histology-specific and mutually exclusive. In liposarcoma it is acquired at dedifferentiation through focal TERT amplification or ALT and identifies DDLPS with inferior survival.

Poly (ADP-ribose) polymerase inhibitors (PARPi) are the only targeted treatment available for early triple-negative breast cancer (TNBC), an aggressive subtype with limited treatment options. While PARPi are effective in patients with BRCA mutations, resistance to these inhibitors can arise. We previously developed BRCA-mutant cell lines, HCC1395, with acquired resistance to talazoparib and olaparib, and have now developed PARPi-resistant MX1 cell lines in an analogous manner. Ribosomal pathways were upregulated in 3/4 cell lines with acquired PARPi resistance. The resistant cell lines showed high and low basal nucleolar stress based on nucleolar morphology and nucleophosmin delocalization from nucleolus to nucleoplasm. Treatment of these cell lines with the combination of olaparib and a ribosome biogenesis inhibitor, BMH-21, demonstrated synergy in the PARPi-resistant cell lines, but not in the parental cells. Interestingly, HCC1395 cells, which had lower baseline nucleolar stress, showed greater nucleophosmin delocalization with combination treatment than MX1 cells, which had higher baseline nucleolar stress. All four cell lines demonstrated sustained DNA damage with the combination. We extended our investigation to 3 BRCA wild-type TNBC cell lines, BT549, Hs578T, and MDAMB231 and identified synergy in the context of intrinsic PARPi resistance. In MDAMB231 cells, combining olaparib with BMH-21 induced a senescence-like phenotype, increasing gH2AX-positive cells by up to 7.3-fold, senescence-associated B-galactosidase (SA-B-gal) staining by 5.6-fold, and p21 by 3.6-fold. These results were mirrored with a second ribosome biogenesis inhibitor, CX-5461. Finally, we identified distinct patterns of ribosomal pathway activity in a cohort of patients with treatment-resistant TNBC, and found correlations between ribosomal pathways with MYC, proliferation, DNA damage, and senescence. Together, these data identify ribosome biogenesis as a potential therapeutic vulnerability in PARPi-resistant TNBC and support its targeting in combination with PARPi, while demonstrating a broader for ribosome biogenesis in treatment-resistant TNBC.

Detecting somatic mutations is a cornerstone of cancer genomics and clinical genotyping, traditionally relying on whole exome (WES) or whole genome sequencing (WGS) data. While RNA sequencing (RNA-seq) is primarily used to assess gene expression, it can also be utilized for somatic variant detection. RNA-seq inherently captures expressed variants, thereby reducing the identification of passenger mutations and mitigating the annotation biases associated with WES. We performed somatic variant calling and cancer driver detection from tumor RNA-seq data from 1,359 RNA-seq samples with matched WGS from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). Our approach using RNA-seq data, alone, identified at least one putative driver gene in 15 of 16 cancer types, consistent with driver predictions from WGS. We further observed that the variant allele frequency (VAF) of RNA-seq-derived variants reflects their predicted functional impact, providing information specific to transcriptomic data. Because RNA-seq data can be generated and analyzed at lower computational cost and time than WGS or WES, it represents a resource-efficient alternative for cancer driver detection. This study provides an extensive pan-cancer resource of RNA-seq-derived variants from the PCAWG consortium and supports the utility of RNA-seq as a complementary approach for characterizing expressed somatic variation in cancer.

PI3K/AKT signalling is a key driver of ovarian cancer progression and an important therapeutic target. Its deregulation is usually explained by genetic changes and altered signalling at the cell surface. Here, we identify an additional layer of pathway control, in which a change in the level of a cancer-associated ribosomal RNA modification alters the translation of proteins that regulate PI3K/AKT activity. SNORA81 is a high-grade serous ovarian carcinoma-associated H/ACA small nucleolar RNA that directs pseudouridylation of 28S ribosomal RNA at position U4636. Integration of tumour transcriptomes with independent SNORA81-depletion datasets identified 22 SNORA81-linked transcripts with reversed disease-associated expression, 19 of them linked to PI3K/AKT signalling. SNORA81 depletion reduced AKT phosphorylation, impaired cell growth, migration, and altered cell-cycle distribution. Molecularly, polysome profiling following SNORA81 depletion identified 524 mRNAs with altered ribosome association, 485 of which changed independently of RNA abundance and included 29 PI3K/AKT regulators. SNORA81 depletion reduced ribosome association of ITGB4, RASGRP2, IGF1 and FGF18 transcripts, and reduced ITGB4 and RASGRP2 protein abundance. IRAK1 and SPC24 acted as downstream RNA-response genes contributing to selected SNORA81-associated phenotypes. ITGB4 expression partially restored cell growth and restored downstream RNA responses after SNORA81 depletion. These findings identify rRNA modification as a translational regulator of PI3K/AKT signalling in ovarian cancer.

New prognostic biomarkers for oesophageal adenocarcinoma (OAC) may help treatment planning as current staging does not accurately predict survival for many patients. We used a 451 cancer-associated gene panel to assess genomic alterations associated with survival for a cohort of 65 OAC patients who underwent surgical resection without perioperative treatment, reflecting institutional practice at the time. Median age at operation was 72 years, 88% were male, median 32 lymph nodes were removed per patient, and minimum follow-up exceeded 11 years. TNM stages (pTNM, 8th ed.) were 14% stage 1, 14% stage 2, 45% stage 3, and 6% stage 4 (non-locoregional nodal metastases). Copy number changes were common, and somatic mutations were similar to those reported previously. Genetic associations with worse survival included amplification of CCND1 (HR=3.08, p=0.02), EGFR (HR=2.98, p=0.01), loss of ARID2 (HR=2.12, p=0.05), KMT2D (HR=1.99, p=0.07) and missense mutation within RYR1 (HR=2.68, p=0.01). This study identifies candidate genomic prognostic biomarkers in OAC using a cohort treated by surgery alone, enabling assessment of tumour biology independent of the confounding effects of peri-operative systemic therapy and radiotherapy. Several of the identified alterations are potentially targetable, supporting further investigation of genomic profiling to refine prognostication and guide treatment selection.

Metastatic melanoma remains highly lethal despite advances in immunotherapy and MAPK-targeted therapy. The Rac1P29S mutation, present in 4-9% of cutaneous melanomas, confers intrinsic resistance to BRAF and MEK inhibitors. Like other small GTPases, Rac1 lacks suitable pockets for small molecule inhibitor binding, motivating indirect approaches to suppressing its activity. We have previously shown that wild-type Rac1 is sensitive to inhibition of de novo GTP biosynthesis in cancer cells, particularly suppression of the rate-limiting inosine monophosphate dehydrogenase (IMPDH) enzymes. Therefore, we asked whether IMPDH inhibition could suppress Rac1P29S and its associated phenotypes in melanoma. We found that IMPDH inhibition reduced Rac1 activity, impaired Rac1-dependent phenotypes, and induced S-phase arrest in Rac1P29S-harboring cells. Moreover, IMPDH inhibition synergized with the BRAF inhibitor vemurafenib and the MEK inhibitor trametinib in Rac1P29S melanoma cells. Dual BRAF and IMPDH inhibition also resulted in enhanced suppression of MEK and ERK phosphorylation in vitro. In syngeneic mouse models, the FDA-approved IMPDH inhibitor mycophenolate mofetil sensitized Rac1P29S-expressing melanoma tumors to trametinib, including tumors made refractory by prior trametinib exposure. We further identified a feed-forward circuit in which Rac1 sustains IMPDH2 expression levels through JNK and c-Jun/AP1 signaling, potentially coupling the GTPase to its own nucleotide supply. These findings establish GTP biosynthesis as a targetable vulnerability in Rac1P29S melanoma and support IMPDH inhibition as a rational partner for MAPK-targeted therapy.

Cisplatin remains as standard chemotherapy for patients with HNSCC, but rapid development of drug resistance has limited patient benefit. The p53 tumor suppressor plays a central role in the cellular response to DNA damage in cancer, triggering apoptosis to prevent propagation of damaged cells in tumor development. TP53 gene mutations occur in 65-86% of HNSCC. Small molecule PG3 induces the integrated stress response (ISR), leading to apoptosis via the HRI-eIF2-ATF4-PUMA axis. We hypothesized that a combination of PG3 plus cisplatin could increase apoptosis in TP53-mutated HNSCC cells through enhanced induction of the ISR and ATF4. PG3 synergized with cisplatin to inhibit cell viability, leading to potent apoptosis in TP53-deficient cells. The effect was regulated through the HRI-ATF4-NOXA pathway. Furthermore, we identified that cisplatin activates HRI and leads to the degradation of CReP (constitutive repressor of eIF2 phosphorylation) via E3 ligase {beta}-TrCP, contributing to the induction of the ISR. We noted decreased ATF4 levels after treatment with cisplatin, CPT, or PG3 and cisplatin. Thus, combined therapy of PG3 plus cisplatin likely results in adaptation and acquired resistance via degradation of ATF4. We targeted the degradation mechanism of ATF4 by inhibiting {beta}-TrCP1, CK1{delta}, or CK2, respectively. Each approach successfully blocked ATF4 degradation induced by cisplatin or PG3 plus cisplatin and enhanced apoptosis. Our results provide a rational strategy for triple treatments, involving an ISR inducer, a DNA damaging drug, and a {beta}-TrCP inhibitor/CK1{delta} inhibitor/CK2 inhibitor, to achieve potent and prolonged anti-tumor effects and overcome chemoresistance in HNSCC.

Purpose Tarlatamab, a bispecific T-cell engager, has generated favorable response and survival outcomes in relapsed small cell lung cancer (SCLC). Factors influencing tarlatamab-associated treatment outcomes and toxicity have yet to be established. We performed a multivariate analysis to identify biomarkers associated with cytokine release syndrome (CRS) and immune effector cell associated neurotoxicity syndrome (ICANS) and integrated these variables into a novel risk stratification tool to identify patients at high risk of clinically significant toxicity. Patients and Methods Logistic and ordinal regression analyses evaluated the predictive value of variables contributing to the presence and severity, respectively, of CRS and ICANS in 115 patients with ES-SCLC receiving tarlatamab. Selected variables were then tuned using 5-fold cross-validation and incorporated into novel elastic net-based prediction models. Results Rates of observed CRS, ICANS, and dysgeusia were 46%, 28%, and 47%, respectively. ORR (overall response rate) and DCR (disease control rate) were 44% and 58.2%, while 6-month PFS (progression free survival) and OS (overall survival) rates were 30.4% and 54.9%, respectively. Excluding patients on tarlatamab <30 days, presence of dysgeusia was associated with a lower rate of disease progression (HR 0.44, p=0.00691) and death (HR 0.34, p=0.0145). The presence of, increased size and number of extracranial metastases as well as elevated baseline LDH were significantly associated with increased likelihood of CRS. Increased ECOG performance status, increased volume of brain metastases, development of CRS, and elevated baseline LDH were all associated with increased risk of developing ICANS. Our cross-validated risk model successfully predicted CRS grade [&ge;]2 and ICANS events with 90.9% and 75% sensitivity, respectively. Conclusions This exploratory analysis identified several predictive biomarkers of toxicity that successfully stratified low and high-risk populations as part of an internally validated novel risk scoring tool.

Despite the advent of immunotherapy in the treatment of human-papilloma-virus (HPV)-negative head and neck squamous cell carcinoma, the overall prognosis still remains dismal. Novel therapeutic approaches are thus urgently needed. We recently reported that SET and MYND containing 3 (SMYD3), a protein methyltransferase that is known to activate the transcription of its target genes through H3K4me3, is overexpressed in ~60% of HPV-negative HNSCC tumors, it drives proliferation and invasion, and induces resistance to immunotherapy in HPV-negative HNSCC. These phenotypes are mediated partially through transcriptional regulation of cell cycle, EMT and immune-related target genes by SMYD3. Despite its enzymatic inhibitory potency in HPV-negative HNSC cell lines, the commercially available SMYD3 inhibitors EPZ031686 and BAY-6035 demonstrated no in vitro phenotypic efficacy in these cell lines, supporting that SMYD3 exerts its oncogenic functions predominantly through catalytically-independent mechanisms. Thus, to effectively target SMYD3, we designed a series of SMYD3 proteolysis targeting chimeras (PROTACs). Treatment of HPV-negative HNSCC cell lines with SMYD3 PROTACs at nanomolar concentrations degraded SMYD3 effectively and induced a drastic decrease in the proliferative and invasive potential of HPV-negative HNSCC cells. One of the designed compounds, IAP-08, showed a promising DC50 at ~177nM with Dmax of ~90%, and effectively induced the formation of ternary complexes with SMYD3 and the XIAP E3 ligase. Furthermore, IAP-08 showed a favorable pharmacokinetic profile in vivo, underscoring the feasibility for further clinical development of this compound. Mass spectrometry analysis of IAP-08 supported its high specificity towards SMYD3. SMYD3 depletion by IAP-08 in HNSCC cells revealed transcriptional regulation of cell cycle, EMT- and type I IFN response genes, in contrast to SMYD3 inhibition which had only a weak transcriptional effect. In summary, we show that inhibition of the enzymatic activity of SMYD3 is not sufficient to repress its oncogenic activity and provide evidence that depletion through PROTACs effectively targets the oncogenic functions of SMYD3 in HPV-negative HNSCC.

Purpose: Existing prognostic models for brain metastases from lung cancer rely on clinical variables and do not capture the biological heterogeneity of host or tumor factors underlying survival outcomes. We evaluated whether MRI-derived radiomic biomarkers improve prognostic stratification beyond clinical variables. We also investigated their biological correlates using matched histopathology. Experimental Design: This retrospective study included 103 patients with brain metastases from lung cancer and matched pre-operative MRI and histopathology. Radiomic features from T1-weighted contrast-enhanced and T2-weighted fluid-attenuated inversion recovery sequences were combined with clinical variables to train Cox proportional hazards, random survival forest, and DeepSurv models for overall survival (OS), CNS progression, and leptomeningeal (LM) progression. Risk groups from an imaging-only model were compared for clinical and histopathologic differences. Results: Imaging features improved prognostic performance beyond clinical variables across all modeling frameworks, with the combined clinical-imaging DeepSurv model achieving the highest concordance index for OS (0.728). Risk groups from the best-performing model for each endpoint differed significantly in OS (median 26.7 vs. 9.1 months, p < 0.001) and LM progression (p = 0.003), but not in CNS progression. Imaging-only risk groups did not differ significantly in any clinical variable, but high-risk patients were less likely to have tumor-infiltrating lymphocytes (46% vs. 77%, p = 0.010) and PD-L1 expression [&ge;] 50% (10% vs. 32%, p = 0.049). Conclusions: MRI radiomic biomarkers provide prognostic information beyond established clinical variables in lung cancer brain metastases and correspond to features of the tumor immune microenvironment, supporting their potential to refine risk stratification.

HER2-directed therapies are expanding across solid tumors, but ERBB2 amplification incompletely captures HER2 expression and pan-tumor IHC lacks standardization. We developed ERBB2 mRNA, bulk HER2 protein and RNA-signature screening benchmarked against IHC/FISH. Screening identified HER2-enriched populations beyond amplification in a pan-tumor discovery cohort of 1,331 tumor biopsies and validated RNA-based screening in an external cohort of 3,898 tumor biopsies. All six objective responses among 51 treated patients in the discovery cohort occurred in tumors positive by ERBB2 mRNA and the combined RNA-signature. In the external dataset (n=102), ERBB2 mRNA positivity was associated with longer time on treatment (hazard ratio 0.42, 95% confidence interval 0.27-0.64) and overall survival (0.41, 0.25-0.65), with concordant associations for the combined RNA signature. Spatial proteomics comprising 2,721 tiles across 88 samples captured HER2 hetero-geneity and identified HER2-enriched profiles below bulk thresholds. These findings support prospective evaluation of RNA and proteomic screening for treatment selection.

Schlafen 11 (SLFN11) is a key determinant of sensitivity to DNA-damaging therapies in multiple cancers including leukemia, Ewing sarcoma, head and neck cancers, mesothelioma and small cell lung cancer (SCLC). Here, utilizing immunofluorescence microscopy and single-cell RNA sequencing we characterized SLFN11 expression across eight different human cancer cell lines and found cell-to-cell heterogenous expression both at the protein and RNA levels. Gene set enrichment and pathway analyses show that SLFN11 is coexpressed with a distinct stress-response state and enhanced genome maintenance programs while being inversely correlated with protein translation pathways. Publicly available single-cell RNA-sequencing datasets of human SCLC tumors confirmed the heterogeneous distribution of SLFN11 expression and confirmed its association with replication-related transcriptional programs. These findings indicate that heterogeneous SLFN11 expression reflects dynamic regulation at the single-cell level. They also underscore the limitations of bulk proteomic and transcriptome profiling and point to a potential reservoir of intrinsic chemotherapy resistance.

Abstract: Background. Class IA PI3K isoforms are candidate therapeutic targets in small-cell lung cancer (SCLC). The transcriptional consequences of isoform-directed inhibitors in SCLC cells have not been compared genome-wide. Methods. We re-analysed GEO series GSE40564: PIK3CA-altered NCI-H69 cells treated for 24 h with vehicle, PIK-75 (p110-directed) or TGX-221 (p110{beta}-directed), three arrays per group (Affymetrix HG-U133 Plus 2.0). Differential expression used limma, with re-processing from raw files and spike-in-anchored normalisation as sensitivity analyses. Gene sets were assessed by effect size, competitive and rotation tests, and size-matched random-set nulls. Isoform dependency was examined in DepMap CRISPR screens. A PIK-75 response score was tested in 81 primary SCLCs against random-signature nulls. Results. PIK-75 reduced SREBP-controlled sterol- and lipid-synthesis genes (SQLE, HMGCS1, HMGCR, LDLR, SCD; log2 fold-change -1.1 to -1.6). Cholesterol, mTORC1, hypoxia and glycolysis gene sets fell far more than size-matched random sets. E2F-target and homologous-repair genes fell more modestly, including BRCA1 (-0.91). The response was broad: 11,645 of 17,458 genes changed at FDR < 0.05, but only 316 decreased and 20 increased significantly beyond two-fold, an asymmetry that persisted under spike-in-anchored normalisation. TGX-221 changed 358 genes, none two-fold. Its set-level effects were four- to nine-fold smaller and depended on two of three replicates. PIK-75 did not induce canonical FOXO targets, and it inhibits kinases other than p110, so the response cannot be attributed to p110 alone. In DepMap, SCLC lines depended more on PIK3CA than on PIK3CB (median Chronos -0.38 vs -0.15), as did other lineages. In patients, the response score was not associated with survival or subtype beyond what random gene signatures achieve (empirical p = 0.14 and 0.11). Conclusion. PIK-75, but not TGX-221, suppresses an SREBP-centred anabolic transcriptional programme in NCI-H69 cells. Attributing this to p110 requires confirmation with selective inhibitors or genetic perturbation.

Purpose: Lung metastases are the primary cause of death in osteosarcoma patients and treatment response often vary due to convergence of genetic and phenotypic influences in the context of a dynamic tumor-host tissue environment. The purpose of this study was to determine how dynamic tumor- and host-driven receptor tyrosine kinase (RTK)-ERK signaling interactions contribute to phenotypic drug response heterogeneity. Experimental Design: Live-cell time-lapse microscopy and data-driven dynamical modeling was used to resolve ERK activity, FOSL1/Fra-1 reporter expression, and spatiotemporal cell fate in living, biosensor-expressing osteosarcoma lung metastases ex vivo following MCL1 inhibitor exposure. RTK inhibitors were then evaluated for their ability to suppress adaptive signaling and enhance MCL1 inhibitor efficacy ex vivo and in vivo. Results: MCL1 inhibition induced extensive tumor-cell death; however, persistent ERKhigh/Fra-1high reporter cells emerged and were enriched at the tumor-lung interface, consistent with adaptive resistance. Experimental and computational approaches revealed that tumor-cell lysis amplified fibroblast growth factor receptor (FGFR)-mediated ERK signaling in neighboring cells, promoting a targetable drug-resistant state marked by adaptive ERK induction, FOSL1/Fra-1 expression, and correlated with upregulation of known drug resistance pathways Nrf2 and HMOX1. Combinatorial inhibition of FGFR with fexagratinib, or broad-spectrum RTK inhibitor, pazopanib, suppressed adaptive ERK activation and enhanced MCL1 inhibitor response resulting in greater efficacy ex vivo and in vivo. Conclusions: Tumor-host and tumor-cell-lysis-induced FGFR-ERK signaling contribute to spatiotemporally heterogeneous adaptive resistance in metastatic osteosarcoma. These data support combinatorial targeting of RTK signaling with cytotoxic or targeted agents as a strategy to block adaptive resistance and improve treatment efficacy.

PhenoAge, a blood-based biological aging clock, is associated with cancer outcomes, a finding taken as evidence that biological aging shapes prognosis. In 3,067 patients undergoing primary tumor resection, PhenoAge acceleration rose with tumor stage. One or two of its eight blood components, differing by cancer type, carried the prognostic signal, and replacing its general-population weights with equal weights did not weaken it. In cancer, PhenoAge may reflect disease burden rather than biological aging.