Oncotarget

The current "gold standard" for diagnosing and assessing treatment response is tumor biopsy; however, biopsies are not always feasible, safe or easily repeated during treatment. Utilization of peripheral blood mononuclear cells (PBMCs) as a surrogate for tumor biopsy allows for longitudinal sampling and is a safer, more readily available option. However, collection conditions, sample transfer time across multiple clinical sites, and PBMC processing conditions are external pre-analytical factors that must be understood and controlled to mitigate bias in downstream functional analyses. This study aims to systematically evaluate the pre-analytical variables affecting PBMC integrity and functional immune readouts as a prerequisite for downstream translational biomarker applications. Peripheral blood samples were collected from 80 treatment-naive patients with a diagnosis of head and neck squamous cell carcinoma. Blood was collected in cell preparation tubes (BD Vacutainer(R) CPT), potassium ethylenediaminetetraacetic acid (EDTA), or sodium heparin (SH) tubes and diluted 1:1 with sterile PBS or remained undiluted. PBMCs were processed and cryopreserved immediately or held for 8- and 24-hours before processing. PBMC viability was measured at cryopreservation and upon thawing. CD8+ T cells or natural killer (NK) cells derived from PBMCs were subjected to cytotoxicity assays using flow cytometry. CPT tubes provided lower cell viability and yield at cryopreservation and upon thaw compared to EDTA and SH tubes while dilution had no effect on viability. NK cell cytotoxicity was similar between EDTA and SH tubes irrespective of dilution. However, diluted EDTA tubes resulted in lower T cell cytotoxicity after 24-hour hold. Viability and NK and T cell cytotoxicity were equivalent between cryopreserved PBMCs that were processed immediately or processed after 8- or 24-hour hold. Here we report cryopreservation methods for reproducibility of viable cells that maintain functional immunological capacity even after significant delay in processing allowing flexibility and feasibility for collection from multiple clinical sites for deferred processing.

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas and the most common cause of disease-associated death for Neurofibromatosis Type 1 (NF1) patients. In the context of NF1, MPSNTs develop from benign premalignant precursors. The transition to malignancy is usually accompanied by loss of the polycomb repressive complex 2 (PRC2), leading to aberrant upregulation of many genes. The specific mechanisms disrupted by PRC2 loss remain incompletely understood. There is a significant gap in our knowledge of which cell-surface targets become derepressed and therapeutically actionable following PRC2 loss, contributing to the current lack of effective targeted therapies for MPNSTs. This study aims to address this gap by using cell-surface capture technology with mass spectrometry to profile MPNST models. In doing so, we define PRC2-dependent effects on the cell surface proteome, including specific biological pathways that are enhanced or suppressed at the cell surface protein level. We also create an MPNST cell-surface protein compendium comprised of proteins that are highly expressed across a variety of well-defined MPNST models. We prioritized proteins that are preferentially expressed in MPNST or other cancers and for which FDA-approved therapies already exist. Specific proteins from this compendium were molecularly targeted with antibody-drug conjugates in these models to surmise their therapeutic efficacy. Results reveal PTK7 as a novel and promising target for MPNST. In total, these efforts represent a step toward addressing the knowledge gap in MPNST genesis and identifying new therapeutic targets for further testing. Additionally, this data serves as a resource for other researchers wishing to characterize specific molecular targets. KEY POINTSPRC2 modulates key MPNST signaling pathways through the cell surface proteome Cell surface proteomics identifies a plethora of therapeutic targets for MPNST targeted therapy Antibody-drug conjugates targeting PTK7 show enhanced efficacy in reducing MPNST viability IMPORTANCE OF THE STUDYThis study utilizes advances in biochemistry to profile the surface proteome of malignant peripheral nerve sheath tumors. In doing so, it identifies many proteins whose presence is abundant on the cell surface of MPNST cells. Pre-clinical drug testing shows that use of antibody-drug conjugates may be effective in killing MPNST cells when targeted to epitopes identified in our MPNST cell surface proteome compendium. This study is a departure from more commonly used transcriptomic methods to identify cell surface proteins by using direct surface capture and mass spectrometry, providing a more direct measurement of cell surface protein abundance. Additionally, it identifies a handful of proteins which can be directly targeted pharmaceutically and one in particular, PTK7, whose targeting is highly effective in killing MPNST cells.

Adenoid cystic carcinoma (ACC) of salivary gland is a "immune-cold" tumour. Annexin A3 (ANXA3) is an apoptotic protein found to be participating in immune cell infiltration in tumour microenvironment (TME) of various cancer cases. Significant low expressions of ANXA3 protein found in adenoid cystic carcinoma. We hypothesized overexpressing ANXA3 transforms ACC "cold" TME to "hot". We cultured UM-HACC-2A and UFH2 spheroids on extracellular matrix and co cultured them with peripheral blood mononuclear cells. We functionalized FDA (The Food and Drug Administration) approved Poly(lactic-co-glycolic acid) PLGA nanoparticles with anti-cMyb antibody and ANXA3 recombinant protein using streptavidin-biotin conjugation. Upon overexpressing ANXA3 in ACC spheroids in immune coculture model using functionalized nanoparticles, significant increase of tumour infiltrating lymphocytes and decrease in the size of the ACC spheroids observed. Apoptotic profiler assay further confirmed significant upregulation of apoptotic proteins, some of them participate in immune infiltration. Overall, this project exhibits promising results showing potential approach to convert ACC into an immune "hot" tumour.

Lung adenocarcinomas frequently harbour actionable oncogenic mutations that are vulnerable to treatment with targeted therapies. While responses to targeted therapies are often initially dramatic, relapse is almost inevitable and prevents durable responses in advanced-stage patients. Relapse is, in part, caused by drug tolerant persister cells (DTPs) which are able to survive treatment by entering a reversible, dormant state. Although long non-coding RNAs (lncRNAs) regulate processes thought to allow DTPs to survive and become stably resistant, the potential roles of lncRNAs in DTPs are largely unknown. In this study, we sought to investigate the expression of lncRNAs in in vitro DTP models of lung adenocarcinoma. We found that the lncRNAs Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1) and Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) were enriched in DTPs and that knocking down MALAT1 enhanced the effect of targeted therapies in both EGFR- and KRAS-mutant DTP models. To better understand pathways that MALAT1 might regulate in DTPs, bulk RNA-sequencing was performed and several pathways that may contribute to the actions of MALAT1 in DTPs were identified. Overall, our work describes a role for the lncRNA MALAT1 in DTPs in NSCLC and suggests that MALAT1 may be a novel target for the prevention of drug tolerance and subsequent resistance to targeted therapy in NSCLC.

The association between higher levels of physical activity and lower cancer risk and mortality is well established. However, a causal link is yet to be proven. Recent studies showed a decrease in the proliferation rates of cultured human cancer cells when the human serum employed to stimulate them was conditioned by acute exercise. Here, we tested the hypothesis that serum mediates some of the putative benefits of exercise on cancer through alterations to the growth pattern and susceptibility to chemotherapy agents of cancer cells. To this end, human non-small cell lung cancer (NSCLC) cells were exposed to serum from two cohorts that differed significantly on their levels of physical activity and, accordingly, cardiorespiratory fitness, but were otherwise identical (master athletes and non-exercisers), collected before and after an acute exercise intervention. Serum levels of glucose, lipids, albumin, C-reactive protein and cytokines were determined and the impact of the serum responses to acute and lifelong exercise on the above-mentioned parameters were analyzed. We found that acute exercise decreased the cells proliferation rate, yet shortened the cells lag phase after detachment, whereas lifelong exercise had the opposite effects. Significantly, we showed, for the first time, that lifelong exercise increased susceptibility to a chemotherapy agent (cisplatin), which may contribute to the decreased cancer mortality rates found among those who exercise regularly. Similar to the cellular effects, changes to serum cytokine levels - several of them linked to the senescence-associated secretory phenotype - depended on whether serum was conditioned by acute or by chronic exercise. Key pointsChronic exercise increased the in vitro susceptibility of lung cancer cells to cisplatin. Acute and chronic exercise modulated the in vitro tumorigenic potential of lung cancer cells. Effects were mediated by serological changes produced by exercise. Acute and chronic exercise had distinct impacts on serological cytokine levels.

In the tumor microenvironment (TME), dynamic interactions between cells and soluble factors promote tumor progression. We previously demonstrated that parathyroid hormone-related peptide (PTHrP), a TME-associated cytokine, enhances the aggressive phenotype of HCT116 colorectal cancer (CRC) cells, and that conditioned medium from PTHrP-treated HMEC-1 endothelial stromal cells (CM) induces epithelial-to-mesenchymal transition (EMT) in CRC cells. Here, Western blot analysis showed that CM modulates Met receptor expression and activation and promotes cancer stem cell (CSC) traits in HCT116 cells. Since PTHrP induces CPT-11 chemoresistance through Met signaling, we investigated the involvement of the CM-Met axis in this process. Viability assays revealed that CM increases cell number and confers CPT11 resistance through Met activation. Transforming growth factor beta 1 (TGF{beta}1), upregulated in PTHrP-treated HMEC-1 cells, was evaluated as a potential mediator. Its neutralization reversed the CM-induced increase in cell number but did not affect chemoresistance. In silico analyses revealed differences between CRC and normal tissues related to TGF{beta}1 signaling and Met activation, along with positive correlations among the analyzed markers. Immunohistochemical observation of human samples is consistent with our previous findings. Overall, these findings support a role for PTHrP in promoting CRC aggressiveness through coordinated effects on tumor and stromal compartments

Common knowledge states that the spontaneous somatic evolution of a normal tissue may lead to a tumor. Once the tumor is formed, it naturally evolves towards a state of higher malignancy. On the other hand, perfect gene expression markers for normal tissue and tumor--the so-called N-genes and T-genes--were recently introduced. We join these two pieces of knowledge in order to argue that: 1) Only N-markers participate in the spontaneous dynamics of a normal tissue. The number of active markers decreases as the tissue approaches the transition point where it becomes a tumor. 2) Only T-markers participate in the spontaneous dynamics of tumors. The number of markers increases as the tumor becomes more malignant. 3) Both sets of genes are connected by the so-called NT-genes, i.e., genes that are simultaneously N- and T-markers. They should play a crucial role at the transition point and, possibly, when the tumor is exposed to a drug or therapy. 4) The pathways or mechanisms protecting the normal tissue from becoming a tumor may be described by a small perfect panel of N-genes. 5) The pathways or mechanisms guiding the evolution of tumors in a tissue may be described by a small perfect panel of T-genes. We illustrate the above statements with the analysis of expression data for prostate adenocarcinoma, one of the most heterogeneous tumors. In this case, there are about 1000 N-genes and 6000 T-genes, and the perfect N- and T-panels contain 11 and 8 genes, respectively. Additionally, we provide examples from lung adenocarcinoma and liver hepatocarcinoma.

Osteosarcoma (OS) is an aggressive bone cancer that most commonly affects children and young adults. OS exhibits a high degree of genomic complexity, as well as cellular plasticity, and dynamic transcriptional regulation is suggested to contribute to treatment resistance and metastasis. Cell lines are well characterized as models to advance our knowledge on OS biology. HOS and U2OS cells have increased invasiveness and higher migratory ability compared with MG63. In this study, we employed a tandem array of consensus transcription factor response elements (catTFREs) proteomic approach to characterize transcription factor (TF) regulatory networks related to OS aggressiveness. We mapped 7,594 proteins and enriched 352 transcription factors and coregulators. When we integrated proteomics with cell line specific gene expression and chromatin accessibility we classified the proteins into different OS cell line dependent sub-clusters and identified TFs and coregulators common for all cell lines and specific for individual cell lines. We demonstrate that RUNX2, MYBL2 and HMGA2 are specifically enriched in HOS and U2OS and may be linked to the cell aggressiveness. ETV5, JUNB, NFIX and ZEB1 were among TFs specific to MG63. Our analysis provides a more comprehensive understanding of the transcriptional drivers that shape OS regulatory landscapes and may have future therapeutic implications.

BackgroundChemo-resistance remains a major clinical challenge in Oral Squamous Cell Carcinoma (OSCC), attributed to the intrinsically resistant cells. Although tumour-derived extracellular vesicles (EVs) have been implicated in cell-cell communication, their role in propagating chemo-resistance remains poorly defined. This study aims to identify salivary EV-associated miRNAs capable of predicting chemoresistance and to delineate the role of miR-1307-5p in modulating CSC-driven therapeutic refractoriness. MethodsSalivary EV-derived expression profile of miR-1307-5p was assessed by qPCR in chemo resistant OSCC patients and further validated in TCGA small RNA sequencing datasets. Expression was validated by qPCR and correlated with clinicopathological outcomes. Functional assays including cell-cycle analysis, apoptosis, migration/invasion, 3D spheroids, angiogenesis, and CAM assays were performed in miR-1307-5p inhibited CD44 CSC subpopulation compared to its vehicular control. Transcriptomic profiling cross-referencing with TCGA was conducted to identify potential novel targets of miR-1307-5p. Chemo-sensitisation was assessed by treating the knockdown chemo resistant cells with low dose cisplatin and validating it using in-vitro functional assays and orthotopic xenograft model. ResultsmiR-1307-5p was significantly elevated in salivary EVs of chemo resistant OSCC patients and correlated with poor overall survival (p = 0.03). The miRNA was markedly enriched in endogenously resistant CD44 CSCs. Silencing of miR-1307-5p induced G2/M arrest, triggered apoptosis, impaired invasion, and reduced angiogenesis both in-vitro and in ex-vivo assays. Transcriptomic profiling, TCGA validation, and integrative pathway analysis identified key oncogenic hubs which converge on PI3K-AKT, MAPK/ERK, and YAP signalling pathways governing EMT. Inhibition of miR-1307-5p restored cisplatin sensitivity in resistant CSCs, with low-dose cisplatin producing substantial tumour suppression in-vitro and in-vivo. Reduced CD44 expression in xenograft models confirmed CSC reprogramming. EVs from anti-miR-treated cells confer chemo sensitisation upon uptake by resistant CSCs. Xenograft models substantiated that EVs can initiate tumour formation and that EV-mediated delivery of anti-miR-1307-5p drives significant tumour regression. ConclusionThis study identifies salivary EV-derived miR-1307-5p as a clinically relevant biomarker of chemoresistance in OSCC and reveals its mechanistic role in sustaining CSC-driven therapeutic failure. Targeting miR-1307-5p offers a promising avenue for restoring cisplatin sensitivity and developing exosome-based therapeutic strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/709730v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@19f88e0org.highwire.dtl.DTLVardef@d36b95org.highwire.dtl.DTLVardef@3c2579org.highwire.dtl.DTLVardef@c04ef5_HPS_FORMAT_FIGEXP M_FIG C_FIG

PurposeTreatment options of advanced oral squamous cell carcinomas (OSCC) are limited, and cisplatin toxicity and drug resistance are major clinical issues. Src is a central kinase that integrates multiple oncogenic pathways and a promising therapeutic target. However, Src inhibitors have shown suboptimal efficacy as monotherapies and their sensitivity in OSCC remains elusive. Experimental DesignWe examined the activation of major oncogenic signaling pathways and the antitumor effects of six Src inhibitors (dasatinib, ponatinib, vandetanib, saracatinib, PP2, bosutinib) in seven human OSCC cell lines (HSC-2, HSC-3, HSC-4, SAS, HO-1-u-1, CAL27, SCC-25). BALB/cAJcl nu/nu mice bearing CAL27 xenografts received dasatinib (30 mg/kg, intraperitoneally, daily), bosutinib (50 mg/kg, intraperitoneally, daily), cisplatin (2 mg/kg or 4 mg/kg, intraperitoneally, weekly), or combinations. Tumor volume, bioluminescence imaging, and body weight were monitored for 17 or 21 days, followed by histopathological assessment. ResultsThe activation of the key pathways, including Src and MAPK, considerably differed among the cell lines and was linked to heterogeneous sensitivity to Src inhibitors. Effective growth suppression required Src dephosphorylation and downstream MAPK pathway inhibition, which vary depending on the cell line. Additionally, combination treatment with a Src inhibitor and cisplatin showed additive antitumor effects, allowing the reduction of cisplatin doses by half without efficacy loss. Notably, dasatinib alone and in combination with cisplatin decreased tumor burden with characteristic internal tumor death in vivo. ConclusionsThese findings elucidate Src signaling dependency on OSCC and the potential of Src inhibition to decrease cisplatin toxicity, paving way for Src targeted therapeutic strategies.

BackgroundThis study investigates the role of the pioneer transcription factor FOXA1 as a master gene in sustaining epithelial cell polarization in early-stage lung adenocarcinoma. The partial loss of FOXA1 is explored to determine if it will affect plasticity and progression of lung adenocarcinoma. The study also addresses the transcriptional circuitry that links polarity defects to lysosome homeostasis. MethodsA multiomics approach was used to define the status of the chromatin in epithelial and mesenchymal states of A549 adenocarcinoma cells obtained with a newly synthetized TGF-{beta} receptor inhibitor or TGF-{beta} respectively. The study leveraged ATAC-seq, RNA sequencing, Cut&Tag sequencing of FOXA1 and histone marks profiling. The functional impact of FOXA1 was examined by partial silencing in vitro and by heterozygous FOXA1 deletion in a KrasG12D mouse model. Three-dimensional organoid culture, high-resolution electron microscopy, spatial transcriptomics and multiplex immunohistochemistry assessed carcinoma cell polarity, proliferation, the tumor microenvironment and organelle content. Group differences were evaluated with two-tailed t tests or one-way analysis of variance. ResultsFOXA1 binding and expression were highest in cells harboring an epithelial phenotype. In mouse KrasG12D LUAD tumors FOXA1 marked polarized, CDH1-positive cells; heterozygous loss diminished CDH1, disrupted apical-basal architecture, lowered organoid-forming efficiency and remodeled the immune microenvironment. Spatial transcriptomics and ultrastructural analyses showed that FOXA1-deficient carcinoma cells accumulated lysosomes, down-regulated vesicle fusion genes of the SNARE family and activated the lysosomal CLEAR gene network. FOXA1 occupied enhancers of lysosome-associated genes and competed with the transcription factor TFE3, thereby suppressing transcription of cathepsin B and cathepsin C and restricting lysosome biogenesis. ConclusionsFOXA1 is a central regulator that preserves epithelial cell polarity and limits lysosome formation in lung adenocarcinoma. Targeting the FOXA1-TFE3-lysosome axis may affect tumor plasticity and provide new therapeutic opportunities.

Cancer genomes tend to accumulate a large number of mutations, and even rare mutations such as those causing the loss of a stop codon can be observed in a significant fraction of the tumors. Stop-loss mutations extend protein translation into the 3 untranslated region (3 UTR), generating altered proteins carrying extra amino acid sequences. These C-terminal extensions can potentially have consequences for tumorigenesis and immune recognition. To investigate the prevalence of stop-loss mutations in cancer, and to identify recurrent mutations with a possible tumor-promoting effect, we have interrogated mutation data from the tumor samples of 20,801 patients. This search has resulted in the annotation of 3,757 stop-loss mutations in 3,249 different protein-coding genes. Around 11% of the mutated genes contain recurrent stop-loss mutations, occurring in more than one patient. The protein extensions created by the mutations tend to be hydrophobic and/or positively charged, and these features are associated with an increased propensity to generate MHC I-bound peptides. We have also found that cancer-related genes contain 37% more stop-loss mutations than non-cancer-related genes, with both oncogenes and tumor suppressor genes showing similar enrichments. Furthermore, three out of the four genes with the highest number of stop-loss recurrences, PTMA, PCDH9 and SOX9, are cancer-related. In PTMA, the gene with the largest number of stop-loss mutations (14 patients), the mutation results in an extension of 9 amino acids. We provide experimental evidence that the mutation is associated with impaired cleavage of thymosin alpha 1, a peptide with immunostimulatory functions that is generated from the N-terminal part of the PTMA protein. The study provides evidence that stop-loss mutations are enriched in cancer-associated genes and constitutes a valuable resource for further studies on the effects of stop-loss mutations in cancer.

Early detection of breast cancer remains essential for improving clinical outcomes, and complementary non-invasive approaches are needed to support existing screening methods, particularly for women with dense breast tissue. We have previously reported plasma lipid biomarker discovery using untargeted high-resolution liquid chromatography tandem mass spectrometry (LC-MS/MS). In this study, we performed biomarker confirmation and developed machine-learning models applied to targeted plasma lipid measurements for the non-invasive detection of early-stage breast cancer across international cohorts with independent external validation. Targeted LC-MS/MS was used to quantify candidate lipid panels in plasma samples from European discovery cohorts (n = 554) and an independent Australian cohort (n = 266) used for external validation. Data-driven feature selection identified a 15-lipid panel with strong performance in European cohorts (AUC [≥] 0.94). External validation prior to confidence stratification yielded 76% sensitivity, 64% specificity, and an AUC of 0.81 in the Australian validation cohort. Clinical assay development requires iterative panel and model testing to support translational feasibility and performance in the intended-use population. An analytically viable panel, excluding lipids requiring complex and costly synthesis, achieved comparable accuracy with improved assay robustness. Confidence-based analysis showed enhanced performance for predictions made with moderate to high confidence, with sensitivity up to 89% and AUC up to 0.85, suggesting that ongoing research should focus on strategies to enhance diagnostic model confidence. Importantly, model predictions were independent of breast density, tumour size, grade, subtype, and morphology, indicating biological specificity of the lipid signature. These results demonstrate that calibrated machine-learning models applied to plasma lipid biomarkers can support non-invasive breast cancer detection. Expanding training datasets to include greater diversity will further improve performance in the ongoing development of this lipid-based detection approach.

HES3/Her3 is a transcription factor that functions in non-canonical STAT3 signaling to promote the renewal of neural stem cells and has roles in multiple cancer contexts. To study its role in development and disease, we previously generated a CRISPR/Cas9 zebrafish knockout of her3, the ortholog to human HES3. HES3 is also a cooperating gene in fusion-positive rhabdomyosarcoma, an aggressive pediatric cancer, where HES3 prevents terminal myogenic differentiation, and high expression correlates with worse patient outcomes. Here, we utilize our her3/HES3 knockout model with chromatin and transcriptional profiling techniques to assess its role during early zebrafish gastrulation with the goal of understanding the function of this transcription factor and how these activities are co-opted in cancer. We found that the Her3/HES3 preferential binding motif is distinct from other HES-family members, including a CG-rich E-box motif, that it leverages to modulate the expression of genes involved in neurogenesis and WNT signaling. We also determined that motif preferences of Her3/HES3 altered its interactions with DNA, allowing it to function canonically as a transcriptional repressor with additional duality as an activator. In the context of PAX3::FOXO1, a monogenic driver of fusion-positive rhabdomyosarcoma, we find that Her3/HES3 plays an influential role in modulating the initial activities of this core oncogenic transcription factor. Upon expressing PAX3::FOXO1 in early developing zebrafish embryos, her3 knockout allowed for enhanced activation of neural programs, which are observed in the human disease, along with alterations to cell adhesion programs. Patient tumor samples could be clustered and stratified based on HES3 expression alone. We saw that patient PAX3::FOXO1-positive tumors with high levels of HES3 contained a more neural identity than those with low levels of HES3, altogether suggesting HES3 plays a critical role in regulating this neural signature during both the initial functions of PAX3::FOXO1 and in established tumors.

IntroductionNovel therapeutic options are urgently required to improve outcomes and survival for patients with lung squamous cell carcinoma (LUSC). In particular, understanding the unique histological features that define LUSC is essential to improving lung cancer mortality. Many pre-clinical models fail to accurately represent intratumour heterogeneity and recapitulate the tumour microenvironment. This is partly responsible for the poor translation of clinical findings to approved therapies. Our objective was to investigate whether patient-derived organoids, replicate the histological morphological, and structural features of keratinizing LUSC, a poor prognostic subtype of lung cancer. MethodsOrganoid cultures were established and maintained from two patients presenting with keratinizing lung squamous cell carcinomas. Immunofluorescent staining of individual organoids and confocal microscopy was performed to confirm expression of tumour markers. Whole organoid domes were fixed, and immunofluorescent staining and imaging was performed to investigate the structural features of the organoid cultures. Findings were compared with histopathological features of the original tumour tissue. ResultsPatient-derived organoids expressed tumour markers specific to the squamous cell carcinoma subtype of non-small cell lung cancer, which were confirmed to be expressed in the parent tissue. Within organoid cultures, keratin pearl structures spontaneously developed, matching the keratinizing pattern demonstrated by hematoxylin and eosin staining of the original tumour. ConclusionsPatient-derived organoids have the capability to replicate key histological features of their parent tumour. This high degree of fidelity makes these 3D models an important and valuable tool for understanding complex tumour biology and as a platform for preclinical drug testing to advance novel therapies into the clinic.

BackgroundChimeric antigen receptor (CAR)-T cell therapies efficacy in solid tumors remains limited, largely due to the profoundly immunosuppressive tumor microenvironment (TME) which drives CAR-T cells to dysfunction and poor persistence. A comprehensive understanding of the dynamic interplay between CAR-T cells and the TME is therefore critical for the rational design of more effective CAR-T strategies for solid cancers. MethodsHere, we performed single-cell RNA sequencing of tumor samples from immunocompetent mice treated with stroma-targeting EDA-CAR-T cells, profiling CAR-T cell states and TME programs at the peak of antitumor response and during subsequent tumor progression. ResultsOur analysis revealed a marked temporal remodeling of EDA-CAR-T cells within the TME, where early antitumor efficacy is associated with concurrent expansion of cytotoxic effector CD8 CAR-T cells and activation of memory CD4 CAR-T subsets. Moreover, EDA-CAR-T cells effectively engaged the myeloid compartment, resulting in strengthened communication networks involving T cell activation. However, by tumor progression, EDA-CAR-T cells suffered a widespread transcriptional reprogramming towards dysfunction, characterized by loss of effector programs alongside induction of exhaustion and immunoregulatory pathways within the TME, including PD-L1/PD-L2 and TGF{beta} signaling, which impairs sustained immune responses. Notably, early CAR-T cell activation led to increased susceptibility to TME-mediated immunosuppression, revealing EDA-CAR-T-specific soluble galectin-mediated cell-to-cell interaction networks. ConclusionsTogether, this works offers a high-resolution view of CAR-T cell dynamics within the solid TME, uncovering cellular and molecular mechanisms of rapid functional decline and identifying regulatory pathways within the TME that can be exploited to improve CAR-T cell therapy efficacy in solid tumors. KEY MESSAGES OF THE ARTICLEO_ST_ABSWhat is already known on this topicC_ST_ABSThe determinants of CAR-T cell therapeutic efficacy in solid tumors remain poorly defined, largely due to the complexity of the immunosuppressive tumor microenvironment. In this effort, it is necessary to perform comprehensive and detailed mechanistic studies that capture CAR-T cell dynamics within the solid tumor microenvironment to understand treatment failure. What this study addsWe performed single-cell profiling of stroma-targeting EDA-CAR-T cells, revealing their dynamic reprogramming toward dysfunction within the solid tumor microenvironment. We dissected CAR-T cell states and their cell-to-cell interactions with the tumor microenvironment across response and tumor progression and identified mechanisms linking CAR-T cell functionality and therapeutic failure. How this study might affect research, practice or policyThis study provides comprehensive mechanistic insights from an immunocompetent model that can be leveraged to identify shared determinants of CAR-T cell functionality in solid tumors and potentially guide the rational development of improved CAR-T cell therapies.

Metastasis remains the major cause of cancer-related mortality, and circulating tumor cells (CTCs) are both candidate liquid-biopsy biomarkers and plausible intermediates of metastatic dissemination. Because CTCs are extremely rare in peripheral blood, platform comparisons have often focused solely on recovery. That focus is insufficient for applications that depend on the quality of the recovered material, including single-cell profiling, short-term culture, and functional testing. Here, we compared four CTC isolation approaches: TellDx CTC System, Genesis System, RosetteSep, and flow cytometry, using spike-in experiments in human blood. Capture efficiency was evaluated across all four platforms; purity was assessed for TellDx, Genesis, and RosetteSep; and post-isolation GFP signal persistence in culture was assessed for TellDx and Genesis as an exploratory proxy for short-term post-isolation preservation. Under the conditions tested, TellDx showed the highest recovery (88.1% {+/-} 3.7%), followed by Genesis (40.6% {+/-} 12.1%), RosetteSep (36.5% {+/-} 9.0%), and flow cytometry (7.6% {+/-} 4.5%). TellDx also showed the highest purity score (3.76), whereas Genesis (2.25) and RosetteSep (2.09) did not differ substantially. In the short-term culture assay, TellDx-derived samples retained a higher normalized GFP signal than Genesis-derived samples at 48 h and 72 h. To synthesize these readouts, we propose the Recovery Performance Index (RPI), a composite score integrating recovery, purity, and post-isolation signal persistence. Within this experimental framework, TellDx achieved the highest RPI. These data support two conclusions. First, platform benchmarking for CTC workflows benefits from multidimensional evaluation rather than recovery alone. Second, under this spike-in model and within the specific workflows used here, TellDx performed best among the platforms tested. The principal contribution of this study is therefore the establishment of a practical benchmarking framework that can be expanded in future work using clinical samples, multiple CTC phenotypes, and orthogonal viability assays.

BackgroundDynamic chromatin behavior, which is related to chromatin accessibility, plays a critical role in various genome DNA functions such as RNA transcription and DNA replication/repair. Previous studies using highly synchronized cells showed that average local chromatin motion, captured by single-nucleosome imaging and tracking on a second time scale, remained almost constant throughout G1, S, and G2 phases in living human cells, although possible effects of prolonged drug treatments for cell-cycle synchronization could not be excluded. ResultsTo avoid possible effects of prolonged drug treatment, we combined single-nucleosome imaging with Fucci probes to visualize cell-cycle progression through G1, S, and G2. Using HeLa and HCT116 cells expressing H2B-HaloTag and Fucci probes, we found that local nucleosome motion remained similar on average throughout interphase, except for elevated motion in early G1. Transcription inhibition similarly increased nucleosome motion throughout interphase. Local nucleosome motion also increased following replication stress or DNA damage. ConclusionOur findings suggest that near-constant chromatin motion supports housekeeping functions under similar physical conditions during interphase. Our findings also suggest that cells can transiently change chromatin motion to perform ad hoc tasks in response to signals from inside and outside the cell, such as DNA damage.

HCT116 is a colorectal cancer cell line frequently used in anti-tumor drug development experiments as well as in studies of the molecular machinery of eukaryotic cells. It is well characterized by the presence of several single-nucleotide and short mutations in multiple oncogenes and tumor suppressor genes, including KRAS, PIK3CA, MLH1, CTNNB1, CDKN2A, TGFBR2, and BRCA2. However, its landscape of large genomic rearrangements (LGRs) and copy number variants (CNVs) is still far from being fully understood. Therefore, the aim of this study was to identify LGRs and CNVs in several HCT116 cell line samples using Oxford Nanopore sequencing technology, including three samples from the SRA NCBI database, and to compare common and unique variants across all samples. Using the recently developed eLaRodON tool, we identified 22,666 common LGRs, among which more than 70% of tandem duplications and deletions larger than 80 kb were confirmed by CNV analysis. Among LGRs affecting protein-coding sequences, two in-frame rearrangements were identified: a deletion of exons 4-6 and a duplication of exon 10 in the CCSER1 gene, which encodes a cell division regulator protein. Given its high rearrangement rate in various tumors and the clinical significance of its overexpression, this finding may be potentially useful in future research on this cell line. Regarding differences between samples, we found that LGRs in the laboratory sample and in one of the three SRA NCBI samples occurred more frequently via ALR/Alpha repeats than via Alu repeats, in contrast to common LGRs and those unique to the other samples, a finding that may indicate the presence of unique mechanisms of genomic instability. Thus, this study reveals a broad spectrum of large genomic rearrangements and copy number variants that can be identified in the HCT116 cell line using Oxford Nanopore sequencing, including rearrangements specific to distinct cell line samples.

Abstract Introduction: MET tyrosine kinase (TKI) therapy has improved outcomes in patients with non-small cell lung cancer (NSCLC) harboring MET alterations. However, primary and acquired resistance ultimately limits durability of response. This study evaluated the safety and efficacy of the MET inhibitor capmatinib with the MEK inhibitor trametinib in patients with metastatic MET-driven NSCLC who had progressed on prior treatment with at least one MET inhibitor. Methods: A multicenter phase I study evaluated capmatinib in combination with trametinib in patients with advanced stage NSCLC harboring activating MET alterations and prior exposure to at least one MET TKI. A 3+3 dose-escalation design was employed to assess safety and tolerability of the combination. Results: Three patients (n = 3) were enrolled in the study and completed a median of 3 cycles of therapy. Dose-limiting toxicities, including rash, edema, and nausea, necessitated dose reductions in the first two patients and initiation of the third patient at a lower dose level. Ultimately, all patients discontinued therapy due to treatment-related adverse events. The study was terminated early due to poor accrual and TRAEs. No radiographic objective responses were observed. Conclusions: In this phase I trial, capmatinib plus trametinib was associated with significant treatment-related adverse events and treatment was discontinued in all participants. Based on these findings, further investigation of this combination of MET and MEK inhibitors is not recommended.