Serotonin plays a regulatory role in cancer progression, but its role in glioblastoma growth, the most frequent and aggressive malignant brain tumor, is unclear. The expression and cellular distribution pattern of key components of the serotoninergic system in glioblastoma cells have not been fully characterized. Using transcriptomic analysis of public datasets, we identified subtype-specific expression pattern of serotonin-related genes. The biosynthetic enzymes tryptophan hydroxylase 1 and 2 and the serotonin transporter (SERT/SLC6A4) were enriched in the classical (CL) and proneural (PN) molecular subtypes, whereas monoamine oxidase-A expression was uniformly distributed across all subtypes. Notably, the serotonin receptors HTR1D and HTR7 transcripts were upregulated in ME and CL tumors. Additionally, by using RT-qPCR and immunofluorescence, we observed a differential expression and intracellular distribution pattern of all serotoninergic system elements in human glioblastoma-derived cell lines. Our findings demonstrate the differential expression and cellular localization of the serotoninergic elements in human glioblastomas and suggest their potential participation in their progression.

Oral cancer has high mortality and recurrence rates. This is attributed to resistance to the process of regulated cell death and resistance to radiotherapy and chemotherapy. Oral squamous cell carcinoma (OSCC) accounts for the majority of oral cancers. Its prognosis varies with the site, clinical stage, and histological grade of the tumor. Owing to the variation in the biological behavior of OSCC, the existing prognostic parameters have some limitations in terms of providing precise information on prognosis. The remarkable biological effects of vitamin D against oral cancer have been documented in various studies. These include antiproliferative and anti-invasive effects, inhibition of angiogenesis, stimulation of mutual adherence of cells, and induction of apoptosis in OSCC. Furthermore, vitamin D increases the sensitivity of OSCC tumor cells to chemotherapy. This phenomenon has been observed in tumors that are resistant to chemotherapy. These findings indicate that the biological effects of vitamin D may provide significant prognostic value in oral cancer patients. In addition, the administration of vitamin D improves the quality of life of patients with inoperable oral cancer lesions in addition to the reported increase in tumor sensitivity to chemotherapy. A low level of vitamin D is associated with increased oral cancer risk. A high frequency of vitamin D deficiency and pleomorphism of the VDR have been reported in oral cancer patients. Poorly differentiated and aggressive OSCCs exhibit more CYP24A1 and VDR polymorphisms and less CYP27B1. Determination of the serum level of vitamin D and identification of VDR, CYP24A1, and CYP27B1 in oral cancer cells may be of significant prognostic value in oral cancer patients and may significantly improve the management of head and neck cancers.

This study investigates the functions of chromobox 6 (CBX6) in esophageal squamous cell carcinoma (ESCC) and delves into its functional mechanisms. The bioinformatics insights suggested that CBX6 was overexpressed in ESCC and linked to dismal prognosis. Cbx6 knockdown was induced in mouse mEC25 cells. This procedure curbed the proliferation and migration of mEC25 cells and reduced exhaustion of the co-cultured CD8+ T cells. In vivo, Cbx6 knockdown in mEC25 cells reduced tumorigenesis while enhancing immune activity in mice. Further experiments showed that CBX6 reduced CD8+ T cell cytotoxicity by secreting C-C motif chemokine ligand 8 (CCL8) and promoting monocarboxylate transporter 4 (MCT4)-mediated lactate transport. Regarding the mechanism, CBX6 regulated the expression of SWI/SNF related BAF chromatin remodeling complex subunit D1 (Smarcd1) to modulate chromatin remodeling, thus promoting transcription of Ccl8 and Slc16a3 (encoding MCT4). Smarcd1 overexpression restored metabolic activity in mEC25 cells, reduced activity of co-cultured CD8+ T cells, and promoted tumorigenesis in vivo. Tissue microarrays analysis suggested that CBX6 and SMARCD1 were linked to immunosuppression and poor prognosis in clinical samples. In conclusion, this study suggests that CBX6 induces CD8+ T cell exhaustion and tumor development in ESCC through SMARCD1-mediated CCL8 secretion and lactate efflux.

Atypical teratoid/rhabdoid tumors (ATRTs) are rare, aggressive Central nervous system (CNS) tumors in young children with poor prognosis. Molecular subgrouping (ATRT-TYR, ATRT-SHH, ATRT-MYC) is crucial for understanding biology, guiding treatment, and predicting outcomes. This study assesses immunohistochemistry (IHC) as a surrogate for molecular subgrouping and is the second study to analyze histomorphological patterns across subgroups.

This study aims to identify core genes closely associated with the diagnosis and prognosis of colorectal cancer (CRC) using transcriptome-based meta-analysis approach and machine learning algorithms. Nine CRC datasets from the GEO database were integrated for differential gene expression analysis and WGCNA to identify key genes. Ninety-six combinations of machine learning algorithms were employed to further refine the selection of core genes and validate their diagnostic performance. Functional enrichment, molecular pathways, and associations with the immune microenvironment of core genes were analyzed using GSEA, CIBERSORT, and ssGSEA. Drug sensitivity predictions were performed to evaluate the impact of core genes on CRC drug response, and molecular docking simulations were used to identify candidate compounds targeting the core genes. A total of 26 core genes were identified, among which the high expression of the SACS gene was significantly associated with poor prognosis, advanced stage, and specific pathological subtypes in CRC patients. GSEA revealed that high SACS expression prominently activates cell cycle regulatory pathways and immune pathways while suppressing metabolic pathways. Furthermore, in vitro experiments demonstrated that SACS is highly expressed in CRC cells and that its knockdown significantly inhibits CRC cell proliferation, suggesting its functional role in tumor growth. Immune analysis showed that high SACS expression was positively correlated with activated NK cells but negatively correlated with Tregs and resting NK cells. Drug sensitivity analysis indicated that high SACS expression reduces sensitivity to oxaliplatin. Molecular docking identified coumestrol and quercetin as potential compounds targeting SACS. SACS promotes CRC progression by regulating cell cycle pathways, the immune microenvironment, and metabolic pathways. And it may serve as a potential therapeutic target for CRC.

Genome-wide association studies (GWAS) have identified numerous single-nucleotide polymorphisms (SNPs) associated with various diseases, including cancer. However, the mechanisms by which these SNPs contribute to disease susceptibility remain largely unclear. While recent studies have explored the transcriptional impact of disease-associated SNPs, their role in post-transcriptional regulation has been less extensively investigated. In this study, we investigated whether cancer-associated SNPs influence gene expression by altering N6-methyladenosine (m6A) RNA methylation. We collected GWAS-identified SNPs across nine cancer types and integrated these with matched tumor and normal m6A RNA immunoprecipitation sequencing (m6A-seq) and RNA sequencing (RNA-seq) datasets. We first identified differentially methylated m6A sites and assessed whether cancer-associated SNPs were enriched within these regions. These analyses revealed that cancer-associated SNPs were significantly enriched within hypermethylated m6A regions in colon cancer. Integrative analysis revealed that SNPs enriched in m6A-modified regions are associated with altered gene expression and RNA splicing, suggesting that m6A methylation mediates the post-transcriptional impact of genetic variants. Experimental validation further confirmed altered gene expression following ALKBH5 knockdown, consistent with patient-derived data. Collectively, our findings support a novel mechanistic connection between genetic variants and RNA methylation-driven transcriptomic regulation in colorectal cancer, underscoring the epitranscriptome as a potential axis of oncogenic control.

Microarray technology has revolutionized cancer genomics by enabling the simultaneous analysis of thousands of gene expressions, providing critical insights into gene regulation and disease mechanisms. However, the inherent challenges of high-dimensionality, noise, and sparsity in microarray data demand robust analytical approaches. Image processing techniques further enhance this analysis by extracting meaningful patterns from histological and microarray-derived visual data, aiding in biomarker discovery and classification. This study presents a novel framework leveraging deep neural networks for gene selection and cancer classification using microarray data, addressing the challenges of high dimensionality, noise, and sparsity. The proposed Gene-Optimized Neural Framework (GONF) integrates the Minimum Redundancy Maximum Relevance (mRMR) gene selection method with a deep Convolutional Neural Network (CNN) for effective feature selection and classification. By optimizing hyperparameters and employing advanced preprocessing techniques, the framework enhances computational efficiency and accuracy. Experiments were conducted on TCGA and AHBA datasets, utilizing metrics such as accuracy, precision and recall for evaluation. The GONF outperformed other methods, achieving a classification accuracy of 97% on the TCGA dataset and 95% on the AHBA dataset. The framework demonstrated significant reductions in false positive and false negative rates, improving cancer subtype predictions and providing biologically interpretable results. The findings highlight GONF's robustness and adaptability, paving the way for its application in other genomic studies and clinical settings.

The link of epithelial-mesenchymal transition (EMT) program with metastasis is well documented. However, the role of ROS in EMT process is self-contradictory. DpdtpA was a dithiocarbamate derivative (an iron chelator) that exhibits excellent growth and wound healing inhibitory effects in colorectal cancer (CRC) cell lines, but the underlying mechanism of action was not fully determined. The present data in this study revealed that the ROS derived from autophagic degradation of ferritin were conducive to EMT repression. Genetically knockdown of NCOA4 promoted expression of mesenchymal characteristics, supporting that NCOA4 involved EMT regulation. In addition, DpdtpA treatment also caused depletion of Gpx4 and xCT, triggering ferroptosis as Erastin acted. The causal relationship analysis demonstrated that depletion of Gpx4 and xCT, (or ferroptosis) contributed to the EMT inhibition. Moreover, there seemed to be a feedback loop between Gpx4 and xCT, knockdown of Gpx4 led to upregulation of xCT, but knockdown of xCT brought about downregulation of Gpx4. Further study demonstrated that the depletion of Gpx4 and xCT was due to enhanced autophagy. In addition, PI3K/AKT/mTOR/pathway was showed involving EMT and ferroptosis regulation. In short, our data suggested that the status of EMT and ferroptosis largely was dominated by the continuous NCOA4-mediated ROS production.

Background Neoadjuvant chemotherapy (NAC) is a standard approach for treating locally advanced gastric cancer (GC), but resistance in some patients can result in treatment toxicity and surgical delays without therapeutic benefit. Identifying biomarkers predictive of NAC response is crucial for personalized treatment strategies. This study evaluated circulating microRNAs (miRNAs) as potential biomarkers for NAC response. Materials and methods Plasma samples from 39 GC patients undergoing NAC followed by gastrectomy (NCT04223401) were collected before treatment. Four miRNAs (miR-19a, miR-21, miR-27a, miR-200c) were analyzed via quantitative real-time polymerase chain reaction. NAC response was assessed in histological specimens using the Becker tumor regression grade (TRG), which classifies patients as Responders (TRG 1-2) or Non-responders (TRG 3). Results Among 39 patients, 20 (51%) were Responders, and 19 (49%) were Non-responders. miR-19a, miR-21, and miR-200c were significantly upregulated in Non-responders (p < 0.05). ROC analysis revealed miR-19a (AUC: 0.693), miR-21 (AUC: 0.700), and miR-200c (AUC: 0.772) as predictive of resistance. Univariate analysis revealed a correlation between higher levels of miR-19a, miR-21, and miR-200c and a low neutrophil count, with increased resistance risk. Multivariate analysis confirmed miR-200c as an independent predictor of resistance (OR: 20.90; 95% CI: 1.54-283.73). Conclusions This pilot study identifies circulating miR-19a, miR-21, and miR-200c as novel biomarkers for poor NAC response in GC, providing a foundation for personalized treatment strategies.

Gallbladder cancer (GBC) is a highly aggressive malignancy with limited therapeutic options, particularly in underrepresented populations, including South Africa. Understanding the molecular landscape of GBC may provide novel insights into its pathogenesis and potential therapeutic targets. Molecular changes are known to be associated with GBC, however, there is a paucity of this information especially in African populations. Furthermore, within the tumour microenvironment, different immune cells contribute to GBC progression. We investigated gene expression patterns in GBC tumours and their association with different immune cells in a cohort of South African patients. RNA sequencing was conducted on 2 normal and 8 gallbladder cancer tissues from South African patients to identify differentially expressed genes. Bioinformatics tools were used for pathway analysis, while immune cell quantification was performed using the quanTIseq software and presented as median [IQR]. Verification studies were further carried out using real-time PCR on an independent cohort comprising 7 gallstone samples and 26 gallbladder tumour samples. A total of 65 genes were found to be significantly differentially expressed between the gallbladder tumours and gallstone controls. We also identified 37 upregulated and 28 downregulated genes in this cohort. Among the most upregulated genes, MUC16 was confirmed to be significantly overexpressed in tumours. Normal tissues exhibited a significantly higher proportion of dysregulated genes associated with B cells (17.132 [14.866-18.483], p < 0.0001) and M1 macrophages (18.943 [1.097-36.790], p < 0.0001) compared to tumours. In contrast, tumours showed a greater association with dysregulated genes linked to regulatory T cells (Tregs) (14.373 [9.696-20.162]) relative to normal tissues. Pathway analysis further revealed the upregulation of defective GALNT12, defective GALNT3, defective C1GALT1C1 and termination of O-glycan biosynthesis, highlighting key mechanisms potentially involved in tumour progression. The study has shown the dysregulation of key genes in South African gallbladder cancer patients. Specifically, MUC16 was verified to be significantly elevated in tumour samples. Furthermore, the association of these dysregulated genes with key immune cells in this patient group may further highlight their roles in dysfunctional immune processes linked with tumourigenesis.

Patients with metastatic testicular cancer (TC) treated with cisplatin-based chemotherapy (CBCT) are prone to develop metabolic syndrome (MetS). In an epigenome wide association study in patients with TC we have shown that DNA methylation was associated to CBCT. The aim of the study was to investigate whether there was a change in DNA methylation after treatment with CBCT, and if methylation status is related to the presence or development of MetS. In a prospective cohort of 67 TC patients who received CBCT, we assessed whole blood global methylation long interspersed nuclear element-1 (LINE-1) and DNA methylation at selected cytosine-phosphate-guanine dinucleotide (CpG) sites associated with MetS using targeted sequencing. Measured samples were taken before, one month after, and one year after CBCT. Development of MetS was assessed before and up to five years after CBCT. Serum platinum levels were measured to assess platinum exposure (PtAUC) within the first year after the start of CBCT. Data were used for paired comparisons, comparisons between groups, statistical modeling to account for covariates, and machine learning approaches to predict occurrence of MetS five years after diagnosis. Global methylation did not change during the first year after the start of CBCT (median 73.7% (25th -75th percentile 72.0-75.2) vs. 73.9% (72.5-75.1)). Seven out of the 16 other selected CpGs decreased. Patients with MetS before start of CBCT (N = 18) showed a larger decrease than patients without MetS (N = 49) for AC090023 (-11.6% vs. -8.2%, p = 0.008), NCAM2 (-6.5% vs. -1.6%, p = 0.030), and TOM1L2 (-5.8% vs. -2.6%, p = 0.003). The 15 patients who did not have MetS prior to CBCT, but developed MetS within five years after treatment showed an increase in global methylation (1.5% vs. - 0.6%, p = 0.008) after one year, and a decrease in TOM1L2 methylation (-4.0% vs. -1.6%, p = 0.015) when compared to patients who did not have prior to CBCT nor developed MetS (N = 34). There was no difference in PtAUC during the first year after the start of CBCT between the latter groups (70.0 vs. 67.9 days*mg/L, p = 0.206). Changes in global DNA methylation and TOM1L2 one year after the start of CBCT are associated with a higher risk for newly developing MetS within five years. This may indicate potential for tailored advice, based on epigenetic status, to patients treated with chemotherapy for TC to prevent development of MetS.

Diffuse intrinsic pontine glioma (DIPG) is a fatal brainstem tumor desperately in need of better treatments. Chimeric antigen receptor (CAR) T cell therapies for DIPG have demonstrated clinical tolerability and bioactivity, but not universal benefit. A major obstacle is insufficient CAR T cell trafficking to the tumor. As our recent clinical trials have demonstrated locoregional elevation of CXCL10, a ligand of the chemokine receptor CXCR3, here we aim to leverage this CXCL10 upregulation to enhance cell trafficking by engineering our B7-H3-targeting CAR T cells to overexpress CXCR3 variants. We demonstrate that, compared to unmodified B7-H3 CAR T cells, CXCR3-A-modified CAR T cells migrate more efficiently toward CXCR3 ligands in vitro, and when delivered intracerebroventricularly in orthotopic DIPG mouse models, CXCR3-A-modified CAR T cells show enhanced trafficking into the tumor and improved therapeutic efficacy. Overall, our data support the potential for engineering CXCR3-A expression to enhance CAR T cell trafficking and efficacy against DIPG.

Increasing evidence indicates that activation of oncogenic pathways contributes to an unfavourable tumour immune microenvironment (TIME), ultimately resulting in resistance to immunotherapy. Here, we aim to identify a critical oncogenic pathway involved in an antigen-expressing c-MYC-lucOSOE/Tp53KO hepatocellular carcinoma (HCC) mouse model that simulates immune response against tumour-associated antigens. Using data-independent acquisition proteomics, we reveal the role of wild-type KRAS in immune escaped mouse HCC tumours, with EGF concurrently activating EGFR/MEK/ERK signalling. Single cell RNA sequencing data analysis reveals that KRAS signalling intrinsically inhibits interferon-mediated MHC-I expression and extrinsically impairs CD8+ T cell activity due to the suppression of CXCL9 through the EGFR/MEK/ERK pathway. We observe KRAS activation in HCC patients who received immune checkpoint inhibitor (ICI) treatments, where it correlates with poor clinical outcomes. Notably, combination therapy with SOS1 inhibitor MRTX0902, Trametinib, and anti-PD-1 antibody effectively increased intratumoural CD8+ T cell infiltration and improved survival. Our study thus reveals that targeting wild-type KRAS signalling in combination with ICIs may serve as an effective treatment strategy for advanced HCC patients.

The clinical data of patients with acute myeloid leukemia (AML) treated at Hebei Yanda Lu Daopei Hospital between August 1, 2024, and March 1, 2025 were retrospectively included, to differentiate AML with the same recurrent t(11;12)(p15;q13) karyotype but harboring distinct rare fusion genes, namely NUP98::RARG::LINE-L2a and NUP98::HOXC13. Two patients were included: Patient 1, a 12-year-old male, visited Hebei Yanda Lu Daopei Hospital on August 8, 2024, due to "fever for 4 days accompanied by sore throat"; Patient 2, a 33-year-old female, visited the hospital on September 22, 2024, due to "recurrent fatigue and cough for over one month". Case 1 and Case 2 carried the NUP98::RARG::LINE-L2a and NUP98::HOXC13 fusion genes, respectively. The patient with NUP98::RARG::LINE-L2a fusion genes exhibited bone marrow morphology and immunophenotypic features resembling acute promyelocytic leukemia (APL) but was resistant to all-trans retinoic acid. Although initial treatment achieved remission, early relapse occurred. The patient with NUP98::HOXC13 fusion genes showed increased myeloblasts, the presence of Auer rods, and an elevated proportion of promyelocytes, along with mutations in FLT3-TKD gene, RUNX1 gene and, WT1 gene, demonstrating resistance to multiple chemotherapy regimens. Both patients underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) without achieving complete remission. After transplantation, they were followed for 8 and 9 months, respectively, with quantitative monitoring of fusion genes showing negative results. Although the patients with NUP98::RARG::LINE-L2a and NUP98::HOXC13 fusion genes have completely identical chromosomal abnormalities, but they are different rare molecular subtypes. Both involve the NUP98 gene. The former partner gene is RARG, with clinical manifestations, bone marrow morphology, and immunophenotype similar to APL. The latter partner gene is HOXC13, with the characteristics of NUP98-AML patients.

Immunotherapy has transformed cancer treatment, highlighting the importance of effective antitumor immunity to fight cancer. However, its success in pediatric cancer remains limited, underscoring the urgent need to identify new immunotherapeutic targets. In this study, we explored the clinical relevance of B cells and tertiary lymphoid structures (TLS) in neuroblastoma (NB), a pediatric tumor with a heterogeneous immune landscape.

This study aimed to investigate the clinical significance of actinin-4 in endometrial carcinoma. Actinin-4, an actin-binding protein involved in cytoskeletal dynamics, has been implicated in the progression of various cancers; however, its precise role in endometrial carcinoma is not fully understood. This research sought to evaluate actinin-4 protein expression and gene amplification and correlate these findings with clinicopathological parameters and patient survival to determine its prognostic value.

The tumor microenvironment (TME) contributes to breast cancer heterogeneity and outcome but is rarely considered in clinical decision-making. We address this gap by systematically characterizing the TME's cellular composition to establish its independent clinical utility across intrinsic and genomic subtypes. We first compare 15 TME profiling methods in 693 samples and then apply the deconvolution algorithm InstaPrism to a meta-dataset of 14,837 expression profiles. We identify seven distinct TME patterns that associate with disease-free survival independently of intrinsic subtype. We also identify TME features that modulate chemotherapy response, relapse, and metastatic risk, with divergent patterns observed across estrogen receptor subtypes. Notably, long-term recurrence was regulated by vascular stromal cells and the innate immune response. Furthermore, the depletion of B cell lineage derivatives in metastatic lesions suggests an opportunity for therapeutic intervention. These results provide evidence for using TME characterization as a prognostic and predictive biomarker and identify potential targets for TME-based intervention.

The mechanisms underlying sustained proliferation and aberrant cellular plasticity that drive early breast tumorigenesis remain unclear. Using CRISPR knockout (KO) screens, we systematically characterized the regulators of cellular fitness in the normal mammary epithelium. We found that loss of METTL3 stimulates mammary epithelial proliferation and reprograms gene expression in an m6A methyltransferase-dependent manner. Single-cell analysis in normal breast organoids revealed that METTL3 ablation causes disruption of the mammary cellular hierarchy through increased aberrant luminal differentiation. Mechanistically, METTL3 loss reduces RNA m6A modification of transcribed transposable elements leading to their increased expression and upregulation of interferon-STAT signaling. This inflammatory response leads to cross talk between STAT and GATA3 transcription factors, resulting in transcriptional activation of luminal genes in the mammary epithelium. These findings identify a cell-intrinsic epigenetic loop contributing to mammary epithelial differentiation and highlight a potential role of loss of METTL3-dependent m6A modification during neoplastic transformation.

The WNT signaling pathway has long been implicated in tumorigenesis across multiple cancer types, including breast cancer. However, the complexity arising from the large number of WNTs and their receptors has made it challenging to pinpoint specific components driving tumor development. Using the MMTV-Wnt1 genetically engineered mouse model, which develops mixed-lineage mammary tumors resembling triple-negative breast cancer and composed of both basal and luminal subtypes, we identify the frizzled class receptor 7 (Fzd7) as a key player. Fzd7 is expressed on mammary tumor cells that show enhanced tumorigenic potential in both orthotopic transplantation and tumor organoid assays. Despite the cellular heterogeneity of MMTV-Wnt1 tumors, treatment with a Fzd7-specific antibody-drug conjugate significantly suppresses tumor growth, suggesting that Fzd7-expressing cells are critical drivers of tumor progression. These findings show that Fzd7 marks a population of putative tumor-initiating cells and that targeting Fzd7 offers a promising therapeutic strategy for breast cancer.

Metastatic outgrowth requires that cancer cells delaminate from the primary tumor, intravasate, survive in circulation, extravasate, migrate to, and proliferate at a distal site. Recurrent genetic drivers of metastasis remain elusive, suggesting that unlike the early steps of oncogenesis, metastasis drivers may be variable. We develop a framework for identifying metastasis regulators using CRISPR/Cas9-based screening in a genetically defined organoid model of colorectal adenocarcinoma. We conduct in vitro screens for invasion and migration alongside orthotopic, in vivo screens for gain of metastasis in a syngeneic mouse model. We identify CTNNA1 and BCL2L13 as bona fide metastasis-specific suppressors which do not confer any selective advantage in primary tumors. CTNNA1 loss promotes cell invasion and migration, and BCL2L13 loss promotes anchorage-independent survival and non-cell-autonomous changes to macrophage polarization. This study demonstrates proof of principle that large-scale genetic screening can be performed in tumor-organoid models in vivo and identifies novel regulators of metastasis.