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.

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.

Citrullination enhances the tumor-suppressor function of p53 by redirecting its gene target selectivity.

Circulating tumour DNA (ctDNA) methylation analysis, a noninvasive liquid biopsy technique, has shown great potential in cancer diagnosis and treatment. This article reviews the progress of research in ctDNA methylation detection. It summarises the advantages and potential of ctDNA methylation analysis, suggesting that it holds the key to unlocking new chapters in cancer diagnosis and therapy.

Intronic PolyAdenylation (IPA) is an important post-transcriptional mechanism that can alter transcript coding potential by truncating translation regions, thereby increasing transcriptome and proteome diversity. This process generates novel protein isoforms with altered peptide sequences, some of which are implicated in disease progression, including cancer. Truncated proteins may lose tumor-suppressive functions, contributing to oncogenesis. Despite advancements in Alternative PolyAdenylation (APA) analysis using RNA-seq, detecting and quantifying novel IPA events remains challenging. To address this, we developed IPScan, a computational pipeline for precise IPA event identification, quantification, and visualization. IPScan has been benchmarked against existing methods using simulated data, different human and mouse cell lines, and TCGA (The Cancer Genome Atlas) breast cancer datasets. Differential IPA events under different biological conditions were quantified and validated via qPCR.

Inflammation is associated with sickness behavior symptoms in patients receiving chemotherapy. However, its impact on symptom burden (i.e., higher number of concurrent symptoms) requires evaluation. Study purposes were to evaluate for differentially perturbed immune and/or inflammatory pathways between outpatients receiving chemotherapy with Low (i.e., 0-8) versus High (i.e., 16-38) symptom burden and identify common immune and/or inflammatory pathways among symptom burden and single sickness behavior symptoms.

The mitogen-activated protein kinase (MAPK) pathway plays a pivotal role in tumorigenesis and immune regulation. However, its prognostic significance in lung adenocarcinoma (LUAD) remains poorly defined. This study aimed to construct a robust MAPK-related gene (MRG) signature by integrating multi-omics data to enhance risk stratification and therapeutic guidance in LUAD.

Long non-coding RNAs (lncRNAs) play important roles in the occurrence and development of multiple cancers, but the role of lncRNAs in breast cancer has not been fully elucidated. We integrated data mining, bioinformatics analysis, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) to pinpoint key lncRNAs that modulate breast cancer development. In vitro functional assays evaluated the impact of lncRNA 11β-hydroxysteroid dehydrogenase type 1-antisense RNA 1 (HSD11B1-AS1) on breast cancer cells proliferation, migration, and invasion. Interactions between HSD11B1-AS1 and Glyoxylate Reductase 1 Homolog (GLYR1) within breast cancer cells were confirmed through bioinformatics prediction, chromatin immunoprecipitation (ChIP), and dual-luciferase reporter assays. Rescue experiments substantiated the involvement of GLYR1 in breast cancer advancement through the regulation of HSD11B1-AS1. HSD11B1-AS1 is markedly downregulated in breast cancer tissues and cell lines, correlating with an unfavorable prognosis for patients. Functional assays revealed that the suppression of HSD11B1-AS1 notably amplified the proliferation, migration, and invasive capabilities of breast cancer cells. Conversely, the overexpression of HSD11B1-AS1 significantly curtailed the proliferation, migration, and invasion of breast cancer cells. Mechanistically, GLYR1 directly binds to the HSD11B1-AS1 promoter and repressess its transcription, thereby enhancing the malignant behaviors of breast cancer cells, including proliferation, migration, and invasion. GLYR1-mediated suppression of HSD11B1-AS1 drives breast cancer progression. The GLYR1/HSD11B1-AS1 axis may represent a promising avenue for diagnostic biomarkers and therapeutic intervention in breast cancer.

Accumulating evidence indicates that circular RNAs (circRNAs) play a pivotal role in tumor initiation and progression. However, their expression profiles and functional roles in serum exosomes from nasopharyngeal carcinoma (NPC) remain undefined. This study aims to explore the expression patterns, biological functions, and potential prognostic significance of circRNAs in serum exosomes of NPC. CircRNA expression profiles in serum exosomes were analyzed using a circRNA microarray, along with mRNA and miRNA data from RNA sequencing and the Gene Expression Omnibus (GEO). Initially, the competitive endogenous RNA (ceRNA) regulatory network was established by integrating multiple online databases and bioinformatics tools. Subsequently, LASSO and COX regression analyses were used to construct and validate the prognostic model. Additionally, the immunological characteristics analysis was conducted using CIBERSORT. qRT-PCR was performed to further validate the expression levels of circRNAs. Finally, a total of 314 differentially expressed circRNAs were identified in NPC serum exosomes, and a ceRNA regulatory network was constructed for three of them. The prognostic risk model effectively predicts outcomes for NPC patients. Immune cell infiltration analysis revealed a significant increase in M1-type macrophages in the high-risk group, whereas the low-risk group exhibited elevated levels of resting mast cells and activated CD4 memory T cells. Additionally, immune checkpoint gene analysis revealed significantly higher expression of CD276 and ICOSLG in the high-risk group compared to the low-risk group. Our findings suggest that serum exosomal circRNAs may be promising prognostic biomarkers in NPC, warranting further functional and clinical validation.

Gastric cancer (GC) is a leading cause of cancer-related deaths worldwide, with peritoneal metastasis commonly seen in advanced cases. Based on RNA-sequencing data from GEO dataset, we focused on the role of SMOC2, SPARC-related modular calcium-binding protein 2, in regulating GC progression and peritoneal metastasis. Our analysis revealed that high SMOC2 expression was associated with poor survival in the population with peritoneal metastases. Functional assays demonstrated that SMOC2 promotes the migration and invasion of GC cells in vitro. In vivo experiments using a mouse peritoneal metastasis model showed that SMOC2 promoted the peritoneal metastasis of GC cells. Additionally, in a co-culture system of GC cells and endothelial cells, SMOC2 overexpression in GC cells promoted the proliferation, migration, and tube formation capability of endothelial cells. Mechanistically, SMOC2 knockdown reduced GSK-3β phosphorylation and nuclear β-catenin levels, accompanied by decreased expression of downstream target genes. These results indicate that SMOC2 promotes GC peritoneal metastasis involving Wnt/β-catenin pathway modulation. In conclusion, our findings highlight SMOC2's significant role in GC progression, potentially involving Wnt/β-catenin pathway modulation and angiogenesis. These results position SMOC2 as a potential prognostic biomarker and therapeutic target for GC peritoneal metastasis.

This study aimed to identify key genes regulating plasma cell (PC) infiltration in kidney renal clear cell carcinoma (KIRC) and construct a novel prognostic model for predicting KIRC. Clear cell renal cell carcinoma is the most common malignant tumor type of the kidney, with an increasing incidence rate and low survival rates in advanced patients. Plasma cells (PCs), as terminally differentiated B cells, produce highly specific antibodies that effectively target and kill tumors through the antibody-dependent cellular cytotoxicity (ADCC) mechanism. Growing evidence has shown that PC infiltration is closely associated with the progression of various malignant tumors, including ccRCC. Therefore, identifying PC infiltration-related biomarkers is of great significance for the prognosis and treatment of ccRCC patients. Machine learning was used to determine PC-related key genes in KIRC patients. A prognostic model termed PC score was developed using TCGA and ArrayExpress data and validated in external cohorts. The molecular background, immune characteristics, and drug sensitivity of the high PC score group were evaluated. Single-cell sequencing was employed to assess the expression of hub genes in KIRC patients. We identified 9 hub genes associated with PC infiltration, including 3 risk genes (ADAM8, KCNN4, and TCIRG1) and 6 protective genes (RAG1, ATPEV1D, CDKL2, RUNDC3B, SLC30A9, and PPARGC1A), and constructed a PC score based on these key genes. Older age, advanced TNM stage, and higher PC score were independent predictors of shorter overall survival. A nomogram model integrating age, stage, and PC score showed significantly higher predictive value than staging alone (P < 0.01). The high PC score group exhibited a higher abundance of immune cells (e.g., activated B cells, activated CD8 + T cells) in the tumor microenvironment. Drug sensitivity analysis revealed that tyrosine kinase inhibitors (e.g., ceritinib, imatinib) potently inhibited cancer cell lines in the high PC score group, while inhibitors like acalabrutinib were effective in the low PC score group. Patients with higher risk scores showed greater sensitivity to ofloxacin and cortivazol (a cortisol hormone). Expression of hub genes in KIRC patients was validated using a local cohort and single-cell sequencing. We identified key genes regulating PC infiltration in KIRC and proposed a predictive model that effectively identifies high-risk KIRC patients.

CD151 belongs to the tetraspanin family and is a transmembrane glycoprotein that forms a complex with integrins. The complex is involved in cancer cell adhesion, growth, migration, and metastasis. Previous studies have shown that CD151 plays distinctly different roles in different types of cancer. Concerning this, we attempted to elucidate the roles that the N-glycosylation of CD151 plays in cell behavior. The expression of CD151 was diverse in different types of cancer cells and was very low in the human breast cancer cell line MCF-7. To clarify the roles of N-glycosylation, we established wild-type CD151 (CD151/WT)-expressing cells and CD151-non-glycosylation mutant (CD151/NQ)-expressing cells in MCF-7 cells, and we found that the tumor growth of CD151/WT was increased, while the invasion activity of CD151/NQ cells was dramatically enhanced without an increment of the cell-surface expression of integrin β1. We also analyzed the glycan structure of CD151 and found that the N-glycan structure of CD151/WT was rich in oligomannose, which is potentially involved in the interaction with integrins according to 3D structural models. In addition, gene expression analyses using public genomics data sets showed that invasive breast cancers exhibit low expression levels of the STT3B gene. STT3B is a key player in the production and modification of N-glycans, and a low level of STT3B therefore results in a predominant expression of non-glycosylated CD151 and in the accumulation of oligomannose-type glycans in CD151. The results suggest that the expression of the non-glycosylated form of CD151 confers an invasive phenotype to cancer cells, and as such, it could be a therapeutic target to block metastasis in breast cancer.

Esophageal squamous cell carcinoma (ESCC) is the most common subtype of esophageal cancer (ESCA). ESCC is one of the malignancies with high incidence and mortality rates. Studies have found that laminin subunit alpha 3 (LAMA3) functions as an oncogene in a variety of cancers. SPI1 is highly expressed in ESCC, but whether LAMA3 and SPI1 regulate the development of ESCC is still unclear. In this study, bioinformatics analysis tools were used to predict the expression of LAMA3 and SPI1 in ESCA. Subsequently, the levels of mRNA and protein were respectively detected by RT-qPCR and WB. Then, the cell biological behaviors were measured by CCK-8, colony formation, EdU, and tube formation assays. To investigate the in vivo effects of LAMA3 knockdown on ESCC, a xenograft tumor model was established, followed by IHC analysis. Additionally, glucose consumption, lactate production, ROS, and Fe2+ levels were determined by the corresponding kits. Besides, the interaction of LAMA3 and SPI1 was examined by ChIP and dual luciferase reporter assays. LAMA3 was highly expressed in ESCC and silencing it could curb the viability and proliferation of ESCC cells, tumor growth in vivo, tube formation of HUVECs, and induce oxidative stress and ferroptosis of ESCC cells. SPI1 was highly expressed in ESCC and could bind to the promoter of LAMA3 to jointly regulate the progression of ESCC. This study elucidated that SPI1 aggravated ESCC by binding to the promoter of LAMA3, thereby stimulating the growth and proliferation of ESCC cells and suppressing oxidative stress and ferroptosis.

Endometrial cancer (EC) is one of the most prevalent gynecologic malignancies, and long non-coding RNA (lncRNA) SOX9-AS1 has been identified as being upregulated in various cancers, indicating its potential role in driving carcinogenesis. However, the involvement and mechanism of SOX9-AS1 in EC have not been thoroughly investigated. The expression of SOX9-AS1 was assessed using qRT-PCR. The impact of molecular intervention on EC cells was evaluated through cell viability, migration, and invasion assays. Survival probability was analyzed using the Kaplan-Meier method. Bioinformatics predictions, dual-luciferase reporter assays, and rescue experiments were conducted to elucidate the specific competitive endogenous RNA (ceRNA) mechanism of the SOX9-AS1/miR-497-5p/E2F3 axis. SOX9-AS1 expression was significantly upregulated in EC tissues and cells, correlating with poor prognosis in EC patients. Knockdown of SOX9-AS1 inhibited the proliferation, migration, invasion, and glycolysis of EC cells. Mechanistically, miR-497-5p suppressed the proliferation, migration, invasion, and glycolysis of EC by targeting E2F3. Molecular interaction analysis indicate that SOX9-AS1 functions as a molecular sponge for miR-497-5p, thereby increasing E2F3 expression. Our work unveiled a novel mechanism by which SOX9-AS1 promotes EC development, suggesting that targeting the SOX9-AS1/miR-497-5p/E2F3 axis may represent a potential therapeutic strategy for EC.