The high mortality rate of metastatic cutaneous melanoma (SKCM) remains a major challenge in clinical treatment. This study used single-cell RNA sequencing (scRNA-Seq) technology to compare the differences between metastatic and primary tumour cells. By manually annotating cell types, significant disparities in cell communication patterns and functional pathways between the two groups were identified. Combined with transcriptomic data, differential gene analysis was performed to screen out a core gene set associated with tumour metastasis. To achieve accurate prediction of tumour metastasis, this study innovatively constructed a binary classification algorithm (PSO-SVM) integrating particle swarm optimisation (PSO) and support vector machines (SVMs). This model optimises SVM parameters via the PSO algorithm, addressing the limitations of traditional machine learning models such as insufficient accuracy and poor generalization ability in tumour metastasis prediction. Verified by comparison with mainstream machine learning methods, the PSO-SVM model exhibited superior classification performance and successfully identified five key metastasis-related genes: SFN, S100A8, KLF5, ARL4D and TINCR. Furthermore, the expression differences of these genes in the metastatic group were verified at the single-cell level, clarifying their regulatory roles in different cell types and states. Through an innovative analytical strategy integrating single-cell and transcriptomic data, this study elucidated the core molecular mechanisms of SKCM metastasis and key regulatory pathways in the tumour microenvironment, providing potential biomarkers and therapeutic targets for the early diagnosis and targeted treatment of SKCM metastasis. This PSO-SVM-integrated analysis method also offers new insights for research on metastasis mechanisms of other cancers.

Current spatial T cell receptor (TCR) profiling approaches lack the resolution needed to link clonal identity, transcriptional state, and spatial positioning of individual T cells in the tumor microenvironment. Here, we introduce a spatial TCR profiling strategy that resolves individual T cell clones together with their transcriptional states at single-cell resolution and applied the method to human head and neck squamous cell carcinoma. Presumed tumor-specific T cells were broadly dispersed throughout the tumor microenvironment, and cells of the same clone occupied distinct transcriptional states in different locations: Immune-rich regions contained more plastic or progenitor cells, whereas tumor-dense regions were enriched for exhausted states. Patients exhibited notably different spatial architectures of antitumor T cell responses, revealing variation that was not captured by high-resolution, spatially agnostic methods such as spectral flow cytometry and single-cell RNA sequencing. These results provide a blueprint for dissecting antigen-specific T cell states in human tumors and reveal how T cell states are spatially coordinated with local cues across the tumor microenvironment.

Although pancreatic cancer is generally refractory to immune checkpoint blockade, recent studies of tumor-infiltrating T cells in human tumor samples demonstrated the presence of in vivo expanded, tumor-reactive T cell receptor (TCR) clonotypes. Here, we explored the T cell repertoire in a murine pancreatic cancer model by combining single-cell transcriptomics with functional TCR characterization. This uncovered a substantial diversity of tumor-reactive TCR clonotypes. Whereas some of these were exclusively reactive against the autologous tumor, most TCRs reacted against syngeneic tumor cells of diverse tissue origin. Immunopeptidome analyses revealed three T cell epitopes reflecting distinct tumor antigen classes also found in human cancers: a mutanome-encoded neoantigen, an epitope encoded by an ectopically expressed endogenous retroviral provirus, and an epitope derived from a cell stress-induced autoantigen. These findings underline the importance of uncovering the antigen specificity of the natural tumor-reactive TCR repertoire to assess its therapeutic potential and safety with regard to personalized immunotherapy.

Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality and is largely driven by metabolic disorders such as obesity and type 2 diabetes. The AMP-activated protein kinase (AMPK) is a master regulator of metabolism, and its activation has been proposed as a therapeutic strategy for treating metabolic disorders. However, although AMPK activity is down-regulated in HCC, the precise role of AMPK in HCC development has not been clearly delineated. Here, we investigated the ability of constitutive AMPK activation to prevent HCC development using a constitutively active AMPK transgenic mouse model and a pharmacological AMPK activator. We observed that AMPK activation substantially reduced tumor formation in both diethylnitrosamine (DEN)-induced and streptozocin-induced (STAM) models of HCC via altered bile acid metabolism and inhibition of hepatic nuclear factor alpha (HNF4α) signaling. These findings provide mechanistic insights into AMPK biology and highlight the potential of AMPK as a therapeutic target, emphasizing the intricate interplay between metabolic dysregulation and cancer development.

Protein kinases play a crucial role in regulating cellular processes, and their dysregulation is frequently implicated in various diseases, including cancer. Targeting protein kinases represents a promising therapeutic strategy for cancer treatment. Esophageal squamous cell carcinoma (ESCC) constitutes over 90% of esophageal cancer cases in high-incidence regions, with a global five-year survival rate below 20%. Here, we report that CK2 is aberrantly activated in ESCC, identified through kinase-substrate enrichment analysis (KSEA) of large-scale proteomic and phosphoproteomic data. Functional enrichment revealed the splicing factor SF3B3 as a clinically relevant CK2 substrate. We demonstrated that CK2-mediated phosphorylation of SF3B3 T1200 plays a pivotal role in ESCC progression. Mechanistically, CK2-mediated phosphorylation of SF3B3 enhances its affinity for the deubiquitinase USP7, leading to SF3B3 deubiquitination and subsequent protein stabilization. This stabilization drives ESCC progression by regulating alternative splicing (AS) events, including a critical event involving the inclusion of exon 4 in the EXOSC2 transcript. Furthermore, we demonstrated that SF3B3 T1200 phosphorylation specifically facilitates its incorporation into the U2 snRNP complex, directly promoting the aforementioned EXOSC2 exon 4 inclusion. Crucially, targeting CK2 or USP7, either individually or in combination, effectively suppressed ESCC progression. Our findings uncover a key molecular mechanism underlying SF3B3 stabilization and AS regulation, offering novel therapeutic opportunities for ESCC.

Invasion plasticity allows malignant cells to toggle between collective, mesenchymal, and amoeboid phenotypes while traversing extracellular matrix (ECM) barriers. Current dogma holds that collective and mesenchymal invasion programs trigger the mobilization of proteinases that digest structural barriers dominated by type I collagen, while amoeboid activity allows cancer cells to marshal mechanical forces to traverse tissues independently of ECM proteolysis. Here, we use cancer spheroid-3-dimensional matrix models, single-cell RNA sequencing, and human tissue explants to identify the mechanisms controlling mesenchymal versus amoeboid invasion. Unexpectedly, collective/mesenchymal- and amoeboid-type invasion programs-though distinct-are each characterized by active tunneling through ECM barriers, with expression of matrix-degradative metalloproteinases. CRISPR/Cas9-mediated targeting of a single membrane-anchored collagenase, MMP14/MT1-MMP, ablates tissue-invasive activity while coregulating cancer cell transcriptional programs. Though changes in matrix architecture, nuclear rigidity, and metabolic stress as well as the presence of cancer-associated fibroblasts are proposed to support amoeboid activity, none of these changes restore invasive activity of MMP14-targeted cancer cells. While a requirement for MMP14 is bypassed in low-density collagen hydrogels, invasion by the proteinase-deleted cells is associated with nuclear envelope and DNA damage, highlighting a proteolytic requirement for maintaining nuclear integrity. Nevertheless, when cancer cells confront explants of live human breast tissue, MMP14 is again required to support invasive activity. Corroborating these results, spatial transcriptomic and immunohistological analyses of human breast cancers identified MMP14 expression in tissue-infiltrating carcinoma cells that were further juxtaposed with proteolyzed type I collagen fragments, underlining the pathophysiologic importance of this proteinase in directing invasive activity in vivo.

Intrinsic and acquired resistance to poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) remains a major barrier in treating homologous recombination (HR) repair-deficient tumors, including those with germline or somatic BRCA1/2 mutations. Although PARPi are FDA approved for adjuvant treatment of locally advanced or metastatic breast cancer in patients with germline BRCA1/2 mutations, emerging data support their use as monotherapy in the neoadjuvant setting. Promising safety profiles of newer-generation PARPi further support this potential. However, resistance mechanisms specific to the neoadjuvant setting are poorly understood. To address this gap, we leveraged resources from a phase II neoadjuvant clinical trial (NCT03499353), analyzing tumors from patients with germline BRCA1/2 mutant breast tumors before and after six months of talazoparib monotherapy. Whole-transcriptome analyses were performed on these samples. Additionally, we established orthotopic patient-derived xenograft models from a subset of the patient tumors and conducted whole-exome and whole-transcriptome analysis. This integrative approach revealed both known and previously unknown PARPi resistance mechanisms. In one case, overexpression of BRN2, encoding a transcription factor that plays a critical role in neurogenesis, led to activation of ATR/RAD51 and STAT3 pathways, restoring HR repair. BRN2-driven resistance could be reversed with ATR and STAT3 inhibitors, resensitizing cells to talazoparib. In another, an HR repair proficient tumor subclone lacking Shieldin 2 expression expanded during treatment and accounted for intrinsic resistance. Our findings highlight the need to determine intrinsic and anticipate acquired resistance pathways in treatment-naïve tumors and support combining PARPi with targeted agents to improve outcomes in the neoadjuvant setting.

Glioma represents a significant challenge in neuro-oncology due to its highly invasive nature and poor prognosis. Recent studies indicate that ferroptosis, a form of regulated cell death, plays a crucial role in the pathogenesis of glioma. Modulating ferroptosis may offer a novel therapeutic approach for glioma treatment. This study aims to identify ferroptosis-related biomarkers and patterns of immune infiltration in glioma using bioinformatics techniques, and to predict potential therapeutic drugs targeting these biomarkers. Gene expression profiles (GSE16011, GSE50161) were retrieved from the GEO database, while ferroptosis-related genes were sourced from the FerrDb database. Intersection genes were identified using the CytoHubba algorithm and a consensus clustering method. Immune infiltration was assessed using the CIBERSORT algorithm. Functional enrichment analysis and gene set enrichment analysis were conducted with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Drug targeting predictions were made based on identified hub genes. We identified 10 hub genes: TP53, RRM2, EZH2, CDKN1A, MYCN, KIF20A, BLM, GLS2, HMOX1, and GOT1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that ferroptosis is primarily associated with apoptosis, reactive oxygen metabolism, the p53 signaling pathway, and immune regulation. Immune infiltration analysis showed significant differences in the expression of plasma cells, CD8 T cells, follicular helper T cells, activated NK cells, and macrophages between groups. qRT-PCR validation in glioma cell lines confirmed the differential expression of key ferroptosis-related genes, supporting the robustness of our bioinformatic findings. Furthermore, molecular docking demonstrates excellent binding properties between the drug components and key targets, and these key targets were further validated by PCR analysis in vitro. In summary, this study highlights the potential of ferroptosis-related biomarkers in glioma and suggests novel drug targets, providing a foundation for future therapeutic strategies.

This study investigated the molecular mechanisms underlying the anticancer effects of Hedyotis Diffusae Herba (HDH) against esophageal squamous cell carcinoma (ESCC) through network pharmacology and molecular docking approaches. We identified active compounds in HDH using the traditional Chinese medicine systems pharmacology database and analysis platform, while ESCC-related targets were retrieved from the GeneCards database. Drug-disease target interactions were analyzed and visualized through Venn diagrams and network topology analysis. We employed Kyoto encyclopedia of genes and genomes pathway enrichment analysis to elucidate potential therapeutic mechanisms and constructed comprehensive "drug-active ingredient-key target-signaling pathway-disease" networks using Cytoscape software. Key active ingredients and targets were prioritized based on network topological parameters, and their binding interactions were validated through molecular docking using AutoDock software. Our analysis identified 15 bioactive compounds in HDH, including quercetin, beta-sitosterol, and stigmasterol, as primary contributors to its anti-ESCC activity, corresponding to 91 potential therapeutic targets. From the GeneCards database, we identified 6262 ESCC-associated genes, including key oncogenes such as TP53, MET, and EGFR. Notably, 43 genes overlapped between HDH targets and ESCC-related genes, including critical cancer drivers such as EGFR, ERBB2, and MYC. Kyoto encyclopedia of genes and genomes pathway enrichment analysis revealed that HDH's anti-ESCC targets are predominantly involved in the MAPK signaling pathway, p53 signaling pathway, and chemical carcinogenesis-receptor interaction pathways. Molecular docking simulations indicated strong binding affinity and conformational stability between key active compounds (quercetin and beta-sitosterol) and critical target proteins (BCL2 and PRKCA). This study infers the molecular mechanisms through which HDH components may regulate ESCC via an integrated multi-omics approach; however, its computational nature primarily necessitates experimental validation.

The leptin receptor (LEPR) serves as a central regulator of energy balance and metabolic homeostasis, with growing interest in its pleiotropic roles in cancer. However, existing evidence on its oncogenic function remains ambiguous, with studies reporting both tumor-promoting and tumor-suppressive effects across different contexts. This duality complicates the interpretation of LEPR's precise role in carcinogenesis. Moreover, conventional observational studies are inherently limited by residual confounding and reverse causality, leaving the causal relationship between LEPR signaling and site-specific cancer risk unresolved. To address this, we performed a drug-target Mendelian randomization analysis to assess the causal effect of genetically proxied LEPR activity on 16 such cancers. We selected cis-expression quantitative trait loci (cis-eQTLs) associated with LEPR expression in blood from the eQTLGen Consortium (n = 31,684) as instrumental variables, and harmonized them with summary-level genome-wide association study data for cancers from the FinnGen R12 release. Among the 16 evaluated malignancies, our primary finding demonstrated that genetically elevated LEPR signaling was significantly associated with a lower risk of pancreatic cancer (odds ratio = 0.91; 95% CI: 0.87-0.96; P = 3.93 × 10-4). This association withstood Bonferroni correction and was consistent across sensitivity analyses. Suggestive inverse associations were also observed for lung squamous cell carcinoma, gastric cancer, and breast cancer subtypes (P <.05), whereas no significant causal links were detected for the remaining ten cancers. No significant heterogeneity or horizontal pleiotropy was detected. In summary, this drug-target Mendelian randomization study provides concise genetic evidence supporting a protective role of LEPR signaling specifically in pancreatic cancer, with suggestive effects in several other malignancies. These findings inform the pathophysiological understanding of leptin in cancer and highlight the relevance of LEPR-modulating strategies for safety assessment in oncology. Limitations include the use of blood-derived eQTLs and restriction to European ancestry, which may affect generalizability.

This study aimed to retrospectively analyze the clinical characteristics, tumor staging, surgical outcomes, and prognosis of children with MEN2B who presented with MTC. By summarizing our single-center experience, we emphasize the importance of early recognition and genetic screening to provide clinical insights for improving prognosis. Clinical data of six pediatric patients diagnosed with MEN2B in BCH, between January 2019 and December 2023, were reviewed. Demographic characteristics, clinical presentation, laboratory and imaging findings, genetic testing, surgical details, and follow-up information were analyzed. Descriptive statistical methods were used for data analysis. The cohort included 6 patients (2 males, 4 females) with a median age of 9.2 years (range 8.1-14.4 years). All patients harbored the de novo p.M918T RET mutation. All patients exhibited the classic MEN2B phenotype (marfanoid habitus, ocular signs, multiple oral mucosal neuromas, vocal cord nodules, high-arched palate, etc.) accompanied by alacrima and gastrointestinal symptoms. All underwent total thyroidectomy and bilateral central compartment neck dissection, with five undergoing concurrent lateral neck dissection due to suspected metastasis. Postoperative pathology confirmed MTC in all cases, with cervical lymph node metastases present in 4 patients (66.7%). Preoperative calcitonin levels were markedly elevated. After a median postoperative follow-up of 2.8 years (range 2.1 to 4.5 years), only one patient (T2N0M0) achieved biochemical remission.

Actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) has been found to be closely associated with the initiation and progression of various tumors; however, its role in oral squamous cell carcinoma (OSCC) remains unclear. AFAP1-AS1 expression in OSCC cells was detected using qRT-PCR. The regulatory effects of AFAP1-AS1 on tumor cell proliferation, migration, and invasive capabilities were systematically evaluated through CCK-8 proliferation, colony formation, wound healing, and Transwell invasion assays. Flow cytometry was employed to quantitatively analyze its impact on cell cycle progression and apoptotic. Based on bioinformatics predictions, a dual-luciferase reporter system was utilized to validate the targeting interactions among AFAP1-AS1, miR-93-3p, and CCND1. Functional rescue experiments were conducted to elucidate the functional regulatory network among them. Furthermore, a xenograft tumor model in nude mice was employed to verify in vivo the promoting effect of AFAP1-AS1 on tumor growth. AFAP1-AS1 was significantly upregulated in OSCC cells. AFAP1-AS1 knockdown inhibited the malignant phenotypes of OSCC cells. Mechanistic studies revealed that AFAP1-AS1 could target miR-93-3p and regulate CCND1 expression, thereby influencing OSCC progression. Subcutaneous tumor model in mice further confirmed the in vivo relevance of the AFAP1-AS1/miR-93-3p/CCND1 axis. AFAP1-AS1 downregulation inhibited OSCC progression through the miR-93-3p/CCND1 axis.

ZNRF3 and RNF43 are closely related transmembrane E3 ubiquitin ligases with significant roles in development and cancer. Conventionally, their biological functions have been associated with regulating WNT signaling receptor ubiquitination and degradation. However, our proteogenomic studies have revealed EGFR as the protein most negatively correlated with ZNRF3/RNF43 mRNA levels in multiple human cancers. Through biochemical investigations, we demonstrate that ZNRF3/RNF43 interact with EGFR via their extracellular domains, leading to EGFR ubiquitination and subsequent degradation facilitated by the E3 ligase RING domain. Overexpression of ZNRF3 reduces EGFR levels and suppresses cancer cell growth in vitro and in vivo, whereas knockout of ZNRF3/RNF43 stimulates cell growth and tumorigenesis through upregulated EGFR signaling. Together, these data suggest ZNRF3 and RNF43 as novel E3 ubiquitin ligases of EGFR and establish the inactivation of ZNRF3/RNF43 as a driver of increased EGFR signaling, ultimately promoting cancer progression. This discovery establishes a connection between two fundamental signaling pathways, EGFR and WNT, at the level of cytoplasmic membrane receptors, uncovering a novel mechanism underlying the frequent co-activation of EGFR and WNT signaling in development and cancer.

Acute myeloid leukemia (AML) harboring BCR::ABL1 is considered a separate diagnostic entity and is classified as adverse in the risk score of the European LeukemiaNet. However, its prognosis could change with the addition of tyrosine kinase inhibitors (TKI) to chemotherapy.

Breast cancer (BC) is the leading cause of cancer death in women. Bidirectional regulation between BC and gut microbiota (GM) is established, but GM's mechanistic role in BC pathogenesis remains unclear. Public BC/control samples and GM genome-wide association study data underwent Mendelian randomization to identify GM-BC associations and GMRGs. DEGs between BC and controls were analyzed. Candidate genes were derived from intersecting DEGs and GMRGs. Machine learning identified biomarkers, validated by expression analysis. GSEA, immune infiltration, drug screening with molecular docking, and scRNA-seq were performed. Intersecting 3455 DEGs with GMRGs yielded eight candidates; MCM6 and NR3C1 were validated as biomarkers, enriched in DNA replication pathways. Immune infiltration showed 13 differential immune cells, with macrophages notably influencing biomarkers. Etoposide exhibited strong binding to biomarkers via docking. scRNA-seq identified epithelial cells as key, with stage-dependent biomarker expression. This study redefines BC as a microbiome-regulated network, identifying the MCM6/NR3C1 biomarker pair for early diagnosis and microbiome-targeted interventions.

Clear cell renal cell carcinoma (KIRC), the most prevalent pathological renal cell carcinoma (RCC) subtype, makes up approximately 75%-84% of total cases. KIRC is characterized by high heterogeneity, high metastasis rates, and a poor prognosis. Its incidence rate has continued to rise in recent years. We sought to construct new prognostic models to optimize treatment decisions, improve clinical benefits, and explore potential therapeutic targets.

Kidney renal clear cell carcinoma (KIRC) is an aggressive malignancy with limited therapeutic options, highlighting the need for novel biomarkers and therapeutic targets. Although endoplasmic reticulum metallopeptidase 1 (ERMP1) has been implicated in cancer progression, its specific role, clinical significance, and underlying mechanisms in KIRC remain poorly defined.

Cholangiocarcinoma (CCA) is a highly aggressive malignancy. 3-Hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), a mitochondrial enzyme involved in ketogenesis, has been linked to tumor progression, but its role in CCA remains unclear. HMGCS2 expression in CCA tissues was analyzed using TCGA data and immunoblotting (IB). Functional assays were performed in CCA cell lines (HuCCT-1 and RBE) and an in vivo xenograft model. Metabolomics explored HMGCS2-mediated metabolic changes. SIRT3-HMGCS2 interactions were examined via molecular docking, IF, CO-IP, GST pull-down, and CHX assays, with mutational analysis identifying interaction sites. IHC assessed clinical samples. HMGCS2 was downregulated in CCA. Overexpression inhibited proliferation and invasion, while knockdown promoted these effects, consistent in vitro and in vivo. Metabolomics showed HMGCS2 enhanced ketone body synthesis, and exogenous ketone bodies mimicked its antitumor effects. SIRT3 deacetylated HMGCS2 at K310 (with plasmid mutation assay), and low HMGCS2/SIRT3 expression correlated with poor patient survival. SIRT3-mediated deacetylation of HMGCS2 promotes ketone body synthesis, suppressing CCA progression. HMGCS2 is a potential therapeutic target for CCA.

Background: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths globally. Although the hypoxia-inducible factor 1A (HIF1A) pathway is crucial in HCC progression, its regulatory mechanisms remain unclear as mutations in its primary regulator, von Hippel-Lindau tumor suppressor (VHL), are rare in HCC. We aimed to elucidate the role of proliferation and apoptosis adaptor protein 15 (PEA15), identified through proteomic analysis, as a regulator of the VHL/HIF1A pathway and a therapeutic target in HCC. Methods: Proteomic and genomic analyses of over 1,000 HCC samples were conducted, identifying PEA15 amplification. Functional validation involved in vitro and in vivo assays, including gene knockdown, ectopic expression, and antisense oligonucleotide (ASO) therapy in xenograft models. Protein interactions were assessed using immunoprecipitation and ubiquitination assays. Results: We identified 3 clinically distinct HCC subtypes and found that PEA15 was selectively amplified and highly expressed in the mesenchymal (MES) subtype, which exhibited the poorest prognosis. PEA15 acted as a regulator of the VHL/HIF1A pathway and a key oncogene in HCC. The amplification of PEA15 was significantly associated with the poor survival of HCC patients. Moreover, by interacting with the β-domain of VHL, PEA15 promoted HCC cell proliferation and migration by inhibiting VHL's interaction with the VHL/elongin C (ELOC)/elongin B (ELOB)/cullin 2 (CUL2) E3 ligase complex, destabilizing the complex and consequently activating HIF1A. Importantly, pharmacologically inhibiting PEA15 using PEA15 ASO drugs attenuated tumor burden and restored VHL function in a xenograft mouse model. Conclusions: This study identified PEA15 as a potential oncogene in HCC, regulating the VHL/HIF1A axis and driving tumor progression. Targeting PEA15 using ASOs offers a promising therapeutic strategy for HCC, particularly in the MES subtype. These findings provide a basis for further exploration of PEA15-targeted therapies to improve HCC outcomes.

Human leukocyte antigen E (HLA-E) plays a role in tumor immune escape and is associated with poor prognosis in neuroblastoma (NB). This study aimed to investigate the regulatory effect of suberoylanilide hydroxamic acid (SAHA) on HLA-E expression via the PERK/ATF4/CHOP pathway in NB.