Spatial transcriptomics reveals molecular differences associated with malignant transformation in oral epithelial dysplasia

Spatially resolved proteomics provides insights into the normal-dysplasia-tumor continuum in oral squamous cell carcinoma.

Spatially resolved proteomics of archived formalin-fixed paraffin-embedded tissues provides a morphology-anchored proteomic continuum of oral malignant transformation in a small spatially matched cohort, suggesting that OSCC progression involves early-shift, progressive, and transient dysplasia-specific programs.

Exploratory transcriptomic analysis of low-grade oral epithelial dysplasia and oral squamous cell carcinoma in Chilean patients

Spatial transcriptomics reveals site-specific cellular and metabolic heterogeneity in bladder carcinoma in situ

Bladder carcinoma in situ (CIS) is a multifocal, non–muscle-invasive disease with a high risk of progression to muscle-invasive cancer. Current management strategies are often guided by genomic profiling of single tumor samples, which incompletely capture tumor heterogeneity and may contribute to treatment failure. In particular, the multifocal nature of CIS raises uncertainty regarding the uniformity of genomic, immunologic, and microenvironmental features across anatomically distinct sites within the same patient. To address this, we performed spatial transcriptomic profiling of CIS-containing tissue from four anatomically distinct sites within a single individual. Unsupervised clustering with marker-based annotation, integrated with metabolic inference, identified epithelial tumor populations alongside stromal, immune, and smooth muscle compartments. While key cellular states were conserved, their spatial organization and relative abundance varied by site. Metabolic analysis further revealed region-specific microenvironments shaped by local cellular architecture. These findings indicate that both cellular composition and metabolic activity are spatially structured. Collectively, these results demonstrate that CIS exhibits significant intra-patient heterogeneity not captured by single-site profiling. These findings require validation in larger cohorts but support multi-region sampling could help improve risk stratification, biomarker development, and prediction of response to intravesical therapies, with potential implications for more personalized treatment strategies.

Integrated identification, functional characterization, and clinical significance of key genes during cervical cancer progression

Introduction: Cervical cancer evolves from normal cervical epithelium through a multifaceted pathway, first to high-grade squamous intraepithelial lesions (HSILs) and subsequently culminating in invasive cancer, yet the specific molecular mechanisms driving this progression remain poorly understood. Objective: To identify genes persistently dysregulated during cervical lesion progression and to evaluate their clinical relevance with respect to prognosis, immune infiltration, and therapeutic response. Methods: Two independent gene expression datasets (GSE7803 and GSE64217) were analyzed to screen persistently differentially expressed genes (DEGs) across normal cervix, HSIL, and cervical cancer. Public databases and clinical samples were used to validate the hub genes initially identified through functional enrichment and protein–protein interaction analyses. Associations with patient survival, immune infiltration, and drug sensitivity were further analyzed using integrated bioinformatics platforms. Results: Eighteen common persistent DEGs were identified, primarily enriched in cell cycle regulation and epithelial differentiation. Four hub genes (AURKA, ECT2, RFC4, and PCNA) showed progressive upregulation as cervical lesions progressed and were associated with clinicopathological features. Elevated RFC4 and PCNA levels were significantly associated with improved survival. Immune analysis revealed distinct correlation patterns for RFC4 and PCNA expression: positive with B cells and effector memory immune cells, and negative with regulatory T cells. Drug sensitivity analysis showed that elevated RFC4 and PCNA expression were associated with lower IC50 values, whereas AURKA and ECT2 were linked to potential drug resistance. Conclusion: AURKA, ECT2, RFC4, and PCNA are key regulators of cervical lesion progression, among which RFC4 and PCNA are promising prognostic biomarkers and potential therapeutic targets.

Transcriptomic Changes and Biomarkers in Barrett’s Metaplasia, Dysplasia and Cancer

ORC6 marks a replication-active malignant epithelial state and is associated with immune-low features in oral squamous cell carcinoma

Introduction Oral squamous cell carcinoma (OSCC) shows marked biological heterogeneity, but markers that connect malignant epithelial states with the tumor immune context remain limited. Origin recognition complex subunit 6 (ORC6) participates in DNA replication licensing, but its disease-specific role in OSCC is not well defined. Methods We integrated anatomically filtered bulk transcriptomic data, external validation cohorts, single-cell transcriptomic profiling, immune-context analyses, proliferation-adjusted sensitivity analyses, virtual perturbation, and in vitro ORC6-knockdown assays to evaluate the clinical and biological relevance of ORC6 in OSCC. Results After reconstruction of a strictly defined TCGA oral cavity OSCC cohort excluding base of tongue and other non-oral cavity subsites, ORC6 remained upregulated in OSCC tissues and cell lines and was associated with adverse clinicopathological features and poorer survival. Exploratory analysis in the HPV-negative GSE41613 cohort further supported the adverse survival association of ORC6. Single-cell analysis showed preferential enrichment of ORC6 in malignant epithelial cells. Within this compartment, high ORC6 expression marked a replication-active state characterized by activation of DNA-replication and cell-cycle programs and weaker transcriptional signatures of interferon response and antigen presentation. These differences were directionally preserved in donor-matched pseudobulk comparisons and after cell-cycle-score regression. At the bulk-tumor level, proliferation-adjusted models showed that ORC6 retained directionally inverse associations with selected immune-related features, including cytolytic activity, IFN-γ response, and MHC-I/antigen-presentation signatures. ORC6 knockdown in CAL27 cells reduced cell growth, migration, invasion, and S-phase fraction while increasing antigen-presentation-associated transcripts and surface HLA-A/B/C expression. Discussion These findings support ORC6 as a marker of a replication-active malignant epithelial state associated with attenuated immune-related features in OSCC, particularly antigen-presentation-related programs. Further functional immune-recognition studies and independent clinical validation are warranted.