Molecular Profiling for Risk Stratification in Appendiceal Cancer

Appendiceal cancer is a rare and heterogeneous malignancy with limited clinically actionable biomarkers for risk stratification. Histologic grade remains one of the strongest determinants of prognosis, but outcomes among patients with lower-grade disease remain variable. This study is designed to characterize the molecular architecture of appendiceal cancer through integrated analysis of DNA methylation and m6A epitranscriptomic profiles generated from archived tumor tissue specimens from the same patient cohort.

The study uses formalin-fixed paraffin-embedded appendiceal cancer tissues, and where available benign or normal appendix tissues, together with matched clinicopathologic and follow-up data. DNA methylation profiling is performed to evaluate tumor-associated methylation patterns, identify differentially methylated regions or features, and assess their association with clinical and survival outcomes. In parallel, m6A epitranscriptomic profiling is performed using m6A-enriched RNA sequencing with matched input RNA sequencing to quantify transcriptome-wide m6A enrichment.

Molecular data are analyzed to identify tumor-associated epigenetic and epitranscriptomic alterations, define molecular subtypes, and construct continuous molecular risk scores. These molecular features are evaluated in relation to histologic grade, histologic subtype, lymph node metastasis, lymphovascular invasion, perineural invasion, peritoneal cancer index, overall survival, and progression-free survival.

The study aims to determine whether DNA methylation and m6A-based profiling can provide complementary molecular information for appendiceal cancer classification, prognostic modeling, and future biomarker development.

Inclusion criteria

• Patients with histologically confirmed appendiceal adenocarcinoma or appendiceal cancer.
• Availability of archived tumor tissue suitable for molecular profiling.
• Availability of tissue for DNA methylation profiling, m6A epitranscriptomic profiling, or both.
• Availability of relevant clinicopathologic data.
• Availability of survival or follow-up information when applicable.
• Age 18 years or older at diagnosis or tissue collection.

Exclusion criteria

• Insufficient tissue quantity or quality for molecular profiling.
• Inadequate DNA or RNA quality for sequencing or molecular assay preparation.
• Missing essential clinicopathologic information required for analysis.
• Non-appendiceal primary tumor or metastatic tumor to the appendix from another primary site.
• Patients who do not meet institutional review board or consent requirements, if applicable.