Gene expression data to identify molecular characteristics of mucinous colorectal cancer

Mucinous adenocarcinoma (MuC), a subtype of colorectal cancer (CRC), exhibits distinct molecular features and a poorer prognosis compared to non-mucinous CRC (NMuC). Standard CRC treatments often fail to address MuC's unique characteristics, especially in stage II, where the benefit of adjuvant chemotherapy is unclear. Biomarkers that improve risk assessment and guide personalized treatment are needed. Based on RNA-seq data and Cox regression models, we developed a signature reflecting the characteristics of MuC which showed a strong prediction ability and clinical utility in both MuC and NMuC. Our signature represents a valuable tool for predicting recurrence and guiding personalized treatment in CRC. RNA-seq data of 140 fresh frozen tissues of mucinous colorectal cancer tissues (n = 140) were generated. Total RNA was isolated by RNeasy Plus Mini Kit (Qiagen, CA, USA), following the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by RNA Integrity Number (RIN) measurements, with only samples achieving RIN value > 8 were selected for further analysis. Sequencing library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the provided protocol. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented and converted into cDNA. Then adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (100PE) using Novaseq 6000 platform (Illumina, CA, USA).