Jingjing Yu, MD
Resident
University of California, Irvine Medical Center
Anaheim, California, United States
Disclosure: I do not have any relevant financial / non-financial relationships with any proprietary interests.
Circulating tumor DNA (ctDNA), the most commonly used liquid biopsy in colon cancer, has poor sensitivity in patients with peritoneal carcinomatosis (PC). Hence, an alternative liquid biopsy that has high sensitivity to detect colon cancer including colon cancer PC is critically necessary. Due to the role of exosomes in cancer communication and progression, we aimed to investigate the feasibility of a liquid biopsy using plasma exosomes in patients with colon cancer.
Methods:
Presurgical frozen plasma samples from patients with colon cancer (non-metastatic (NM) n=14, visceral metastasis (VM) n=16, PC n=12) were obtained. Plasma exosomes from patients and healthy controls (n=10) were isolated through precipitation technique. Isolated exosomes were verified using nanoparticle tracking analysis (NTA) and western blot. Next Generation Sequencing (NGS) analysis of the isolated exosomal RNA was performed to identify differentially expressed genes (DEGs).
Results:
In the patient cohort (n=42), right sidedness, grade II/III, and KRAS mutations were detected in 62%, 67%, and 36% respectively. Isolated plasma exosomes had a mode size of 86.9 nm on NTA and expressed common exosomal markers CD9 and tumor susceptibility gene 101 (TSG101). Pair-wise group comparisons of DEGs by DESeq2 analysis discovered 1,566 genes (mRNAs, microRNAs & lincRNAs) with baseMean read values >10 with Benjamini-Hochberg adjusted p-values < 0.0001 for any one pair-wise comparison. Highly prevalent tRNA transcripts were excluded from this group of 1,566 genes, resulting in 448 genes that we characterized as the ExoSig 448 gene signature. With hierarchical clustering, control samples clustered apart from colon cancer samples due to lack of gene expression (Figure). Six exosomal subtypes emerged in the colon cancer group, suggestive of tumor biological grouping.
Conclusions:
We have identified a specific plasma exosomal gene signature with 448 genes in patients with colon cancer that is distinct from healthy controls. ExoSig 448 can potentially be used as a liquid biopsy to identify patients with various stages of colon cancer including PC with high accuracy.