Identification of liquid biopsy-based mutations in colorectal cancer by targeted sequencing assays. (February 2023)

• Record Type: Journal Article
• Authors: Szász, István; Kiss, Tímea; Mokánszki, Attila; Koroknai, Viktória; Deák, János; Patel, Vikas; Jámbor, Krisztina; Ádány, Róza; Balázs, Margit
• Is Part Of: Molecular and cellular probes. Volume 67(2023)
• Publication Date: 2023-02
• Subjects: Colorectal cancer -- Tumor tissue and plasma samples -- cfDNA -- Next generation sequencing -- Liquid biopsy; Molecular probes -- Diagnostic use -- Periodicals; Pathology, Cellular -- Technique -- Periodicals; Cell Biology -- Periodicals; Molecular Biology -- Periodicals; Sondes moléculaires -- Utilisation diagnostique -- Périodiques; Cytopathologie -- Technique -- Périodiques; 572
• DOI: 10.1016/j.mcp.2022.101888
• Languages: English
• ISSNs: 0890-8508

Abstract

Abstract: Recently, liquid biopsy, as a promising approach was introduced for the analysis of different tumor-derived circulating markers including tumor DNA and cell free DNA (ct/cfDNA). Identification of mutations in cfDNA may allow the early detection of tumors, as well as predicting and monitoring treatment responses in a minimally invasive way. In the present study, we used commercially available gene panels to verify the mutation overlap between liquid biopsy and abnormalities detected in colorectal tumor tissue. The two panels (Archer®VariantPlex®Solid Tumor and LIQUIDPlexTM ctDNA) overlap in 23 genes, which enables a comprehensive view of tumor-plasma mutational status by next generation sequencing. We successfully analyzed 16 plasma and 16 tumor samples. We found that 87% of tumor tissues contained 44 mutations in 12 genes and 43.8% of cfDNA harbored 13 mutations in 5 genes. To verify whether the mutation pattern of the tumor DNA could be consistently detected in plasma cfDNA, we compared the alterations between cfDNA and matched tissue DNA in nine patients. Six of the 9 tumor tissues harbored mutations in TP53, KRAS or MET genes, those were not detectable by the ctDNA kit, even eventhough the exons of these genes overlap in both panels. Comparing the mutational patterns of the matched samples, we found that only one cfDNA had the same mutations ( KRAS, SMAD4 and TP53 ) in the paired tissue. The results of the comparison between tumor tissue DNA and matched plasma cfDNA underline the importance of studying the paired solid tumor and plasma samples together. Highlights: Commercially available gene panels are used to define mutation overlap between cfDNA and tumor tissue of CRC patients. cfNDA concentration was significantly higher in patients' plasma with metastasis compared to patients with primary tumors. Mutations in plasma were associated mainly with metastasis, highlighting that mutations accumulate as the tumor progresses. cfDNA analysis can identify heterogeneous tumor cell subpopulations, indicative for metastasis and need different treatment.