Identification of Circulating Genomic and Metabolic Biomarkers in Intrahepatic Cholangiocarcinoma

• Published in: Cancers Vol. 11; no. 12; p. 1895
• Main Authors: Winter, Helen, Kaisaki, Pamela J, Harvey, Joe, Giacopuzzi, Edoardo, Ferla, Matteo P, Pentony, Melissa M, Knight, Samantha J L, Sharma, Ricky A, Taylor, Jenny C, McCullagh, James S O
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 28.11.2019; MDPI
• Subjects: Abundance; Alleles; Bile ducts; Biomarkers; Breast cancer; Cancer; Cancer therapies; Chemotherapy; Cholangiocarcinoma; Copy number; Dehydrogenases; Deoxyribonucleic acid; Diagnosis; DNA; DNA methylation; DNA sequencing; Enzymes; Feasibility studies; Genes; Genomes; Genomics; Isocitrate dehydrogenase; Kinases; Liquid chromatography; Mass spectroscopy; Metabolism; Metabolites; Mutation; Patients; Proteins; Radiation therapy; Signal transduction; Statistical analysis; Statistics; Tumors; Whole genome sequencing; metabolomics; IDH1; CAD; Intrahepatic cholangiocarcinoma; 2-hydroxyglutarate; circulating DNA; orotic acid; TYMS; UMPS; DHODH
• ISSN: 2072-6694; 2072-6694
• DOI: 10.3390/cancers11121895

Intrahepatic cholangiocarcinoma (ICC) is an aggressive cancer arising from the bile ducts with a need for earlier diagnosis and a greater range of treatment options. mutations are common in ICC tumours and 6-32% of patients also have isocitrate dehydrogenase 1 and 2 ( and ) gene mutations associated with metabolic changes. This feasibility study investigated sequencing circulating tumour DNA (ctDNA) combined with metabolite profiling of plasma as a method for biomarker discovery in ICC patients. Plasma was collected from four ICC patients receiving radio-embolisation and healthy controls at multiple time points. ctDNA was sequenced using Ampliseq cancer hotspot panel-v2 on Ion Torrent PGM for single nucleotide variants (SNV) detection and with Illumina whole genome sequencing for copy number variants (CNV) and further targeted examination for SNVs. Untargeted analysis of metabolites from patient and control plasma was performed using liquid chromatography coupled with high-resolution tandem mass spectrometry (LC-MS/MS). Metabolite identification was performed using multi-parameter comparisons with analysis of authentic standards, and univariate statistical analysis was performed to identify differences in metabolite abundance between patient and control samples. Recurrent somatic SNVs and CNVs were identified in ctDNA from three out of four patients that included both and mutations linked to ICC. Plasma metabolite analysis revealed biomarker metabolites associated with ICC and in particular 2-hydroxyglutarate (2-HG) levels were elevated in both samples from the only patient showing a variant allele in . A reduction in the number of CNVs was observed with treatment. This study demonstrates that ctDNA and metabolite levels can be identified and correlated in ICC patient blood samples and differentiated from healthy controls. We conclude that combining genomic and metabolic analysis of plasma offers an effective approach to biomarker identification with potential for disease stratification and early detection studies.