Examination of genomic profile of true single circulating tumor cells (sCTC) from hepatocellular carcinoma and its effect on mutational features.
Authors: Bharde Atul , Shafi Gowhar , Dongare Manoj , Jadhav Vikas Leelavati Balasaheb , Khutale Ganesh , Andhari Saloni , Prajapati Sangeeta , Jadhav Bhagwat , Mobeen Fauzul , Hariramani Kanchan , Basavalingegowda Madhura , Deshpande Richa , Zhou Wenhui , Uttarwar Mohan , Patel Kaushal Babubhai , Kishore Sirish , Singhal Manish Kumar , Gupta Vineet Govinda , Thirumalairaj Raja , Khandare Jayant 
Published: June 2024

e15039

Background: Hepatocellular carcinoma (HCC) is the fifth leading cause of cancer-related deaths worldwide. Despite numerous NGS studies unveiling diverse mutational patterns through tissue biopsies, the absence of tissue for biopsy and distinct biomarkers complicates both diagnosis and treatment. The utilization of sCTC genomics holds promise in furnishing clinically relevant and actionable insights to tailor personalized diagnostics and therapy for HCC. We present a comparative analysis of sCTC and paired ctDNA obtained from primary HCC patients for better Tx possibilities. Methods: Genomic profile from 24 sCTCs/CTC clusters (19 sCTCs, 79%; 5 CTC clusters, 21 %) revealed distinct mutational patterns compared to paired ctDNA. Live sCTCs/CTC clusters were isolated from peripheral blood of treatment naïve 12 Hepatobiliary Cancer with advanced and metastatic disease patients using OncoRadar technology. Whole genomes from sCTCs/CTC clusters were amplified, target enriched with hybridization capture using a comprehensive 1080 gene panel-OncoIndx to obtain sequencing libraries, and sequenced on Illumina NextSeq2000 platform in paired end mode (depth 500x). The raw sequence alignment and variant calling was performed using iCare software. Paired ctDNA samples were sequenced the same way, except at the depth of 5500x. Results: Pathogenic (P)/likely pathogenic (LP) variants were detected from all sCTCs, while ctDNA was negative for 40% samples. sCTCs showed at least twice as many P variants compared to paired ctDNA. ATM (50%), PIK3CA (42%), ARID1A /1B (42%), TP53/RB1 (34%), and IDH1 (34%) were among the most frequently mutated genes, while 42% sCTCs showed amplified CCND1/2 variants. In comparison, paired ctDNA had no distinct mutational pattern. Genomic profile of sCTC showed concordance with paired ctDNA for at least one gene mutation when compared at patient level. At pathway level, all sCTCs were mutated for at least one HRR pathway component, while 60% sCTCs had at least one mutation in receptor tyrosine kinase (RTK) pathway (FGFR1, ERBB, ALK, ROS1). sCTC population showed a strong cooccurrence of HRR mutation and epigenetic regulatory pathway mutations (OR =4, CI=0.4-60). At individual mutation level, 30 % concordance was observed in sCTC population, suggesting high mutational heterogeneity. Besides actionable targets, 50% sCTC were enriched with resistance conferring variants such as STK11, NF1, STAT5B, and RB1. Conclusions: The genomic profile of sCTCs in primary HCC pts revealed a complex mutational landscape, offering complementarity to ctDNA for clinical insights. sCTCs exhibited more actionable targets and greater heterogeneity compared to paired ctDNA, making sCTC genomics valuable for pts ineligible for tissue biopsy or lacking clinically relevant information from ctDNA.