Comparison of Genetic Profiling between Primary Tumor and Circulating Tumor Cells Captured by Microfluidics in Epithelial Ovarian Cancer: Tumor Heterogeneity or Allele Dropout?

Abstract

Epithelial ovarian cancer (EOC) is a leading cause of cancer mortality among women but unfortunately is usually not diagnosed until advanced stage. Early detection of EOC is of paramount importance to improve outcomes. Liquid biopsy of circulating tumor cells (CTCs) is emerging as one of the promising biomarkers for early detection of solid tumors. However, discrepancies in terms of oncogenomics (i.e., different genetic defects detected) between the germline, primary tumor, and liquid biopsy are a serious concern and may adversely affect downstream cancer management. Here, we illustrate the potential and pitfalls of CTCs by presenting two patients of Stage I EOC. We successfully isolated and recovered CTCs by a silicon-based nanostructured microfluidics system, the automated Cell RevealTM. We examined the genomics of CTCs as well as the primary tumor and germline control (peripheral blood mononuclear cells) by whole exome sequencing. Different signatures were then investigated by comparisons of identified mutation loci distinguishing those that may only arise in the primary tumor or CTCs. A novel model is proposed to test if the highly variable allele frequencies, between primary tumor and CTCs results, are due to allele dropout in plural CTCs or tumor heterogeneity. This proof-of-principle study provides a strategy to elucidate the possible cause of genomic discrepancy between the germline, primary tumor, and CTCs, which is helpful for further large-scale use of such technology to be integrated into clinical management protocols.

RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data

“…We found that KMT2D p.E869∗ mutation could cause its truncation leading to tumor progression. In addition, TP53 p.A276G mutation had been found to locate within the DNA binding domain of the TP53 protein and presumably have deleterious impacts on protein functions ( Chang et al, 2021 ) with pathogenic ClinVar database ( Landrum et al, 2020 ) interpretation (Accession: VCV000185319.3). These findings confirmed that RNA-seq data could provide valuable supplementary information useful for clinical decisions and improve diagnostic yield in extreme cases when DNA failed to detect actionable mutations.…”

Isolation of TTF-1 Positive Circulating Tumor Cells for Single-Cell Sequencing by Using an Automatic Platform Based on Microfluidic Devices

“…Cell Reveal TM machine (CytoAurora Biotechnologies, Inc., Hsinchu, Taiwan) was used for the CTCs enrichment and staining as described in our previous reports [ 23 , 24 ]. The system is a fully automatic CTC enrichment and staining system centered on an immune-affinity microfluidic chip, V-BioChip (CytoAurora Biotechnologies, Inc., Hsinchu, Taiwan) [ 25 , 26 ]. After placing the required reagents in the machine and setting the experiment condition and procedure, the prepared blood sample was injected into the instrument, and then the whole process would automatically proceed.…”