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Updated: Oct 9, 2025
Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
Published on: August 24, 2017
CNA Profiling of Single CTCs in Locally Advanced Esophageal Cancer Patients during Therapy Highlights Unexplored
Giulia Gallerani1, Tania Rossi1, Martina Valgiusti2
1Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, Italy.
Background:
Here, we monitored the evolution of CTCs spread in 11 patients affected by locally advanced EC who were undergoing therapy.
Methods:
In this perspective study, we designed multiple blood biopsies from individual patients: before and after neoadjuvant chemo-radio therapy and after surgery. We developed a multi-target array, named Grab-all assay, to estimate CTCs for their epithelial (EpCAM/E-Cadherin/Cytokeratins) and mesenchymal/stem (N-Cadherin/CD44v6/ABCG2) phenotypes. Identified CTCs were isolated as single cells by DEPArray, subjected to whole genome amplification, and copy number aberration (CNA) profiles were determined. Through bioinformatic analysis, we assessed the genomic imbalance of single CTCs, investigated specific focal copy number changes previously reported in EC and aberrant pathways using enrichment analysis.
Results:
Longitudinal monitoring allowed the identification of CTCs in at least one time-point per patient. Through single cell CNA analysis, we revealed that CTCs showed significantly dynamic genomic imbalance during treatment. Individual CTCs from relapsed patients displayed a higher degree of genomic imbalance relative to disease-free patients' groups. Genomic aberrations previously reported in EC occurred mostly in post-neoadjuvant therapy CTCs. In-depth analysis showed that networks enrichment in all time-point CTCs were inherent to innate immune system. Transcription/gene regulation, post-transcriptional and epigenetic modifications were uniquely affected in CTCs of relapsed patients.
Conclusions:
Our data add clues to the comprehension of the role of CTCs in EC aggressiveness: chromosomal aberrations on genes related to innate immune system behave as relevant to the onset of CTC-status, whilst pathways of transcription/gene regulation, post-transcriptional and epigenetic modifications seem linked to patients' outcome.
Insights
Monitoring circulating tumor cells (CTCs) in esophageal cancer (EC) patients revealed dynamic genomic changes during treatment. Relapsed patients showed greater genomic imbalance in CTCs, linked to specific gene regulation pathways.
Area of Science:
- Oncology
- Genomics
- Cancer Biology
Background:
- Locally advanced esophageal cancer (EC) treatment involves complex therapeutic strategies.
- Monitoring circulating tumor cells (CTCs) offers insights into treatment response and disease progression.
- Understanding CTC evolution is crucial for managing EC aggressiveness.
Purpose of the Study:
- To longitudinally monitor the genomic evolution of circulating tumor cells (CTCs) in patients with locally advanced esophageal cancer (EC) undergoing therapy.
- To correlate CTC genomic profiles with treatment response and patient outcomes.
- To investigate the phenotypic and genomic characteristics of CTCs during different treatment phases.
Main Methods:
- Developed a multi-target 'Grab-all assay' to detect CTCs with epithelial and mesenchymal/stem phenotypes.
- Utilized DEPArray for single-cell isolation of CTCs followed by whole genome amplification.
- Determined copy number aberration (CNA) profiles of single CTCs and performed bioinformatic analysis for genomic imbalance and pathway enrichment.
Main Results:
- CTCs were identified longitudinally in all 11 patients, exhibiting dynamic genomic imbalance during treatment.
- CTCs from relapsed patients showed significantly higher genomic imbalance compared to disease-free patients.
- Genomic aberrations reported in EC were prevalent in post-neoadjuvant therapy CTCs.
- Innate immune system pathways were enriched in all CTCs, while transcription/gene regulation pathways were uniquely affected in relapsed patients.
Conclusions:
- Chromosomal aberrations in innate immune system genes are relevant to CTC-status onset in EC.
- Aberrant transcription/gene regulation, post-transcriptional, and epigenetic modifications in CTCs are linked to patient outcomes.
- Genomic profiling of CTCs provides valuable insights into EC aggressiveness and treatment response.
