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Extrachromosomal DNA Detection and Ultrastructural Profiling in Lung and Colorectal Cancer Models.

Astari Dwiranti1, Gina Zulfa Nabila1, Tiara Aulia Zalyanti1

  • 1Cellular and Molecular Mechanisms in Biological Systems (CEMBIOS) Research Group, Department of Biology, Faculty of Mathematics and Natural Science, Universitas Indonesia, Depok, Indonesia.

Genes, Chromosomes & Cancer
|March 9, 2026
PubMed
Summary

Extrachromosomal DNA (ecDNA) was detected in lung and colorectal cancer cells, contributing to cancer aggressiveness and drug resistance. This study characterized ecDNA in A549 and HT-29 cells, revealing its presence and potential as a therapeutic target.

Keywords:
A549HT‐29cancerextrachromosomal DNAultrastructure

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Area of Science:

  • Oncology and Molecular Biology
  • Cancer Research
  • Genetics

Background:

  • Lung and colorectal cancers are leading causes of cancer mortality worldwide.
  • Drug resistance in these cancers is linked to cancer cell heterogeneity, partly due to extrachromosomal DNA (ecDNA).
  • ecDNA, found in cancer cells, carries amplified oncogenes and promotes cancer aggressiveness.

Purpose of the Study:

  • To detect and characterize ecDNA in A549 (lung) and HT-29 (colorectal) cancer cell lines.
  • To investigate the prevalence and structural features of ecDNA in these specific cell lines.

Main Methods:

  • Giemsa staining
  • DAPI staining
  • Scanning Electron Microscopy (SEM)

Main Results:

  • ecDNA was identified in 15% of A549 cells and 10% of HT-29 cells.
  • ecDNA structures varied in size and fluorescence intensity, with SEM confirming ring-like circular forms.
  • The presence of ecDNA was confirmed across different cancer cell lines.

Conclusions:

  • ecDNA is present in A549 and HT-29 cancer cells.
  • ecDNA may serve as a potential biomarker for cancer.
  • ecDNA represents a promising target for future cancer therapies.