# Integrated CIRCLE-seq with RNA-seq to decipher the quantity, localization, and functional features of eccDNA in AML

## TL;DR

This study explores the role of circular DNA in acute myeloid leukemia, revealing its increased presence and link to cancer-related genes.

## Contribution

The study is the first to use CIRCLE-seq and RNA-seq to characterize eccDNA in AML, revealing its functional and prognostic significance.

## Key findings

- AML cells have significantly more eccDNA than healthy controls, with distinct size peaks at 202 and 368 bp.
- AML eccDNA localizes near regulatory regions and activates oncogenic pathways like MAPK and ErbB signaling.
- 570 genes, including FLT3 and RUNX1, are upregulated in both eccDNA and mRNA, correlating with poor AML outcomes.

## Abstract

Extrachromosomal circular DNA (eccDNA) plays critical roles in cancer, yet its landscape in acute myeloid leukemia (AML) remains unexplored.

We used CIRCLE-seq and RNA-seq to characterize eccDNA in 12 AML patients and 4 healthy controls.

AML cells showed significantly increased eccDNA counts and gene involvement versus healthy controls, with distinct size peaks at 202 and 368 bp. eccDNAs localized non-randomly to chromosomes 1, 2, and 10–19, enriching near transcription start sites and regulatory regions. Functional analysis revealed activation of oncogenic pathways (e.g., MAPK, ErbB signaling) in AML-associated eccDNA. Integrative analysis identified 570 genes upregulated at both the eccDNA and mRNA levels, including myeloid leukemia-related genes (e.g., FLT3, RUNX1, and CD33) and oncogenes. Prognostic analysis showed that high expression of these genes correlated with poor outcomes in AML.

This study unveils the eccDNA landscape in AML by direct CIRCLE-seq, linking its accumulation to transcriptional dysregulation and leukemogenesis, and highlights eccDNA as a potential biomarker and therapeutic target.