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Characterization of extrachromosomal circular DNAs in plasma of patients with clear cell renal cell carcinoma

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Abstract

Background and Purpose

Extrachromosomal circular DNAs (eccDNAs) have been recognized for their significant involvement in numerous biological processes. Nonetheless, the existence and molecular characteristics of eccDNA in the peripheral blood of patients diagnosed with clear cell renal cell carcinoma (ccRCC) have not yet been reported. Our aim was to identify potentially marked plasma eccDNAs in ccRCC patients.

Methods and Materials

The detection of plasma eccDNA in ccRCC patients and healthy controls was performed using the Tn5-tagmentation and next-generation sequencing (NGS) method. Comparisons were made between ccRCC patients and healthy controls regarding the distribution of length, gene annotation, pattern of junctional nucleotide motif, and expression pattern of plasma eccDNA.

Results

We found 8,568 and 8,150 plasma eccDNAs in ccRCC patients and healthy controls, respectively. There were no statistical differences in the length distribution, gene annotation, and motif signature of plasma eccDNAs between the two groups. A total of 701 differentially expressed plasma eccDNAs were identified, and 25 plasma eccDNAs with potential diagnostic value for ccRCC have been successfully screened. These up-regulated plasma eccDNAs also be indicated to originate from the genomic region of the tumor-associated genes.

Conclusion

This work demonstrates the characterization of plasma eccDNAs in ccRCC and suggests that the up-regulated plasma eccDNAs could be considered as a promising non-invasive biomarker in ccRCC.

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Data availability

The data that supports the findings of this study are available in the supplementary materials and the raw data are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank Cloud-Seq Biotech Ltd. Co. (Shanghai, China) for eccDNA sequencing service.

Funding

This work was supported by University Natural Science Research Project of Anhui Province (KJ2021ZD0102).

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Author notes

  1. Qing Li and Rui-Xuan Zhang Zhang contributes equally to this work.

Authors and Affiliations

  1. Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, No.2, West Zheshan Road, Wuhu, 241001, Anhui, China

    Qing Li, Rui-Xuan Zhang, Jing-Jing Yang & Gang Feng

  2. Department of Urology, The First Affiliated Hospital of Wannan Medical College, Wuhu, 241001, Anhui, China

    Hou-Bao Huang

  3. Department of Urology, North Hospital, CHU of Saint-Etienne, 42055, Saint-Etienne, France

    Gang Feng & Guo-Rong Li

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  1. Qing Li
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Contributions

Gang Feng and Guo-Rong Li designed the study. Rui-Xuan Zhang, Jing-Jing Yang, and Hou-Bao Huang collected the samples and data. Qing Li, Rui-Xuan Zhang, Jing-Jing Yang, and Hou-Bao Huang analyzed the data. Gang Feng, Qing Li and Guo-Rong Li drafted and revised the manuscript. All authors gave final approval of the final version and agreed to its submission.

Corresponding author

Correspondence to Gang Feng.

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Approval for this research was granted by the Scientific research IRB of Wannan Medical College Yijishan Hospital. Consent was obtained from 6 participants included after they were provided with written information.

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Li, Q., Zhang, RX., Yang, JJ. et al. Characterization of extrachromosomal circular DNAs in plasma of patients with clear cell renal cell carcinoma. World J Urol 42, 328 (2024). https://doi.org/10.1007/s00345-024-05031-z

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