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HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia

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Abstract

Human endogenous retroviruses (HERVs) are LTR retrotransposons that are present in the human genome. Among them, members of the HERV-K (HML-2) group are suspected to play a role in the development of different types of cancer, including lung, ovarian, and prostate cancer, as well as leukemia. Acute myeloid leukemia (AML) is an important disease that causes 1% of cancer deaths in the United States and has a survival rate of 28.7%. Here, we describe a method for assessing the statistical association between HERV-K (HML-2) transposable element insertion polymorphisms (or TIPs) and AML, using whole-genome sequencing and read mapping using TIP_finder software. Our results suggest that 101 polymorphisms involving HERV-K (HML-2) elements were correlated with AML, with a percentage between 44.4 to 56.6%, most of which (70) were located in the region from 8q24.13 to 8q24.21. Moreover, it was found that the TRIB1, LRATD2, POU5F1B, MYC, PCAT1, PVT1, and CCDC26 genes could be displaced or fragmented by TIPs. Furthermore, a general method was devised to facilitate analysis of the correlation between transposable element insertions and specific diseases. Finally, although the relationship between HERV-K (HML-2) TIPs and AML remains unclear, the data reported in this study indicate a statistical correlation, as supported by the χ2 test with p-values < 0.05.

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Data Availability

The datasets generated during and/or analysed during the current study are available at Zenodo https://doi.org/10.5281/zenodo.7770141.

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Acknowledgements

We would like to thank the following HPC bioinformatics platforms for their support: the French Bioinformatics Institute (https://www.france-bioinformatique.fr) and IRD (https://bioinfo.ird.fr/).

Funding

Simon Orozco-Arias was supported by a Ph.D. grant from the Ministry of Science, Technology and Innovation (Minciencias) of Colombia, Grant no. 785/2017.

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Authors and Affiliations

  1. School of Biology, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia

    Nicolás Camargo-Forero

  2. Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia

    Simon Orozco-Arias

  3. Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia

    Simon Orozco-Arias

  4. School of Medicine, Universidad de Manizales, Manizales, Caldas, Colombia

    Juan M. Perez Agudelo

  5. UMR DIADE, Université de Montpellier, Institut de recherche pour le développement, CIRAD, Montpellier, France

    Romain Guyot

  6. Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia

    Romain Guyot

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RG and SO-A contributed to the study conception and design. Material preparation, data collection, and analysis were performed by NC-F. The first draft of the manuscript was written by NC-F, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Simon Orozco-Arias.

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Camargo-Forero, N., Orozco-Arias, S., Perez Agudelo, J.M. et al. HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia. Arch Virol 168, 125 (2023). https://doi.org/10.1007/s00705-023-05747-0

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