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Gene biomarkers and classifiers for various subtypes of HTLV-1-caused ATLL cancer identified by a combination of differential gene co‑expression and support vector machine algorithms

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Abstract

Adult T-cell leukemia/lymphoma (ATLL) is pathogen-caused cancer that is progressed after the infection by human T-cell leukemia virus type 1. Four significant subtypes comprising acute, lymphoma, chronic, and smoldering have been identified for this cancer. However, there are no trustworthy prognostic biomarkers for these subtypes. We utilized a combination of two powerful network-based and machine-learning algorithms including differential co-expressed genes (DiffCoEx) and support vector machine-recursive feature elimination with cross-validation (SVM-RFECV) methods to categorize disparate ATLL subtypes from asymptomatic carriers (ACs). The results disclosed the significant involvement of CBX6, CNKSR1, and MAX in chronic, MYH10 and P2RY1 in acute, C22orf46 and HNRNPA0 in smoldering subtypes. These genes also can classify each ATLL subtype from AC carriers. The integration of the results of two powerful algorithms led to the identification of reliable gene classifiers and biomarkers for diverse ATLL subtypes.

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Availability of data and materials

All data generated or analyzed during this study are included in this article. The SVM-RFECV code was deposited in https://github.com/Mohadesehzarei/SVM-RFECV.

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Authors and Affiliations

  1. Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran

    Mohadeseh Zarei Ghobadi & Rahman Emamzadeh

  2. Independent Researcher, Tehran, Iran

    Elaheh Afsaneh

Authors
  1. Mohadeseh Zarei Ghobadi
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  2. Elaheh Afsaneh
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  3. Rahman Emamzadeh
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Contributions

MZG and EA performed bioinformatics and statistical analysis. MZG interpreted the results and wrote the manuscript. EA revised the manuscript. RE supervised the project. All authors approved the final manuscript.

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Correspondence to Mohadeseh Zarei Ghobadi or Rahman Emamzadeh.

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Edited by Matthias J. Reddehase.

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Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary data file 1.

The gene lists in the specific modules for each ATLL subtype. (XLSX 241 KB)

Supplementary data file 2.

The pathway enrichment analysis of the specific modules. (XLSX 12 KB)

Supplementary data file 3.

The unique DEGs considering p. adj. value <0.05 for each ATLL subtype (XLSX 33 KB)

Supplementary data file 4.

The shared genes between unique DEGs and the genes in each specific DiffCoexGMs of each subtype (XLSX 11 KB)

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Zarei Ghobadi, M., Afsaneh, E. & Emamzadeh, R. Gene biomarkers and classifiers for various subtypes of HTLV-1-caused ATLL cancer identified by a combination of differential gene co‑expression and support vector machine algorithms. Med Microbiol Immunol 212, 263–270 (2023). https://doi.org/10.1007/s00430-023-00767-8

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