A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia

Suomela T, Zhang L, Vera J, Bruns H, Lai X (2025)

Publication Type: Book chapter / Article in edited volumes

Publication year: 2025

Journal

Methods in Molecular Biology Humana Press

Publisher: Humana Press Inc.

Series: Methods in Molecular Biology

Book Volume: 2883

Pages Range: 403-426

DOI: 10.1007/978-1-0716-4290-0_18

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. They have been associated with several diseases and cancers, including chronic lymphocytic leukemia (CLL). CLL is the most common form of adult leukemia, and its pathogenesis is driven by the deletion of miRNAs, such as the miR-15a/16-1 cluster. In addition to initiating the development of CLL, the function of miRNAs in regulating the progression of this tumor remains to be investigated. Here, we present a computational pipeline, from the processing of miRNA sequencing files to functional analysis, including differential gene expression and gene set enrichment analysis. We exemplified the utility of the pipeline by applying it to genome-wide small RNA sequencing data from a cohort of CLL patients. The analysis revealed dysregulated expression profiles of miRNAs in CLL. The target genes of these miRNAs are not only associated with the response of CLL patients to current therapies but also involved in several cancer hallmarks, including the avoidance of cell death, the deregulation of cellular energetics, the activation of invasion and metastasis, and genome instability. The identified miRNA–gene interactions offer valuable insights for developing targeted therapies for CLL. In addition, we underscored the importance of a practical and robust computational pipeline to ensure the reliability and reproducibility of miRNA sequencing data analysis.

Authors with CRIS profile

Julio Vera González Professur für Tumorimmunologie (Schwerpunkt Systembiologie) Heiko Bruns Department of Medicine 5 – Haematology and Oncology

Involved external institutions

University of Tampere (UTA) / Tampereen yliopisto (Tay) FI Finland (FI)

How to cite

APA:

Suomela, T., Zhang, L., Vera, J., Bruns, H., & Lai, X. (2025). A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia. In (pp. 403-426). Humana Press Inc..

MLA:

Suomela, Tuulikki, et al. "A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia." Humana Press Inc., 2025. 403-426.

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