Suomela Tuulikki, Zhang Liang, Vera Julio, Bruns Heiko, Lai Xin
Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
Department of Dermatology, Universitätsklinikum Erlangen and Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
Methods Mol Biol. 2025;2883:403-426. doi: 10.1007/978-1-0716-4290-0_18.
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.
微小RNA（miRNA）是一类调控基因表达的小型非编码RNA。它们与多种疾病和癌症相关，包括慢性淋巴细胞白血病（CLL）。CLL是成人白血病最常见的形式，其发病机制由miRNA的缺失驱动，如miR-15a/16-1簇。除了引发CLL的发展，miRNA在调节这种肿瘤进展中的功能仍有待研究。在这里，我们展示了一个计算流程，从miRNA测序文件的处理到功能分析，包括差异基因表达和基因集富集分析。我们通过将其应用于一组CLL患者的全基因组小RNA测序数据来举例说明该流程的实用性。分析揭示了CLL中miRNA的表达谱失调。这些miRNA的靶基因不仅与CLL患者对当前疗法的反应相关，还涉及多个癌症特征，包括避免细胞死亡、细胞能量代谢失调、侵袭和转移激活以及基因组不稳定。所确定的miRNA-基因相互作用为开发CLL的靶向疗法提供了有价值的见解。此外，我们强调了实用且强大的计算流程对于确保miRNA测序数据分析的可靠性和可重复性的重要性。
