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Bioinformatics Prediction and Analysis of MicroRNAs and Their Targets as Biomarkers for Prostate Cancer: A Preliminary Study

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Abstract

Prostate cancer (PCa) is the second most common form of cancer in men around the world. Due to its heterogeneity, presentations range from aggressive lethal disease to indolent disease. There is a need to identify core biomarkers that are important for early detection and progression, allowing a more precise method for the treatment and management of Pca. We obtained metastatic prostate cancer associated microRNA array profiles from the GSE28029 dataset in the GEO database. MicroRNA target prediction was done using the databases, TargetScanHuman, miRDB and DIANA microT, six target genes (FOXC1, CDKN1A, BIRC2, CTNND1, ELK1 and LRP8) were found to be common among the three different databases. Differential expression of the target genes was performed via the GENT2 database in the GPL96 platform (HG-U133A). Results indicated all genes were downregulated. Gene Ontology (GO) was used to perform enrichment analysis. The GO enrichment analysis indicated that the downregulated genes were enriched in cellular response to gamma radiation, regulation of transcription and response to drugs as well as protein binding and receptor signaling protein activity. The study suggested that CDKN1A, FOXC1 and BIRC2 might be core genes for prostate cancer that play an important role in its diagnosis, development and progression.

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Acknowledgements

The authors thank the Biotechnology Department at UWC, the NIC and DST Minetk for their aid in the project.

Funding

Funding for part of this work was provided for by the Nanotechnology Innovation (NIC) Centre with the aid of the Department of Science and Technology (DST) Mintek South Africa.

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Authors and Affiliations

  1. Department of Biotechnology, University of the Western Cape, Cape Town, South Africa

    Chipampe Patricia Lombe, Mervin Meyer & Ashley Pretorius

  2. Biology Department, Mukuba University, Garneton itimpi, Kitwe, Zambia

    Chipampe Patricia Lombe

  3. Biotechnology Innovation Division, Aminotek, PTY, Cape Town, South Africa

    Ashley Pretorius

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  1. Chipampe Patricia Lombe
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The corresponding author conceived the idea, performed the experiments, guided the aim of study, interpreted the project results and drafted the manuscript. The other authors supervised the project and reviewed the manuscript. All authors read and approved the final version of the manuscript.

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Appendix

Appendix

See Tables 5 and 6.

Table 5 Primer sequences
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Table 6 Cell lines used to investigate the expression levels of the microRNAs
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Lombe, C.P., Meyer, M. & Pretorius, A. Bioinformatics Prediction and Analysis of MicroRNAs and Their Targets as Biomarkers for Prostate Cancer: A Preliminary Study. Mol Biotechnol 64, 401–412 (2022). https://doi.org/10.1007/s12033-021-00414-8

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