Biological role and diagnostic utility of ribosomal protein L23a pseudogene 53 in cutaneous melanoma

Tomasz Kolenda; Paulina Poter; Kacper Guglas; Joanna Kozłowska-Masłoń; Alicja Braska; Urszula Kazimierczak; Anna Teresiak

doi:10.5603/RPOR.a2023.0030

Biological role and diagnostic utility of ribosomal protein L23a pseudogene 53 in cutaneous melanoma

Rep Pract Oncol Radiother. 2023 Jun 26;28(2):255-270. doi: 10.5603/RPOR.a2023.0030. eCollection 2023.

Authors

Tomasz Kolenda^{1

2}, Paulina Poter^{3

4}, Kacper Guglas^{1

2

5}, Joanna Kozłowska-Masłoń^{1

2

6}, Alicja Braska², Urszula Kazimierczak^{7

8}, Anna Teresiak^{1

2}

Affiliations

¹ Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland.
² Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland.
³ Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Center, Poznan, Poland.
⁴ Department of Pathology, Pomeranian Medical University, Szczecin, Poland.
⁵ Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland.
⁶ Faculty of Biology, Institute of Human Biology and Evolution, Adam Mickiewicz University, Poznań, Poland.
⁷ Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.
⁸ Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Poznan, Poland.

Abstract

Background: Skin melanoma is one of the deadliest types of skin cancer and develops from melanocytes. The genetic aberrations in protein-coding genes are well characterized, but little is known about changes in non-coding RNAs (ncRNAs) such as pseudogenes. Ribosomal protein pseudogenes (RPPs) have been described as the largest group of pseudogenes which are dispersed in the human genome.

Materials and methids: We looked deeply at the role of one of them, ribosomal protein L23a pseudogene 53 (RPL23AP53), and its potential diagnostic use. The expression level of RPL23AP53 was profiled in melanoma cell lines using real time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and analyzed based on the Cancer Genome Atlas (TCGA) data depending on BRAF status and clinicopathological parameters. Cellular phenotype, which was associated with RPL23AP53 levels, was described based on the REACTOME pathway browser, Gene Set Enrichment Analysis (GSEA) analysis as well as Immune and ESTIMATE Scores.

Results: We indicted in vitro changes in RPL23AP53 level depending on a cell line, and based on in silico analysis of TCGA samples demonstrated significant differences in RPL23AP53 expression between primary and metastatic melanoma, as well as correlation between RPL23AP53 and overall survival. No differences depending on BRAF status were observed. RPL23AP53 is associated with several signaling pathways and cellular processes.

Conclusions: This study showed that patients with higher expression of RPL23AP53 displayed changed infiltration of lymphocytes, macrophages, and neutrophils compared to groups with lower expression of RPL23AP53. RPL23AP53 pseudogene is differently expressed in melanoma compared with normal tissue and its expression is associated with cellular proliferation. Thus, it may be considered as an indicator of patients' survival and a marker for the immune profile assessment.

Keywords: BRAF mutation; RPL23AP53; TCGA; biomarkers; immunology; lncRNA; non-coding RNA; pseudogene.