Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies

Abstract

Background: Phosphatase and tensin homolog, widely known as PTEN, is a major negative regulator of the PI3K/AKT/mTOR signaling pathway, involved in the regulation of a variety of important cellular processes, including cell proliferation, growth, survival, and metabolism. Since most of the molecules involved in this biological pathway have been described as key regulators in cancer, the study of the corresponding genes at several levels is crucial.

Objective: Although previous studies have elucidated the physiological role of PTEN under normal conditions and its involvement in carcinogenesis and cancer progression, the transcriptional profile of PTEN has been poorly investigated.

Methods: In this study, instead of conducting the "gold-standard" direct RNA sequencing that fails to detect less abundant novel mRNAs due to the decreased sequencing depth, we designed and implemented a multiplexed PTEN-targeted sequencing approach that combined both short- and long-read sequencing.

Results: Our study has highlighted a broad spectrum of previously unknown PTEN mRNA transcripts and assessed their expression patterns in a wide range of human cancer and non-cancer cell lines, shedding light on the involvement of PTEN in cell cycle dysregulation and thus tumor development.

Conclusion: The identification of the described novel PTEN splice variants could have significant implications for understanding PTEN regulation and function, and provide new insights into PTEN biology, opening new avenues for monitoring PTEN-related diseases, including cancer.

Keywords: Phosphatase and tensin homolog; alternative splicing; cytogenetic; long-read sequencing; splice variants; tumor suppression.

Fig. (1)

Visualization of the aligned sequencing reads representing novel transcript variants of the human PTEN gene via Integrative Genomics Viewer (IGV) tool.

Fig. (2)

Detailed structure of the newly identified PTEN transcript variants comprising the annotated exons. Exons are shown as rectangles and introns as lines. The length of every exon/intron is also shown. The highlighted regions in rectangles depict the ORFs in each transcript variant. Finally, the positions of the annotated initiation and stop codons are indicated with arrows (↓) and asterisks (*) accordingly.

Fig. (3)

Next-generation sequencing reads that support the existence of novel PTEN exons and alternative splice sites. For visual purposes, the nucleotide bases of each exon are demonstrated in a different color.

Fig. (4)

Detailed structure of the novel PTEN transcripts that include newly detected cryptic exons. Exons are shown as rectangles and introns as lines. The length of every exon/intron is also shown. The highlighted regions in rectangles depict the ORFs in each transcript variant. Finally, the positions of the annotated initiation and stop codons are indicated with arrows (↓) and asterisks (*) accordingly.

Fig. (5)

Heatmap indicating the relative abundance of each PTEN transcript compared to the main mRNA. Yellow coloring is indicative of a higher relative abundance of the corresponding transcript variant, whereas purple coloring corresponds to low-frequent or even undetectable transcripts.

Fig. (6)

Gene ontology analysis of the putative new isoforms encoded by the described PTEN mRNA transcripts. (A) Plot demonstrating the GO scores of each predicted new isoform in terms of cellular components. (B) Scatterplot providing the GO scores for the molecular function. (C) Heatmap showing the probability of each putative PTEN isoform to participate in a wide spectrum of biological processes.