E-Poster Presentation 34th Lorne Cancer Conference 2022

Bioinformatics prediction of microRNAs targeting PTEN and its pseudogene, PTENp1 (#316)

Glena Travis 1 , Ann M. Simpson 1 2 , Najah T. Nassif 1 2
  1. School of Life Science, University of Technology Sydney, Sydney, NSW, Australia
  2. Centre for Health Technologies, University of Technology Sydney, Sydney, NSW, Australia

The phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is a tumour suppressor that is under post-transcriptional regulation by microRNAs, which bind to the 3’-untranslated region (UTR) and decrease vital PTEN cellular levels1. The pseudogene of PTEN, (PTENp1) is transcribed as a long non-coding RNA, with high sequence similarity to PTEN and is able to sponge microRNAs that target PTEN to increase PTEN levels1. This study aimed to predict microRNAs targeting the 5’-UTR, CDS and 3’-UTR of both PTEN and PTENp1 in silico using bioinformatics tools.

The online bioinformatics tool, miRWalk 3.02 was used to predict microRNAs targeting PTEN. microRNAs targeting the 3’-UTR of PTEN were predicted using TargetScan release 7.23 and microRNAs targeting the 3’-UTR of PTEN and PTENp1 were predicted using StarBase-ENCORI v3.04. microRNAs targeting the 5’-UTR, CDS and 3’-UTR of PTEN and PTENp1 were predicted by inputting mined sequences into the custom prediction tool in miRDB v6.05 and exported. Duplicates were removed and Venn diagrams for each region identified microRNAs targeting both the respective regions of PTEN and PTENp1. The microRNAs were mapped onto pair-wise alignments of PTEN and PTENp1 transcripts based on sequence complementarity. The mapped microRNAs were ranked based on the number of bioinformatics tools that predicted the microRNA. A literature search identified cancer associated microRNAs from the ranked microRNAs.

Of the predicted miRNAs, 16 out of 19, 37 out of 40 and 56 out of 108 matched the pair-wise aligned 5’-UTR, CDS and 3’-UTR of the PTEN and PTENp1 sequences, respectively. Of these, a total of 21 (of 109) microRNAs received the highest rankings as potential targets for the 5’-UTR (7/21), CDS (3/21) and 3’-UTR (11/21) of PTEN and PTENp1, respectively. Some of the predicted microRNAs have been previously described as targeting PTEN with 4 representing potential novel targets of the 3’-UTR of PTEN and PTENp1.

This study provides some novel predicted microRNAs targeting the 5’-UTR, CDS and 3’-UTR of PTEN and PTENp1 for experimental validation.

 

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