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Accessing a New Dimension in TP53 Biology: Multiplex Long Amplicon Digital PCR to Specifically Detect and Quantitate Individual TP53 Transcripts.

TP53, the most commonly-mutated gene in cancer, undergoes complex alternative splicing. Different TP53 transcripts play different biological roles, both in normal function and in the progression of diseases such as cancer. The study of TP53's alternative RNA splice forms and their use as clinical bi...

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Published in:Cancers Vol. 12; no. 3; pp. 769 - 770
Main Authors: Lasham, Annette, Tsai, Peter, Fitzgerald, Sandra J., Mehta, Sunali Y., Knowlton, Nicholas S., Braithwaite, Antony W., Print, Cristin G.
Format: research tables/charts Journal Article
Published: MDPI Mar2020
Online Access:View this record in EBSCOhost
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      dt: Mar2020
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      pub: MDPI
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        10.3390/cancers12030769
        142523972
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        atl: Accessing a New Dimension in TP53 Biology: Multiplex Long Amplicon Digital PCR to Specifically Detect and Quantitate Individual TP53 Transcripts.
      aug:
        au:
          Lasham, Annette
          Tsai, Peter
          Fitzgerald, Sandra J.
          Mehta, Sunali Y.
          Knowlton, Nicholas S.
          Braithwaite, Antony W.
          Print, Cristin G.
        affil: Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1142, New Zealand
      sug:
        subj:
          Mutation
          Gene Amplification
          Polymerase Chain Reaction Methods
          Sequence Analysis
          Genetic Engineering
          Breast Neoplasms Diagnosis
          Human
          RNA
          Tumor Markers, Biological
          Gene Expression
      ab: TP53, the most commonly-mutated gene in cancer, undergoes complex alternative splicing. Different TP53 transcripts play different biological roles, both in normal function and in the progression of diseases such as cancer. The study of TP53's alternative RNA splice forms and their use as clinical biomarkers has been hampered by limited specificity and quantitative accuracy of current methods. TP53 RNA splice variants differ at both 5' and 3' ends, but because they have a common central region of 618 bp, the individual TP53 transcripts are impossible to specifically detect and precisely quantitate using standard PCR-based methods or short-read RNA sequencing. Therefore, we devised multiplex probe-based long amplicon droplet digital PCR (ddPCR) assays, which for the first time allow precise end-to-end quantitation of the seven major TP53 transcripts, with amplicons ranging from 0.85 to 1.85 kb. Multiple modifications to standard ddPCR assay procedures were required to enable specific co-amplification of these long transcripts and to overcome issues with secondary structure. Using these assays, we show that several TP53 transcripts are co-expressed in breast cancers, and illustrate the potential for this method to identify novel TP53 transcripts in tumour cells. This capability will facilitate a new level of biological and clinical understanding of the alternatively-spliced TP53 isoforms.
      pubtype: Academic Journal
      doctype:
        research
        tables/charts
        Journal Article
      ougenre: Article
    language: English
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