Review the detection and bioinformatic analysis of alternative 3′ utr isoforms as potential cancer biomarkers

Nitika Kandhari; Calvin A. Kraupner-Taylor; Paul F. Harrison; David R. Powell; Traude H. Beilharz

doi:10.3390/ijms22105322

Review the detection and bioinformatic analysis of alternative 3^′ utr isoforms as potential cancer biomarkers

Nitika Kandhari, Calvin A. Kraupner-Taylor, Paul F. Harrison, David R. Powell, Traude H. Beilharz

Research output: Contribution to journal › Review Article › Research › peer-review

6 Citations (Scopus)

Abstract

Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinfor-matically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could ad-vance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.

Original language	English
Article number	5322
Number of pages	18
Journal	International Journal of Molecular Sciences
Volume	22
Issue number	10
DOIs	https://doi.org/10.3390/ijms22105322
Publication status	Published - 2 May 2021

Keywords

3 focused RNA-seq
Alternative polyadenylation
Bioinformatics
Cancer biomarkers
ScRNA-seq

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.3390/ijms22105322Licence: CC BY

Cite this

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title = "Review the detection and bioinformatic analysis of alternative 3′ utr isoforms as potential cancer biomarkers",

abstract = "Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinfor-matically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could ad-vance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.",

keywords = "3 focused RNA-seq, Alternative polyadenylation, Bioinformatics, Cancer biomarkers, ScRNA-seq",

author = "Nitika Kandhari and Kraupner-Taylor, {Calvin A.} and Harrison, {Paul F.} and Powell, {David R.} and Beilharz, {Traude H.}",

note = "Funding Information: Funding: This research was funded by grants from the National Health and Medical Research Council (NHMRC: APP1128250) and the Australian Research Council (ARC: DP170100569 and FT180100049). N.K. and C.A.K.-T. were supported by PhD stipends from the Monash University Biodiscovery Institute. Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2021",

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doi = "10.3390/ijms22105322",

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AU - Powell, David R.

AU - Beilharz, Traude H.

N1 - Funding Information: Funding: This research was funded by grants from the National Health and Medical Research Council (NHMRC: APP1128250) and the Australian Research Council (ARC: DP170100569 and FT180100049). N.K. and C.A.K.-T. were supported by PhD stipends from the Monash University Biodiscovery Institute. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

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N2 - Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinfor-matically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could ad-vance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.

AB - Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinfor-matically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could ad-vance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.

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KW - Alternative polyadenylation

KW - Bioinformatics

KW - Cancer biomarkers

KW - ScRNA-seq

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Review the detection and bioinformatic analysis of alternative 3^′ utr isoforms as potential cancer biomarkers

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

The transcriptome dynamics that refine eukaryotic gene expression

The mechanism and function of 3'UTR switching in eukaryotic cells

An investigation into the role of 3'UTR dynamics in breast cancer metastasis

Bioinformatics Platform

Cite this

Review the detection and bioinformatic analysis of alternative 3′ utr isoforms as potential cancer biomarkers

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Projects

The transcriptome dynamics that refine eukaryotic gene expression

The mechanism and function of 3'UTR switching in eukaryotic cells

An investigation into the role of 3'UTR dynamics in breast cancer metastasis

Equipment

Bioinformatics Platform

Cite this

Review the detection and bioinformatic analysis of alternative 3^′ utr isoforms as potential cancer biomarkers