In Silico Design of Quantitative Polymerase Chain Reaction (qPCR) Assay Probes for Prostate Cancer Diagnosis, Prognosis, and Personalised Treatment

Sep 23, 2026

Uploaded by James

Prostate cancer remains a leading cause of cancer-related mortality worldwide, and commonly used options such as PSA testing and androgen deprivation therapy (ADT) can suffer from limitations. Many gene mutations drive prostate cancer development and can shape resistance or vulnerability to targeted treatments. This in silico study evaluates four genes—AR, ATM, PTEN, and TP53—selecting 28 mutations for qPCR primer and probe design. Primer/probe sets fall within intended ranges and support improved diagnostic and prognostic assay development, pending experimental validation.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages13

Reading Time33 min

AccessFree to download

Introduction

Background on prostate cancer risks, diagnosis, and treatment

Androgen receptor (AR) and ADT resistance/susceptibility

ATM gene role in DNA damage response and cancer subset

PTEN loss and PI3K/AKT/mTOR pathway signaling

Article In Silico Design of Quantitative Polymerase Chain Reaction (qPCR) Assay Probes for Prostate Cancer Diagnosis, Prognosis, and Personalised Treatment Trevor Kenneth Wilson and Oliver Tendayi Zishiri * Academic Editor: Stergios Boussios Received: 26 March 2025 Revised: 16 April 2025 Accepted: 17 April 2025 Published: 19 April 2025 Citation: Wilson, T.K.; Zishiri, O.T. In Silico Design of Quantitative Polymerase Chain Reaction (qPCR) Assay Probes for Prostate Cancer Diagnosis, Prognosis, and Personalised Treatment. Curr. Issues Mol. Biol. 2025, 47, 292. [https://](https://)[ ](https://)[doi.org/10.3390/cimb47040292](doi.org/10.3390/cimb47040292) [Copyright:](Copyright:) © 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ([https://creativecommons.org/](https://creativecommons.org/)[ ](https://creativecommons.org/)[licenses/by/4.0/](licenses/by/4.0/)) . Discipline of Genetics, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; [218014013@stu.ukzn.ac.za](218014013@stu.ukzn.ac.za) * Correspondence: [zishiri@ukzn.ac.za](zishiri@ukzn.ac.za) Abstract: Prostate cancer is one of the world’s leading causes of cancer-related mortalities. There are several diagnostic tools and treatment plans readily available, such as prostatespecific antigen (PSA) tests and androgen deprivation therapy (ADT) . However, these all come with their setbacks. Therefore, alternatives must be developed to assist those patients for whom standardised treatment does not work. There are many genes whose mutations lead to prostate cancer development and progression. These mutations may also lead to higher resistance/vulnerability to specific therapies. In this in silico study, four genes, AR, ATM, PTEN, and TP53, were assessed, and mutations were chosen for qPCR primer and probe design. A total of 28 mutations were selected from the four genes, with PTEN (13) making up the majority of the mutations, followed by TP53 (six), then ATM (five), and finally, AR (four) . All primer/probe combinations fall within the desired ranges for this study and provide valuable additions to prostate cancer’s diagnostic/prognostic landscape. These assays will require further experimental validation, but they are the first step toward a better future in the fight against this horrible disease. Keywords: prostate cancer; diagnosis; prognosis; personalised treatment; genetic mutations; qPCR assay 1. Introduction Prostate cancer is the second most common cancer in men worldwide [1] . There are several risk factors associated with prostate cancer, including age, ethnicity, obesity, and familial risk through inherited gene alterations [2] . Standard diagnostic tools currently inuse for prostate cancer include digital rectal examinations, prostate-specific antigen (PSA) tests, and prostate biopsies [3] . However, these tests can be invasive and harbour risks of false-positive diagnoses [4] . Currently, the most common treatment options for prostate cancer are Androgen deprivation therapies, radical prostatectomy, or radiation [2] . Many men often experience relapsed prostate cancer after treatment, with more aggressive forms such as metastatic castration-resistant prostate cancer (mCRPC) being common [4] . An accurate depiction of prostate cancer in Africa is not available due to minimal testing being conducted. However, from the known data, prostate cancer is the most common cause of cancer-related deaths among African men, with as many as 38 in 100,000 men having this form of cancer and with as high as 64% of new cases showing advanced stages of the disease [5] . Gene alterations are found regularly in prostate cancer, with several genes playing a crucial role in this disease. One such gene is the Androgen receptor (AR) gene, encoding the Androgen receptor, a

FAQs

What is the goal of the in silico study?

To design qPCR primer and probe assays for specific prostate cancer-related gene mutations, supporting improved diagnosis, prognosis, and personalised treatment planning.

Which genes and how many mutations were assessed for qPCR probe design?

The study assessed AR, ATM, PTEN, and TP53 and selected 28 mutations in total, with PTEN contributing 13 mutations as the largest group.

What is the status of the designed qPCR assays?

All primer/probe combinations fit the desired design ranges for the study, but the assays require further experimental validation before clinical use.

Sep 23, 2026

Uploaded by James