Predicting prostate cancer progression with a Multi-lncRNA expression-based risk score and nomogram integrating ISUP grading

Sabrina Ledesma-Bazan; Florencia Cascardo; Juan Bizzotto; Santiago Olszevicki; Elba Vazquez; Geraldine Gueron; Javier Cotignola

doi:10.1016/j.ncrna.2024.01.014

Predicting prostate cancer progression with a Multi-lncRNA expression-based risk score and nomogram integrating ISUP grading

Noncoding RNA Res. 2024 Jan 23;9(2):612-623. doi: 10.1016/j.ncrna.2024.01.014. eCollection 2024 Jun.

Authors

Sabrina Ledesma-Bazan^{1

2}, Florencia Cascardo^{1

2}, Juan Bizzotto^{1

2

3}, Santiago Olszevicki^{1

2}, Elba Vazquez^{1

2}, Geraldine Gueron^{1

2}, Javier Cotignola^{1

2}

Affiliations

¹ Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Inflamación y Cáncer, C1428EGA, CABA, Buenos Aires, Argentina.
² CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), C1428EGA, CABA, Buenos Aires, Argentina.
³ Universidad Argentina de la Empresa (UADE), Instituto de Tecnología (INTEC), Buenos Aires C1073AAO, Argentina.

Abstract

Prostate cancer is a highly heterogeneous disease; therefore, estimating patient prognosis accurately is challenging due to the lack of biomarkers with sufficient specificity and sensitivity. One of the current challenges lies in integrating genomic and transcriptomic data with clinico-pathological features and in incorporating their application in everyday clinical practice. Therefore, we aimed to model a risk score and nomogram containing long non-coding RNA (lncRNA) expression and clinico-pathological data to better predict the probability of prostate cancer progression. We performed bioinformatics analyses to identify lncRNAs differentially expressed across various prostate cancer stages and associated with progression-free survival. This information was further integrated into a prognostic risk score and nomogram containing transcriptomic and clinico-pathological features to estimate the risk of disease progression. We used RNA-seq data from 5 datasets from public repositories (total n = 178) comprising different stages of prostate cancer: pre-treatment primary prostate adenocarcinomas, post-treatment tumors and metastatic castration resistant prostate cancer. We found 30 lncRNAs with consistent differential expression in all comparisons made using two R-based packages. Multivariate progression-free survival analysis including the ISUP group as covariate, revealed that 7/30 lncRNAs were significantly associated with time-to-progression. Next, we combined the expression of these 7 lncRNAs into a multi-lncRNA score and dichotomized the patients into low- or high-score. Patients with a high-score showed a 4-fold risk of disease progression (HR = 4.30, 95 %CI = 2.66-6.97, p = 3.1e-9). Furthermore, we modelled a combined risk-score containing information on the multi-lncRNA score and ISUP group. We found that patients with a high-risk score had nearly 8-fold risk of progression (HR = 7.65, 95 %CI = 4.05-14.44, p = 3.4e-10). Finally, we created and validated a nomogram to help uro-oncologists to better predict patient's risk of progression at 3- and 5-years post-diagnosis. In conclusion, the integration of lncRNA expression data and clinico-pathological features of prostate tumors into predictive models might aid in tailored disease risk assessment and treatment for patients with prostate cancer.