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. 2024 Aug 23;10(5):46.
doi: 10.3390/ncrna10050046.

MicroRNA Profiling as a Predictive Indicator for Time to First Treatment in Chronic Lymphocytic Leukemia: Insights from the O-CLL1 Prospective Study

Affiliations

MicroRNA Profiling as a Predictive Indicator for Time to First Treatment in Chronic Lymphocytic Leukemia: Insights from the O-CLL1 Prospective Study

Ennio Nano et al. Noncoding RNA. .

Abstract

A "watch and wait" strategy, delaying treatment until active disease manifests, is adopted for most CLL cases; however, prognostic models incorporating biomarkers have shown to be useful to predict treatment requirement. In our prospective O-CLL1 study including 224 patients, we investigated the predictive role of 513 microRNAs (miRNAs) on time to first treatment (TTFT). In the context of this study, six well-established variables (i.e., Rai stage, beta-2-microglobulin levels, IGVH mutational status, del11q, del17p, and NOTCH1 mutations) maintained significant associations with TTFT in a basic multivariable model, collectively yielding a Harrell's C-index of 75% and explaining 45.4% of the variance in the prediction of TTFT. Concerning miRNAs, 73 out of 513 were significantly associated with TTFT in a univariable model; of these, 16 retained an independent relationship with the outcome in a multivariable analysis. For 8 of these (i.e., miR-582-3p, miR-33a-3p, miR-516a-5p, miR-99a-5p, and miR-296-3p, miR-502-5p, miR-625-5p, and miR-29c-3p), a lower expression correlated with a shorter TTFT, whereas in the remaining eight (i.e., miR-150-5p, miR-148a-3p, miR-28-5p, miR-144-5p, miR-671-5p, miR-1-3p, miR-193a-3p, and miR-124-3p), the higher expression was associated with shorter TTFT. Integrating these miRNAs into the basic model significantly enhanced predictive accuracy, raising the Harrell's C-index to 81.1% and the explained variation in TTFT to 63.3%. Moreover, the inclusion of the miRNA scores enhanced the integrated discrimination improvement (IDI) and the net reclassification index (NRI), underscoring the potential of miRNAs to refine CLL prognostic models and providing insights for clinical decision-making. In silico analyses on the differently expressed miRNAs revealed their potential regulatory functions of several pathways, including those involved in the therapeutic responses. To add a biological context to the clinical evidence, an miRNA-mRNA correlation analysis revealed at least one significant negative correlation between 15 of the identified miRNAs and a set of 50 artificial intelligence (AI)-selected genes, previously identified by us as relevant for TTFT prediction in the same cohort of CLL patients. In conclusion, the identification of specific miRNAs as predictors of TTFT holds promise for enhancing risk stratification in CLL to predict therapeutic needs. However, further validation studies and in-depth functional analyses are required to confirm the robustness of these observations and to facilitate their translation into meaningful clinical utility.

Keywords: Beta-2-microglobulin (B2M); CLL; IGVH mutations; NOTCH1; Rai stage; del11q; del17p; microRNA; prognosis; time to first treatment (TTFT).

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Conflict of interest statement

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Kaplan–Meier curve of TTFT in the 224 CLL cases from our prospective O-CLL1 study.
Figure 2
Figure 2
Risk score histogram distribution of 224 cases from O-CLL1 study based on the 16 miRNAs significantly associated with TTFT in multivariate Cox regression model.
Figure 3
Figure 3
Dot plot displaying the magnitude of negative correlation between the 16 miRNAs significantly associated with TTFT in the 224 CLL cases from our prospective O-CLL1 study and the 50 AI genes from the same cohort. AI genes are sorted by significance magnitude from the bottom to the top. The first 10 genes represent the top AI-based selected genes that were significantly associated with TTFT. The greater intensity of the color in the circle shapes corresponds to a higher magnitude of the negative correlation measured by a Spearman test. rho (or Spearman’s correlation coefficient, measured using a Spearman test) is a non-parametric measure that evaluates the strength and direction of a monotonic relationship between two ordinal or quantitative variables using the ranks of the observations instead of their absolute values.
Figure 4
Figure 4
Interaction analysis between miRNAs and genes which were found to be associated with TTFT. Interaction networks between has-miR-29c-3p with 4 AI genes ANKRD52, KDM5B, PRICKLE1, and ZBTB34 or hsa-miR-625-5p with IGF1R are shown. Arrows, circles, and squares indicate the miRNA–mRNA interaction scores, miRNA, and mRNA log-transformed fold-change (Log FC), respectively. Log FC values for miRNA (◯) and mRNA (□) are indicated by a color gradient scale. Regulation score parameter values related to the IGHV mutational status (arrows) are highlighted by a scale color gradient from light gray that represents a midpoint value of 0 to red that indicates positive values (interaction score).

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