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

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.

Genes selection using deep learning and explainable artificial intelligence for chronic lymphocytic leukemia predicting the need and time to therapy.

Analyzing gene expression profiles (GEP) through artificial intelligence provides meaningful insight into cancer disease. This study introduces DeepSHAP Autoencoder Filter for Genes Selection (DSAF-GS), a novel deep learning and explainable artificial intelligence-based approach for feature selection in genomics-scale data. DSAF-GS exploits the autoencoder's reconstruction capabilities without changing the original feature space, enhancing the interpretation of the results. Explainable artificial intelligence is then used to select the informative genes for chronic lymphocytic leukemia prognosis of 217 cases from a GEP database comprising roughly 20,000 genes. The model for prognosis prediction achieved an accuracy of 86.4%, a sensitivity of 85.0%, and a specificity of 87.5%. According to the proposed approach, predictions were strongly influenced by CEACAM19 and PIGP, moderately influenced by MKL1 and GNE, and poorly influenced by other genes. The 10 most influential genes were selected for further analysis. Among them, FADD, FIBP, FIBP, GNE, IGF1R, MKL1, PIGP, and SLC39A6 were identified in the Reactome pathway database as involved in signal transduction, transcription, protein metabolism, immune system, cell cycle, and apoptosis. Moreover, according to the network model of the 3D protein-protein interaction (PPI) explored using the NetworkAnalyst tool, FADD, FIBP, IGF1R, QTRT1, GNE, SLC39A6, and MKL1 appear coupled into a complex network. Finally, all 10 selected genes showed a predictive power on time to first treatment (TTFT) in univariate analyses on a basic prognostic model including IGHV mutational status, del(11q) and del(17p), NOTCH1 mutations, ß2-microglobulin, Rai stage, and B-lymphocytosis known to predict TTFT in CLL. However, only IGF1R [hazard ratio (HR) 1.41, 95% CI 1.08-1.84, P=0.013), COL28A1 (HR 0.32, 95% CI 0.10-0.97, P=0.045), and QTRT1 (HR 7.73, 95% CI 2.48-24.04, P<0.001) genes were significantly associated with TTFT in multivariable analyses when combined with the prognostic factors of the basic model, ultimately increasing the Harrell's c-index and the explained variation to 78.6% (versus 76.5% of the basic prognostic model) and 52.6% (versus 42.2% of the basic prognostic model), respectively. Also, the goodness of model fit was enhanced (χ2 = 20.1, P=0.002), indicating its improved performance above the basic prognostic model. In conclusion, DSAF-GS identified a group of significant genes for CLL prognosis, suggesting future directions for bio-molecular research.

Nutrition Education Program and Physical Activity Improve the Adherence to the Mediterranean Diet: Impact on Inflammatory Biomarker Levels in Healthy Adolescents From the DIMENU Longitudinal Study.

Adherence to Mediterranean diet (MD) and physical activity (PA) in adolescence represent powerful indicators of healthy lifestyles in adulthood. The aim of this longitudinal study was to investigate the impact of nutrition education program (NEP) on the adherence to the MD and on the inflammatory status in healthy adolescents, categorized into three groups according to their level of PA (inactivity, moderate intensity, and vigorous intensity). As a part of the DIMENU (Dieta Mediterranea & Nuoto) study, 85 adolescents (aged 14-17 years) participated in the nutrition education sessions provided by a team of nutritionists and endocrinologists at T0. All participants underwent anthropometric measurements, bio-impedentiometric analysis (BIA), and measurements of inflammatory biomarkers such as ferritin, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) levels. Data were collected at baseline (T0) and 6 months after NEP (T1). To assess the adherence to the MD, we used KIDMED score. In our adolescents, we found an average MD adherence, which was increased at T1 compared with T0 (T0: 6.03 ± 2.33 vs. T1: 6.96 ± 2.03, p = 0.002), with an enhanced percentage of adolescents with optimal (≥8 score) MD adherence over the study period (T0: 24.71% vs. T1: 43.52%, p = 0.001). Interestingly, in linear mixed-effects models, we found that NEP and vigorous-intensity PA levels independently influenced KIDMED score (ß = 0.868, p < 0.0001 and ß = 1.567, p = 0.009, respectively). Using ANOVA, NEP had significant effects on serum ferritin levels (p < 0.001), while either NEP or PA influenced ESR (p = 0.035 and 0.002, respectively). We also observed in linear mixed-effects models that NEP had a negative effect on ferritin and CRP (ß = -14.763, p < 0.001 and ß = -0.714, p = 0.02, respectively). Our results suggest the usefulness to promote healthy lifestyle, including either nutrition education interventions, or PA to improve MD adherence and to impact the inflammatory status in adolescence as a strategy for the prevention of chronic non-communicable diseases over the entire lifespan.