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Chronic consumption of ‘Pera’ orange juice (POJ), a rich source of flavanones, has been associated with beneficial cardiovascular and metabolic effects. However, individual responses to dietary interventions vary considerably, and the molecular mechanisms underlying this variability remain incompletely understood. Biological factors such as sex, BMI, genetic background, age, and gut microbiota may contribute to these differential responses. Therefore, this study aimed to investigate sex-dependent nutrigenomic adaptations induced by chronic POJ consumption through transcriptomic profiling in women and men. Healthy volunteers (10 women and 10 men) consumed 500 mL of POJ daily for 60 days. Peripheral blood mononuclear cells (PBMCs) were isolated before and after the intervention, and transcriptomic analysis was performed using the Clariom microarray platform. Differentially expressed genes, functional enrichment analyses, transcription factor prediction, and non-coding RNA analyses were performed to identify biological pathways modulated by POJ consumption. Transcriptomic profiling showed marked sex-dependent molecular adaptations following chronic POJ consumption, with women exhibiting predominantly metabolic responses and men showing stronger immunomodulatory signatures. A total of 530 and 934 differentially expressed genes were identified in women and men, respectively. In women, POJ consumption primarily affected pathways involved in lipid metabolism, adipocyte differentiation, cholesterol transport, endothelial function, oxidative stress regulation, and insulin signaling, suggesting a metabolic remodeling response. Downregulation of GSK3B (-1.71), together with upregulation of its regulatory miRNAs miR-548 (1.68) and miR-1185 (2.31), suggests coordinated transcriptional and post-transcriptional regulation of adipocyte function, insulin signaling, and metabolic homeostasis. Reduced KEAP1 expression (-1.59), a negative regulator of the NRF2 pathway, suggests enhanced antioxidant defense, while decreased STAT5 (-1.58) and ICAM3 (-2.08) expression supports potential beneficial modulation of inflammatory and vascular processes. In men, POJ consumption predominantly affected immune and inflammatory pathways. Downregulation of genes involved in inflammasome activation, inflammatory signaling, and metabolic stress, including NLRP3 (-2.94), NAMPT (-11.07), IER3 (-6.54), and FYN (-1.85), indicates a stronger immunomodulatory response. Transcription factor analysis further supported these differences, with STAT3 and NFKB2 pathways being specifically associated with the male response. Sex-dependent regulation was also observed at the post-transcriptional level, with differential expression of miRNAs, lncRNAs, and snoRNAs, suggesting additional regulatory mechanisms involved in POJ-induced adaptations. Overall, women exhibited predominantly metabolic and antioxidant response, whereas men showed stronger modulation of immune and inflammatory signaling. These findings identify sex as an important determinant of nutrigenomic responses to chronic orange juice consumption and provide new insights into personalized dietary strategies based on bioactive compounds. This work was supported by the Food Research Center (FoRC), the Research, Innovation and Dissemination Center (CEPID) of the São Paulo Research Foundation (FAPESP) (grants 2013/07914-8, 2022/05463-8, and 2024/03926-6), and the National Council for Scientific and Technological Development (CNPq) (grants 141878/2019-3 and 311517/2025-0).
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