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The Quest for Human Health in the Genomic Era: Nutrigenomics...
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The Quest for Human Health in the Genomic Era: Nutrigenomics Approaches to Natural Products

A special issue of Nutrients (ISSN 2072-6643). This special issue belongs to the section "Nutrigenetics and Nutrigenomics".

Deadline for manuscript submissions: 15 January 2026 | Viewed by 691

Special Issue Editors

Dr. Flores Naselli

E-Mail Website
Guest Editor
Department Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90133 Palermo, Italy
Interests: nutrigenomics; epigenetics; genetics; gene expression; precision nutrition; nutrition in health
Special Issues, Collections and Topics in MDPI journals
Dr. Ilenia Cruciata

E-Mail Website
Guest Editor
Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
Interests: nutrigenomics; epigenetics; genetics; gene expression; DNA fragmentation

Special Issue Information

Dear Colleagues,

In the genomic era, nutrition is no longer seen merely as a source of energy but as a powerful tool in influencing human health. Nutrigenomics reveals how natural dietary compounds can modulate biological pathways and (epi)genetic mechanisms. This growing field highlights how natural dietary components may contribute to health promotion and disease prevention.

This Special Issue will focus on the role of phytocompounds and plant extracts enriched in specific bioactives, exploring their molecular mechanisms and nutrigenomic effects.

Particular attention will be given to bioactive molecules such as polyphenols, flavonoids, and plant extracts. These substances have demonstrated the ability to influence transcription factors, non-coding RNAs, and epigenetic markers, with implications for the prevention and management of chronic diseases. Moreover, many of these natural compounds exhibit protective effects against toxic xenobiotics commonly found in food and water, reducing their impact on cellular homeostasis and gene regulation.

We aim to highlight how these compounds influence key signaling pathways and epigenetic markers, offering new opportunities for personalized nutrition.

We welcome original research, reviews, and case studies that examine how natural products can be used as genomic modulators to promote human health in the context of diet-related chronic diseases, aging, metabolic dysfunction, and inflammation.

Dr. Flores Naselli
Dr. Ilenia Cruciata
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Nutrients is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • nutrigenomics
  • epigenetics
  • DNA methylation
  • methylome
  • gene expression
  • phytochemicals
  • bioactive compounds
  • Mediterranean diet

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Published Papers (1 paper)

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Research

28 pages, 2285 KB  
Article
Methylomic Signature and Epigenetic Damage Modulation of Bronte Pistachio (Pistacia vera L.) Hydrophilic Extract in Differentiated CaCo-2 Cells
by Ilenia Cruciata, Flores Naselli, Sara Volpes, Paola Sofia Cardinale, Laura Greco, Federico Martinelli, Matteo Ramazzotti, Anna Perrone, Graziella Serio, Carla Gentile and Fabio Caradonna
Nutrients 2025, 17(16), 2678; https://doi.org/10.3390/nu17162678 - 19 Aug 2025
Viewed by 598
Abstract
Background/Objectives: Nutrigenomics explores how dietary components influence genome function, especially via epigenetic mechanisms like DNA methylation. A key challenge is identifying healthy food-derived molecules capable of counteracting epigenetic damage from harmful dietary elements. Pistachio nuts (Pistacia vera L.), particularly the Bronte [...] Read more.
Background/Objectives: Nutrigenomics explores how dietary components influence genome function, especially via epigenetic mechanisms like DNA methylation. A key challenge is identifying healthy food-derived molecules capable of counteracting epigenetic damage from harmful dietary elements. Pistachio nuts (Pistacia vera L.), particularly the Bronte variety from Sicily, are rich in antioxidant polyphenols. In this study we used a methylomic approach to assess the nutrigenomic potential of a hydrophilic extract from Bronte pistachio (BPHE) in a model of human intestinal epithelium, as well as its capacity to modulate arsenic (As)-induced epigenotoxicity. Methods: BPHE was obtained via ethanol/water Soxhlet extraction. CaCo-2 cells were treated with BPHE, alone and after exposure to sodium arsenite. The methylation pattern of the genomic DNA was assessed by methylation-sensitive arbitrarily primed PCR and the methylomic signature was defined by Next-generation bisulfite sequencing. Results: BPHE alone did not alter DNA methylation pattern but, at the highest dose, modulated the changes induced by As. The identification of differentially methylated gene promoters in cell treatment vs. untreated controls revealed that BPHE and As primarily induced hyper-methylation, with a synergistic effect when combined. In particular, all the treatments increased methylation levels of gene categories such as pseudogenes, key genes of specific pathways, genes for zinc-finger proteins, homeobox proteins, kinases, antisense RNA, and miRNA. Notably, in co-treatment with As, BPHE promoted hypo-methylation of genes involved in tumor suppression, detoxification, mitochondrial function, and cell division. Conclusions: These findings suggest that Bronte pistachio polyphenols may epigenetically steer gene expression toward a protective profile, reducing risks of genomic instability and disease. This supports their potential as nutraceuticals to counter harmful epigenetic effects of toxic food components like arsenic. Full article
(This article belongs to the Special Issue The Quest for Human Health in the Genomic Era: Nutrigenomics Approaches to Natural Products)
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