A recent study casts a spotlight on the alarming connection between our diets and our very DNA! It has been discovered that a high consumption of ultra-processed foods (UPFs) is linked to significant changes in DNA methylation among women. This finding hints at early biological modifications that may shed light on how our eating habits can leave lasting marks on our health at the molecular level.
In a compelling Brief Report published in the journal Nutrients, researchers delved into the impact of ultra-processed foods on epigenetic mechanisms—specifically, the process of DNA methylation in peripheral blood leukocytes among women. What they uncovered was striking: women who indulged in higher quantities of UPFs demonstrated noticeable variations in DNA methylation across 80 distinct regions, with the majority showing reduced methylation activity—an indicator of potential epigenetic changes that could correlate with health outcomes. However, it’s crucial to note that causation cannot be directly established from these observations.
What Exactly Are Ultra-Processed Foods?
So, what qualifies as ultra-processed? According to the NOVA classification system, UPFs encompass a wide array of readily available products like instant meals, packaged snacks, and sugary beverages. These items undergo intense processing and often include various preservatives, flavor enhancers, colors, and additional chemicals. They are crafted to be convenient and flavorful, which is why they tend to be so appealing to consumers.
The Rising Tide of UPFs and Related Health Dilemmas
The increased global consumption of UPFs is alarming, as this trend coincides with a rising prevalence of obesity and chronic health conditions. In wealthier nations, up to 50% of daily caloric intake can come from these food products, which are generally high in calories yet low in essential nutrients. They frequently harbor large amounts of unhealthy fats, sugars, and salts, contributing to a poor dietary profile.
Moreover, the risk posed by UPFs extends beyond their lack of nutrition. They may adversely affect health due to their structural changes, possible contaminants, and added ingredients. Studies have linked high UPF consumption to various health issues, including mental health challenges, heart problems, weight gain, metabolic disorders, and even rapid biological aging.
Epigenetics: The Missing Link Between Diet and Health
Though the biological pathways that connect diet to these health concerns are still being unraveled, epigenetic modification, particularly through DNA methylation, presents a compelling avenue of research. This process can determine how genes respond to environmental influences like our diet.
Research Overview and Participant Criteria
In this study, the researchers conducted a cross-sectional pilot investigation involving 30 women aged between 20 and 40 years, with body mass indices (BMI) ranging from 18.5 to 39.9 kg/m², recruited from a prior study. Exclusions were made for participants with factors affecting metabolism, such as excessive exercise, certain medical conditions, or specific medications, ensuring a more homogeneous study group. Ethical approval was granted, and each participant provided informed consent.
Analyzing Dietary Habits and Categorizing UPFs
Participants recorded their dietary intake over three days (spanning two weekdays and one weekend day). Foods consumed were classified based on the NOVA system, allowing researchers to calculate the share of total energy derived from UPFs. To minimize variability, the Multiple Source Method (MSM) was employed for estimating habitual intake.
The women were categorized into tertiles based on UPF consumption, with those in the lowest and highest tertiles selected for the epigenetic analysis. In addition, measures of body composition and biochemical markers were documented.
Decoding DNA Methylation and Statistical Analysis
DNA was extracted from the participants' blood, with genome-wide methylation profiling conducted using next-generation sequencing (NGS) following the enrichment and bisulfite conversion of the DNA. Bioinformatics tools processed the data, allowing the identification of differentially methylated regions.
Statistical analyses—including t-tests and Mann–Whitney U tests—were conducted to compare the variables between groups, while correlations among methylated regions were examined utilizing Pearson’s correlation test. Regions exhibiting over fourfold differences in methylation levels were highlighted for graphical representation via heatmaps.
Notable Discoveries and Their Biological Significance
The analysis showed that those in the low-UPF group consumed, on average, only 14% of their total energy from UPFs, while the high-UPF group derived a staggering 45% from these products. From the 20 DNA samples analyzed, five were excluded due to inadequate sequencing quality, leaving 15 samples (seven from the low-UPF group and eight from the high-UPF group) for valid assessment.
Participants had a median age of 31 and an average BMI of 24.7 kg/m², with no significant differences in their body compositions or measurements across the groups. Interestingly, biochemical tests indicated unexpectedly elevated total, low-density lipoprotein (LDL), and non-high-density lipoprotein (non-HDL) cholesterol levels in the low-UPF group. This observation aligns with earlier research, including findings from Dicken et al. (2025), suggesting that short-term UPF consumption does not necessarily correlate with higher blood lipid levels, highlighting the complexity of the relationship between UPFs and lipid profiles. Dietary comparisons indicated that the low-UPF participants consumed a greater proportion of unprocessed foods, protein, and polyunsaturated fats.
The broad genome-wide analysis revealed 80 distinct regions of differential methylation, predominantly within gene promoter areas. Post filtering for significant differences, seven regions emerged as showing the largest variations, including RNA5S7, RNA5S9, RNA5S13, LINC00396, FOXP1-AS1, LOC124902961, and REPIN1-AS1, which were visually emphasized for reference.
The majority of the identified differential methylation regions appeared hypomethylated in the group with higher UPF intake, pointing towards a troubling association between increased UPF consumption and reduced DNA methylation levels across various genomic areas.
Wrapping Up: Study Insights and Path Forward
This pilot study stands as the first to apply next-generation sequencing techniques to examine genome-wide methylation shifts linked to UPF consumption. The identification of 80 altered regions, notably hypomethylated in those with higher UPF intake, is an important finding. Several affected genes like FOXP1-AS1 and REPIN1-AS1 play roles in metabolic regulation and cancer pathways, hinting at biological connections between UPFs and negative health impacts.
Although the study employed rigorous high-resolution NGS methods, the small sample size presents a hurdle in gaining statistical power, and the design of the study—being cross-sectional—limits our ability to draw causal conclusions. Since the reported p-values were nominal and unadjusted for multiple comparisons, they primarily serve exploratory purposes, increasing the potential for false-positive outcomes. Moreover, the patterns of DNA methylation were evaluated in blood, which may not accurately reflect alterations in other tissues, and micronutrient data were not included. Due to the small cohort size, confounder variables like BMI and age could not be adequately adjusted.
Nevertheless, this research opens the door to the intriguing possibility that UPF consumption may affect gene expression through epigenetic alterations, paving the way for more extensive studies in larger, longitudinal populations.
