Genomics: Insight

Research Question: What is the correlation between the methylation and mutations of specific loci in the genome and the risk factor for expressing Cow’s Milk Allergy?

Background:

Cow’s milk allergy (CMA) is one of the most common food allergies in infants and young children, affecting roughly 2-7% of the pediatric population worldwide.¹ CMA is an immune-mediated reaction to milk proteins such as casein and whey. Reactions to CMA vary greatly in severity. While CMA is one of the most common food allergies in children, many patients outgrow it, typically by early childhood and adolescence. However, severe life-threatening anaphylaxis can still occur. For example, in some countries such as the United Kingdom and Italy, CMA has emerged as a leading cause of fatal food-induced anaphylaxis.² As it is the third most common cause of anaphylactic reactions, CMA poses a significant threat to children around the world.³ Therefore, it is key to understand the epigenetic factors associated with CMA to develop early detection and treatment methods. This research article presents a review of the current findings about the correlation between the methylation and mutations of specific loci in the genome to the risk factor for expressing Cow’s Milk Allergy.

Genomic Marker Associations, Environmental Variables, and Genetic Risk Scoring in CMA

Chinese researchers, Lin Hou et al,⁴ conducted a study that looked at 5 separate loci, rs17616434, rs2069772, rs1800896, Rs855791, and rs20541, that have been linked to many other allergens to see how mutations at those loci correlate with CMA. Their study included 200 infants with clinically diagnosed CMA and 799 infants with no allergies as a control group. The researchers collected blood samples from the infants and collected the DNA, and then used the Illumina Asian Screening Array to test for Single Nucleotide Polymorphisms (SNPs) in the genome. They also looked at environmental factors such as sex, gestational age, birth weight, feeding patterns, season of birth, delivery mode, pregnancy history, and parental age. The researchers found that the only statistically significant environmental factor was parental allergen history, which increased risk by 87%. While examining the 5 loci, they identified only one locus as independently raising the risk of CMA.  After using statistical analysis tools such as Chi-squared analysis and logistic regression modeling, only Loci rs1800896 was statistically significant across all trials, and having a risk allele at that locus alone raises the risk of CMA by ~60-70%. While that locus was the only one that independently increased risk, they identified that the other loci, in combination with each other, raised the risk of having CMA. They created a genetic risk score (GRS), calculated by adding the number of risk alleles that were at each locus, which allowed them to combine the risk of having multiple of the SNPs and used those numbers to create a high-risk group (GRS>6) and a low-risk group (GRS≤5). They identified that with each single risk allele increase, there is an 11% higher risk of having CMA, and infants in the high-risk group had about a 45% higher risk of CMA than those in the low-risk group. 

With each single risk allele increase, there is an 11% higher risk of having CMA, and infants in the high-risk group had about a 45% higher risk of CMA than those in the low-risk group.

Epigenome-Wide Methylation Profiling and CMA Risk Factors at Specific Loci

A study published by Hong et. al.⁵ analyzed the correlation between DNA methylation (DNAm) at specific loci and CMA at an epigenomic-wide scale. The study used a two-stage approach, with a discovery stage and a validation stage. In the discovery stage, blood samples were collected from a group of 106 Caucasian children with CMA and a control group of 76 non-allergic Caucasian children. The results were then confirmed in the validation stage with two more trials with samples collected from 25 Caucasian children and 140 African-American children. After analyzing the DNAm at 485,512 loci within the genomes of each individual, 575 differentially methylated positions (DMPs) were identified in the genomes of individuals with CMA compared to the control group, with 568 being hypomethylated and 7 being hypermethylated. Many of these DMPs showed very minor DNAm differences compared to controls, and only 5 loci showed an absolute mean DNAm difference ≥ 5%. Furthermore, the study found a correlation between the DNAm at five more loci and the Th1-Th2 pathway, which is a balance between two types of T-helper cells that detect antigens and activate immune responses. The Th1-Th2 pathway controls broad immune responses, and it is understood to be associated with but not directly a cause of CMA. The researchers used two replications, as well as a webtool, and confirmed the results of the discovery stage. This study not only confirmed the correlation between genes associated with the Th1-Th2 pathway and CMA but also identified three new genes with strong correlation to CMA: NDFIP2 (cg11770323), EVL (cg18550847) and TRAPPC9 (cg09377531). 

Similarly, in a study published by Paparo et. al,⁶ researchers established a strong correlation between DNA Methylation and the likelihood of CMA in the FOXP3 locus. They chose the FOXP3-TSDR locus because it is the main gene that controls the regulatory T cells, which suppress immune overreactions and maintain tolerance. In other words, if FOXP3 doesn’t work properly, allergies are more likely. In their study, they had a total of 40 children from infancy to 12 years of age: 10 children with active cow’s milk allergy (CMA) (group 1), 20 children who had outgrown CMA (tolerant Group) (group 2 and 3), and 10 healthy controls (with no CMA). They concluded active CMA patients exhibit lower demethylation levels in the FOXP3 TSDR locus (~1–2%) than tolerant and healthy children (~15–20%). 

CONCLUSION

As several members of our group grew up with life-threatening food allergies, this area of study was particularly of interest. In fact, one of our members struggled with severe CMA as a child and took two trips to the emergency room due to anaphylaxis caused by accidental ingestion of milk. This individual's experience reflects the challenges faced by countless families around the world that manage severe Cow’s Milk Allergy. Despite advances in linking risk factors for CMA to methylation patterns of specific loci, current findings are still insufficient to identify a definitive epigenetic cause. Therefore, additional research investigating current potential causes, as well as identifying new ones, is necessary to ensure accurate risk prediction. To supplement epigenetic data, the future of CMA risk prediction will likely move beyond identifying single genetic variants or isolated methylation changes towards multi-layered precision-based immune profiling, combining genomic, epigenomic, environmental, and clinical data. Advances in risk prediction will allow early detection and proactive, rather than reactive, treatment, greatly improving the quality of life for those struggling with CMA.

References: 

1. Hao, Li, et al. “Cow’s Milk Protein Allergy: A Comprehensive Review of Epidemiology, Pathogenesis, Clinical Manifestations, Diagnostics, and Management Strategies.” PubMed, vol. 34, no. 3, National Institutes of Health, June 2025, pp. 298–307, https://doi.org/10.6133/apjcn.202506_34(3).0004.
2. Badina, Laura et al. “Life‐Threatening Anaphylaxis in Children with Cow's Milk Allergy during Oral Immunotherapy and after Treatment Failure.” Immunity, Inflammation, and Disease, vol. 10, no. 4, 2022, https://pmc.ncbi.nlm.nih.gov/articles/PMC8962636/pdf/IID3-10-e607.pdf
3. Roua Lajnaf, et al. “Recent Advances in Selective Allergies to Mammalian Milk Proteins Not Associated with Cow’s Milk Proteins Allergy.” Food and Chemical Toxicology, vol. 178, Elsevier BV, Aug. 2023, pp. 113929–29, https://doi.org/10.1016/j.fct.2023.113929. 
4. Hou, Lin, et al. “Genetic Susceptibility to Cow’s Milk Allergy in Chinese Children.” Asia Pac J Clin Nutr, vol. 31, no. 1, 2022, pp. 147–55, https://doi.org/10.6133/apjcn.202203_31(1).0016.
5. Hong, Xiumei, et al. “Epigenome-Wide Association Study Links Site-Specific DNA Methylation Changes with Cow’s Milk Allergy.” The Journal of Allergy and Clinical Immunology, vol. 138, no. 3, Elsevier BV, Sept. 2016, pp. 908-911.e9, https://doi.org/10.1016/j.jaci.2016.01.056.
6. Paparo, Lorella, et al. “Preparing to Download ...” Nih.gov, 2026, pmc.ncbi.nlm.nih.gov/articles/PMC4981981/pdf/13148_2016_Article_252.pdf. Accessed 27 Feb. 2026.