Maternal Genetics Shapes Variation in Human Milk

Written by: Alla Katsnelson, Ph.D | Issue # 124 | 2025

Human milk contains hundreds of components and varies tremendously between lactating mothers. However, very little is known about the genetics that shape this variation or how differences in milk composition might affect infant health. In a new study, researchers have begun to characterize these relationships [1].

The study begins to lay the foundation for a biological understanding of how breastmilk production is regulated and how it shapes infant health, says lead author Kelsey E. Johnson, a postdoctoral researcher at the University of Minnesota, co-advised by Frank Albert, Ran Blekhman, and Ellen W. Demerath. “If you’re interested in seeing how variation in a particular component of milk matters for infant growth or development you can use genetics to address that question,” Johnson said. “But first you have to be able to identify these genetic associations with the milk itself.” 

Johnson and her colleagues tracked how variants of maternal genes affect the genetic regulation of gene expression in milk. They also explored how the expression of milk related genes is associated with milk composition, as well as the composition of the infant’s gut microbiome. They found 482 points in the genome that affect the expression of genes specific to lactating mammary glands, and they uncovered a link between these lactation-specific genes and breast cancer risk, as well as human milk oligosaccharide composition.  

Previous research [2] has demonstrated that RNA in milk provides a profile of gene expression inside the lactating mammary gland, but the current work is the first to explore such profiles across hundreds of mother infant pairs. The researchers studied a cohort of 300 mother-infant pairs assembled by Demerath and colleagues that included genetic and gene expression data as well as milk samples. About half the pairs also had infant fecal samples reflecting the infant microbiome.

The researchers first set out to test how the expression of milk-related genes correlates with maternal traits and milk composition.  One interesting association that emerged was that the volume of milk a mother produced was inversely correlated with the expression levels of PER2, a gene known to be a key regulator of circadian rhythm. This aligns with studies demonstrating that circadian genes have been “kind of co-opted by the mammary gland to control production,” Johnson said [3]. 

The researchers also extracted and sequenced the RNA from the cells in milk samples. Using a statistical analysis approach that correlates this type of bulk RNA sequencing with data from single cell RNA sequencing studies of human milk, they estimated the proportion of different cell types in the milk samples. The most abundant cell type was mammary epithelial cells, and several immune cell types were increased in milk samples with higher concentrations of IL-6, a cytokine marker of inflammation. 

To determine how different gene variants in the genome affect the expression of milk-related genes, Johnson and her colleagues used a measure called “expression of quantitative trait loci” (eQTLs). They tested about 17,000 genes that were highly expressed in their human milk samples and homed in on 3000 genes that had nearby gene variants that affect their expression. 

Johnson and her colleagues then compared mammary tissue-specific eQTLS from their samples with genes associated with milk related traits in dairy cattle and determined how the gene expression patterns they observed aligned with that in other tissue types. The patterns of variants they observed in lactating mammary tissue were most similar to those in salivary tissue. “I think that makes sense,” said Johnson, because mammary and salivary tissue share biological commonalities in terms of secretion, immune system role, and evolutionary history. 

Next, the team explored whether genetic variants associated with milk gene expression were also associated with other traits. “Breast cancer was a clear place to look because there’s a strong epidemiological relationship between lactation and breast cancer risk, where women who have a longer lifetime duration of lactation have a lower lifetime risk of breast cancer,” Johnson explained. 

Johnson looked for overlaps between eQTLs in lactating mammary tissue and genetic studies of breast cancer, landing on a transcription factor called LMX1B. Although the finding is a preliminary hint that must be explored in further studies, it suggests that the activation of this gene specifically during lactation may be a link to breast cancer. 

Finally, the team turned to milk composition. Among the genetic variants that are associated with gene expression of milk-related genes, the team identified three that affect the composition and abundance of human milk oligosaccharides (HMOs). “This is another example of how we can use the eQTLs to identify not just genetic associations with HMOs, but the particular gene whose expression is shaped by the HMO composition,” Johnson said. She and her colleagues also explored how variation within milk might affect an infant’s microbiome. They first sequenced the samples to identify the lineup of bacteria in the microbiomes, then used a machine learning approach to identify correlations between the genes expressed in milk samples and the microbes present in the microbiomes of the corresponding infants. They identified several biological pathways within these correlations—the most prominent one being the inflammation-related JAK-STAT pathway, which was inversely correlated with the abundance and growth of Bifidobacterium in the infant gut at 1 month and Escherichia at 6 months. 

Johnson noted that mammary inflammation was a major theme that emerged across many of the results in the study. “There seems to be this big axis of variation shaping the milk transcriptome related to this inflammation pathway,” she said. None of the mothers in the study had active infections such as mastitis, but the findings might mean that subclinical infection of the mammary gland is not uncommon, she added. 

Building on the areas of insight established in the study will enable researchers to better understand the biology of human milk, said Johnson. She plans to continue looking at genetic associations with milk traits and molecular phenotypes, such as gene expression, and to use genetics to further probe the link between lactation to larger health outcomes, such as breast cancer.  

References

1. Johnson KE, Heisel T, Allert M, Fürst A, Yerabandi N, Knights D, Jacobs KM, Lock EF, Bode L, Fields DA, Rudolph MC, Gale CA, Albert FW, Demerath EW, Blekhman R. Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome. Cell Genom. 2024;4(10):100638. 
2. Lemay DG, Ballard OA, Hughes MA, Morrow AL, Horseman ND, Nommsen-Rivers LA. RNA sequencing of the human milk fat layer transcriptome reveals distinct gene expression profiles at three stages of lactation. PLoS One. 2013; 8(7):e67531.
3. McQueen CM, Schmitt EE, Sarkar TR, Elswood J, Metz RP, Earnest D, Rijnkels M, Porter WW. PER2 regulation of mammary gland development. Development. 2018;145(6):dev157966.

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