BRCA1/2 Mutation Carriers Show Fewer Active Ribosomal DNA Copies in Blood

Healthy women who carry inherited, disease-causing variants in the BRCA1 or BRCA2 genes have measurably fewer active copies of their ribosomal DNA than women without such variants, according to a new study published in Breast Cancer Research. The difference was small—on average about ten copies—but statistically significant in BRCA1 carriers and, in the youngest age group, present in BRCA2 carriers as well. Because the study participants had never been diagnosed with cancer, the finding hints that an epigenetic signature linked to cancer susceptibility may already be visible in the blood of genetically predisposed women long before any tumor appears.

Ribosomal DNA, or rDNA, is the stretch of the genome that encodes the RNA components of ribosomes, the molecular machines that build every protein in the body. The 45S rDNA transcription units, which produce the 18S, 5.8S and 28S ribosomal RNAs, sit in long tandem arrays on the short arms of the acrocentric chromosomes. Remarkably, the absolute number of these units varies enormously between healthy people, from fewer than 200 to more than 1,000 copies per diploid genome. Despite this dramatic variation, surprisingly little is known about what it means for health, largely because these repetitive, CpG-rich regions are difficult for standard genome sequencing technologies to analyze.

The research team, led by Sarah Kießling and Thomas Haaf at Würzburg University, tackled this problem with a two-pronged measurement strategy. They combined droplet digital PCR, which counts the absolute number of rDNA copies in a DNA sample without a standard curve, with deep bisulfite sequencing, which reads the methylation state of the promoter region controlling each copy. Copies whose promoters carry little or no methylation—at or below 10 percent—are generally considered active, while heavily methylated copies are presumed silenced. By multiplying the absolute count by the fraction of hypomethylated reads, the researchers could estimate how many rDNA copies each person likely keeps switched on.

The study enrolled 90 unrelated healthy women carrying a pathogenic BRCA1 variant and 71 carrying a pathogenic BRCA2 variant, all identified through predictive genetic testing and classified according to ACMG/AMP criteria. They were compared with 146 age-matched women who tested negative for such variants. All DNA came from blood samples, and all measurements were performed in duplicate, with strong correlations between technical replicates. The participants ranged in age from 18.2 to 78.5 years.

The first key result was a null finding: absolute rDNA copy number was essentially identical across the three groups. BRCA1 carriers averaged 397 copies, BRCA2 carriers 400, and controls 393, with no statistically significant differences. This matters because rDNA instability—gains or losses of copies in tumors compared with healthy tissue—is considered a hallmark of cancer progression. The new data suggest that this genomic instability does not precede tumor development in BRCA1/2 carriers but instead arises later, during tumor evolution.

The epigenetic picture was different. The number of hypomethylated, presumably active rDNA copies averaged 142 in BRCA1 carriers and 145 in BRCA2 carriers, versus 152 in controls. The difference reached statistical significance for BRCA1 carriers (P = 0.023) and was borderline for BRCA2 carriers (P = 0.085). Consistent with earlier work by the same group, hypomethylated copy number declined with age in the control group, with a Spearman correlation of −0.21. Intriguingly, that age-related decline was not statistically detectable in either carrier group, suggesting that carriers may start adult life with a reduced pool of active copies rather than losing them faster over time.

To probe this age pattern, the team split the cohort at an admittedly somewhat arbitrary threshold of 45 years, chosen to keep both subgroups large enough for analysis. Among the 214 younger women, BRCA1 carriers had about 145 hypomethylated copies compared with 157 in controls, a significant difference (P = 0.015), and BRCA2 carriers showed a borderline difference (P = 0.150) of roughly ten copies fewer. Among the 93 women older than 45, the between-group differences disappeared entirely. In other words, the epigenetic gap between carriers and controls is most visible in young adulthood and fades with age, as the carriers’ counts converge with the naturally declining counts of controls.

The authors propose that this reduced pool of active rDNA copies might contribute to cancer susceptibility in BRCA1/2 variant carriers, potentially preceding tumor development. They point to supporting evidence from an entirely different population: carriers of Robertsonian translocations, the most common balanced chromosome rearrangement in humans, who lose two of their ten rDNA arrays in the fusion event. These individuals show a significantly increased risk of several cancers, including childhood leukemia, non-Hodgkin lymphoma and breast cancer, even without any BRCA mutation. Together, these lines of evidence suggest that a lower rDNA copy number, or a lower active fraction, may be one of many modulating factors in multifactorial disease.

Important caveats temper the excitement. The effect size is genuinely small: ten copies on a background where copy number varies naturally by hundreds, and carriers’ values remained well within the normal range of human variation. Previous analyses by the group suggest that as few as 50 active copies may suffice for normal cell function, so no individual’s result should be read as a red flag. The authors are explicit that at the level of a single person, rDNA copy number cannot be used as a predictive marker for cancer risk; the association is meaningful only at the population level. The study also could not control for confounders such as physical activity, diet, body mass index, hormones, alcohol, smoking or other environmental exposures, because the samples were anonymized and none of this information was available.

There is also a functional gap. Without RNA samples or cell lines from the participants, the researchers could not directly demonstrate that the hypomethylated copies are actually being transcribed; the evidence that low promoter methylation marks active rDNA remains circumstantial, albeit supported by independent work showing that silent rDNA arrays carry high promoter methylation, lack key transcription proteins, and can be reactivated by demethylation. Other mechanisms, including RNA polymerase I factor modifications, chromatin changes and long non-coding RNAs, also regulate rDNA expression. The authors call for multicenter studies with larger cohorts and explicit control of confounding factors to replicate the association, and for parallel analyses in breast epithelial cells, since haploinsufficiency effects may be cell-type specific. For now, the study stands as an intriguing early signal that inherited cancer risk may leave a subtle, measurable fingerprint in the epigenetic architecture of the genome’s most repetitive corner—one that appears years before disease, but only if you know where, and at what scale, to look.

Subject of Research: The association between germline BRCA1/2 pathogenic variants and reduced numbers of hypomethylated ribosomal DNA copies in healthy women

Article Title: Pathogenic germline variants in BRCA1/2 are associated with a decreased number of hypomethylated rDNA copies

Article References: Kießling, S., Durackova, J., Michler, A., Geisen, A. B. C., Santana Acevedo, N., & Haaf, T. (2026). Pathogenic germline variants in BRCA1/2 are associated with a decreased number of hypomethylated rDNA copies. Breast Cancer Research, 28(1), Article 161. https://doi.org/10.1186/s13058-026-02387-5

Image Credits: AI Generated

DOI: 10.1186/s13058-026-02387-5

Keywords: BRCA1, BRCA2, ribosomal DNA, DNA methylation, epigenetics, breast cancer, ovarian cancer, copy number variation, droplet digital PCR, bisulfite sequencing, genetic predisposition, cancer susceptibility