Human rDNA copy number is unstable in metastatic breast cancers

ABSTRACT

Chromatin-mediated silencing, including the formation of heterochromatin, silent chromosome territories, and repressed gene promoters, acts to stabilize patterns of gene regulation and the physical structure of the genome. Reduction of chromatin-mediated silencing can result in genome rearrangements, particularly at intrinsically unstable regions of the genome such as transposons, satellite repeats, and repetitive gene clusters including the rRNA gene clusters (rDNA). It is thus expected that mutational or environmental conditions that compromise heterochromatin function might cause genome instability, and diseases associated with decreased epigenetic stability might exhibit genome changes as part of their aetiology. We find the support of this hypothesis in invasive ductal breast carcinoma, in which reduced epigenetic silencing has been previously described, by using a facile method to quantify rDNA copy number in biopsied breast tumours and pair-matched healthy tissue. We found that rDNA and satellite DNA sequences had significant copy number variation – both losses and gains of copies – compared to healthy tissue, arguing that these genome rearrangements are common in developing breast cancer. Thus, any proposed aetiology onset or progression of breast cancer should consider alterations to the epigenome, but must also accommodate concomitant changes to genome sequence at heterochromatic loci.

KEYWORDS:

• Ribosomal DNA (rDNA)
• invasive breast carcinoma
• heterochromatin
• repeat
• qPCR
• copy number polymorphism

Acknowledgments

GFP-BLM cell lines were obtained from Dr. Mary Yagle and Dr. Nathan Ellis. The University of Arizona Cancer Center provided core and facilities support, funded through National Institutes of Health Support Grant P30CA023074. Blood DNA (Figure 6(a-b,e)) or blood samples (Figures 6(c) and 7) were obtained from the AHSC Biorepository at The University of Arizona College of Medicine. Ovary samples (Figure 2) were obtained from the Univeristy of Arizona Tissue Acquisition and Cellular/Molecular Analysis Shared Resource (TACMASR). TACMASR also performed the tissue sections of the breast tumour samples. Support also came from the Department of Cellular and Molecular Medicine, the Univeristy of Arizona College of Medicine, the Arizona State Museum, and Transformative Research Award (R01) GM123640, granted to Keith A. Maggert. Finally, Dr. Nicholas Ratterman’s excellent sociolinguistic parsimony and keen advice was invaluable, as were the delicate urgings of Dr. Diana Darnell.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the NIH [GM123640].