Widespread Non-Canonical Epigenetic Modifications in MMTV-NeuT Breast Cancer.
Breast tumors in (FVB × BALB-NeuT) F1 mice have characteristic loss of chromosome 4 and sporadic loss or gain of other chromosomes. We employed the Illumina GoldenGate genotyping platform to quantitate loss of heterozygosity (LOH) across the genome of primary tumors, revealing strong biases favoring chromosome 4 alleles from the FVB parent. While allelic bias was not observed on other chromosomes, many tumors showed concerted LOH (C-LOH) of all alleles of one or the other parent on sporadic chromosomes, a pattern consistent with cytogenetic observations. Surprisingly, comparison of LOH in tumor samples relative to normal unaffected tissues from these animals revealed significant variegated (stochastic) deviations from heterozygosity (V-LOH) in every tumor genome. Sequence analysis showed expected changes in the allelic frequency of single nucleotide polymorphisms (SNPs) in cases of C-LOH. However, no evidence of LOH due to mutations, small deletions, or gene conversion at the affected SNPs or surrounding DNA was found at loci with V-LOH. Postulating an epigenetic mechanism contributing to V-LOH, we tested whether methylation of template DNA impacts allele detection efficiency using synthetic oligonucleotide templates in an assay mimicking the GoldenGate genotyping format. Methylated templates were systematically over-scored, suggesting that the observed patterns of V-LOH may represent extensive epigenetic DNA modifications across the tumor genomes. As most of the SNPs queried do not contain standard (CpG) methylation targets, we propose that widespread, non-canonical DNA modifications occur during Her2/neuT-driven tumorigenesis.
Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Sara J
SJ
Felts
Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Virginia P
VP
Van Keulen
Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Michael J
MJ
Hansen
Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Michael P
MP
Bell
Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Kathleen
K
Allen
Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Alem A
AA
Belachew
Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA; Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA.
Richard G
RG
Vile
Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA.
Julie M
JM
Cunningham
Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.
Tanya L
TL
Hoskin
Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.
V Shane
VS
Pankratz
Department of Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA. Electronic address: pease.larry@mayo.edu.
Larry R
LR
Pease
D000483:Alleles; D000818:Animals; D001943:Breast Neoplasms / Q000235:genetics*; D002471:Cell Transformation, Neoplastic / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics*; D005260:Female; D005787:Gene Frequency / Q000235:genetics; D016147:Genes, Tumor Suppressor / Q000502:physiology; D005838:Genotype; D006579:Heterozygote; D019656:Loss of Heterozygosity / Q000235:genetics; D051379:Mice; D008807:Mice, Inbred BALB C; D020641:Polymorphism, Single Nucleotide / Q000235:genetics