A team of researchers has developed a mouse DNA methylation microarray that will enable the research community to accelerate their epigenetics studies. The team presented the design and functionality of the new microarray in a publication in Cell Genomics on July 13, where they described several applications including aging and tumorigenesis research.
Currently, over 200,000 genetically engineered strains of mice are commercially available through entities such as the Jackson Laboratory. However, researchers working with mouse models have not had access to affordable tools to study the murine DNA methylation landscape. Due to the lack of such tools for mice, researchers have been limited in their ability to identify DNA methylation biomarkers that may further the understanding of human diseases.
Peter Laird and Hui Shen of the Van Andel Institute, Wanding Zhou of the Children’s Hospital of Philadelphia, and researchers at Foxo Technologies recognized the gap that could be filled by a mouse-specific DNA methylation array, and they worked with Illumina to develop the Infinium Mouse Methylation BeadChip.
By designing a mouse-specific array on the Infinium array platform, the researchers hoped to provide a tool that can enable epigenome-wide association studies (EWAS), cancer research, epigenetic aging studies, and more in a ubiquitous model for life science research.
Validating the Mouse Methylation BeadChip
To enable the applications described above in mouse models, Laird, Shen, and Zhou designed the array to offer comprehensive coverage of the mouse methylome. The BeadChip is composed of over 285,000 CpG sites covering CpG islands, transcription start sites, enhancers, imprinted loci, gene body regions, repetitive element regions, lamin attachment domains, CCCTC-binding factor binding sites, and hypermethylated regions in cancer.
Once developed, the team performed validation studies with the BeadChip, processing over 1,000 mouse DNA samples and summarizing their results in Cell Genomics. The authors showed that the Mouse Methylation BeadChip can be used in patient-derived xenograft models of cancer for analysis of stromal features. Moreover, they demonstrated the array’s compatibility with formalin-fixed paraffin-embedded (FFPE) tissue, a common sample type for studying tumors. These two features will facilitate studies of DNA methylation in tumor pathology.
The authors also showed that the BeadChip can detect changes in DNA methylation in response to exogenous chemicals. This feature may open the door to translational studies in which changes in mouse DNA methylation are used as a biomarker for therapeutic efficacy in preclinical trials.
Moreover, the BeadChip was able to provide high-resolution data for mice across different strains, along with a portion of probes that can be used in rat species.
Laird, Shen, and Zhou have collaborated for several years with a focus on research areas like cancer, epigenetics, and bioinformatic analysis.
The collaborations among the three authors started at the Van Andel Institute, where Laird has served as a professor and researcher since 2014. Shen has also worked at the institute since 2014, serving as an associate professor in the Center for Epigenetics. Zhou, lead author of the paper, joined Van Andel in 2015 as a postdoctoral researcher. He now works as an assistant professor at the Children’s Hospital of Philadelphia.
The three are co-authors on several papers, including a comprehensive evaluation of another Infinium Methylation BeadChip, MethylationEPIC, which was published in 2017. Zhou is also the creator of SeSAMe, a popular tool for bioinformatic analysis of methylation array data, and the three are listed as authors of the introductory paper.
Additionally, the authors have published work as part of The Cancer Genome Atlas, a 12-year project described as “a landmark cancer genomics program, molecularly characteriz[ing] over 20,000 primary cancers and matched normal samples spanning 33 cancer types.” Laird served as principal investigator for DNA methylation data production on the project.
New Technology, New Capabilities
The advent of DNA methylation microarrays has brought throughput capabilities normally seen in genotyping studies to the study of epigenetics. The first DNA methylation microarray, known as the GoldenGate Assay, measured the methylation state of 1,536 CpG sites in 96 samples simultaneously. Today’s most comprehensive human DNA methylation microarray, MethylationEPIC, allows for genome-wide coverage of greater than 850,000 CpG sites.
With the expanded capabilities of DNA methylation measurement technology, several new applications have come to light. For instance, EWAS have steadily increased in popularity over the past several years. These types of studies help identify epigenetic variants associated with phenotypes, such as diseases, in a population. Beyond disease, EWAS have identified epigenetic signatures for environmental exposures to smoking, pesticides, pollution, and more.
DNA methylation studies have also been important in our understanding of cancer. Cancer is associated with characteristic changes in DNA methylation activity, and often these changes are tumor-specific. Identifying tumor-specific methylation signatures enables molecular classification of those tumors. In fact, methylation profiling has been incorporated into the World Health Organization Classification of Tumors in recent years. Methylation arrays specifically can be used to subclassify central nervous system and sarcoma tumors with web-based classifiers developed by the German Cancer Research Institute (DKFZ).
Methylation-based epigenetic aging clocks have also emerged as a novel use case for DNA methylation arrays. Epigenetic aging clocks are a measure of biological age, as opposed to chronological age. Because epigenetic aging clocks are associated with disease, mortality, and general wellness, they are being investigated as biomarkers for human health.
Laird, Shen, Zhou, and colleagues wrote that they expect the Mouse Methylation BeadChip will contribute to these advances and they anticipate will it “rapidly contribute large amounts of epigenetic data by taking advantage of the powerful mouse genetics and complementing the extensive phenotype characterization.”
For Research Use Only. Not for use in diagnostic procedures.