CpG Methylation System Revealed in Western Honey Bee

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Last week Science published several new reports on Apis mellifera, the honey bee, including a report from Wang et. al on the functional CpG methylation system in this newly sequenced genome. The methylation report has a number of key findings and implications for further research:

  • While the widely used genetics model Drosophila melanogaster shows only limited DNA methylation, the honey bee exhibits a fully functional CpG methylation system, including the identification of the deoxycytosine methyltransferase Dnmt2, as well as an ortholog for de novo methylation (AmDnmt3) and two orthologs for maintenance methylation (AmDnmt1a and AmDnmt1b).
  • Analysis thus far indicates that non-CpG methylation in the honey bee is either extremely rare or non-existent.
  • The authors propose that DNA methylation is widespread in insects, and thus Drosophila may be useful for understanding “unexplored evolutionary aspects of genome regulation.”
  • Since honey bees exhibit the underlying mechanisms that underlie imprinting, they could be used to test the kin-conflict theory.
  • All detected methylation in the honey bee was limited predominantly to coding regions.
  • The overall level of methylation in the honey bee is lower compared to vertebrates.
These findings could be important in providing a new understanding of how DNA methylation has evolved over time. Link

Orion Teams with Mayo for Validation of Breast Cancer Detection

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St. Louis-based Orion Genomics has announced a collaboration with the Mayo Clinic to establish the utility of using its breast cancer biomarkers in the early detection of other cancers, such as lung, ovarian, and colon cancers. Mayo will be used to “validate the tumor specificity of Orion’s breast cancer biomarkers by analyzing the cross reactivity of these epigenetic biomarkers in more than a dozen additional cancer types.” By screening breast cancer samples using Orion’s proprietary MethylScope platform, the company has identified over 50 novel biomarkers (a change in methylation pattern between breast cancer and control samples) to date. Link

Johns Hopkins/USC Cancer Centers to Analyze Methylation Profiles in Cancers

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The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University in Baltimore, Md, in a joint partnership with the Norris Comprehensive Cancer Center at the University of Southern California, has been selected as one of seven Cancer Genome Characterization Centers (CGCCs) by the National Cancer Institute. The two cancer centers will take up the task of detecting “changes in methylation profiles associated with transcribed genes in cancer samples.” The tumor types chosen to analyze for the 3-year, $100 million Cancer Genome Atlas Pilot Program are lung, brain (glioblastoma), and ovarian cancers.

    Additionally, SRA International Inc. of Fairfax, Va., has been selected to develop the Data Coordinating Center (DCC) for the TCGA Pilot Project. The DCC will track data produced by components of TCGA, ensuring that this data meets quality standards set for the project, and make TCGA data publicly accessible through databases supported by NCI’s Cancer Biomedical Informatics Grid (caBIG™) and the National Library of Medicine’s National Center for Biotechnology Information (NCBI). The DCC will establish public data resources that scientists can use in their research to generate new insights into the causes and potential targets for interventions in cancer. Access to all TCGA data will be provided in a manner that meets the highest standards for protection and respect of the research participants. Link

An Epigenetic Factor in Increased Infant Mortality

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Epigenetics may play a role in the higher rates of infant mortality and low birth weight babies born to black women. The News and Advance reports this from Dr. Michael Lu of the UCLA School of Medicine and School of Public Health, as well as a co-principal investigator on a three-year, $15 million study on improving birth outcomes in Los Angeles.

    One hypothesis Lu cited is that during critical periods of development the fetus is impacted by the mother’s level of stress and the hormones it produces, which pass through the placenta. For critical developmental periods, that may affect organs or organ development in a way that “they don’t function optimally for an entire life course.”

    He said the new field of “epigenetics” takes the concept to the molecular level, as a “volume control for genes.” Gene expression can be turned up or down, switched on or off, by environmental exposure, “including pre-natal exposure.”

    With this theory, he said, identical genetic codes could play out very differently if one was developed under very high stress.

    Stress affects immune function, and some infections increase the possibility of pre-term labor, which leads to early delivery and low birth-weight babies.


Carnivals of Interest

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A couple of carnivals recently published may interest the loyal readers here at Epigenetics News:

  • Tangled Bank #64, hosted by The Neurophilosopher’s Weblog. This collection of the Web’s best science writing from the past two weeks includes a nice synopsis of the discovery of RNAi by Fire and Mello, which earned them the Nobel Prize in Chemistry.
  • Mendel’s Garden #8, hosted by Discovering biology in a digital world. This genetics carnival includes a number of interesting pieces this week, such as the origins of gene structure and the truth about ethidium bromide.

Progress in Development of Lung Cancer Screening Tools

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Epigenomics AG recently announced that it has identified novel biomarkers that could be used in the development of clinical tests to aid in the early detection of lung cancer.

    …Epigenomics identified a large number of genes showing higher levels of DNA methylation in lung cancer compared to healthy lung tissue and other healthy and cancerous controls. The results were statistically significant. Importantly, a considerable number of these candidate DNA methylation biomarkers detected both major types of lung cancer, small cell lung cancer (SCLC) as well as non-small cell lung cancer (NSCLC). Link
Earlier this year a review was published summarizing the link between epigenetics and lung cancer.