UK scientists extensively map the brain methylome, providing a valuable resource for the epigenetics and neuroscience research communities.
Dynamic changes to the epigenome play a critical role in establishing and maintaining cellular phenotype during differentiation, but little is known about the normal methylomic differences that occur between functionally distinct areas of the brain. Now, researchers from King‘s College London (UK) have characterized intra- and inter-individual methylomic variation across whole blood and multiple regions of the brain from multiple donors, creating a baseline resource for use in future research efforts.
In the recent study, the UK-based team profiled the methylomes of multiple dissected brain regions and blood from several individuals. “The key motivation for this study was that very little is known about ‘normal‘ patterns of epigenetic variation across different regions of the brain, and how intraindividual patterns of DNA methylation differ across brain and blood,” commented Jonathan Mill from the Institute of Psychiatry, King‘s College London, who led the research group.
The study saw researchers employ methylated DNA immunoprecipitation sequencing to investigate brain segments, including the inferior frontal gyrus, middle frontal gyrus, entorhinal cortex, superior temporal gyrus of the temporal cortex, visual cortex and cerebellum from samples without any neuropathology or neuropsychiatric disease.
“We hoped to identify regions of the methylome that define different types of tissue, and understand more about whether blood can be used as a proxy for brain in epidemiological studies aiming to identify disease biomarkers,” explained Mill.
Indeed, distinct tissue-specific patterns of DNA methylation were identified, with a highly significant over-representation of tissue-specific differentially methylated regions (TS-DMRs) observed at intragenic CpG islands and low CG-density promoters.
These between-brain region TS-DMRs were found to be associated with stable gene-expression differences and involved in functionally relevant neurobiological pathways. Furthermore, the researchers discovered that despite between-tissue variation in DNA methylation greatly exceeding between-individual differences within any one tissue, some interindividual variation was found across brain and blood, implying that peripheral tissues may have some utility in epidemiological studies of complex neurobiological phenotypes.
The study also brought to light some unexpected findings: “It was interesting that intraindividual intertissue variation in DNA methylation far exceeded interindividual variation in any given tissue. DNA methylation across intragenic CpG islands and low CG content promoters was found to be particularly important in defining tissue-specific variation. We also observed that although brain tissue and blood have very distinct methylomic profiles, as would be expected, some interindividual variation is correlated across tissues. It is plausible that some of this may result from genetic effects on DNA methylation, or the effects of environmental or stochastic events occurring early in development,” commented Mill.
So how will the data be used now? By making the University of California, Santa Cruz (CA, USA) tracks available on the Mill laboratory website, and by starting to integrate the raw data into the Human Epigenome Atlas (part of the NIH Epigenomics Roadmap Initiative) for others to freely use, the King‘s College group anticipate that their data will become a valuable resource for further genomics efforts.
Mill concludes that: “Understanding these things is an important first step in our efforts to examine the role of epigenetic processes in disorders such as schizophrenia, autism and dementia,” going on to further explain that “These results are important because regions defined as TS-DMRs are likely to be key regulators of cellular phenotype, and altered DNA methylation across these regions could play a key role in regulating health and disease.”
– Written by Natalie Harrison
Source: Davies MN, Volta M, Pidsley R et al. Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biol. 13(6), R43 (2012).
In this study, researchers sequenced the complete normal and cancer genomes of 37 young medulloblastoma patients. Recurrent mutations were detected in 41 genes not previously implicated in medulloblastoma. Including several that target components of the epigenetic machinery. A high percentage of patients with WNT-subtype medulloblastoma had DDX3X mutations. The study also linked alterations in CDH1 and PIK3CA to the development and spread of the WNT subtype. Subtype 3 and 4 medulloblastoma often had alterations in genes affecting cell maturation and were characterized by a gain in EZH2. Some of these subtypes also had KDM6A inactivated. The work marks progress towards more targeted therapies against medulloblastoma and adds evidence to theories that epigenetic changes are involved in fuelling childhood cancer.
– Written by Francesca Lake
Source: Robinson F, Parker M, Kranenburg TA et al. Novel mutations target distinct subgroups of medulloblastoma. Nature doi:10.1038/nature11213 (2012) (Epub ahead of print).
A rapid new method called tissue-accessible chromatin (TACh) has been found to be capable of identifying accessible chromatin derived from frozen tissue samples. The NIH researchers propose that this simple, robust approach can be applied across a broad range of clinically relevant samples to allow demarcation of regulatory elements of considerable prognostic significance.
To date, the standard tool for looking at chromatin accessibility has been DNaseI; a method that requires large amounts of fresh samples, an hour-long preparation time to isolate nuclei and a narrow concentration range to work within. This presents a problem as clinical samples are often frozen solid, only available in minute amounts and often with unknown cell numbers. The formaldehyde assisted isolation of regulatory elements method is able to identify regulatory elements in frozen samples, but its success depends on many factors and does not always provide consistent results.
For that reason, the NIH researchers developed the TACh methodology; a quick way to analyze the chromatin state of frozen clinical specimens. Unlike DNaseI, TACh uses one of the two robust endonucleases, benzonase or cyanase, to efficiently digest DNA and RNA under harsh conditions which are fully active under a range of stringent conditions such as high levels of detergent and dithiothreitol.
In a proof-of-concept study, the team performed TACh on frozen mouse livers. They found that pulverizing the frozen tissue before digestion gave the best signal-to-noise ratio. Both benzonase and cyanase yielded similar results to each other, and when nuclei were isolated from fresh mouse livers and results were compared with DNaseI tratement, outcome was similarly comparable. All three enzymes recognized most of the highly accessible regions; however, the variability was more noticeable in less accessible regions.
The researchers conclude that benzonase and cyanase identified accessible regions that correlated with low nucleosomal occupancy, euchromatin-specific epigenetic marks and transcription, making TACh an ideal technique for extracting the chromatin information in frozen clinical samples.
– Written by Natalie Harrison
Source: Gr⊘ntved L, Bandle R, John S et al. Rapid genome-scale mapping of chromatin accessibility in tissue. Epigenetics Chromatin 5(1), 10 (2012).
A news release published by Merck Serono, a biopharmaceutical division of Merck (Darmstadt, Germany), has recently announced that it is to expand its collaboration with the leading molecular diagnostic company, MDxHealth SA (Liege, Belgium). The collaboration will cover the development and worldwide commercialization of MDxHealth‘s MGMT diagnostic test (PredictMDx™ for glioblastoma), which assesses the methylation status of the MGMT gene promoter. It is hoped that the test will help identify glioblastoma patients who might be more likely to benefit from cilengitide-based therapies in combination with temozolomide and radiotherapy.
“Our collaboration with MDxHealth reflects the importance of diagnostics in the field of personalizing cancer care, an approach that Merck Serono is actively investing in with the ultimate goal to identify those patients who are most likely to benefit from a certain treatment through the use of a biomarker-guided approach,” commented Annalisa Jenkins, Head of Global Drug Development and Medical for Merck Serono. “We are hoping that this will help to improve the future treatment of patients with glioblastoma, a disease which today has high unmet medical needs.”
As outlined in the news release, cilengitide is Merck‘s cancer drug candidate currently in Phase III development for newly diagnosed glioblastoma, an aggressive form of brain cancer. As part of the expanded collaboration, Merck has agreed to support MDxHealth‘s development and regulatory activities for the MGMT test, which has already been used for the identification and stratification of newly diagnosed glioblastoma patients enrolled in cilengitide clinical studies. Furthermore, after regulatory approval, Merck has agreed to the coordinated launch together with cilengitide in glioblastoma.
The gene the test assesses, MGMT, is believed to contribute to cellular DNA repair; methylation alters the expression of the gene, leading to a proposed increase in responsiveness of tumor cells to some chemotherapeutic regimens.
“With this agreement, MDxHealth and Merck are collaborating to bring PredictMDx for glioblastoma to the clinical community – as a companion diagnostic in the US if approved by the US FDA and as a validated assay in other regions of the world – enabling personalized treatment of newly diagnosed glioblastoma patients. Today, we are excited to be partnering with Merck, one of the most advanced pharmaceutical companies in the field of personalized medicine,” concludes Jan Groen, chief executive officer of MDxHealth.
– Written by Natalie Harrison
Source: Merck Serono News Release: www.merckserono.com/corp.merckserono_2011/en/images/20120705_en_MDX_tcm1494_96883.pdf
In a bid to understand human aging in terms of the constrained genetic setting, researchers from the Bellvitge Biomedical Research Institute (Barcelona, Spain) have performed whole-genome bisulfite sequencing of newborn and centenarian genomes. The study offers clues about how and why we age and constitutes a unique DNA methylation analysis of the extreme points of human life at a single-nucleotide resolution level. The findings are reported in the June 2012 issue of Proceedings of the National Academy of Sciences.
Led by Manel Esteller, the researchers studied the epigenomes of a newborn baby boy and 103-year old man and discovered that the centenarian DNA had a lower DNA methylation content and a reduced correlation in the methylation status of neighboring CpGs throughout the genome in comparison with the more homogeneously methylated newborn DNA.
The newborn had methyl groups turning genes off at more than 80% of all possible sites. This compared with 73% in the centenarian; a difference of nearly half a million sites between the two.
These findings imply that very tight control of genes at the beginning of our lives may be being lost as we age, with more genes being switched on over time. Furthermore, as Esteller highlights, epigenetics is playing a central role in aging, and epigenetic changes between newborns and centenarians are affecting a plethora of genes, which could in turn affect some of the physical traits associated with aging.
The finding of increased hypomethylated DNA sequences in the advanced age group was confirmed by the researchers using a 450,000 CpG-site DNA methylation microarray in an extension study which included a larger cohort of newborn and nonagenarian samples.
The results of the present study raise the question of whether there is anything we can do to our epigenome in order to live a longer or lead a healthier life. As Esteller concludes: “If it is something we can intervene from outside, maybe we can change the epigenome to change or slow aging.”
– Written by Natalie Harrison
Source: Holger Heyn, Ning Li, Ferreira HJ et al. Distinct DNA methylomes of newborns and centenarians. Proc. Natl Acad. Sci. USA 109(26), 10522–10527 (2012).