In a recent study, published in Nature, a team of researchers from Brigham and Women‘s Hospital (MA, USA), Columbia University (NY, USA), Mount Sinai (NY, USA) and the University of Pennsylvania (PA, USA), have investigated the role of de novo mutations in the development of congenital heart disease (CHD).
CHD affects 0.8% of live births, making it the most common birth defect. In many cases, affected individuals have healthy parents and siblings, suggesting a role for de novo mutations.
The team used recently developed sequencing technologies to compare the protein-coding regions of the genomes of both healthy children and those affected by CHD and their families. The incidence of de novo mutations was analyzed in 362 families with a CHD-affected child and healthy parents (with no family history of CHD) and 264 healthy control families.
It was observed that all of the children had approximately the same number of de novo mutations, but the location of these mutations differed significantly between the two groups. Mutations in genes that are highly expressed in the developing heart were found more frequently in children with CHD, with an odds ratio of 7.5 for damaging mutations. Mutations were found in a selection of genes but there was a marked excess of de novo mutations in one pathway affecting the epigenome in children with CHD.
An excess of mutations affecting histone methylation at two sites previously known to be involved in the regulation of key developmental genes was observed. Specifically, mutations were observed in genes involved in the removal, production or reading of H3K4 methylation. Two de novo mutations were also observed in SMAD2, which is known to regulate H3K27 methylation in the embryonic left–right organizer.
The team found that, overall, de novo mutations contribute to 10% of severe CHD cases and approximately a third of these cases are due to mutations in the histone-methylation pathway. It was found that a mutation in just one copy of a gene in this pathway could significantly increase the risk of CHD.
This method of searching for significant de novo mutations by direct sequencing of the protein-coding regions of the genome has also been applied to autism. In that study, researchers from Yale University (CT, USA) and the University of Washington (WA, USA) observed mutations in some of the same genes and the same histone-modification pathway is believed to play a role. The identification of the mutations responsible for severe congenital defects may help physicians to understand these conditions and improve outcomes for their patients.
– Written by Caroline Telfer
Source: Zaidi S, Murim C,Wakimoto H et al.De novo mutations inhistone-modifying genes in congenitalheart disease. Nature 498, 220–223 (2013).
In a recent study published in Cancer Cell, a collaboration of researchers from the University of Basel (Basel, Switzerland) and the Friedrich Miescher Institute (Basel, Switzerland) have discovered a master regulator of cancer metastasis.
Metastasis is the predominant cause of death in cancer patients. The epithelial-to-mesenchymal transition (EMT), the process by which fixed, specialized cells transform into invasive, unspecialized cells, is central to metastasis. The molecular processes responsible for EMT are still largely unknown.
Using gene expression profiling during TGF-β-induced EMT in normal and cancerous breast epithelial cells, the team identified the transcription factor Sox4 as a master regulator of metastasis. Sox 4, which is upregulated during EMT, is essential for primary tumor growth and metastasis in vivo, and cell survival and EMT in vitro. Sox4 is responsible for regulating the expression of Ezh2, which encodes the polycomb group histone methyltransferase that trimethylates H3K27me3, causing gene repression. The team observed that forced expression of Ezh2 in Sox4-deficient cells was enough to restore EMT, whereas inhibition of Ezh2 led to the prevention of EMT. Ezh2-mediated H3K27me3 marks were discovered to be associated with known EMT genes.
This study has highlighted Sox4 as a master regulator of EMT by regulating the expression of the enzyme Ezh2, which exerts epigenetic effects on the cells. This research highlights an epigenetic signature that could be used to predict patient survival. It also raises the possibility of therapeutically inhibiting Sox4 or Ezh2 for the treatment of metastatic cancer.
– Written by Caroline Telfer
Source: Tiwari N, Tiwari V, Waldmeier L et al.Sox4 is a master regulator of epithelial–mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming. Cancer Cell 23(6), 768–783 (2013).
Researchers from the University of Pennsylvania (PA, USA) have highlighted a role for epigenetics in the association between paternal stress and neuropsychiatric diseases in the offspring. The paradigm of the influence of maternal stresses during pregnancy on neurodevelopment is relatively well established. However, the specific role of paternal factors is largely unknown. Offspring with neuropsychiatric disease often demonstrate hypo- or hyper-reactivity of the hypothalamic–pituitary–adrenal (HPA) axis, which is a region of the brain that directs responses to stress.
The team exposed male mice to 6 weeks of chronic stress (e.g., movement of habitat, presence of predator scent, and noise or unknown objects being placed in the cage) prior to breeding, either throughout puberty or in adulthood.
Surprisingly, the offspring of both paternal stress groups displayed a significantly blunted HPA stress axis responsivity, with reduced levels of the stress hormone corticosterone in response to stress. The team also conducted gene set enrichment analyses in brain regions known to be involved in stress regulation, the paraventricular nucleus and the bed nucleus of stria terminalis. This revealed an increased expression of glucocorticoid-responsive genes and other global pattern changes indicative of epigenetic reprogramming and associated with altered stress responsivity. Analysis of a series of sperm miRNAs that contribute to post-fertilization gene expression revealed a significant increase in nine miRNAs in both paternal stress groups.
These results highlight a lifelong role for paternal experience in the epigenetic reprogramming and HPA stress axis regulation of the offspring. This provides novel insight into the mechanisms contributing to neuropsychiatric disease risk. The next step will be to examine the mechanisms by which the highlighted sperm miRNAs act at fertilization, with the view of using them as biomarkers of human disease.
– Written by Caroline Telfer
Source: Rodgers A, Morgan C, Bronson S et al. Paternal stress exposure alters sperm microRNA content and reprograms offspring HPA stress axis regulation. J. Neurosci. 33(21), 9003–9012 (2013).
Epigenetic alterations are increasingly understood to play an important role in the development of cancer. Now, for the first time, researchers from St Jude Children‘s Research Hospital (TN, USA) and Weill Cornell Medical College (NY, USA) have performed an integrated analysis of genetic and epigenetic alterations in acute lymphoblastic leukemia (ALL), the most common childhood cancer.
In the study, published online in the Journal of Clinical Investigation, researchers used microarray analysis of DNA copy number alterations and gene expression, and genome-wide cytosine methylation profiling to analyze tissue samples from over 160 B- and T-cell leukemia patients, including representatives of all known ALL subtypes, and 27 healthy children.
The results of the study indicate that the distinct subtypes of ALL have unique methylation patterns that correlate with gene expression. Charles Mullighan, an associate member of the St Jude Department of Pathology and co-corresponding author of the paper, explains: “It is well known that different leukemia subgroups have distinct patterns of gene expression that are important in the development of leukemia. We have assumed that the underlying genetic changes are important determinants of those gene expression profiles. We now know that changes in methylation state also have key roles in influencing gene expression.”
In addition, the data show an ‘epigenetic signature‘, a core set of abnormally methylated genes in all ALL cells analyzed. More than a third of the 71 genes that are genetically altered in ALL are also abnormally methylated, including known tumor suppressor genes or oncogenes, such as CDKN2A, CDKN2B, PTEN and KRAS. Mullighan says: “The findings suggest these genes are inactivated or deregulated more frequently than suggested by simply analyzing structural changes in the genome.”
The researchers explained that these results highlight the role of cytosine methylation in ALL and may represent important early steps in the development of leukemia. Ari Melnick, Gebroe Professor Hematology/Oncology at Weill Cornell Medical College and the second co-corresponding author of the paper, explained his optimism regarding the results: “The data show that aberrant epigenetic gene programming can now be considered a hallmark of ALL, occurring in all patients regardless of the presence of genetic mutations. This offers the opportunity for development of epigenetic targeted therapies for patients with ALL that could be broadly applicable to many patients.”
– Written by Karen Vincent
Sources: Figueroa ME, Chen SC, Andersson AK et al. Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukaemia. J. Clin. Invest. doi:10.1172/JCI66203 (2013) (Epub ahead of print); St Jude Children‘s Research Hospital news release. Epigenetic factor likely plays a key role in fueling most common childhood cancer: www.stjude.org/mullighan-epigenetic-all
In a recent study published in Current Biology, a group of researchers from the Fred Hutchinson Cancer Research Center (WA, USA) and the Howard Hughes Medical institute in Seattle (WA, USA) have unraveled the mechanism by which doxorubicin affects chromatin.
Doxorubicin is one of the most commonly used anticancer drugs. It is an anthracycline DNA intercalator that causes DNA double-stranded breaks in rapidly dividing cells. It was previously unknown whether the drug has an effect on chromatin properties.
Using a metabolic labeling strategy, the team measured nucleosome turnover in squamous cell carcinoma cell lines that had been derived from genetically defined mice. It was observed that doxorubicin treatment was associated with an increase in nucleosome turnover around gene promoters. This increase correlated with time of exposure, suggesting the direct action of the drug.
Of interest, the enhancement of nucleosome turnover in response to doxorubicin was observed in cells deficient in p53 or ATM, suggesting that the underlying mechanism is independent of the DNA damage checkpoint. The same effect was demonstrated with aclarubicin, another anthracycline drug.
This study indicates that doxorubicin affects DNA topology, promoting nucleosome turnover around promoters; a possible mechanism for cell killing during cancer chemotherapy. Understanding these molecular effects may provide insights into the design of cancer therapies to target chromatin regulators.
– Written by Caroline Telfer
Source: Yang F, Kemp CJ, Henikoff S et al. Doxorubicin enhances nucleosome turnover around promoters. Curr. Biol. 23(9), 782–787 (2013).