Are You What Your Mom Ate?

To ensure they give birth to a healthy baby, pregnant mothers will take the necessary precautions, such as eating a balanced diet or avoiding exposure to cigarette smoke. This is because there appears to be a link between exposure to environmental factors early in development and disease in adulthood. One explanation for this relationship may involve epigenetic modifications, such as DNA methylation of transposable elements.

The study featured in the article, Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development, sought to explore the effects of chemical exposure, specifically bisphenol A, during early development on the epigenome and whether or not these effects could be counteracted by nutrient supplementation.

Epigenetic modifications established during early development create epialleles, or alleles that would be identical if not for methylation differences. One example of an epiallele is the Agouti gene in the yellow agouti mouse. The A^vy allele of this gene resulted from the insertion of a retrotransposon into the 5' end of the gene. Methylation of cytosines in cytosine-guanine (CpG) dinucleotide sites in and near the A^vy gene results in a wide variation in coat color, ranging from yellow (unmethylated) to pseudoagouti (methylated).

Bisphenol A (BPA) is a chemical used in the manufacture of polycarbonate plastics. It can be found in products such as food and beverage containers and baby bottles. Although reviews of the BPA literature have conflicting conclusions as to its potential as a human health risk, rodent studies have found that exposure to BPA, either as an embryo or fetus or as a newborn, is associated with higher body weight, increased breast and prostate cancer, and altered reproductive functions. The current study looked at the effect on the epigenome of offspring of maternal BPA exposure alone and in combination with nutritional supplements.

The study showed that maternal BPA exposure shifted the coat color distribution of genetically identical heterozygous offspring towards the yellow coat color phenotype. Twenty-one percent of offspring exposed to BPA during development were yellow compared with ten percent of offspring with no BPA exposure. Bisulfite treatment and sequencing was used to measure the DNA methylation at nine CpG sites in the promoter region of the A^vy allele. The offspring that were exposed to BPA had 27+/- 2.8% methylation across the nine sites compared with 39 +/- 2.6% in the offspring without BPA exposure. The sites that exhibited the greatest difference in methylation appear to be important in modifying chromatin structure and Agouti gene expression. Early stem cell development must to be sensitive to BPA exposure since the patterning of DNA methylation at the A^vy locus was similar in tissues from three of the germ layers (ectoderm, mesoderm, and endoderm).

Additionally, results from a statistical approach, known as mediational regression analysis, suggest that BPA exposure does not directly regulate coat color. Instead, coat color is determined by the methylation at the A^vy gene. BPA exposure just so happens to affect methylation and therefore indirectly affects coat color.

The study investigated the relationship between BPA exposure and maternal nutritional supplements that are methyl donors, such as folic acid. Previous studies suggest that these supplements will counteract the hypomethylation effect of BPA exposure. Female mice that received a BPA diet supplemented with methyl donors or genistein (not a methyl-donating compound) produced offspring that exhibited the coat color distribution found in offspring from females that were not exposed to BPA. These findings suggest that maternal nutritional supplementation, with either methyl-donors or non-methyl-donors, counteracts the hypomethylation caused by maternal BPA exposure.

BPA exposure is linked to modifications of the epigenome and disease pathologies that are passed down through the germ line. This study’s findings suggest that nutrition interventions during early development have the potential to reduce disease susceptibility in adulthood. Be sure to thank your mom for eating healthy during her pregnancy!

Not So Identical

Diane Arbus, Identical Twins - Stencil                                       

Identical twins have largely the same genes. So, how can identical twins not look exactly the same or have the same susceptibility to disease? The phenotypic differences we see in twins prove that our genes are not the only factors in determining physical attributes. One explanation for the differences seen in identical twins is the presence of epigenetic differences.

The article, Epigenetic differences arise during the lifetime of monozygotic twins, features a study which examined the difference in DNA methylation and histone acetylation between 80 identical twins over various ages. Identical twins are the perfect subjects to evaluate the epigenetic causes of phenotypes because the differences between the twin pairs must be a result of factors other than gene sequence.

The epigenome controls the differential expression of genes. DNA methylation and histone modifications, such as acetylation, store epigenetic information that controls heritable states of gene expression. In the article, the study examined different epigenetic characters, which included the abundance of DNA methylation and histone acetylation, as well as the distribution of DNA methylation in chromosomes.

Christoph Bock (Max Planck Institute for Informatics)

Histones are proteins that, together with DNA, are found in the chromatin in a cell's nucleus. This study examined the acetylation of two specific histones, H4 and H3,  as well as methylation of DNA. The technique known as Amplification of Intermethylated Sites (AIMS) was used to determine the specific methylated DNA sequences, which allowed for the determination of the distribution of DNA methylation on chromosomes.

35% of the twin pairs studied had significantly different epigenetic characters between pairs. The twins that were the most epigenetically different were older in age, while the youngest pairs were epigenetically similar. Also, twins with similar amounts of DNA methylation and histone acetylation, and methylation patterns, shared a common distribution of DNA methylation in their chromosomes. 

Twins by Elsie esq.

Using the statistical methods, ANOVA and ESD, the epigenetic variability was compared within the twin population and between pairs. Results from these methods determined that the epigenetic variability among individuals is high and similar, regardless of age group. However, older identical twins have higher epigenetic variability between pairs than younger twins. When comparing 3-year old twins with 50-year old twins, the 50-year-old twins were found to have extremely different gene expression. In an older twin pair, there were four times as many differently expressed genes than in the younger twin pair.

Besides age, other factors that were found to possibly contribute to the epigenetic modification pattern differences between twin pairs included the time twins spent with each other and differences in their medical history. Twins who spent the least amount of their lifetimes together or had different medical history were those who also showed the greatest differences in levels of DNA methylation and histone acetylation of histones. Even when comparing different cell types (epithelial mouth cells, intraabdominal fat, and skeletal muscle biopsies), there are striking epigenetic differences in older twins with different lifestyles and that had spent less of their lives together.

twins by cesarastudillo

The difference in epigenetic patterns that arise during the lifetime of identical twins explains their phenotypic differences. External factors, such as smoking habits, physical activity, or diet, have been proposed to have a long-term influence on epigenetic modifications. Internal factors, such as small defects in transmitting epigenetic information through successive cell divisions, may also play a role in causing different epigenetic modification patterns. Further studies must be done to fully understand the effects of these external and internal factors on the the epigenome. We have much more to learn about the growing research field of epigenetics and how different phenotypes can result from the same genotype.

The benefits of RNA in curing cancer

Many techniques used to treat cancer lead to side effects and illnesses. For example, a majority of cancer drugs cause those cells that rapidly divide due to the fact that rapid cell division is known to result in the formation of cancer. However, rapid cell division is “a property of normal cells in the bone marrow, digestive tract, and hair follicles,” and if these cells are also killed, it will lead “to a host of debilitating side effects.”

Neils Pierce of the California Institute of Technology (Caltech) has developed a new method of killing cancer cells. Pierce’s main goal was to develop a therapy that did not result in side effects and create an innovative way of killing cancer cells using small RNA molecules. Pierce and his colleagues used a method using two types of small conditional RNA molecules, which are 30 base pairs in length. According to the researchers, one of the RNA molecules “is designed to be complementary to, and thus to bind to, an RNA sequence unique to a particular cancer cell.” The RNA hairpin then changes form by opening and exposing a sequence that can spontaneously bind to the second type of RNA hairpin that will bind to the cancer mutation; this process continues from one hairpin to the next.

“In this way, detection of the RNA cancer marker triggers the self-assembly of a long double-stranded RNA polymer.” In order to search for long double-stranded viral RNA in the human cells, they used a protein known as protein kinase R (PKR). If the protein is able to find the long double-stranded RNA in the cell, PKR will trigger the cells to undergo apoptosis, a cell death pathway to destroy the cell. The results of their study showed that small RNAs were able to “trick” the cancer cells to self-destruct.

Pierce concluded that small RNA molecules were advantageous due to the fact that they were useful in the diagnosis and treatment of the disease “one cell at a time.” However, further studies will need to be conducted in order to see if the small RNAs can be useful for the diagnosis in human patients.” Pierce’s approach to finding a way to “program” cancer cell death is beneficial to those diagnosed with cancer due to the fact that these patients would not have to be overwhelmed with the additional side effects that come about from cancer drugs and therapy.

Citation: California Institute of Technology. "Scientists create new process to 'program' cancer cell death." ScienceDaily, 8 Sep. 2010. Web. 28 May 2011.

Epigenetic and Breast Cancer Sub-types

Recent work by Dedeurwaerder et al. has shown that epigenetics really does play a major role in development of breast cancer sub-types. This discovery came through the study of DNA methylation’s level and the associated breast cancer subtype. It was previously known that epigenetic mechanisms such as histone methylation play an important role in development of tumors and that DNA methylation is usually found in regions of the genome that are functionally silenced. We know there are genes called estrogen-receptor on breast tissues and when estrogen binds to them, they stimulate cell proliferation, which could subsequently lead to mutations and cancer development. As a result, estrogen-receptor genes are usually over expressed in majority of breast tumors. Until this study, the details of existing various sub-types of tumors that were as a result of DNA methylation were not yet known. The study was performed on numerous independent breast tissue samples known to be cancerous by assaying for the level of DNA methylation. They found two distinct types of tumors, positive and negative for estrogen receptor, and each with different levels of DNA methylation. Further analysis revealed that the level of DNA methylation was inversely related to the activation of

estrogen-receptor genes and DNA methylation was acting to negatively regulate the expression of these genes, i.e. DNA was highly methylated when the estrogen-receptor genes were not expressed. This revelation could redefine our current understanding of cancer, and perhaps open doors for research on the role of epigenetic on other diseases. Most importantly, this discovery could potentially lead to improved and more efficient cancer diagnosis and treatment based on the sub-type of cancer.

S. Dedeurwaerder et al. Epigenetic Portraits Of Human Breast Cancers. Annals of

Oncology, 2011; 22: Supplement 2

Retrieved May 26, 2011, from

http://annonc.oxfordjournals.org/content/22/suppl_2.toc

New Target for Breast Cancer?

In the UK four out of five women who suffer from hormonal breast cancer are oestrogen positive which means that the receptor for oestrogen is overexpressed. Oestrogen is required for the proliferation and growth of breast cancer. Overexpressed oestrogen receptors are diagnosed in 50-80% of breast tumors cases. Recently researcher in UK found 3 new genes, C6ORF96, C6ORF97, and C6ORF211, located just upstream of the known oestrogen receptor gene ESR1. ESR1 is an important breast cancer biomarker oestrogen receptor. The 3 new genes have been shown to tightly co-expressed with ESR1 but behave separately from it. At the nucleotide level, all three ORFs show some homology with ESR1, indicating that they may have emerged from gene duplication events. This discovery is astonishing because ESR1 has been extensively studied and is located in one of the most heavily studied areas of the genome.

Further analysis revealed that the protein encoded by C6ORF211 was expressed mainly in the cytoplasm. C6ORF211 was shown to drive the growth of tumor. In a proteomic screen the protein has been found to interact with SAP18, a Sin3A-associated cell growth inhibiting protein. This reported interaction was hypothesized as one of the reasons that there was a suppression of proliferation in cultured cells where C6ORF211 was knocked down. Contrarily, a high level of activity of C6ORF97 predicted an improvement of “disease-free survival” in tamoxifen-treated dataset, independently from ESR1. The gene was a good predictor of response to tamoxifen. Less was known about C6ORF96, but it was being researched by the team.

Tamoxifen works by competitively blocking binding of oestrogen to receptors and therefore decreasing the transcriptional activation level of genes required for tumor growth. Tamoxifen is not shown to efficiently affect the activity of the new discovered genes, thus opening up a possible synergistic drug treatment for breast cancer along with the current treatment. Professor Mitch Dowsett, who lead the team at the Breakthrough Breast Cancer Research Centre at the ICR, added:

"This research is exciting because it shows that while the oestrogen receptor is the main driver of hormonal breast cancer, there are others next door to it that also appears to influence breast cancer behavior. We now need to better understand how they work together and how we can utilize them to save lives of women with breast cancer."

Hopefully the discovery of the new genes will help us to develop new drugs can cure breast cancer. The problem with the current treatment is that he tumors develop resistance overtime and may come back after the surgery and spread to another place. Perhaps with better and more advanced technologies, cancer can be treated as a curable disease.

Citation:

Scientist discover three genes link to breast cancer. Thursday, 5th May 2011. Mackenzie, Carla.
<http://www.figo.org/news/scientists-discover-three-genes-linked-breast-cancer-003612>
C6ORF211 Genes Catalyze the Growth of Tumor in Breast. Wednesday, 4th May 2011. Wilkins, Dave.
<http://topnews.us/content/239524-c6orf211-genes-catalyze-growth-tumor-breast>
Three gene discovery may lead to new breast cancer treatments. 4th May 2011. Kraft, Sy.
<http://www.medicalnewstoday.com/articles/224227.php>
Oestrogen receptors and breast cancer. Elledge, Richard M. Osborne, C Kent. University of Texas Health Science Center, San Antonio, TX 78284-7884, USA.

BMJ 314 : 1843 (Published 28 June 1997).
<http://www.bmj.com/content/314/7098/1843.full>
ESR1 is co-expressed with closely adjacent uncharacterized genes spanning a breast cancer susceptibility locus at 6q25.1. Anita K. Dunbier, Helen Anderson, Zara Ghazoui,Elena Lopez-Knowles, Sunil Pancholi, Ricardo Ribas,Suzanne Drury, Kally Sidhu, Alexandra Leary, Lesley-Ann Martin, Mitch Dowsett. May 12th, 2011. London, United Kingdom.

<http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001382>

Autism, Where Did It Come From?

Autism is a developmental disorder that impairs social behavior and communication in children before the age of 3. While the current estimate of a sibling recurrence risk is at 15%, the population of children with an autism spectrum disorder is about 1 per 150. How has autism become so common within these young children? Geneticists have found a couple of important genes called NHE9 and DIA1 as possible disruptions to cause the disorder.

A study done by Morrow et. al, investigated the coding regions of NHE9, a nearby gene encoding a membrane protein that exchanges intracellular H-ions for sodium. It was sequenced to find a loss of function mutation in a nonconsanguineous family. They also found a gene called DIA1 (deleted in autism1), an uncharacterized protein, to be completely removed from chromosome 3q.

Morrow et. al, used DNA microarrays to study various consanguineous families from the Middle East and were able to identify common inherited regions of affected individuals with homozygous segments. These individuals were completely deficient for the genes in the deleted intervals and these regions were predicted to cause the autism spectrum disorder in the family.

These scientists also found similar loss of function mutations causing an epileptic phenotype in mice. These mutations also caused a phenotype with autistic symptoms and epilepsy in the related NHE6 gene. Mice can be tested for autism by monitoring the reduction of social response to other individuals. They can also be startled by an auditory signal in order to measure its response, frozen time, and its force applied to the floor. Combining these findings support dysregulation of NHE9 as a contributing or casual factor in a family with affected individuals.

Overall, this study points out some important clues towards autism susceptibility. Since autism is a neurodevelopmental disorder, the genes mentioned above have expression changes due to stimulation of neuronal activity. As the brain develops after birth, synapses mature as a function of experience-dependent neuronal activity and of the gene-expression that follows. Scientists have been able to establish dysregulation of synaptic development as an idea for autism research. Although more studies are necessary to confirm this idea, the possibility that dysregulation of these genes results in synaptic development disruption is a fascinating hypothesis.

Sutcliffe, James S. Insights into the Pathogenesis of Autism. Science 11 July 2008: 208- 209. [DOI:10.1126/science.1160555]

Anders J, Baxter B, Pi C, Dunn C, Fahimi F, Yamdagni N. Novel Measures of Mouse Social Behavior. December 2004. http://homepages.cae.wisc.edu/~bme402/mouse_stress/reports/Final_Paper.pdf

Gliding Bacteria: Myxococcus xanthus

Did you know that E. coli is not the only bacteria model organism? Myxococcus xanthus has been the subject of recent research. People are interested in their biofilm self-organization and their motility. An interesting trait is that M. xanthus do not have flagella. They move by twitching or gliding. The mechanisms involved in twitching motility have been characterized, but the mechanics behind gliding have been a mystery. One model suggests that gliding is conducted by substrate-bound motors that run along a track inside the cell. Recently, Sun and his colleagues discovered indirect evidence that can support this model.

AglZ is a regulatory factor involved in gliding mobility. Sun’s team observed AglZ fused with yellow florescence protein. AglZ localizes to the leading cell pole and focal adhesion complexes distributed along the cell body. In a moving Myxococcus xanthus cell, the focal adhesion complexes would remain fixed relative to the cell surface, even if the cell moved several microns. However, when observing cells immobilized to a surface, they found focal adhesion complexes moving from one pole to the other. They then observed small beads attached to the surface of immobilized cells and found they moved from the leading pole to the lagging cell pole. The beads colocalize with AglZ in the focal adhesion complexes.(1) This all proves that the traction force is generated at the focal adhesion complexes.

Sun et al. hypothesized that motors were moving on cytoskeletal filaments in the cytoplasm and transmitting force through the cell wall to dynamic adhesion complexes, causing the cell to move forward. After observing the involvement of the AglZ protein, they found that gliding mobility requires a protein gradient, suggesting that the bacterial gliding and swimming may be linked to a common form of molecular motor, a proton channel.(1)

Sun et al. searched the Myxococcus genome for a homolog of bacterial motors that could be involved in a proton channel and identified the aglRQS locus. aglRQS encodes for the AglQ/AglR/AglS protein complex. AglR is homologous to bacterial motors MotA/TolQ/ExbB; AglQ and AglS are homologous to MotB/TolR/ExbD.(2) After further analysis, they concluded that the aglRQS locus indeed encodes a proton-conducting channel essential for gliding motility.

What is the importance of gliding bacteria? By understanding gliding motility in M. xanthus, researchers can investigate similar gliding motor proteins in other bacteria and eukaryotes. Sun et al. discovered AglQ/AglR/AglS as the first bacterial motor able to move in a directed manner between subcellular regions. If aglQ/Aglr/AglS can move around a bacteria cell in a controlled manner, then it is possible that other proteins can too. Søgaard-Andersen suggests that it is possible that motor proteins similar to aglQ/Aglr/AglS may be involved in organizing bacteria cells by moving proteins, DNA, or mRNA to their subecellular addresses.(2) With the discovery of this prokaryotic gliding mechanism, Myxococcus xanthus has great potential in further our understanding of the mechanism and organization of bacterial cells.

Works cited:
1. Sun, Mingzhai and et al. “Motor-driven intracellular transport powers bacterial gliding motility.” Proceedings of the National Academy of Sciences of the United States of America. 108.18 (2011): 7559-7564. UC Davis University Library, Davis, CA. 25 May 2011 < http://www.pnas.org/content/108/18/7559.full>
2. Lotte Søgaard-Andersen “Directional intracellular trafficking in bacteria.” Proceedings of the National Academy of Sciences of the United States of America. 108.18 (3 May 2011): 7283-7284. UC Davis University Library, Davis, CA. 27 May 2011 < http://www.pnas.org/content/108/18/7283.long>.