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>.

Using Genetically Engineered Mosquitoes to Battle Malaria

Malaria is a well-known disease that plagues much of the world. Over the years, various techniques including the use of mosquito nets and pesticides have been implemented in an effort to combat the disease.

One scheme that has been thought up to prevent the spread of malaria is to make mosquitoes themselves resistant to the malaria pathogen as a more indirect way to prevent the transmission of the pathogen from mosquito to human. Several labs across the world including some in the United States and Europe have been testing this idea by working with transgenic mosquitoes that have been genetically manipulated to be immune to malaria.

While transgenic mosquitoes are a step in the right direction, there have been road bumps in their usage in the fight against malaria. It has been found that lab-created malaria-resistant mosquitoes are not as “fit” as their wild-type relatives and therefore are outcompeted in the natural world. This is in addition to the fact that the wild type mosquito population is so dense that it would be very difficult for a lab-synthesized gene to fully assimilate into the general mosquito population.

A team of scientists led by Bruce Hay and Chun-Hong Chen at the California Institute of Technology has been working to address this issue through the use of the model organism Drosophila melanogaster. The team devised a technique in which they produced a “selfish gene” named Medea that silences a gene needed for normal embryonic development. Female mosquitoes that carry Medea express a toxin that passes on to their oocytes. Embryos that do not inherit Medea die from the toxin. Embryos that inherit Medea live due to the expression of an antidote during embryogenesis that counteracts the toxin.

These scientists are working to transfer this work to mosquitoes. The idea is to link a Medea-type gene to a malaria resistant gene as an effective way to incorporate a malaria resistant gene into the general mosquito population.

Although this research has been groundbreaking, there remains controversy surrounding the idea of introducing a genetically modified organism into the ecosystem as well as whether this is a cost-effective solution to eradicating malaria.

Levy, Sharon. "Mosquito Modifications: New Approaches to Controlling Malaria."BioScience. Biosciencemag.org, Nov. 2007. Web. 27 May 2011.

Lichtman, Flora. "Killing Disease with Bugs." Sciencefriday.com. 30 Mar. 2007. Web. 27 May 2011.

Links:

http://www.sciencefriday.com/newsbriefs/read/125

http://www.its.caltech.edu/~haylab/publication/comments2007/BioScience.pdf

De Novo Mutations and Autism

Rates of autism have risen to extraordinary levels over the last several decades. Whereas 50 years ago an autism diagnosis was made for 1 in 360 children, today, autism spectrum disorder affects 1 in every 66 boys. Some of this increase can be attributed to changes in the timing and nature of diagnoses, but even accounting for these factors the rates have risen dramatically and continue to rise. Autism is a difficult disease to study because it is not likely to have a single functional cause. The disease onset is in children and it affects a core human characteristic: it impairs social communication. In trying to identify causal factors that lead to autism, researchers have been focused on environmental agents that interact with heritable traits as possible causes for the disease. The results of these studies have not yet shown a single pathway or mechanism. Researchers are also trying to define distinct mechanisms for different sub-groups with the goal of accounting for the heterogeneous aspects of the disease.

A new study used modern genetic techniques to examine unique properties of autistic children’s DNA that might be associated with the disorder. The authors searched for point mutations that occur spontaneously or what are called “de novo mutations.” These are mutations in the child that are not present in the parents. Researchers at the University of Washington selectively sequenced the exomes (protein coding regions) of 20 families with autistic children by what they called trio-based exome sequencing (TBES). In contrast to relatively coarse micro-array studies, TBES can look with high resolution at individual point mutations in patients.

The study reports that the de novo mutation rate in autistic children does not differ from the rate in controls. However, the de novo mutations in the autistic children were located in crucial places in the genome, and that such de novo mutations do not occur at similar places in controls. The study estimates that the new technique may identify up to 40-50 percent of the genetic causes of the disease.

In several children they found mutations they believed were causative to their diagnosis. The four genes implicated were FOXP1, GRIN2B, SCN1A, and LAMC3. LAMC3 was not previously implicated in autism, but the gene does have some association with the limbic system and frontal cortex; these are brain regions that researchers believe are abnormal in some autistic brains. Looking at the specific mutations that arise spontaneously in autism is an innovative approach to studying autism. As whole genome sequencing becomes more accessible and less expensive, more data can be collected to find all of the genes implicated in autism.

O’Roak et al, “Exome Sequencing In Sporadic Autism Spectrum Disorders Identifies Severe de Novo Mutations”. Nature Genetics. Online May 15, 2011.

Gray L. “Sporadic Mutations Idenitified in Children with Autsim Spectrum Disorders.” University of Washington Press Release. May 16th, 2011.

New Cystic Fibrosis Gene Modifier Loci Discovered

Cystic Fibrosis (CF) is one of the most common hereditary diseases afflicting today's global population. CF causes body-wide defects including exocrine pancreatic inefficiency, male infertility, poor digestion, and excess mucus buildup in sinuses. However, 90% of deaths caused by CF are due to the excess mucosal blockages in pulmonary air channels. Past research showed that the recessive allele mutation of the cystic fibrosis transmembrane conductance regulator protein (CFTR) is the sole culprit of causing CF when inherited from a carrier at the parental generation. Researchers concluded at the time that the recessive allele inheritance of CFTR was the sole reason of acquiring CF, yet the severity of the symptoms a patient suffers with CF can vary. This led researchers to believe that the diverse severity of CF symptoms observed from different patients attributed to secondary factors besides just the CFTR recessive mutant.

This month, researchers from the University of North Carolina, Chapel Hill have discovered two loci that could be the so called secondary factors. Using an extensive genome-wide association study (GWAS), researchers took samples from three research study groups, totaling over 3,000 patients suffering from CF, and analyzed them by their severity of their phenotype symptoms. After narrowing down to using subjects with the common homozygous CFTR variant, p.Phe508del, and eliminating any outlier cases, the study found that chromosome loci 11p13 and 20q13 heavily influenced the severity of CF symptoms expressed in various patients from the study groups. Furthermore, both genes were found to be inhibitory factors involved in apoptotic suppression pathways. Their roles as inhibitors could explain the decrease of neutrophilic-triggering apoptosis, in which inflamed neutrophils within pulmonary air channels would fail to be eradicated, and thus impair pulmonary function.

This study was not the first attempt from CF researchers in finding genetic modifiers. While three previous small-scale association studies on other loci modifiers. There modifiers could not be replicated in a genome-wide scale by both this study and a previous one conducted in 2009. Nevertheless, the discovery of two possible modifiers from this GWAS study has shed new light and potential opportunities in creating better or possibly more individualized therapies to CF sufferers. For instance, a new therapy treatment could be created to suppress the activation of these modifiers as a method to reduce the severity of the symptoms CF patients exhibit or bring a new perspective road map for scientists to now tackle the disease by also integrating these modifiers in the equation. Therefore, this discovery of CF-modifying genes could completely change the methods we could use against this devastating disease.

Witt, Heiko. Nature Genetics 43, 508–509 (2011).

Wright, Fred A. et al. Nature Genetics 43, 539–549 (2011).

Epigenetics during Pregnancy Can Influence Obesity

Obesity has become prevalent all across the world, yet what is to blame for the condition, genetics or the environment? Recently, a third factor has been linked to obesity: epigenetics. Studies have found that the connection between skinny mothers and obese children is partly due to epigenetics in the womb that causes the child to have an increase in appetite. The mothers must have felt a little relieved after finding this out!

Rat studies at the University of Auckland in New Zealand showed that undernourished rats during pregnancy produced overweight offspring. In a later study in 2005 they were able to show that the offspring turned out normal when the methyl tags were removed.

As for humans, two studies have been performed in the United Kingdom. The studies analyzed the diets of pregnant women, extracted the DNA from the child’s umbilical cord, then measured the body fat of the child to look for specific epigenetic marks correlated with obesity. The first test analyzed children at nine and the second test analyzed children at six. Both of the tests gave similar results, showing that epigenetics can be seen early in a child’s development. Seventy-eight genes were analyzed for epigenetic marks and only the methylation at RXRα gene was correlated with obesity. The genetic changes in RXRα had no correlation with fat levels, which indicates that epigenetics, not genetics, explains the differences in RXRα expression. The researchers also found a link between a low carbohydrate diet early in pregnancy and methylation levels of RXRα. Methylation of RXRα is thought to contribute 25% of the differences in fat levels. The statistics of the studies show that “as the percentage of the RXRα genes that were methylated went from 40% to 80%, the children’s percentage of body fat went up from 17% to 21%”. Obesity is classified as being greater than 30% BMI, so 4% can make a difference in a person’s preset conditions for obesity.

The RXRα gene is called Retinoid X Receptor-α and codes for a protein involved in the fat cell and fat metabolism pathway. Researchers think that the reason for RXRα gene methylation in mothers with a low carb diet is that somehow the mom programs the child to live in a world with scarce food resources by increasing the child’s appetite and food storage capacities. Since many of us do not live in a food-scarce world, however, these children overeat and become obese compared to children with less RXRα methylation. Fortunately, there are preventative measures in treating RXRα methylation. Mothers can add carbs to their diet to prevent methylation of the RXRα gene, and treatments for altering epigenetic tags are available. One type of treatment would be to administer micronutrients to the child. While these results have not yet been proven to be considered true, the take home message here is that pregnant women should not try to diet but should eat a healthy amount of carbs just to be safe.

Finkel, Elizabeth. "Why Skinny Moms Sometimes Produce Fat Children - ScienceNOW." Science/AAAS | News - Up to the minute news and features from Science.. Science Now, 22 Apr. 2011. Web. 27 May 2011. .

"Obesity and Overweight for Professionals: Defining | DNPAO | CDC." Centers for Disease Control and Prevention. Centers of Disease Control and Prevention, 10 June 2010. Web. 27 May 2011. .

Obesity and Genetics!

Obesity is one of the biggest concerns of the American population. In 2007-2008, 34% of adults over 20 years old had been diagnosed with obesity. One of the mysteries of obesity is locating the genes responsible for it and understanding its inheritance. We all know that obesity is mostly caused by the environment, and we know there is a genetic component involved, but we do not clearly understand it. A paper was published in 2010 that discussed rare variants discovered in early onset obese patients. Since researchers knew obesity was heritable, they wanted to investigate the copy number variation to obesity in Caucasian patients who were diagnosed with early onset obesity. They first found that early onset obesity is associated with rare number variants causing rare developmental disease, such as autism and mental retardation. They discovered a large chromosomal deletion about 500 kilobases on chromosome 16p11.2, and these deletions were occurring very rarely at <1%. The 16p11.2 region of the chromosome is involved in many genes, but there is a gene that has been involved in leptin and insulin signaling called SH2B1. They found a delayed and exaggerated insulin secretion in patients who have a SH2B1 deletion. In Gene-wide association studies, they identified common single nucleotide polymorphisms (SNPs) near the SH2B1 locus which were associated with Body Mass Index (BMI). After gathering all the data, researchers proposed a mechanism to explain why the deletions are a more frequent source of loss of function at SH2B1 loci; they believe this could occur through a segmental duplication of 16p11.2 by non-allelic homologous recombination. This paper sheds light on a topic that has been very difficult to understand for a very long time.

Bochukova et al. “Large, rare chromosomal deletions associated with severe early-onset obesity.” Nature 463, 666-670.

Centers for Disease Control and Prevention. http://www.cdc.gov/nchs/fastats/overwt.htm