New Genetic Loci Associated with Type 2 Diabetes Risk

Diabetes mellitus is a chronic condition characterized by high levels of sugar in the blood which affects 2.8% of the world population. Type 2 Diabetes results from insulin resistance which may be combined with reduced insulin secretion (impaired beta cell function) and accounts for 90-95% of the U.S. diabetes population. Insulin is a hormone that causes cells in the liver, muscle, and fat tissue to take up glucose from the blood, so reduced insulin secretion or insulin resistance will result in higher blood glucose levels.

The researchers in this report conducted association studies concentrating on the identification of genetic variants that affect fasting glucose levels in adult non-diabetics of European descent. They ended up identifying nine new SNPs associated with fasting glucose levels and one SNP associated with insulin resistance, as well as confirmed a number of previously-found associations. In addition, among these SNP loci, five were identified as having an association with type 2 diabetes risk.

This study demonstrates that genetic studies of glycemic traits can identify type 2 diabetes risk loci. It is essential that there is a continued identification of these loci, which would allow for individuals to undergo more effective genetic predisposition tests for the condition, so that measured steps may be taken to minimalize chances of contracting type 2 diabetes for those individuals.

Link to Article: http://www.nature.com/ng/journal/v42/n2/abs/ng.520.html

Dupris, Josée et al. “New Genetic Loci Implicated in Fasting Glucose Homeostasis and Their Impact on Type 2 Diabetes Risk”. Nature Genetics 42.2 (2010): 105-116.

Genetics of the Pleb Plebis

“Our biggest fear is a power-failure” Dr. Pui-Yan Kwok of the University of California at San Francisco notes, a fear shared by tropical aquarium enthusiasts everywhere. However, unlike amateur aquarists, Dr. Kwok is working on human genetic research on a massive scale. Using recent advances in genetic technology that allows for rapid analysis of a human genome, researchers at Kaiser Permanente in Oakland and at UCSF are working to analyze over 130,000 samples of DNA in order to uncover the roots of genetic disorders and to work out just how it is that some people live longer than others.

This project dwarfs others of its kind. Most genome wide studies work with samples of under 10,000, and possibly by using some previously published data from smaller studies. Access to over 130,000 samples, simply put, will provide an enormous statistical pool from which to draw information. Several advances in technology and shifts in the political winds have allowed this to be possible. Although the Human Genome project, started in the early nineties, took over a decade to sequence a group of under a dozen genomes, this project is working on analyzing 2,500 samples… in one week. Politics have also come in to play, as advances in technology have aligned with the Obama Administration’s resolve to keep science and research well funded. The team received the $25 million grant that made this large scale operation possible from Obama’s Federal Stimulus package, passed last year.

There are three prongs to this endeavor. The first is the collection of samples. For this, Kaiser’s large pool of patients is being tapped. Almost two million patients were asked about participation in 2007, and a large group assented. This large pool was winnowed down to the 130,000 participants, who received little plastic cups in which to spit by mail. The saliva of the participants contained enough genetic material for a full analysis. Dr Kwok’s lab at UCSF will analyze the genomes in order to compare genomes of people with diseases such as cancer and multiple sclerosis to healthy genomes, hopefully to pinpoint the genetic causes. Another UCSF researcher, Nobel laureate Dr. Elizabeth Blackburn, will analyze the genomes with a different aim. Her lab will be measuring the length of the chromosome’s telomeres. Telomeres are bits of DNA on the tops and bottoms of chromosomes that seem to regulate lifespan.

The DNA samples are stored in specialized cardboard boxes at room temperature while they await analysis. Special robots costing a quarter of a million dollars each take the saliva samples and processes them, storing the data. This is where Dr. Kwok’s fear of a power failure comes from, as each array filled with 96 analyzed DNA samples costs $10,000. Although some scientists, such as Dr. David B. Goldstein of Duke University, think the money would be better spent on more specialized research focusing on total sequencing of a smaller number of genomes rather than a large number being scanned for variations, it is hard to argue that the scale of this operation will not produce useful data. Even if the UCSF researchers are unable to glean anything useful from the research, this large amount of data will be available for future studies. This study is a landmark, as genome analysis has typically relied on smaller numbers of genomes self selected by paying for a service, or by researchers just taking small samples of people. The technology has moved to the point where truly large numbers of people’s information can be processed, and this study of 130,000 is just the beginning. Kaiser is currently planning to sample 400,000 more patients over the coming years. This huge pool of genetic material will hopefully provide science and medicine with powerful insights into the way our bodies are built, and more importantly, ways to fix ailing ones.

Article by Sabin Russel of the new york times.Original article can be viewed at:www.nytimes.com/2010/05/30/science/30sfgenome.html

Hutchison-Gilford Progeria Syndrome: Insight Into Normal Human Aging

Hutchison-Gilford Progeria Syndrome is a disease in which children experience very rapid aging. In all cases these children will experience rapid decay in their vascular, muscular, and skeletal systems until they die at about 15 years old usually from cardiovascular problems (stroke or heart attack). The Massachusetts Medical Society enrolled 15 children into this study ranging from ages 1 to 17 years of age, nearly half of the worlds known patients with this syndrome. The stereotypic phenotype we see from these individuals include sclerosis of the skin, joint contractures, bone abnormalities, alopecia (hair loss), and stunted growth. When studying the cardiovascular system they saw weakening heart function, high blood pressure, and hardening/thickening of the arterial walls. All of these problems are seen in normal human aging and if we can better understand the phenotypic malfunctions in Hutchinson-Gilford Progeria Syndrome then we may gain insight into normal human aging and bring us closer to finding ways to slow normal human aging.

The Medical Society also looked at this disease from a genetic standpoint. If you look at the LMNA gene's 12 exons you get two main splice products. Lamin C is encoded by exons 1 to 9 and a portion of exon 10. Lamin A results from alternative splicing which adds exons 11 & 12 and removes the Lamin C-specific portion of exon 10. It is during this splicing which the disease occurs. If LMNA gene is working properly the nuclear structure is maintained, transcription is regulated, there is proper differentiation of mesenchymal cells types (adipose and skeletal muscle tissues), and correct chromatin organization within the nucleus. In Hutchison-Gilford Progeria Syndrome there is a mutation in the LMNA gene where it encodes for Lamin A. At this particular location we see a change from glycine (GGC) to glycine (GGT). This causes an activation of cryptic splice site which leads to truncated proteins. This does not allow for proper nuclear structure (causes nuclear blebbing), disorganizes chromatin placement, and interrupts transcription. The next step in studying this disease is to see if this same malfunction in the LMNA gene occurs over a longer period of time in unaffected humans and if so, we can take steps to delay the onset of normal human aging.

New England Journal of Medicine, 2008, pgs. 592-604. www.nejm.org

With so much variation, how can we make sense of it all?

The field of Evolutionary Genetics focuses on the interplay between genetic events, speciation, and phenotypic diversity. A noticeable part of genetics that has been seen to vary between species is gene expression. Despite this common trend, little research has been performed to assess the extent to which transcription factor (TF) binding differs among individuals of the same species and closely related species, as well as the overarching connection between TF binding and genetic variability. In order to figure out some of the mystery, Maya Kasowski et al. decided to look at the variation in TF binding among humans.

The researchers decided to use 10 individuals (5 of European ancestry, 2 of eastern Asian ancestry, and 3 of Nigerian ancestry) with extensive genetic data already existing for them, as well as one chimpanzee as a point of comparison because of how closely related they are to humans. Once they picked their people, they used chromatin immunoprecipitation plus sequencing (ChIP-seq: For a quick reminder check this out! http://en.wikipedia.org/wiki/Chromatin_immunoprecipitation ) to figure out the binding sites of two TF, RNA polymerase II (Pol II) and nuclear factor kB (NFkB). This two transcription factors were not picked randomly of course! Pol II catalyzes reactions that make the precursors of mRNA, snRNA, and microRNA while NFkB is a key regulator of immune responses as it acts as the last component that actually binds to the DNA to start transcription. As you can see, these factors are very important, and what’s more is that their different binding regions have links to many high interest diseases. For instance, type I diabetes, chronic lymphatic leukemia, and schizophrenia relate to Pol II genes while asthma, Crohn’s disease, and rheumatoid arthritis relate to NFkB.

Overall, the results they found were that differences of 7.5% and 25% exist in TF binding for NfkB and PolII respectively between the individuals they studied, but the estimated value for sequence variation in coding sequences is only 0.025% between humans. Basically, what they found was that there was a very strong role in binding variation in human diversity. When I first read the article, 7.5% and 25% did not seem like large enough numbers, but compared to 0.025% this is a very significant difference that deserves further research. An interesting finding of theirs is that these differences were more likely to be found in variable regions of the genome, such as those involved in immune response. This makes sense because the individuals that had more variability in their immune responses would survive preferentially due to their increased ability to adapt to novel diseases or viruses. Further research after this study could expand upon their studies. How can they apply their findings to human medicine once they recognized the disease loci? Will they now be able to even more accurately explain speciation events and phenotypic diversity? I don’t know what will come of the further research, but the endless possibilities are sure to be central to evolutionary genetic research for years.

Kasowski, M. et al., 2001, Variation in Transcription Factor Binding Among Humans, Science, v. 328, p. 232.

Reconstructing a Mammoth Hemoglobin

The reconstruction of a Mammoth just might be possible! Well not quite yet, but researchers are getting closer and closer. A team led by Kevin L. Campbell of the University of Manitoba in Canada, has reconstructed the Mammoth’s hemoglobin. People usually associate these furry creatures with the frozen arctic; however, they actually originated in the tropics about seven million years ago. Their split from the elephants is what led them to adaptations in the cold northern latitudes. The split occurred in physical appearance such as smaller ears, a thick furry coat, and in protein structure such as hemoglobin.

Hemoglobin is the protein that is responsible for the transport of oxygen from the lungs to the rest of the body. It is an assembly of four globular protein subunits which are made of globin chains and these are tightly associated with a heme (iron) group. In humans, most of our blood contains two alpha chains and two beta chains; however, elephant hemoglobin is slightly different. It is composed of 2 alpha globins chains and 2 fused delta-beta chains. It was assumed that Mammoths also had the same structure of hemoglobin; therefore, with that knowledge Dr. Campbell was able to construct tools necessary to fish out these chains from a 43,000 year old, well preserved mammoth. They discovered that the alpha chains differed from elephants in one of its amino acid units and the beta-delta chain differed in three units. This was all reported to Nature Genetics, because with this type of information, they could potentially reconstruct a mammoth hemoglobin.

The next step for Dr. Campbell and his team was to figure out a way to synthesize copies of the mammoth’s two globin genes. Dr. Campbell came up with a technique to just alter the DNA units of an elephant’s globin genes one by one at the four different sites until it matched that of the mammoth’s. This globin gene was then inserted into bacteria which was then synthesized into the mammoth globin chains. After inserting the required iron atoms, the globin chains were assembled into working hemoglobin molecules. This new development led Dr. Campbell to state, “It’s the same as if I went back 43,000 years in a time machine and took blood from a mammoth!”

This was a significant discovery in proving adaptive mutations for survival. As arteries carry blood down to the feet, they warm up the blood traveling up through the veins. Therefore, with this heat transfer, the blood at the toes are cold which prevents much heat loss. However, oxygen release from the hemoglobin becomes much less efficient at lower temperatures. With the construction discovery of the mammoth’s hemoglobin, scientists were able to determine how such an arctic mammal was capable of survival. The way the mammoth’s hemoglobin had evolved, it allowed for oxygen to be released from hemoglobin much more readily at lower temperatures.

Two years ago, scientists at Penn State University sequenced a large portion of the mammoth genome from a clump of well preserved hair. Now, with this completed reconstruction of their hemoglobin, scientists are getting closer to reconstructing the whole animal. Dr. Campbell states his optimism on the possibility; however, he also says “I’m 42 years old, but I doubt I’ll ever see a living mammoth.” We still have years of research left, but every step is one step closer!

Kevin L Campbell et. Al
Nature Genetics Volume: 42, Pages: 536–540 Year published: (2010)
DOI: doi:10.1038/ng.574 Received 18 December 2009 Accepted 31 March 2010
Published online 02 May 201

Link to article: http://www.nature.com/ng/journal/v42/n6/abs/ng.574.html#/

The Search for the Origin of Our Favorite Canine Companion

The search for the origin of the domesticated dog has been a long process and full of controversy. We all have heard how dogs were domesticated from wolves, but knowing when and where is a bit of a mystery. “New Finding Puts Origins of Dogs in Middle East” by Nicholas Wade reports on a new study that has yet another theory on the origin of dog domestication- the Middle East.
Bridgett M. vonHoldt and Robert K. Wayne of UCLA led a team that analyzed a large collection of wolf and dog DNA from around the world. Using two dog genomes previously sequenced (a poodle and a boxer) they developed a dog SNP chip that was used to scan for variable sites in the DNA of a variety of dogs and wolves and cluster them into groups of who is most related to who. Not only did this allow them to place the origin of the domesticated dog in the Middle East, but also showed that dogs with common functions (such as herding dogs and scent hounds) are closely related- showing that these functions are not an example of convergent evolution but that breeds with a common function are closely related.
This team concluded that dogs were domesticated in the Middle East, and later spread to East Asia (where previous studies have put the origin of domesticated dogs). In Asia, some of the dogs bred with local wolves, part of the reason the genetic evidence is so convoluted. The team also used their SNP chips to scan for areas that showed signatures of selection. There is evidence supporting that the dogs lovable personality and their unique ability to “read” human expression were both selected (whether naturally or artificially) in the dog domestication process.
All theories on the origin of a species must be checked with archeological evidence, especially since most DNA samples taken are from modern dogs and wolves and is only a reflection of what was. A Middle Eastern origin fits the archeological evidence better than the other theories presented. This study puts the origin of a domesticated species, dogs, at the same place of domestication of many other plants and animals. According to this study, dogs were domesticated 15,000 years ago- a time when hunter gathers were converting to more stationary societies. Dogs may not only be our best friends, but what allowed us to settle and grow into what we are today.

P.S: Check out the family tree from this article: http://www.nytimes.com/2010/03/18/science/18dogs.html?scp=6&sq=Dog+DNA&st=nyt

P.S.S. If you search for the study this paper was based on, you can get an even better tree!

Reference:
Wade, Nicholas. "New Finding Puts Origins of Dogs in Middle East." New York Times 17 March 2010: Web. 16 May 2010.

Original Article:
vonHoldt, Bridgett M., John P. Pollinger, Kirk E. Lohmueller, Eunjung Han , and others. "Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication." NATURE 464.8 April 2010: 898-903. Web. 28 April 2010.

CpG methylation influences mutation rates

DNA Sequence Itself Influences Mutation Rate, New Research Indicates

Natural selection, accomplished by mutations and heritability, is the driving force of evolution. Neutral selection defines any region of DNA which is changing at a random rate, and not under any selection preferences. Thus, scientists are usually more interested in those regions which do experience selection, and often overlook the neutral sequences. But what makes these regions neutral? Not all regions under selection are in genes, or affect phenotypic expression; thus why is there neutrality or selection at all?

This paper recognizes that there is a need to look at the neutral mutation rate, since this rate is important in keeping genomic stability. A lot of errors/mutations are caught in the proofreading processes of transcription and replication. Seemingly random, they seem inconsequential. But according to Walser and Furano, mutation rates in mammals differ at methylated cytosines, with 10-50 times more mutations at these sites.

Methylation of cytosine (CpG) in endogenous DNA sequences is critical for many organisms. Euchromatin activation is driven by methylation, and in plants, methylation is indicative of host genome recognition against foreign pathogen DNA. The high CpG rate results from the spontaneous deamination of methyl-C to T and incomplete restoration of the ensuing T:G mismatches to C:Gs (Walser et al. 2010). The concentration and ratio of CpG seems to positively correlate with the rate of mutation. However chemically modified CpG are prone to mutation as well, and the age of the mutation can be assessed.

Interestingly enough, in older inactive retrotransposons latent within the primate genome, the overall mutation rates have dropped and are now neutrally evolving. However this is not due to chromosomal location (by the centromere, etc.), but due to the inherent DNA sequence itself. The article concludes that these methylated areas promote mutations at the methylated sites, as well as the surrounding DNA. Future studies of methylated mutation rates will probably still continue to focus on genomic stability and repair.

Science Daily article: http://www.sciencedaily.com/releases/2010/05/100524092348.htm

Walser J, Furano A. The mutational spectrum of non-CpG DNA varies with CpG content. Genome Research, 2010; DOI: 10.1101/gr.103283.109