Researchers Successfully Used The 454 Sequencing System For Sensitive Detection Of HIV Tropism

454 Life Sciences, a Roche company, announced today that a team of researchers from the BC Centre of Excellence in HIV/AIDS and the University of British Columbia, Canada have used the Genome Sequencer FLX system to monitor low frequency HIV variants from human samples in a recent study. The preliminarily results of the study were presented by Dr. Richard Harrigan, the Centre's Director of Research Labs at the HIV DART 2008 conference in Puerto Rico in a presentation entitled "Quantification of HIV Tropism by Deep Sequencing Shows a Broad Distribution of X4 Variants in Clinical Samples Associated with Virological Outcome."

The background of this research study is that correct determination of "HIV tropism" is critical for the administration of a new class of drugs called CCR5 antagonists used for the treatment of AIDS. HIV tropism refers to the type of cell the HIV virus infects, as determined by so-called co-receptors that the virus employs for entry into the cell. Determining the co-receptor that a HIV strain uses, either CCR5, CXCR4 or a combination of both, is a critical component of monitoring and treating HIV.

The preliminary results of the study found that conventional genotyping methods lack sufficient sensitivity for detection of the CXCR4 variant which is a contraindication for adminstering CCR5 antagonists. By using deep sequencing with the Genome Sequencer FLX system, the researchers were able to quantify low-frequency variants associated with poor response to CCR5 antagonists and accurately determine HIV tropism across all individuals' samples.

"The sensitivity of the Genome Sequencer FLX platform allowed us to monitor HIV sequence variation from 48 or 96 individuals´ samples simultaneously, and still have far greater ability to spot minority variants than using standard approaches," explained Dr. Richard Harrigan. "The result was the ability to detect HIV tropism accurately in all samples from this study. Standard methods were missing up to 35 percent of the answers. This has important implications for therapy monitoring. The fact that the Genome Sequencer FLX system gives a quantitative measure of sequence variance within a sample is a bonus".

"The sequencing technology of 454 Life Sciences is a critical tool for research on viral diseases and their possible treatment. The system shows potential for sensitive profiling of viral populations for enhanced monitoring and for the development of more personalized therapies," said Christopher McLeod, President and CEO of 454 Life Sciences. "We believe that, in the near future, the 454 Sequencing system will transform the way HIV is monitored and treated."

454 Life Sciences, a center of excellence of Roche Applied Science, develops and commercializes the innovative 454 Sequencing system for ultra-high-throughput DNA sequencing. Specific applications include de novo sequencing and re-sequencing of genomes, metagenomics, RNA analysis, and targeted sequencing of DNA regions of interest. The hallmarks of the 454 Sequencing system are its simple, unbiased sample preparation and long, highly accurate sequence reads, including paired-end reads. The technology of the 454 Sequencing system has enabled hundreds of peer-reviewed studies in diverse research fields, such as cancer and infectious disease research, drug discovery, marine biology, anthropology, paleontology and many more.

About Roche

Headquartered in Basel, Switzerland, Roche is one of the world's leading research-focused healthcare groups in the fields of pharmaceuticals and diagnostics. As the world's biggest biotech company and an innovator of products and services for the early detection, prevention, diagnosis and treatment of diseases, the Group contributes on a broad range of fronts to improving people's health and quality of life. Roche is the world leader in in-vitro diagnostics and drugs for cancer and transplantation, a market leader in virology and active in other major therapeutic areas such as autoimmune diseases, inflammation, metabolism and central nervous system. In 2006 sales by the Pharmaceuticals Division totaled 33.3 billion Swiss francs, and the Diagnostics Division posted sales of 8.7 billion Swiss francs. Roche employs roughly 75,000 worldwide and has R&D agreements and strategic alliances with numerous partners, including majority ownership interests in Genentech and Chugai. Roche's Diagnostics Division offers a uniquely broad product portfolio and supplies a wide array of innovative testing products and services to researchers, physicians, patients, hospitals and laboratories world-wide.

For further information, please visit www.roche.com

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How Much Do Genetic Covariances Alter The Rate Of Adaptation?

Organisms are composed of suites of correlated traits. If these traits have a shared genetic basis, these relationships can influence their evolution.

While this possibility is well known, it remains unclear how commonly genetic relationships between traits affects their evolution in nature. Here we introduce a new metric for quantifying whether the relationships between traits affects the rate of adaptation, and evaluate it using data from the literature.

We find little evidence for the widespread intuition that genetic correlations restrict the rate of adaptation. Understanding when and whether the correlations among traits will affect their evolution remains an ongoing challenge.

Proceedings of the Royal Society B: Biological Sciences

Proceedings B is the Royal Society's flagship biological research journal, dedicated to the rapid publication and broad dissemination of high-quality research papers, reviews and comment and reply papers. The scope of journal is diverse and is especially strong in organismal biology.

http://www.publishing.royalsociety.org/proceedingsb

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SNPs Of ABC Transporter Genes Linked To Lung Cancer Risk

Individuals with particular variants of certain genes involved in metabolizing the most potent carcinogen found in cigarette smoke have an increased risk of developing lung cancer. That is the conclusion of a new study published in the February 1, 2009 issue of CANCER, a peer-reviewed journal of the American Cancer Society. The study's results may help shed light on how lung cancer develops and could have important implications for preventing smoking-related cancers.

Tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a component of cigarette smoke that has been shown to cause lung cancer in rodents. Certain enzymes act to protect the body from this type of chemical by turning it into nontoxic forms or by transporting it from cells. For example, ATP-binding cassette transporters encoded by genes known as ABCB1 and ABCC1 are involved in eliminating carcinogens from the lungs, protecting them against inhaled toxins.

Researchers suspect that individuals with alterations in these genes might have an increased susceptibility to develop lung cancer. Recently, a team of scientists led by Dr. Daru Lu and Dr. Haijian Wang of the Fudan University in Shanghai identified common variants at the beginning and end of the ABC1 and ABCC1 genes. They then analyzed these variants in 500 patients with lung cancer and 517 cancer-free controls in a Chinese population.

The investigators found that certain variants were found much more often in individuals with lung cancer than in cancer-free controls. Patients who had the variant allele of either ABCB1 rs3842 or ABCC1 rs212090 had a significantly increased risk of developing lung cancer. The former variant was particularly associated with an increased risk of cancer in women and in individuals under age 60 years. It also was linked to a major type of lung cancer called adenocarcinoma.

Dr. Wang and his colleagues previously identified other common genetic variants associated with lung cancer risk in NNK disposition pathways, such as CYP2A13, the most active P450 for the phase metabolic activation of NNK (Cancer Res 2003; 63: 8057) and the receptor (ADRB2) in its non-genotoxic pathway (Cancer Lett 2006; 240: 297). This study shed new insight into the toxicogenomics of NNK and further supported the hypothesis proclaiming genetic components in the metabolism and disposition machines of NNK as modifiers of risk of lung cancer.

"Because tobacco smoking is the leading preventable cause of cancer and the cancer-prone genotypes of these genetic components are relatively prevalent in the human population, our findings have important implications for the prevention of tobacco smoking-related cancers," the authors write.

Article: "Genetic susceptibility of lung cancer associated with common variants in the 3' untranslated regions of the adenosine triphosphate-binding cassette B1 (ABCB1) and ABCC1 candidate transporter genes for carcinogen export." Haijan Wang, Guangfu Jin, Haifeng Wang, Gaifen Liu, Ji Qian, Li Jin, Qingyi Wei, Hongbing Shen, Wei Huang, and Daru Lu. CANCER; Published Online: December 22, 2008 (DOI: 10.1002/cncr.24042); Print Issue Date: February 1, 2009.

Source:
David Sampson http://www.cancer.org/

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Genes Determining Asymmetry Probably Arose In The First Bilaterally Symmetric Organisms

Biologists have tracked down genes that control the handedness of snail shells, and they turn out to be similar to the genes used by humans to set up the left and right sides of the body.

The finding, reported online in advance of publication in Nature by University of California, Berkeley, researchers, indicates that the same genes have been responsible for establishing the left-right asymmetry of animals for 500-650 million years, originating in the last common ancestor of all animals with bilateral body organization, creatures that include everything from worms to humans.

"Previous studies indicated that the methods for breaking left-right symmetry in animals seem to differ widely, so there was nothing suggesting that the common ancestor of humans, snails and other bilateral organisms had a common strategy for left-right asymmetry," said Nipam H. Patel, UC Berkeley professor of integrative biology and of molecular and cell biology, and an investigator of the Howard Hughes Medical Institute.

"Indeed, scientists thought that one of the genes that is critical for setting up left-right asymmetry in vertebrates was only present in vertebrates and related groups and not in any other animals," said UC Berkeley post-doctoral fellow Cristina Grande. "But we found that gene in snails, which has a lot of evolutionary implications. This cellular pathway was present already in the ancestors of most animals."

The finding, the researchers say, could help to track down the ultimate cause of symmetry-breaking in snails and other organisms, and the cascade of gene activation that leads to complex shapes, such as coiled shells.

Despite humans' superficial symmetry - our left and right sides appear to be mirror images - we are anything but symmetric. Most people's hearts are towards the left side of the body, which means the left lung is slightly smaller to make room for the heart, and our intestines are arranged in an asymmetric coil. This asymmetry is unrelated to being left- or right-handed, a preference determined in the brain.

While a small percentage of people have their insides flipped, their overall internal arrangement is a mirror image of the norm. Anyone with a random arrangement of internal organs would be dead, Patel said, because his or her organs wouldn't fit together properly.

Other vertebrates are the same. In fact, scientists have identified a gene called "nodal" that - in all vertebrates checked to date - is expressed on the left side of the body and necessary to set up left-right asymmetry. If nodal doesn't work or is knocked out, internal organs are jumbled and the organism dies.

"In vertebrates, a set of genes tells the body it has to form a heart toward one side, and nodal is one of those genes," said Grande, who recently took a position at the Centro de Biología Molecular "Severo Ochoa" in Madrid, Spain.

"There are a lot of asymmetric molecules in the body, that is, molecules that are active on only one side of the body, but nodal is always expressed on the left side in all vertebrates, which is evidence of a conserved pathway," Patel said.

Genes similar to nodal have been found throughout the so-called deuterostomes, one of the three subgroups of bilateral animals that includes not only vertebrates, but also sea urchins and sea squirts.

But the most common lab animals, fruit flies and nematodes, apparently do not have a gene like nodal, despite their asymmetry. As a result, biologists have assumed that fruit flies and all other non-deuterostomes - snails included - use some other mechanism to establish right and left. Fruit flies and nematodes are in the clade Ecdysozoa, while snails and worms are members of the clade Lophotrochozoa.

Grande approached Patel four years ago to collaborate in a test of this assumption in snails, which have an obvious and easy-to-check handedness: Their shell either coils right, like a standard screw, or left. Patel, a biologist who focuses on the genetics and evolution of crustacean and insect development, such as the formation of segments and appendages in shrimps and crabs, invited Grande to join his lab, even though he had never before worked with snails.

Snail handedness becomes obvious very early in the embryo, Patel said. When the four-cell embryo divides to become eight cells, the new cells blossom from their predecessors in a clockwise spiral, in which case the snail ultimately forms a right-handed, or dextral, shell; or a counter-clockwise spiral, creating a left-handed, or sinistral, shell. Biologists had earlier shown that this decision is made by the mother snail, which dumps many proteins and RNA molecules into the egg to jump-start embryonic development and, in the process, imprints her offspring with specific characteristics.

"No one knows what that maternal gene is, and you can't track it down using the standard approach of looking for genetic markers because there are not yet enough markers in snails, so we looked for any molecular entry into the cause of asymmetry," Patel said.

That proved to be the genome of the marine limpet Lottia gigantea, a right-handed snail whose genome was sequenced recently by the Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, Calif. Grande looked for genes in Lottia similar to nodal, and found one, as well as a gene analogous to the gene, Pitx, which is activated by nodal and also involved in setting up left-right asymmetry in vertebrates.

She used this information to look for and find similar genes in the left-handed snail Biomphalaria glabrata, the fresh-water host of the parasite that causes schistosomiasis. Experimental tests showed that nodal and Pitx were active or expressed on the right side of embryos in the right-handed snail Lottia, and on the left side in the left-handed snail Biomphalaria.

A key test of the critical nature of nodal involved treating the snails with a chemical known to inhibit the activity of nodal. While most treated snails died, some lost the asymmetric expression of Pitx and, most strikingly, developed a straight shell, Patel said.

Grande has since found analogs of nodal in the genome of the marine worm Capitella, which was sequenced by JGI, suggesting that nodal is active throughout the Lophotrochozoa.

"Everybody thought using nodal and Pitx for left-right asymmetry was an invention of this one group, the deuterostomes," Grande said. "The fact that we find them setting up asymmetry in snails and worms means that is not true; the ancestor of all bilaterians already used these genes to set up left-right asymmetry."

Because the ancestral snail was right-handed and thus, presumably, expressed nodal and Pitx on the right side of the body - similar to sea urchins, an early offshoot of the deuterostome branch leading to humans - the authors propose that the common ancestor of all bilateral animals had left-right asymmetry controlled by nodal and Pitx expressed on the right side of the body.

The discovery also could help Grande and Patel track down the maternal factors that ultimately determine handedness in snails.

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Newly Identified Gene Powerful Predictor Of Colon Cancer Metastasis - Low Gene Activity - Higher Survival Rate

Cancer Researchers at the Max Delbruck Center for Molecular Medicine (MDC) Berlin-Buch and the Charite - Universitats Medizin Berlin (Germany) have identified a gene which enables them to predict for the first time with high probability if colon cancer is going to metastasize. Assistant Professor Dr. Ulrike Stein, Professor Peter M. Schlag, and Professor Walter Birchmeier were able to demonstrate that the gene MACC1 (Metastasis-Associated in Colon Cancer 1) not only promotes tumor growth but also the development of metastasis.When MACC1 gene activity is low, the life expectancy of patients with colon cancer is longer in comparison to patients with high MACC1 levels. (Nature Medicine, doi: 10.1038/nm.1889)*.

According to the National Institutes of Health in Bethesda, Maryland, USA, more than 108,000 people developed colon cancer in the US in 2008. Despite surgery, chemo- and radiotherapy, only 50 percent of patients can be cured because 20 percent of the patients have already developed metastasis by the time their colon cancer is diagnosed. In addition, one-third of patients whose treatment of the original colon cancer was successful will, nevertheless, go on to develop metastasis.

The MDC and Charité researchers are convinced that the identification of the MACC1 gene will aid medical doctors in identifying those patients as early as possible who are at high risk of developing life-threatening metastasis in the liver and the lungs. As a result, more intensive treatment and follow-up care could be offered to high risk patients.

MACC1 turns on a signaling pathway which is important for tumor growth and the formation of metastasis. Researchers call this pathway HGF/Met signaling pathway. Once MACC1 has activated this HGF/Met signaling pathway, tumor cells proliferate much faster, get rid of their ties within the cellular tissue, and eventually settle down as metastasis at various sights throughout the body far from the original tumor.

High MACC1 Levels - Higher Risk for Metastasis

The researchers discovered the MACC1 gene by comparing tissue from healthy persons with tissue from 103 patients with colon cancer between 20 to 88 years of age. Sixty (60) cancer patients had no metastasis at the time they underwent surgery.

Of these 60 patients, 37 had no metastasis five years after surgery and treatment. These patients were shown to have had low levels of MACC1 when first diagnosed with colon cancer. In contrast, 23 patients had developed metastasis in the course of five years after surgery. Researchers detected high levels of MACC1 in their colon cancer tissue. Thus, patients with high MACC1 levels have a much higher risk for developing metastasis than patients with a MACC1 gene that is not very active.

The researchers are convinced that MACC1 will enable physicians to decide if a patient needs a more intense therapy or if a less aggressive treatment is sufficient. "The expression analysis of MACC1 in the original tumor tissue will probably contribute to individualize and optimize colon cancer therapy", they assume.

Now the MDC and Charite researchers and their colleagues want to find out if the MACC1 gene also allows for a more precise prediction about the outcome of lung cancer, breast cancer, and stomach cancer.

MACC1, a newly identified key regulator of HGF-Met signaling, predicts colon cancer metastasis

Ulrike Stein1,2, Wolfgang Walther1,2, Franziska Alt1,2, Holger Schwabe2, Janice Smith1, Iduna Fichtner1, Walter Birchmeier1, Peter M. Schlag 1,2

1Max Delbrück Center for Molecular Medicine, Robert RössleStrasse 10, 13125 Berlin, Germany 2Department of Surgery and Surgical Oncology, Robert Rössle Cancer Hospital Charité University Medicine Berlin, Lindenberger Weg 80, 13125 Berlin, Germany

Foundation under Public Law
Directors:
Prof. Walter Birchmeier, PhD., Cornelia Lanz

Member of the Hermann von Helmholtz Association of National Research Centres

Further information: http://www.cancer.gov/cancertopics/types/colon-and-rectal

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