Tangled Bank #58


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Salto sobrius, a blog dedicated to “archaeology, skepticism and sundry musings kept by an archaeologist in Stockholm, Sweden,” hosts the latest edition of Tangled Bank, a collection of the latest science writing from around the blogosphere.

Tangled Bank #58 opens with a link here to the recent post concerning the epigenetics of lung cancer, but it also contains links to a lot of other interesting and informative posts, including discussion of new research into how cells divide, sex differences in gene expression, and the potentional evolutionary implications of two genes central to the development of the brain.

Breast Cancer Detection Improves through Methylation-Specific PCR


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Researchers at Johns Hopkins University have found a way to test for breast cancer in body fluid that doubles the rate of detection of the life threatening disease. Their work, reported in the June 1 edition of Clinical Cancer Research, shows an improvement in diagnosis from 33 percent through traditional cytology methods to 71 percent using a quantitative multiplex methylation-specific PCR (QM-MSP).

    Cytopathologists correctly identified seven of 21 (33 percent) fluid samples containing cancer, and ruled out the disease in nearly all cases negative for cancer (92 of 93 samples, 99 percent). QM-MSP doubled the cancer detection rate to 71 percent by spotting 15 of 21 samples known positive for cancer. Of 76 samples negative for cancer, QM-MSP concurred on 63 (83 percent).
The test works by checking for the methylation states of five to ten genes found to be more highly methylated in breast cancer cells from breast fluid. The percent of methylation at the specific sites are then added together for a cumulative score, and compared with a standard threshold value. If the methylation score is higher than the threshold value, cancer cells may be present.

The researchers note that the accuracy in detecting breast cancer through methylation detection in breast fluid would likely improve by being able to obtain fluid from all of the breast ducts, which is currently being investigated by other researchers. Link

The Epigenetics of Lung Cancer


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Lung cancer and epigenetics have become inextricably linked. That’s the word from Dr. Annalese Semmler and colleagues from the The University of Queensland and The Prince Charles Hospital in Queensland, Australia in the journal Respirology.

In an invited review exploring the link between epigenetics and lung cancer, the Australian scientists do an admirable job of summarizing many of the discoveries made that offer new hope in lung cancer diagnostics and therapeutics.

For instance, both DNA hypomethylation (a loss of methylation) and DNA hypermethylation (an increase in methylation) have been linked to studies examining genes that are differentially methylated between normal and cancerous lung tissue. The genes that have been linked to altered methylation include those involved in cell cycle regulation, DNA repair, RAS signaling and invasion.

Epigenetics also provides an intriguing opportunity for the early detection of lung cancer. Various genes have been found to be differentially methylated in various body fluids that are potential biomarkers for the early detection of lung cancer, including sputum, bronchial lavage, and peripheral blood. These same biomarkers may also be useful in assessing the risk of a patient developing lung cancer, which could afford a chance for primary prevention (smoking cessation).

Demethylating drugs are also being investigated for their potential in the treatment of lung cancer. However, the authors stress that it will likely require new developments in demethylating agents to induce noticeable effects in lung cancer patients.

These and other links between epigenetic alterations and lung cancer provide researchers with a number of novel strategies for combating a cancer that affects millions around the world. Link

Nature’s Top 50 Science Blogs: A Technorati Ranking


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This week Nature recognized the top 50 science blogs (written by scientists), and ranked them according to their Technorati ranking. It seems that the aim of this list was to use an objective method to make a list of some of the most popular science blogs around.

But I think the important thing to recognize with this list is how much credibility Nature has given these blog authors by formal recognition of their influence with a list such as this. Sure, it’s partly a gimmick to get free links from dozens of science blogs to the Nature Web site. But more importantly, the list establishes that the editors of one of the top peer-reviewed science journals in the world thinks that these blogs are important enough to point out to their scholarly audience.

That should be the story of this story, rather than who falls at what ranking and why X blog is not included. Link

Multiple Marker Approach to Colorectal Cancer Detection


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Epigenomics AG released clinical data this week showing that a new approach to early colorectal cancer detection in blood can be used to detect most colon polyps.

    Colon polyps are benign proliferations that can give rise to cancer. The risk is considerably high if they are greater than 1 cm in size. Their timely removal is therefore a major contribution to saving patients’ lives.

    The study was based on a total of 49 blood plasma samples from patients with colon polyps and 22 patients without polyps. Researchers studied two proprietary Epigenomics markers alone and in combination: Septin9, a marker which has already been presented by Epigenomics earlier this year and ALX4, a previously undisclosed marker identified by Epigenomics.

    The combination of the two markers detected clinically relevant polyps with very high sensitivity. Detection rate for polyps larger than 1cm was 67% (12 out of 18 plasma samples from patients with polyps). Sensitivity for large dysplastic polyps (adenomas greater than 1 cm) was 100% and for adenomas with intraepithelial neoplasia, i.e. a substantial likelihood of developing invasive cancer was 80%. The specificity of the combination as tested in asymptomatic patients over 50 years of age was 91%.

Link