Tag: cancer

Food for Thought: Weekly Wrap-Up

John Markoff reports in the New York Times about scientists who created online video game EteRNA in which players can come up with novel ways of folding RNA. The scientists claim it is “democratizing science” by attracting thousands of citizens to participate in constructing new ways to understand and use the folding of RNA.

Finally, the NYT reports about wine. While archaeologists discovered the earliest winemaking facility of the world in Armenia where wine was being made there as early as 7,400 years ago – proving that mankind must have found something positive in consuming red wine, today’s scientists still grapple at understanding the benefits. Dealing with the halt of the last resveratrol trial in which biotech company Sirtis (now GSK) tried to prove that this particular ingredient of red wine is able to extend the life span of obese Rhesus Monkeys, Nicholas Wade casts doubt about the usefulness of resveratrol and resveratrol-mimicking chemicals as anti-aging drugs.

The Economist this week deals with epigenetics in a story featuring that not only mothers but fathers as well may be able to pass on a propensity to obesity if they themselves have been starved during their life before fathering offspring. The findings are from mice.

A separate story deals with attempts by British researchers to attach glowing proteins to cancer cells so that they emit red light. However to detect it doctors would have to use a specially developed camera that scans the body slice by slice. Such cameras are expensive, and the £500,000 ($750,000) they cost may be the greatest hurdle to deploying the technique.

Djuke Veldhuis reports in New Scientist about a simple blood test for Down’s syndrome that successfully detected all 86 cases confirmed by other methods. The validation study is published in BMJ 2011; 342:c7401.

In The Scientist, Vanessa Schipani elaborates why it is not a good idea to use the usually well-fed, parasite-free and genetically similar lab animals to study immunology. Instead, she makes a case for ecoimmunology, a new field studying immunology in wild animals and still trying to attract more researchers and funding. Jef Akst reports about cancer researchers identifying an increasing number of proteins that have a dual nature in cancer: they may initially promote the development of tumors, but in the long run make them less aggressive, or vice versa. “One problem in identifying such two-faced proteins may stem from the fact that these opposing effects are rarely demonstrated in the same research paper,” Jef writes, adding that both reviewers and funding agencies do not like this kind of complex stories and rather prefer focusing on one side of the coin.

Speaking of peer reviews, Martina Lenzen-Schulte in the German Frankfurter Allgemeine Zeitung (FAZ)  reports about efforts of peer-reviewed journals like the British Medical Journal or the EMBO Journal to make the peer review process more transparent by disclosing the names of the reviewers and the review or even the complete review process. Goals are to improve the quality of the process and of reviews in general and to prevent reviewers from either stealing ideas or putting a spoke in competitors’ wheels.

Volker Stollorz in Frankfurter Allgemeine Sonntagszeitung (FAS) provides a concise review of the ongoing debate whether the chronic fatigue syndrome (CFS) is caused by the newly discovered retrovirus XMRV or whether contamination of specimens, the lab or chemicals used in experiments have produce results that could be mistaken for XMRV. The article clarifies that there are increasing doubts about the hypothesis as many independent researchers have not been able to find the virus in the blood of CFS patients and/or from blood banks.

Focus reports on new efforts to combat AIDS by learning from the about 1% of humans resistant to the virus. The article cites James Hoxie, of Penn Center for AIDS Research, who is trying to cure AIDS by removing from immune cells of AIDS patients those genes that provide entry to HIV. Subsequently, the immune cells are transferred back to the patient. Focus states the approach goes back to findings in Germany at Charité Berlin where a patient suffering from both AIDS and leukemia received a bone marrow transplant from a HIV resistant donor. Citing an article in Blood (DOI 10.1182/blood-2010-09-309591), Focus states the patient is now virus-free and off AIDS medications.

Food for Thought: Why tissue sample quality matters for personalized medicine

“We now have the technical ability to get the wrong answers with unprecedented speed.” Carolyn Compton, Director, Office of Biorepositories and Biospecimen Research

When the U.S. National Cancer Institute recently started its Cancer Genome Atlas initiative and asked biobanks all over the world for cancer biopsy samples, it was puzzled to find that the quality of the donated samples was so poor that the NCI was unable to meet the moderate target of collecting 1,500 biopsy samples per cancer. In a telling article in “Wired magazin”, Steve Silberman gives the example of a university biobank, which claimed to have more than 12,000 samples of glioblastoma in its collection. However, the initiative judged only 18 of those as good enough to use. After contacting biobanks on a global scale, the researchers did not even get to 500 glioblastoma samples of satisfactory quality and barely got to 500 in ovarian cancer, the 5th most common cancer in women. In lung cancer, the initiative was unable to start because it simply could not obtain the minimum number of biopsy samples of adequate quality. „However, all biobanks thought they were doing a superb job,“ resumed Carolyn Compton, director of NCI‘s Office of Biorepositories and Biospecimen Research OBBR and responsible for the biopsy sampling part.
The reason for the poor quality is simple: minutes after cutting tissue off from blood supply, cells start to react with massive changes in gene methylation patterns, gene expression and translation, proteome composition, enzymatic activities, surface protein patterns, etc. The changes affect hundreds of genes, and it is reality in many hospitals that the resected cancer tissue lies around for hours at room temperature in the operation theater before it is put in the freezer to get formalin-fixed a few days later.
Even more, the medication the patient has been given prior to or during operation (sedatives, anesthetics, etc.) has a profound impact on these parameters as well.
Therefore, very often it is impossible to judge whether the changes observed between individual patients is a result of their inherently different metabolisms/genetic makeup or a consequence of different sampling and handling of the biopsies and medications.
“We now have the technical ability to get the wrong answers with unprecedented speed,” Compton says. “If we put the wrong stuff into the front end of our analytical pipeline, we will not only lose the war on cancer, we’ll pollute the scientific literature with incorrect data that will take us a long time to sort out. This is a crisis that requires disruptive innovation.”
OBBR is now systematically looking into the problem and has chosen one company to perform the first systematic studies: Hamburg-based Indivumed GmbH. The company did pioneering research and devised standards for cancer biopsy samplings that are applied in a network of clinics Indivumed is collaborating with in the Hamburg and the Washington DC area. The company runs the only ISO-certified biobank in the world and is offering biospecimens, related patient data, and services including biomarker development for the purpose of developing personalized cancer therapies. By employing specially trained nurses, the company guarantees that each sample is frozen or fixed within 12 minutes, and each sample comes with a data package comprising several hundred data on the patient‘s medical history and life style. Further information about Indivumed, a client of akampion, can be found here.

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