​Can the length of strands of DNA in patients with heart disease predict their life expectancy?
Researchers from the Intermountain Heart Institute at Intermountain Medical Center in Salt Lake City, who studied the DNA of more that 3,500 patients with heart disease, say yes it can.
In the new study, the researchers were able to predict survival rates among patients with heart disease based on the length of strands of DNA found on the ends of chromosomes known as telomeres—the longer the patient’s telomeres, the greater the chance of living a longer life.
Previous research has shown that telomere length can be used as a measure of age, but these expanded findings suggest that telomere length may also predict the life expectancy of patients with heart disease.

Telomeres protect the ends of chromosome from becoming damaged. As people get older, their telomeres get shorter until the cell is no longer able to divide. Shortened telomeres are associated with age-related diseases such as heart disease or cancer, as well as exposure to oxidative damage from stress, smoking, air pollution, or conditions that accelerate biologic ageing.

‘Chromosomes by their nature get shorter as we get older,’ said John Carlquist, PhD, director of the Intermountain Heart Institute Genetics Lab. ‘Once they become too short, they no longer function properly, signalling the end of life for the cell. And when cells reach this stage, the patient’s risk for age-associated diseases increases dramatically.’

Dr. Carlquist and his colleagues from the Intermountain Heart Institute at Intermountain Medical Center tested the DNA samples from more than 3,500 heart attack and stroke patients.

‘Our research shows that if we statistically adjust for age, patients with longer telomeres live longer, suggesting that telomere length is more than just a measure of age, but may also indicate the probability for survival. Longer telomere length directly correlate with the likelihood for a longer life—even for patients with heart disease,’ said Dr. Carlquist. Intermountain Medical Center Heart Institute

Researchers from the Masonic Cancer Center, University of Minnesota, and the University’s Brain Tumor Program, have developed a new mouse model of malignant peripheral nerve sheath tumours (MPNST) that allow them to discover new genes and gene pathways driving this type of cancer.
Utilising the Sleeping Beauty transposon method, researchers in the lab of David Largaespada, Ph.D., professor in the Medical School and College of Biological Sciences, were able to use an unbiased approach to generate mouse models of MPNST development that lead to the identification of genes related to this tumour’s development.

MPNST is a genetically diverse, aggressive form of sarcoma impacting connective tissue surrounding nerves that occurs sporadically or in association with Neurofibromatosis Type 1 (NF1) syndrome. The exact cause of MPNST is not known, but symptoms include swelling in the arms and legs, soreness and stiffness at the site of the tumour. MPNSTs are the most common malignancy in adults with NF1 syndrome and leading cause of NF1-related mortality.

Due to the invasive nature and high incidence of metastasis of MPNSTs, surgical resection, radiotherapy and chemotherapeutic treatments have proven to be ineffective for long-term treatment, resulting in 5-year survival rates of less than 25 percent with metastatic disease.

One of the most surprising findings in this research showed the gene FOXR2 is intrinsically linked to the growth of MPNSTs. This gene has not been heavily studied as researchers had not identified a clear function of this gene.

‘By using an unbiased approach, it helped us identify FOXR2 as an important gene in MPNST development and develop experiments to pinpoint the role FOXR2 plays in maintaining the aggressive nature of these tumours,’ said Eric Rahrmann, Ph.D., the paper’s lead author and a postdoctoral fellow in the Largaespada lab. ‘When we turn off FOXR2, the growth ability of these MPNSTs drastically decreases.’

Other findings showed interesting evidence of pathways that could be viable targets for therapeutics. The activation of the Wnt signalling pathway was shown to drive MPNSTs. This pathway has been highly implicated in colon cancer but not previously linked to MPNSTs.

Researchers also found many of the MPNSTs have dual loss of the genes called NF1 and PTEN. This pairing of lost genes causes MPNST formation. Both of these genes have previously been shown as pathways related to MPNSTs but it wasn’t clear the extent to which they work together.

Now, researchers are applying these findings to the testing of therapeutics currently on the market for other drugs. This research is continuing both in the mouse model and within primary tumour settings of human cell lines.

‘We want to know if these drugs, which are not currently directed at MPNSTs, could be repurposed to provide alternate therapies for patients,’ said Largaespada.

Researchers are also looking into more direct ways to target tumours through the Wnt pathway and paired NF1 and PTEN pathways, utilising mouse models and human cell lines in the lab setting. University of Minnesota

Researchers at the University of Wisconsin-Madison have found a new way to accelerate a workhorse instrument that identifies proteins. The high-speed technique could help diagnose cancer sooner and point to new drugs for treating a wide range of conditions.
Proteins are essential building blocks of biology, used in muscle, brain, blood and hormones. If the genes are the blueprints, the proteins patterned on them are the hammers and tongs of life.

Proteins are not only numerous — humans have more than 100,000 varieties — but each one has a complex structure that determines its exact function in the biological realm. Just as tissue from cats and kangaroos can be distinguished by studying the individual ‘letters’ of their genetic codes, protein A can be distinguished from protein B by looking at the amino-acid sub-units that compose all proteins.

The fastest way to count and identify proteins is to use a mass spectrometer, a precise instrument that measures chemical compounds by mass. ‘Mass spec is an essential part of modern biology, and most people use it to look at variations in proteins,’ says Joshua Coon, a professor of chemistry and biomolecular chemistry.

Because mass spectrometers are expensive, and proteins are both numerous and ubiquitous, chemists have recently learned to double up their samples so they can, for example, compare normal tissue to diseased tissue in a single run.

Knowing how the proteins change when good tissue goes bad suggests what has gone wrong.

Now, Coon has doubled-down on the doubling-up process with a technique that has the potential to run as many as 20 samples at once. The new process has already gone to work, says Alexander Hebert, a graduate student who was first author on the new publication.

‘Working with John Denu at the Wisconsin Institute for Discovery, we are looking at mice that lived with or without caloric restriction,’ says Hebert. Caloric restriction is known to increase lifespan in many animals, and scientists are eager to unravel the biochemical pathways that explain this life extension. ‘Some of these mice have lost a certain gene related to metabolism, so we are comparing four types of tissue all at once. We can look at the brain, liver or heart, and ask, how does the abundance of proteins vary?’
Already, Coon and Hebert have performed six simultaneous analyses using the new technique; but it could actually do batches of 20, Coon says.

Key to the original doubling-up process was inserting a ‘tag’ into the amino acids that gives the proteins a slightly different mass. The tags are isotopes — chemically identical atoms that have different masses.

To prepare two samples, one would receive an amino acid containing common isotopes, and the other special, heavier isotopes. The result — proteins that are chemically identical but have different masses — can easily be identified in a mass spectrometer.

The new journal report by Coon and Hebert describes a way to use amino acids built from a broader range of isotopes that would be expected to have identical mass, but do not because some of their mass has been converted to energy to hold the atomic nuclei together. Without this energy, the positively charged proteins would repel each other and the atomic nucleus would be destroyed. The tiny loss of mass due to this conversion to binding energy can be detected in the new, ultra-precise mass spectrometers that are now installed in several labs on campus.

The mass difference in the new technique is more than 1,000 times below the mass differences in the existing doubled-up technique, but it is enough to count and identify proteins from six — and, theoretically, 20 — samples at once. The researchers applied for a patent last fall and assigned the rights to the Wisconsin Alumni Research Foundation. University of Wisconsin-Madison

The Red Cross Blood Transfusion Service of Upper Austria has become the first laboratory in Europe to receive accreditation from the European Federation for Immunogenetics (EFI) for the use of human leukocyte antigen (HLA) tests based on next-generation sequencing with Roche’s GS Junior System. This new method will allow more precise and much more rapid tissue-typing and donor selection for stem cell transplants than has been possible to date. In addition, the HLA testing method previously only used for research will now also be available as a standard routine diagnostic procedure.
“Worldwide, around 50,000 people a year urgently require a stem cell transplant, and the chances of finding an allogeneic stem cell donor are about 1:500,000,” said Thomas Schinecker, Head of Roche Sequencing Solutions. “This accreditation is an example of how the potential of next-generation sequencing can be successfully translated from research into medicine and made widely available to patients in areas of high medical need.”
Underlining the benefits of the new standard method, Dr Christian Gabriel, Medical Director of the Red Cross Blood Transfusion Service of Upper Austria, said: “Standardized laboratory procedures are needed to promote positive therapeutic outcomes for patients. EFI accreditation is an important step, allowing large numbers of patients to benefit from the latest technologies.”

www.roche.com

To the list of oncogenic drivers of lung cancer that includes ALK, EGFR, ROS1 and RET, results of a University of Colorado Cancer Center study presented at ASCO 2013 show that mutations in the gene NTRK1 cause a subset of lung cancers.

‘We’re reconceptualising lung cancer as many, related diseases. And we need to learn to identify and treat each individually. We can treat the forms of the disease that depend on ALK and EGFR mutations. We’re getting very close to treating lung cancers that depend on ROS1 and RET. And now we show another oncogenic driver of the disease that begs its own targeted treatment,’ says Robert C. Doebele, MD, PhD, investigator at the CU Cancer Center and assistant professor of medical oncology at the CU School of Medicine.

The group, in collaboration with Pasi A. Jänne, MD, PhD from the Dana-Farber Cancer Institute, started with lung cancer tumour samples from 36 ‘pan-negative’ patients, meaning that no other driver oncogene had been identified. So if not EGFR, ALK and the like, what was driving the cancer? Doebele and colleagues took the question to Foundation Medicine (Cambridge, MA), which used targeted, next-gen sequencing to analyse the samples for possible mutations in a couple hundred potential oncogenes identified as drivers of other cancers. NTRK1 had been identified as a driver of thyroid cancer and so was included in the panel (though drug development had stalled due in part to the relative rarity of the thyroid disease). Sure enough, next-gen sequencing identified NTRK1 gene fusions as the potential driver in two of these samples.

Doebele and colleagues took the lead back to the CU labs, where Marileila Varella Garcia, PhD, developed a specific test for NTRK1 fusions based on fluorescence in situ hybridisation (FISH), similar to what is used for ALK, ROS1 and RET fusions. This allowed the group to validate the finding of NRTK1 as a novel oncogene in these patient samples.

But the study went a step beyond identifying the oncogene. Doebele describes the relative ease with which genes that are improperly activated can be silenced – ‘whether a drug is already is in clinical trials, or already approved for another cancer, or just sitting on the pharma shelf somewhere, many drugs exist that turn off these candidate genes,’ Doebele says.

In this case, Doebele describes ‘walking up the street to Array BioPharma (Boulder, CO), who happened to have several compounds specific for this gene.’

The group showed that mutated NRTK1 genes in cells treated with drug candidates ARRY-772, -523, and -470 and others was effectively turned off.

‘This is still preclinical work,’ Doebele says, ‘but it’s the first – and maybe even second and third! – important steps toward picking off another subset of lung cancer with a treatment targeted to the disease’s specific genetic weaknesses.’ University of Colorado Cancer Center