Archive for the ‘RAS subfamily’ Category

SNaPshot: Screening for Many Mutations at Once

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Posted 12 Nov 2011 — by James Street
Category ALK, EGFR, Gene sequencing, genetic research, KRAS, Lung Cancer, Personalized, Tumor biomarkers

Zosia Chustecka

November 11, 2011 — Sending off a tumor sample for a broad screening of genetic aberrations, instead of just a single test, increases the chance of finding a therapy that the patient will respond to, and it might also improve survival, say researchers from Massachusetts General Hospital (MGH), in Boston, who are already using the screen in routine clinical practice.

The broad genetic screen, known as SNaPshot, is advertised around the hospital with a poster that depicts a fingerprint, declaring: “Our patients are unique. So are their tumors.”

The screen can test for more than 50 well-known mutation sites (hot spots) in 14 key cancer genes, and has a turnaround time of less than 3 weeks.

“To our knowledge, we are the first center to offer this broad multiplexed genetic screening to all nonsmall-cell lung cancer [NSCLC] patients,” said Lecia Sequist, MD, MPH, a thoracic medical oncologist at MGH and assistant professor of medicine at Harvard Medical School. She is first author of a paper that reports on the use of the screen in 552 patients with NSCLC, published online November 9 in the Annals of Oncology.

Broad Screen Found Extra Patients

Up to now, genotyping strategies have typically homed in on 1 genetic mutation; for example, lung cancer patients are tested for the epidermal growth-factor receptor (EGFR) gene to identify those who will respond to the EGFR inhibitors erlotinib and gefitinib.

However, “employing a broad gene panel enabled us to provide a therapeutic alternative to lung cancer patients whose tumors harbored much less frequent genetic abnormalities, such as mutations in PIK3CA and BRAF or rearrangements in ALK,” explained senior author Dora Dias-Santagata, PhD, director of the Translational Research Laboratory at MGH.

“These individuals accounted for about 10% of our patient population, but they would have remained ‘invisible’ in the absence of a comprehensive genotyping panel, like the one used here,” she said in a statement.

Identifying these genetic aberrations allowed the researchers to offer patients treatment with targeted therapies that act specifically on those aberrations, which increases the likelihood that the patient will respond to treatment. “Choosing the right therapy can raise response rates in NSCLC patients from around 20% to 30% to 60% to 70%, and may improve survival,” Dr. Sequist said

Use in Other Cancers

The team is currently offering the screening to patients with other solid tumors, such as colorectal and breast cancers, and gliomas, and they are planning to extend the analysis to hematologic malignancies.

“Our study is exciting because it demonstrates that it is possible today to integrate testing for multiple genetic biomarkers in a busy clinic and steer patients toward personalized therapies,” Dr. Sequist explained.

“My message to oncologists is that now is the time to begin thinking about how best to work with pathology — as well as surgery, radiology, and pulmonology — colleagues, to try to adapt their practice toward broad-based genotyping,” she told Medscape Medical News.

“It is something that can be done at most hospitals. We, as a field, need to update our diagnostic practices to accommodate this important test,” Dr. Sequist added.

Pioneering Work

This is a superb initiative.

“This is a superb initiative,” said Jean-Charles Soria, MD, PhD, current president of the European Society for Medical Oncology. This group at MGH is a pioneer in this field, and has “accomplished a tour de force by offering this comprehensive analysis to all their NSCLC patients since 2009,” he told Medscape Medical News.

Although ahead of the game, this work is not entirely unique, he said. A similar approach is being developed at many other large cancer centers, including the Dana-Farber Cancer Institute in Boston; the University of Texas M.D. Anderson Cancer Center in Houston; The Royal Marsden in London, United Kingdom; Val d’Hebron in Barcelona, Spain; and his own center, Institute Gustave Roussy in Villejuif, France.

Medscape Medical News has previously reported on the broad-screen genotyping carried out at M.D. Anderson and by the Lung Cancer Mutation Consortium, which involves 14 centers in the United States. However, these initiatives are focused on enrolling patients in clinical trials, whereas the MGH team is using their broad screen in routine clinical practice.

“This approach will become standard practice in all major academic centers in Europe and North America…in 3 to 5 years at most, in my opinion,” Dr. Soria predicted.

At the moment, this approach belongs in academia and large care centers, said Alex Adjei, MD, a thoracic oncologist who is senior vice president of clinical research and professor of medicine at the Roswell Park Cancer Institute in Buffalo, New York. He agrees that broad-based genotyping is something that oncologists need to think about, but argued that this approach is not ready for widespread use. “It will become relevant to community oncologists, but that is a few years away,” he told Medscape Medical News.

Dr. Adjei explained that, at the moment, the main problem with this approach is that a lot of the information obtained is of academic interest and has little practical relevance. There are currently only a few targeted drugs available that home in on genetic aberrations. Although there are many under development, the only way to get a patient on these is to enroll them in a clinical trial, which best done in academic hospitals and large cancer centers, he said.

It makes sense to screen for many different mutations and genetic aberrations all at once, rather than one at a time, but for this approach really to come into its own, “we need to have more drugs available,” he said.

Right now it’s not ready for general use.

“For this to become routine and for this to make sense, we have to have more actionable mutations,” he said. “There is no point looking at 15 genes and finding 50 mutations when you can treat only a few of them.”

“SNaPshot is a great idea and has great utility because it is going to simplify molecular testing. This is the way of the future, but right now it’s not ready for general use,” Dr. Adjei concluded.

A slightly different opinion comes from community oncologist Patrick Cobb, MD, from Billings, Montana. Some practices are sending off tumor samples for broad genotyping. “It is already starting to happen at the community level,” he said.

“It is relevant to us,” he explained. Community oncologists are having to keep up with research and to change their practices accordingly, Dr. Cobb said. It is already standard practice to test colorectal cancer for KRAS (and BRAF) mutations and to use Oncotype Dx in breast cancer. These test results are influencing treatment decisions, and sparing some patients unnecessary adverse effects, he said. His own practice is considering EGFR and ALK testing for lung cancer, but hasn’t done so yet; however, they are testing melanoma for BRAF mutations.

“There’s much more collaboration nowadays between medical oncologists and pathologists,” Dr. Cobb said. “We’ve always been tied at the hip,” but in recent years, with pathologists providing information on mutations as well as histology, that collaboration has intensified.

“As an oncologist, this is an exciting time. We are really seeing the benefit of bench research starting to affect the way we are treating our patients,” he said.

Between the top academic centers and community practices are the middle-sized hospitals. Curtis Miyamoto, MD, is a professor of radiation oncology at just such a hospital — Temple University Hospital in Philadelphia, Pennsylvania. He thinks that “this broad genetic testing will be mainstream in the future, probably 5 years from now, but it’s not mainstream yet.”

“SNaPshot is great idea,” Dr. Miyamoto told Medscape Medical News, “and I do think it will become a standard of care in the future…. It provides valuable information that can change the way a patient is treated and can make a big difference, especially for patients who are being treated nonspecifically and who may be missing opportunities to get well because they are not getting the testing done.”

However, such genetic testing needs to be placed in the larger picture of strained healthcare resources and decreasing investment in new drug development, he said. “It’s very nice to have these profiles, but what about the drugs to treat patients with these results?”

Dr. Miyamoto echoed the point made by Dr. Adjei — that for many of the mutations, targeted drugs “are not available yet…. How many will be developed under the current financial constraints…, and further down the line…, will we be able to afford to use them?”

First Cohort of Patients

In their paper, the MGH team reports on the first cohort of NSCLC patients screened with SNaPshot. A total of 589 patients were referred for genotyping, and 95% of these (n = 552) had sufficient tumor tissue for the screen.

The median age of the patients was 64 years (range, 22 to 89), 58% were female, and 92% were white, “reflecting our clinic’s racial homogeneity,” the researchers write. Histology was predominantly adenocarcinoma (81%), and about a quarter of the patients (24%) were never smokers.

The screen identified driver mutations in 51% of the patients. Most of the tumor samples had 1 mutation, but 5% had 2 mutations, and 2 tumors had 3 mutations.

The most commonly occurring mutations were KRAS (in 24% of tumor samples), EGFR (in 13%), and translocations involving ALK (5%).

There is wide agreement that it is important to identify patients with EGFR and ALK aberrations, the researchers note, because targeted therapies directed at the aberration (erlotinib and gefitinib for EGFR and crizotinib for ALK) are available.

There are also data that support directing patients with certain genotype findings “away” from therapies; for example, patients with KRAS mutations are directed away from erlotinib.

In addition, there are investigational therapies aimed at some of the other mutations that were found (such as MRK inhibitors for KRAS mutations), and therapies that are aimed at BRAF, PIK3CA, and HER2 mutations.

Of all the patients with genotypes, 22% have begun treatment with a genotype-specific therapy in response to SNaPshot results, the team reports.

Determining the percentage of these patients who would have received targeted therapy in the absence of SNaPshot is difficult, “because it would depend on whether any genetic testing was being done, and if it was, how much,” Dr. Sequist told Medscape Medical News.

Two steps are required before patients receive genotype-specific therapy: “step 1 is doing the testing and step 2 is having the drugs available,” she explained. “I think it is fair to say that EGFR mutation testing is fairly routine in most places around the world currently, and ALK testing is becoming more and more common because the new ALK inhibitor crizotinib has been approved by the US Food and Drug Administration in the United States. As the portfolio of drugs that target these various cancer mutations expands, not only through clinical trials but also through new drug approvals, there will be more of a pressing need to make broad genotyping the standard clinical practice of oncology. Our paper is important because it shows that this type of broad testing can be woven into the everyday care of patients already,” Dr. Sequist said.

What about the clinical outcomes of patients who are identified on screening and are then treated with targeted therapies?

“The field of targeted cancer therapy is still in its infancy, Dr. Sequist told Medscape Medical News. “At the current time, we have not seen that targeted drugs can cure cancers that were not curable otherwise. However, it is likely that survival can be lengthened by these types of treatments. Although not addressed in [our Annals of Oncology paper], our group recently published a study demonstrating that ALK-mutated patients receiving the ALK inhibitor crizotinib survived longer than ALK-mutated patients who did not get the drug” (Lancet Oncol. 2011;12:1004-1012). These data on crizotinib were previously reported by Medscape Medical News.

“We are getting much smarter in treating cancer, and focusing on these genetic changes and using targeted therapies is getting us closer to the ideal of personalized medicine,” said Dr. Cobb.

We are confident that these breakthroughs will make a difference in outcomes for patients, he noted. “There is really no reason why they shouldn’t, but we haven’t really proven that,” Dr. Cobb told Medscape Medical News. “To prove it, you have to marry what we see in the lab with what happens in the patient.”

There is a precedent here that bodes well for the future of this approach. Already in breast cancer, targeting treatment (tamoxifen to estrogen-receptor status and trastuzumab to HER2-receptor status) has led to a marked improvement in survival and cure rates, Dr. Cobb explained. However, this level of data is not available yet for treatment modified according to genetic mutations, he said.

“I don’t think anybody thinks that this is not going to be important,” he added. “There’s plenty of excitement about it; we just haven’t proven it yet.”

Dr. Sequist reports consulting for Clovis Oncology, Merrimack Pharmaceuticals, Daichi-Sankyo, and Celgene. Dr. Dais-Santagata and her colleague at the Translational Research Laboratory at MGH, John Iafrate, MD, PhD, have submitted a patent for the SNaPshot tumor genotyping assay. Dr. Soria reports receiving honoraria from Abbott, Amgen, Bristol-Myers Squibb, GlaxoSmithKline, Pfizer, Roche, Merck, MSD, Servier, sanofi-aventis, and Eli Lilly. Dr. Adjei has disclosed no relevant financial relationships.

Ann Oncol. Published online November 9, 2011. Abstract

Cancer’s secrets come into sharper focus

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Posted 19 Aug 2011 — by James Street
Category genetic research, KRAS, MicroRNA, PTEN, RAS subfamily, RNAi, Understanding Cancer
By George Johnson / New York Times News Service

Published: August 19. 2011 4:00AM PST

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For the last decade cancer research has been guided by a common vision of how a single cell, outcompeting its neighbors, evolves into a malignant tumor.

Through a series of random mutations, genes that encourage cellular division are pushed into overdrive, while genes that normally send growth-restraining signals are taken offline.

With the accelerator floored and the brake lines cut, the cell and its progeny are free to rapidly multiply. More mutations accumulate, allowing the cancer cells to elude other safeguards and to invade neighboring tissue and metastasize.

These basic principles — laid out 11 years ago in a landmark paper, “The Hallmarks of Cancer,” by Douglas Hanahan and Robert Weinberg, and revisited in a follow-up article this year — still serve as the reigning paradigm, a kind of Big Bang theory for the field.

But recent discoveries have been complicating the picture with tangles of new detail. Cancer appears to be even more willful and calculating than previously imagined.

Most DNA, for example, was long considered junk — a netherworld of detritus that had no important role in cancer or anything else. Only about 2 percent of the human genome carries the code for making enzymes and other proteins, the cogs and scaffolding of the machinery that a cancer cell turns to its own devices.

These days “junk” DNA is referred to more respectfully as “noncoding” DNA, and researchers are finding clues that “pseudogenes” lurking within this dark region may play a role in cancer.

“We’ve been obsessively focusing our attention on 2 percent of the genome,” said Dr. Pier Paolo Pandolfi, a professor of medicine and pathology at Harvard Medical School. This spring, at the annual meeting of the American Association for Cancer Research in Orlando, Fla., he described a new “biological dimension” in which signals coming from both regions of the genome participate in the delicate balance between normal cellular behavior and malignancy.

As they look beyond the genome, cancer researchers are also awakening to the fact that some 90 percent of the protein-encoding cells in our body are microbes. We evolved with them in a symbiotic relationship, which raises the question of just who is occupying whom.

“We are massively outnumbered,” said Jeremy Nicholson, chairman of biological chemistry and head of the department of surgery and cancer at Imperial College London. Altogether, he said, 99 percent of the functional genes in the body are microbial.

In Orlando, he and other researchers described how genes in this microbiome — exchanging messages with genes inside human cells — may be involved with cancers of the colon, stomach, esophagus and other organs.

These shifts in perspective, occurring throughout cellular biology, can seem as dizzying as what happened in cosmology with the discovery that dark matter and dark energy make up most of the universe: Background suddenly becomes foreground and issues once thought settled are up in the air. In cosmology the Big Bang theory emerged from the confusion in a stronger but more convoluted form. The same may be happening with the science of cancer.

Exotic players

According to the central dogma of molecular biology, information encoded in the DNA of the genome is copied by messenger RNA and then carried to subcellular structures called ribosomes, where the instructions are used to assemble proteins. Lurking behind the scenes, snippets called microRNAs once seemed like little more than molecular noise. But they have been appearing with increasing prominence in theories about cancer.

By binding to a gene’s messenger RNA, microRNA can prevent the instructions from reaching their target — essentially silencing the gene — and may also modulate the signal in other ways. One presentation after another at the Orlando meeting explored how microRNAs are involved in the fine-tuning that distinguishes a healthy cell from a malignant one.

Ratcheting the complexity a notch higher, Pandolfi, the Harvard Medical School researcher, laid out an elaborate theory involving microRNAs and pseudogenes. For every pseudogene there is a regular, protein-encoding gene.

While normal genes express their will by sending signals of messenger RNA, the damaged pseudogenes either are mute or speak in gibberish.

Or so it was generally believed. Little is wasted by evolution, and Pandolfi hypothesizes that RNA signals from both genes and pseudogenes interact through a language involving microRNAs.

His lab at Beth Israel Deaconess Medical Center in Boston is studying how this arcane back channel is used by genes called PTEN and KRAS, commonly implicated in cancer, to confer with their pseudotwins. The hypothesis is laid out in more detail this month in an essay in the journal Cell.

In their original “hallmarks” paper — the most cited in the history of Cell — Hanahan and Weinberg gathered a bonanza of emerging research and synthesized it into six characteristics. All of them, they proposed, are shared by most and maybe all human cancers. They went on to predict that in 20 years the circuitry of a cancer cell would be mapped and understood as thoroughly as the transistors on a computer chip, making cancer biology more like chemistry or physics — sciences governed by precise, predictable rules.

Now there appear to be transistors inside the transistors. “I still think that the wiring diagram, or at least its outlines, may be laid out within a decade,” Weinberg said in an email. “MicroRNAs may be more like minitransistors or amplifiers, but however one depicts them, they still must be soldered into the circuit in one way or another.”

In their follow-up paper, “Hallmarks of Cancer: The Next Generation,” he and Hanahan cited two “emerging hallmarks” that future research may show to be crucial to malignancy — the ability of an aberrant cell to reprogram its metabolism to feed its wildfire growth and to evade destruction by the immune system.

Unwitting allies

Even if all the lines and boxes for the schematic of the cancer cell can be sketched in, huge complications will remain. Research is increasingly focused on the fact that a tumor is not a homogeneous mass of cancer cells. It also contains healthy cells that have been conscripted into the cause.

Cells called fibroblasts collaborate by secreting proteins the tumor needs to build its supportive scaffolding and expand into surrounding tissues. Immune system cells, maneuvered into behaving as if they were healing a wound, emit growth factors that embolden the tumor and stimulate angiogenesis, the generation of new blood vessels. Endothelial cells, which form the lining of the circulatory system, are also enlisted in the construction of the tumor’s own blood supply.

All these processes are so tightly intertwined that it is difficult to tell where one leaves off and another begins. With so much internal machinery, malignant tumors are now being compared to renegade organs sprouting inside the body.

Unseen enemies

At a session in Orlando on the future of cancer research, Dr. Harold Varmus, the director of the National Cancer Institute, described the Provocative Questions initiative, a new effort to seek out mysteries and paradoxes that may be vulnerable to solution.

“In our rush to do the things that are really obvious to do, we’re forgetting to pay attention to many unexplained phenomena,” he said.

Why, for example, does the Epstein-Barr virus cause different cancers in different populations? Why do patients with certain neurological diseases like Parkinson’s, Huntington’s, Alzheimer’s and Fragile X seem to be at a lower risk for most cancers? Why are some tissues more prone than others to developing tumors? Why do some mutations evoke cancerous effects in one type of cell but not in others?

With so many phenomena in search of a biological explanation, “Hallmarks of Cancer: The Next Generation” may conceivably be followed by a second sequel — with twists as unexpected as those in the old “Star Trek” shows. The enemy inside us is every bit as formidable as imagined invaders from beyond. Learning to outwit it is leading science deep into the universe of the living cell.