A nationwide study by 20 institutes, including TGen, Broad Institute and Dana-Farber Cancer Institute, has unveiled the most comprehensive picture to date of the genetic blueprint of multiple myeloma also called plasma cell myeloma or Kahler’s disease. Multiple myeloma is an all-too-common form of bone marrow cancer in which abnormal plasma cells (myeloma cells) multiply, raising the number of plasma cells to a higher than normal level. Since these cells normally make proteins, this may increase the level of abnormal proteins circulatinng. Health problems caused by multiple myeloma can affect your bones, immune system, kidneys and red blood cell count. The disease is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood.

?This is arguably the largest cancer genome discovery study done to date,? said Dr. John Carpten, Director of the Integrated Cancer Genomics Division at the Phoenix-based Translational Genomics Research Institute, a key member of the national Multiple Myeloma Research Consortium, and a co-author of the research paper titled “Initial genome sequencing and analysis of multiple myeloma.” that will appear in the March 24 issue of the journal Nature.

The study, led by scientists at the Broad Institute and Dana-Farber Cancer Institute, involved whole genome sequencing of normal and tumor DNA from 38 multiple myeloma patients to assess tumor-specific changes across the entire 3-billion-letter human genome, yielding new and unexpected insights into the events that lead to this form of cancer.

Gene expression profiling microarrays
But first, TGen provided an initial analysis of 250 multiple myeloma tumor samples. Using gene expression profiling microarrays and genome copy number arrays ? powerful high-throughput investigative technologies that can assess the state of the vast majority of human genes ? TGen scientists identified numerous overly active genes that likely play a role in multiple myeloma.

?Our data was used to identify several of the gene sets that became the targets in the study investigated with our collaborators,? said Dr. Angela Baker, a staff molecular biologist in Dr. Carpten?s lab and a co-author of the scientific paper in Nature.

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Dr. Jeffrey Trent, TGen?s President and Research Director, and also a co-author of the paper, said this pioneering study will have a major impact in the field of multiple myeloma, and will influence research into other forms of cancer, too.

?This study sets the stage for ever-more-precise and detailed investigations that should eventually pinpoint the genetic and genomic origins of this devastating disease,? Dr. Trent said. ?The next stage will be to look at how these genes affect cellular growth and proliferation that can lead to cancer.?

The second most common blood cancer
Multiple myeloma is the second most common blood cancer in the United States and causes about 20,000 new cases in this country every year. The disease?s five-year survival rate is less than 40%, which is low compared to other forms of cancer. Multiple myeloma begins in the bone marrow, where plasma cells (a type of white blood cell) become malignant, crowding out normal cells and attacking solid bone. No one knows the cause of the disease ? it can develop in people with no known risk factors and in many cases, no family history of multiple myeloma.

The emerging genome-wide picture of multiple myeloma reveals genes never before associated with cancer as well as multiple genetic mutations that disrupt just a handful of common pathways, or chains of chemical reactions that trigger a change in a cell. Individually, each of these mutations is fairly uncommon and might have remained undiscovered had the researchers not looked at such a large collection of samples.

?Already, we can see that mutations are funneling into a limited number of pathways,? said co-senior author Todd Golub, director of the Broad?s Cancer Program and Charles A. Dana Investigator in Human Cancer Genetics at the Dana-Farber Cancer Institute. ?This is a demonstration of the value of looking at more than just a single tumor at great depth.?

Never before have scientists taken an in-depth look at so many multiple myeloma samples. Over the last six years, ?next-generation? sequencing technologies ? machines that can sequence DNA at a rapid pace and deliver massive amounts of data in a short period of time ? have surged. Sequencing the full genome of a tumor is still a feat of technical and analytical prowess and only a few studies to date have looked across more than one. The team of researchers studied 38 multiple myeloma patients, comparing the patients? normal genomes to the genomes from their malignant cells.

With the whole cancer genome in view, one of the most challenging aspects of multiple myeloma research is now separating so called driving events ? the important mistakes that drive cells toward becoming cancerous ? from passenger mutations, genetic alterations that are merely along for the ride. A team of researchers led by co-senior author Gad Getz, director of Cancer Genome Analysis at the Broad Institute, has developed computational tools to address this.

?Next-generation sequencing has the great potential and promise to allow us to comprehensively analyze the cancer genome at extremely high resolution and see all of the events that happen in cancer,? said Getz. ?These tools that we?ve developed are state-of-the-art. We?ve been able to dramatically decrease the error rate for detecting all types of mutations. Now, we can find those genes whose mutations occur more than expected by chance.?

The researchers found sets of mutations affecting many genes in the same pathways, including the NF-kB pathway. If this pathway is turned on at the wrong time, it can activate genes that allow a cancer cell to grow and divide unchecked. Previously, multiple myeloma researchers had suspected that this pathway was involved in the cancer?s development, but it was unclear exactly what events were turning this pathway on. In this latest study, the researchers discovered 11 different genes involved in this pathway that were altered in at least one multiple myeloma sample.

New genes
Additionally, the study has brought to light new mutations affecting genes that had never previously been tied to cancer. ?These genes, which are frequently mutated, were not on anyone?s radar before when thinking about multiple myeloma specifically or cancer in general,? said Golub, who is also an investigator at Howard Hughes Medical Institute, and professor of pediatrics at Harvard Medical School. ?This shows that there are entirely new cancer-causing genes that are going to be discovered through these sequencing efforts.?

In half of the study?s patients, the researchers found mutations in genes that control two fundamental cellular processes: how RNA is processed and proteins are folded. Two of these genes, DIS3 and FAM46C, appear to play important roles in the stability of RNA and hence its translation into protein. Researchers also found genes involved in blood clotting mutated in multiple myeloma patients, a new and surprising discovery. Follow-up studies will be needed to understand what role these defective genes play in cancer and how they can inform treatment.

?It?s going to take a lot of biological research to sort out whether these will make good drug targets,? said Golub, ?but this is an example of how genetic analysis can help point the field in the right direction very dramatically.?

BRAF mutation
One finding with more immediate clinical importance is the discovery of BRAF mutations in a small number of multiple myeloma patients. BRAF mutations have ?never been
a part of the multiple myeloma lexicon before,? according to Golub, but have been previously seen in other forms of cancer, including melanoma and colon cancer. Drugs are now in clinical development to target this particular gene and have shown promising early results in patients with melanoma.

When the scientists looked at samples from over 150 patients with multiple myeloma, they found BRAF mutations in about four percent of cases. Further studies will be needed to see if drugs that inhibit BRAF are as effective in patients with multiple myeloma as they have been in patients with melanoma.

Golub pointed out that with more samples and the analytical tools to look genome-wide, a new picture of the multiple myeloma genome is beginning to develop, and with it, new genetic insights. ?This study shows that there really are entirely new cancer-causing genes that are going to be discovered through these efforts,? he said. All of the data generated through this project have been made publicly available to cancer researchers worldwide. Funding for this project was provided by the Multiple Myeloma Research Foundation and tissue samples were provided by the Multiple Myeloma Research Consortium tissue bank.

For more information:
Chapman MA et al. Initial genome sequencing and analysis of multiple myeloma. Nature. March 24, 2011. DOI: 10.1038/nature09965. Published online 23 March 2011.

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