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Gene Fusion Revealed By Fine Grained Scan of DNA In Lung Cancer Cells

by Rukmani Krishna on November 5, 2013 at 12:58 AM
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 Gene Fusion Revealed By Fine Grained Scan of DNA In Lung Cancer Cells

Scientists at Dana-Farber Cancer Institute and the report in a new paper in the journal Nature Medicine that a fine-grained scan of DNA in lung cancer cells has revealed a gene fusion - a forced merger of two normally separate genes - that spurs the cells to divide rapidly.

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Treating the cells with a compound that blocks a protein encoded by one of those genes - NTRK1 - caused the cells to die.

The finding suggests that the fusion of NTRK1 to other genes fuels the growth of some lung adenocarcinomas (a form of non-small cell lung cancer), and that drugs that target NTRK1's protein product could be effective in patients whose lung tumors harbor such fusions.

"Treatment with targeted therapies is now superior to standard chemotherapy for many patients with lung cancers that harbor genetic changes including those with fusions involving the gene ALK," says Pasi A. Janne, MD, PhD, of Dana-Farber, the senior co-author of the paper with Robert C. Doebele, MD, PhD, of CU Cancer Center. "We know of several other genes that are fused in lung cancer and that offer attractive targets for new therapies. Our discovery places lung adenocarcinomas with NTRK1 fusions squarely within that group."

In the study, researchers performed next-generation DNA sequencing tests - which read the individual elements of the genetic code over long stretches of chromosomes - on tumor samples from 36 patients with lung adenocarcinomas whose tumors did not contain any previously known genetic alterations that could be found with standard clinical tests. In two of those samples - both from women who had never smoked - investigators found that a key region of the NTRK1 gene had become fused to normally distant genes (to the gene MPRIP in one patient; and the gene CD74 in the other).

NTRK1 holds the blueprint for a protein called TRKA, which dangles from the surface of cells and receives growth signals from other cells. The binding of NTRK1 to other genes causes TRKA to issue cell-growth orders on its own, without being prompted by outside signals.

In the laboratory, investigators mixed NTRK1-inhibiting agents into lung adenocarcinoma cells harboring NTRK1 fusions. The result was a dampening of TRKA's activity and the death of the cancer cells.

Investigators then designed a new test using fluorescence in situ hybridization (FISH) to detect NTRK1 fusions and tested an additional 56 tumor samples. In total, three of 91 tumor samples which had no other sign of cancer-causing genetic abnormalities, had fusions involving NTRK1.

"These findings suggest that in a few percent of lung adenocarcinoma patients - people in whose cancer cells we had previously been able to find no genetic abnormality - tumor growth is driven by a fusion involving NTRK1," Janne says. "Given that lung cancer is a common cancer, even a few percent is significant and translates into a large number of patients. Our findings suggest that targeted therapies may be effective for this subset of lung cancer patients."

"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."

The co-lead authors of the study are Aria Vaishnavi, BS, of the University of Colorado School of Medicine and Marzia Capelletti, PhD, of Dana-Farber. Co-authors include Anh Le, BA, Severine Kako, Sakshi Mahale, MS, Kurtis Davies, PhD, Dara Aisner, MD, PhD, Amanda Pilling, PhD Eamon Berge, MD, and Marileila Varella-Garcia, PhD, of the University of Colorado School of Medicine; Mohit Butaney, Dalia Ercan, and Peter Hammerman, MD, PhD, of Dana-Farber; Levi Garraway, MD, PhD, of Dana-Farber and the Broad Institute of MIT and Harvard; Gregory Kryukov, PhD, of the Broad Institute; Jhingook Kim, MD, of Samsung Medical Center, Seoul, Korea; Hidefumi Sasaki, MD, of Nagoya City University, Nagoya, Japan; Seung-il Park, MD, PhD, of Asan Medical Center, Seoul, Korea; Julia Haas, PhD, and Steven Andrews, PhD, of Array BioPharma; Doron Lipson, PhD, Philip Stephens, PhD, and Vince Miller, MD, of Foundation Medicine.

The research was supported by the Colorado Bioscience Discovery Evaluation Grant Program, the National Institutes of Health, and the Boettcher Foundation's Webb-Waring Biomedical Research Program, the Cammarata Family Foundation Research Fund, and the Nirenberg Fellowship at Dana-Farber.
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About Dana-Farber Cancer Institute
Dana-Farber Cancer Institute (www.dana-farber.org ) is a principal teaching affiliate of the Harvard Medical School and is among the leading cancer research and care centers in the United States. It is a founding member of the Dana-Farber/Harvard Cancer Center, designated a comprehensive cancer center by the National Cancer Institute. It provides adult cancer care with Brigham and Women's Hospital as Dana-Farber/Brigham and Women's Cancer Center and it provides pediatric care with Boston Children's Hospital as Dana-Farber/Boston Children's Cancer and Blood Disorders Center. Dana-Farber is the top ranked cancer center in New England, according to U.S. News & World Report, and one of the largest recipients among independent hospitals of National Cancer Institute and National Institutes of Health grant funding. Follow Dana-Farber on Facebook: www.facebook.com/danafarbercancerinstitute and on Twitter: @danafarber .

About University of Colorado Cancer Center
The University of Colorado Cancer Center is Colorado's only National Cancer Institute-designated comprehensive cancer center. NCI has given only 41 cancer centers this designation, deeming membership as "the best of the best." CU Cancer Center is headquartered on the University of Colorado Anschutz Medical Campus and is a consortium of three state universities (Colorado State University, University of Colorado Boulder and University of Colorado Denver) and six health delivery institutions: University of Colorado Health System (including University of Colorado Hospital, Poudre Valley Hospital, Medical Center of the Rockies and Memorial Hospital), Children's Hospital Colorado, Denver Health, Denver VA Medical Center, National Jewish Health and Kaiser Permanente Colorado.

Source: Newswise
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