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'Jumping Genes' Unusually Active in Many Gastrointestinal Cancers, Studies Find - 08/18/2015

'Jumping Genes' Unusually Active in Many Gastrointestinal Cancers, Studies Find

Rogue gene insertions could one day speed diagnosis
Release Date: August 18, 2015

Fast Facts:

  • Jumping genes, also known as transposons, are stretches of DNA that can copy and insert themselves into new places in the genome.
  • The active transposon in the human genome, known as LINE-1, causes disease when it interrupts the sequence of some important genes.
  • A trio of new studies finds that new LINE-1 insertions are common in several cancers of the gastrointestinal tract, and the insertions appear to occur early in tumor development.

Results of a trio of studies done on human cancer tissue biopsies have added to growing evidence that a so-called jumping gene called LINE-1 is active during the development of many gastrointestinal cancers. The Johns Hopkins scientists who conducted the studies caution there is no proof that the numerous new “insertions” of these rogue genetic elements in the human genome actually cause cancers, but they say their experiments do suggest that these elements, formally known as transposons, might one day serve as a marker for early cancer diagnosis.

Collectively, the studies focus on insertions of a stretch of DNA — the LINE-1 transposon — that, as its name suggestions, can produce copies of itself that hop into new areas of the genome and may interrupt normal DNA sequences.

This particular genetic interloper, the investigators say, has been in the human genome for so long that an estimated 17 percent of it is made up of LINE-1 copies, the vast majority of which are now “rusty hulks” of their former selves, unable to move at all. A few, however, are still mobile. Summaries of two of the studies appeared online Aug. 10 in the journals Nature Medicine and Genome Research, and a report on the third appears this week in the Proceedings of the National Academy of Sciences.

Researchers previously reported cases in which new LINE-1 insertions disabled cancer-fighting genes inside tumors, but no one knew how common it was for jumping genes to play a role in cancer development, says Haig Kazazian, M.D., professor of pediatrics at the Johns Hopkins University School of Medicine's McKusick-Nathans Institute for Genetic Medicine, who participated in two of the studies. “A challenge we had to overcome to begin to answer that question was detecting new copies of LINE-1 when the human genome already contains so many — it was like finding a needle in a haystack,” he adds.

After Kazazian and then-graduate student Adam Ewing devised a method to find LINE-1 insertions using powerful genetic sequencing technology, the two worked with research fellow Szilvia Solyom, Ph.D., and other colleagues to analyze the insertions in several types and stages of gastrointestinal cancer tissues biopsies. They compared the DNA insertions they found in colon, pancreatic and gastric cancer to those in healthy tissue from the same people. Results showed that new insertions of the still-mobile LINE-1 transposons tended to occur early in cancer development, Solyom says. For example, she says, a total of 29 new insertions were found in colon polyps, and 24 new insertions were found in samples from seven patients with pancreatic cancer. Of those, 13 were found in both the primary cancer and metastasized cancer cells, indicating that they had occurred before the tumor metastasized. The group’s findings about the timing of insertions in cancer appear in the Genome Research article.

In the study that appears in Nature Medicine, researchers led by Kathleen Burns, M.D., Ph.D., an associate professor of pathology at Johns Hopkins, homed in on LINE-1 insertions in pancreatic cancers. Using tissues from autopsies of 22 people with pancreatic cancer, they compared insertions in normal tissues, primary tumors and metastases. Of these, 21 of the cancers had LINE-1 insertions that were not present in the patients’ healthy tissue, Burns says, and there tended to be more insertions in the metastasized tumors than in the primary tumors, indicating that the insertions are occurring concurrently with cancer progression.

In the third study, graduate student Tara Doucet in Kazazian’s laboratory and others examined LINE-1 insertions in esophageal cancer and a condition known as Barrett’s esophagus that is sometimes a precursor to cancer. They found new insertions in some, but not all of both patients whose Barrett’s esophagus had not progressed to cancer after 15 or more years, and patients with both Barrett’s esophagus and cancer.

“The key question is whether these insertions are driving cancer development or whether they are just a byproduct of cancer,” says Kazazian. To help answer that question, his group hopes to analyze the genomes of individual cells to see whether most insertions seen in cancer cells also crop up in normal cells.

Whatever LINE-1’s role in cancer biology turns out to be, says Burns, the fact that the transposons are more active in gastrointestinal cancer cells than in healthy cells could eventually make them a powerful tool for early detection.

Other authors on the Nature Medicine paper are Nemanja Rodi?, Jared P. Steranka, Alvin Makohon-Moore, Allison Moyer, Peilin Shen, Reema Sharma, Cheng Ran Huang, Daniel Ahn, Paolo Mita, Martin S. Taylor, Norman J. Barker, Ralph H. Hruban and Christine A. Iacobuzio-Donahue of The Johns Hopkins University; Zachary A. Kohutek of Memorial Sloan Kettering Cancer Center; and Jef D. Boeke of New York University.

Other authors on the Proceedings of the National Academy of Sciences paper are Nemanja Rodi?, Reema Sharma, Isha Darbari, Gabriela Abril, Jungbin A. Choi, Ji Young Ahn, Yulan Cheng, Robert A. Anders and Stephen J. Meltzer, all of the Johns Hopkins University School of Medicine.

Other authors on the Genome Research paper are Anthony Gacita, Laura D. Wood, Florence Ma, Dongmei Xing, Min-Sik Kim, Srikanth S. Manda, Gabriela Abril, Gavin Pereira, Alvin Makohon-Moore, Ralph H. Hruban, Robert A. Anders, Akhilesh Pandey, Christine A. Iacobuzio-Donahue, Katharine E. Romans, Bert Vogelstein and Kenneth W. Kinzler of The Johns Hopkins University; and Leendert H.J. Looijenga and Ad J.M. Gillis of the University Medical Center Rotterdam.

The Nature Medicine study was funded by the Sol Goldman Pancreatic Cancer Research Center, the Fred and Janet Sanfilippo Fund in the Department of Pathology at the Johns Hopkins University School of Medicine, a Burroughs Wellcome Fund Career Award for Biomedical Scientists Program, the National Cancer Institute (grant numbers F31CA180682, R01CA163705, P50CA62924, R01CA179991), the National Institute for General Medical Sciences (grant numbers R01GM103999 and P50GM107632) and the National Science Foundation (project #DBI-0959894).

Work described in the Proceedings of the National Academy of Sciences paper was funded by the National Institute of General Medical Sciences (grant numbers 1R01GM099875 and P50GM107632), the Saul-Goldman Award, the Burroughs Wellcome Fund Career Award for Biomedical Scientists, the National Cancer Institute (grant numbers R01CA163705, CA190040, CA146799 and CA173390), the National Institute of Diabetes and Digestive and Kidney Diseases (grant number DK087454), and the ACS Clinical Research professorship.

The Genome Research study was funded by the National Institute of General Medical Sciences (grant numbers 1R01GM099875 and 1P50GM107632), the Sol Goldman Pancreatic Cancer Research Foundation, the Johns Hopkins GI Core Center, the 2013 AACR Basic Cancer Research Fellowship (grant number 13-40-01-SOLY), the Mater Foundation, the National Cancer Institute (grant numbers P50 CA62924, F31CA180682, CA140599, CA179991, RO1-CA43460 and RO1-CA57345), the Virginia and D.K. Ludwig Fund for Cancer Research, Lustgarten Foundation for Pancreatic Cancer Research, and the Sol Goldman Center for Pancreatic Cancer Research.