The research teams also found mutations in the Notch family of genes, suggesting their role as regulators of an important stage in cell development may be impaired.
"This adds a new dimension to head and neck cancer biology that was not on anyone's radar screen before," said Levi Garraway, MD, PhD, a senior associate member of the Broad Institute, an assistant professor at Dana-Farber Cancer Institute and Harvard Medical School, and a senior author of one of the Science papers, in a press release. "Head and neck cancer is complex and there are many mutations, but we can infer there is a convergence on a cellular process for which we previously did not have genetic evidence."
The mutational analysis of Notch clearly indicated the power of genetic changes determining the function of these genes, added Kenneth Kinzler, PhD, professor of oncology and a molecular geneticist at Johns Hopkins, co-director of the Ludwig Center at Johns Hopkins, and an author of one of the Science papers.
"It gives us an important clue to start studying their function," he said.
Head and neck cancer is the sixth most common nonskin cancer in the world, with more than half a million new cases each year. Smokers, drinkers, and people infected with the human papillomavirus (HPV) have the highest risk of developing head and neck cancer, which is the collective name for tumors found in the oral cavity, including the mouth, larynx, and pharynx.
Jennifer Grandis, MD, a professor of otolaryngology and pharmacology and chemical biology at the University of Pittsburgh School of Medicine and a senior author of one of the Science papers, bemoaned the dearth of genetic information about head and neck cancer several years ago at a conference where Dr. Garraway had given a talk about the genomic landscape of melanoma.
"There was a really big gap in knowledge that was an obstacle to doing the right kind of research" about head and neck cancer, she said. "If we didn't know the spectrum of the mutations that were in our patients' tumors, we couldn't begin to develop more appropriate therapies because we were sort of playing in the dark."
Drs. Grandis and Garraway decided to study a University of Pittsburgh collection of 74 pairs of tumor and normal tissue samples using whole-exome sequencing. The exome represents the tiny fraction of the genome that encodes proteins. Focusing on just these protein-producing genes allows scientists to zero in on mutations that alter key proteins involved in cancer growth.
Meanwhile, another collaboration was unfolding among the cancer geneticists, sequencing experts, clinical researchers, and surgical oncologists at Johns Hopkins, MD Anderson, and Baylor College of Medicine. They studied 32 pairs of head and neck tumor and normal tissue samples by whole-exome sequencing and validated the findings in an additional 88 samples.
Both teams found mutations in the p53 gene in a little more than half of the tumors they studied. The next most common mutation occurred in Notch1, which showed up in about 15% of tumors.
Normally, Notch1 controls how cells differentiate into other kinds of cells, mature, stop dividing, and ultimately die. In head and neck cancer, the scientists saw mutations that turn Notch1 off, blocking differentiation and trapping cells in a proliferative, procancer state. Their maturation is arrested, leaving them stuck in an earlier stage, where other damage from smoking or alcohol or even p53 mutations can destabilize the genome.
Notch1's inactivation in head and neck cancer was surprising because in other cancers, such as leukemia, too much Notch signaling leads to cancer, the researchers noted.
"Our study suggests that a gene's role can depend on the tumor type. In some cases, a gene can act as a growth promoter in cancer, and in other cases, such as head and neck cancer, the same gene behaves as a growth suppressor," said Dr. Kinzler.
Efforts to combat the mutated p53 tumor suppressor gene with targeted drugs, for example, have so far been unsuccessful.
The next step, the researchers say, is to tease out how the genes function in normal cells and whether they form the lining of the larynx, pharynx, or another anatomical site affected by head and neck cancer.