Startup PapGene Develops DNA Test for Ovarian, Endometrial Cancers

Johns Hopkins startup PapGene is developing a test to detect early-stage ovarian cancer.

Johns Hopkins Technology Ventures

Although physicians have used the Pap test to detect early-stage cervical cancer for decades, there’s no analogous test on the market to detect early-stage ovarian cancer.

Johns Hopkins startup PapGene plans to change that.

In a specially designed laboratory at the FastForward Homewood innovation hub, PapGene scientists are developing a next-generation DNA sequencing test to look for specific somatic mutations suggesting the presence of ovarian or endometrial cancer cells. Somatic mutations are genetic alterations acquired by cells, and key somatic mutations correlate to different types of cancer, explains Howard Kaufman, PapGene’s CEO.

While the Pap test retrieves cells from the cervix to check for the presence of cervical cancer or its precursor, PapGene’s test takes that same patient sample and looks for mutant DNA shed from cells originating elsewhere in the gynecological tract, including from ovarian or endometrial cancer tumors.

“If a somatic mutation is there, it’s a specific sign that a patient has a gynecological cancer,” says Isaac Kinde, PapGene’s chief scientific officer and a recipient of an M.D. and a Ph.D. in cellular and molecular medicine from The Johns Hopkins University last May.

The Johns Hopkins scientists involved with the original research behind the test found cells with mutant DNA from ovarian and endometrial cancers on the cervix—a surprising discovery, Kaufman says, given the distance the cells had to have traveled from their place of origin.

Those scientists, who filed a patent on their discovery in 2013, included Chetan Bettegowda, assistant professor of neurosurgery and oncology at the Johns Hopkins University School of Medicine; Luiz Diaz Jr., associate professor of oncology at the School of Medicine; Kinde; Kenneth Kinzler, professor of oncology at the School of Medicine; Nickolas Papadopoulos, professor of oncology at the School of Medicine; Bert Vogelstein, Clayton Professor of Oncology and Pathology at the School of Medicine; and Yuxuan Wang, a graduate student at the university pursuing both a medical degree and a doctoral degree in cellular and molecular medicine.

Kinde, Kinzler, Papadoupoulos and Vogelstein also filed a patent in 2012 on a DNA sequencing system that detects small percentages of mutations. The system helps surpass a significant barrier to detecting mutations in a commonly collected clinical sample, such as that collected in a Pap test.

Both patents were filed through Johns Hopkins Technology Ventures, and PapGene, which the scientists incorporated in March 2014, received licenses for both technologies to develop a test for early-stage ovarian and endometrial cancers in January 2015. The scientists hired Kaufman, a former senior director of technology assessment and business development for technology development company Hologic Inc., as CEO in fall 2014.

Because PapGene scientists are developing such a sensitive test, they need access to laboratory rooms with different air pressures, and the rooms must be arranged to facilitate ideal workflows and minimize cross-contamination. The Technology Ventures office connected PapGene with the architects, building engineers and on-site contractors building out the FastForward Homewood hub in the Stieff Silver Building to ensure the startup’s lab space was appropriate for its work.

PapGene scientists are planning clinical studies to collect additional samples and demonstrate the usefulness of the test, Kaufman adds. They hope to roll out the test initially to high-risk women—those with a family history of ovarian or endometrial cancer, or who have cells with inherited genetic alterations in their BRCA1 or BRCA2 genes. Eventually, as use of the test spreads and testing costs decrease, the test could be available on a wider scale, Kaufman explains.

In 2015 in the United States, about 14,000 women will die from ovarian cancer and 10,000 from endometrial cancer, according to the National Cancer Institute. Although endometrial cancer is more common, ovarian cancer is more lethal, as it’s often not discovered until reaching an advanced stage, when it’s generally too late for effective treatment.

“The path we’re taking is for early diagnostics,” Kaufman says. “When detected early, most cancers can be cured with the therapies available today—a more promising option than developing new treatments for advanced cancers.”

PapGene has raised $3 million, and it received a Baltimore Business Journal Health Care Innovators Award in June.

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