Mass General Brigham recently announced a new plan to invest $50 million to improve its community and mental health care offerings.

{image id=1352663 align=left size=large byline=true caption="The Massachusetts General Hospital, home to Mass Eye and Ear and part of the Mass General Brigham system, is located in Boston."

Harvard Medical School-affiliated researchers recently revealed a new technique to help doctors detect head and neck cancers caused by strains of human papillomavirus up to 10 years prior to diagnosis.

Researchers at the Head and Neck Cancer Research Center at Mass Eye and Ear introduced their tool, HPV-DeepSeek, in the Journal of the National Cancer Institute earlier this month. The minimally invasive test may allow patients to seek treatment before symptoms appear — opening the door for both preemptive measures and increased survival rates.

While cancer-causing strains of HPV are best known for causing cervical and genital cancers, the prevalence of HPV-associated oropharyngeal cancers in the U.S. is much higher. But while cervical and genital cancers caused by HPV can be detected early on, there was no similarly applicable test for head and neck cancer.

“There’s been a big explosion in the cancer research world, the general topic of which is liquid biopsy,” Daniel L. Faden, the principal investigator and HMS assistant professor said. “Using those to do lots of different things — like diagnose cancer, screen for cancer, better, monitor for cancer after treatment, decide what treatments you need.”

HPV-DeepSeek is a whole-genome sequencing-based test designed to identify fragments of HPV DNA that shed from tumors into the bloodstream. Earlier work by the same team demonstrated that the test could reach 98.7 percent specificity and sensitivity when diagnosing cancer at a patient’s first clinic visit — outperforming existing diagnostic methods.

“This new paper takes the next step and says ‘can we actually detect the cancer before patients ever have symptoms, and how far ahead of time can we detect it?’ ” Faden said.

The researchers analyzed 56 blood samples from the Mass General Brigham Biobank: 28 from individuals who eventually developed head and neck cancers and 28 from healthy controls. The test successfully detected cancer-causing HPV DNA in 22 of the 28 pre-diagnosis cancer samples, with detection up to 7.8 years before diagnosis, while all 28 control samples tested negative.

Though research was primarily focused on HPV strains that cause oropharyngeal cancers, Faden is hopeful detection methods like HPV-DeepSeek can be used to identify patients with other types of HPV-related cancers.

“An ongoing area of research in our lab is understanding how these approaches could be used in other HPV associated cancers,” said Faden. “Those screening approaches, in some scenarios, are not ideal or not perfect, so there’s opportunities to improve.”

The researchers further improved the accuracy of their testing method by feeding data from HPV-DeepSeek to a machine learning algorithm trained on 153 cancer patients and 153 matched control samples. With artificial intelligence, the test correctly flagged 27 of the 28 eventual cancer cases up to 10.3 years pre-diagnosis — only misidentifying the sample with the longest lead time of 10.8 years.

“Increasing the number of samples that we have will improve our training set,” Dipon Das, first author of the paper and HMS research fellow, said. “It should improve the accuracy of the machine learning models, and, definitely, we are also planning to increase the parameters.”

The team plans to continue the research, extending the capabilities of HPV-DeepSeek to detect other types of cancers and fine-tuning the output to determine if the data points to an active tumor or a pre-cancerous state.

“Another major focus for our lab that also uses HPV-DeepSeek is actually not in the screening setting, but looking at our ability to use tests like this after treatment — particularly after surgery — to understand if the cancer was removed completely, and therefore help decide if patients should get more treatment or not,” Faden said.

Since much of the research conducted by Faden’s lab is funded through federal channels, recent changes to federal funding for research may “impact the pace and scale of the work” that they can perform, said Faden.

But Das remains optimistic that their team will continue to advance cancer detection research.

“This is just the beginning,” Das said.

—Staff writer Andrew Park can be reached at andrew.park@thecrimson.com. Follow him on Twitter at @AndrewParkNews.