By Catherine Shaffer

April 25, 2016 | A new study by UCLA researchers demonstrates the use of next generation sequencing to predict survival of brain cancer patients treated with a cancer vaccine. The vaccine, an autologous dendritic cell therapy called DCVax-L, is under development by Northwest Biotherapeutics Inc., of Bethesda, Md., for glioblastoma multiforme (GBM). It is designed to activate the adaptive immune system, including T lymphocytes (T cells).

The study was published last month in Cancer Immunology Research (doi: 10.1158/2326-6066).

In a Phase I/II clinical trial of DCVax-L in 39 patients with glioblastoma, median survival was three years, or around 2.5 times the usual duration of survival for patients receiving standard of care treatment only. However, there was a large difference between subgroups of patients who showed significant benefit from the therapy and subgroups who appeared to receive no benefit at all.

The clinical trial lead investigator, Linda Liau, and her collaborator Robert Prins at the University of California, Los Angeles, teamed up with Seattle, Wash.-based Adaptive Biotechnologies Corp. to revisit the clinical trial data for deep sequencing of the T cell receptors inside the tumors and in peripheral blood. The technology allowed the team to quantitatively measure tumor-infiltrating lymphocytes (TILs) and compare specific T cell receptor sequences between tumor and peripheral blood.

They learned that elevated T cell levels in the glioblastoma tumor predicted a longer survival time and that significant overlap in sequence between T cell receptors in the tumor and in the peripheral blood was correlated with extended survival.

Prins told Clinical Informatics News that identifying matching T cell receptor sequences in the tumor and in the peripheral blood gives the researchers important new information, “You can see whether an immune response has been mounted after vaccination.”

The results suggest that patients who have higher levels of TIL and have matching T cell receptors sequences in the tumor and peripheral blood already have some level of immune response that can be boosted with dendritic cell therapy. Patients that don't have any T cells inside their tumors, have little response. “Their immune systems were ignorant or ‘tolerized’ to the tumor; they didn't seem to respond as well,” said Prins.

Vaccinating the Model Immune System

The DC vaccine is a personalized immunotherapy created using activated dendritic cells to mobilize the immune system against a cancer. It is prepared using the patient's own tumor lysate to educate the immune system to recognize the cancer cells. This is important because patients with the same cancer can have large variation in tumor profiles.

In addition to the completed Phase I/II trial in GBM, Northwest is running a double blind, randomized, Phase III trial of DCVax-L in 348 patients with newly diagnosed GBM and a Phase I/II trial of another product, DCVax-Direct, in 60 patients with all types of inoperable solid tumors.

This was the first study using high throughput next generation sequencing to monitor systemic T cell response. Adaptive Biotechnologies combines high throughput sequencing and bioinformatics technologies for profiling of T cell and B cell receptors. Harlan Robins, Chief Scientific Officer of Adaptive, said that T cells have huge genetic diversity. This is because the surface receptors on the cell are used to recognize immune system targets. “It's almost like a bar code,” Robins said. “So we can track them and compare them between different tissues.”

Previous high throughput sequencing technologies are not designed for the repeated, quantitative sequencing that is required to characterize those “bar codes” on T cells and B cells. Adaptive was built around developing technology that could sequence at an extremely deep level. “No one ever thought you'd want to sequence the same piece of DNA a hundred million times,” Robins said. “We needed to go very deep in one particular locus, and we had to be able to create technology to do that.”

To achieve its goals, Adaptive developed a synthetic, or “fake” immune system to test the accuracy of its methods. The synthetic immune system is encoded by a custom-synthesized strand of DNA including all of the elements and properties of the adaptive immune system.

Once it had a full synthetic immune system for comparison, Adaptive was able to develop accurate methods for sequencing test DNA. “The first time we did it, we did not get the right answer. We were off by a mile,” said Robins. “Since we had this control, we could continue to make it better. Now it's almost perfect.”

The majority of Adaptive's prior diagnostic development has been in blood cancers, where the T cell or B cell itself is the cancer cell. The glioblastoma study was an expansion of applications for the technology into profiling an immune response to cancer. “What we're really seeing is that we can assess the systemic effect by looking at a comparison of blood and tumor. That's the real power of the technology,” said Robins.

GBM is one of the most deadly cancers. About 18,000 people per year in the U.S. die of glioblastoma, and average survival after diagnosis is only 12 to 24 months. Initial clinical results for DCVax-L in GBM are promising, but only a subset of patients respond strongly to the therapy, and currently no biomarkers exist to predict or track response to therapy. T cell receptor sequencing has the potential to be developed as a clinical diagnostic to identify patients who can benefit, or even potentially bridge the gap if mechanisms can be revealed, but further study is needed, Prins said.

“We have to do more to convince ourselves that it can tell us what we think it's telling us,” he added. “This is sort of a first foray to using this technology in a translational way.”