Novartis team perseveres to develop more personalized approach to breast cancer therapy.
About a decade ago, after years of effort, researchers at Novartis had an experimental compound they thought might benefit cancer patients. They had a strong hunch, based on their research so far, that the cancer patients most likely to benefit had cancer with a mutation in a gene called PIK3CA, so they designed a clinical trial to test the drug in exactly those patients.
Back then, most cancer centers weren’t equipped to sequence the genes of their patients’ tumors and identify mutations. “This was very fancy at that time,” says Cornelia Quadt, a clinical program leader in oncology at the Novartis Institutes for BioMedical Research (NIBR) who worked on the trial.
For decades, doctors had focused on the location of tumors in the body rather than the specific mutations spurring their growth. Oncologists were accustomed to treating tumors with radiation and chemotherapy. They often weren’t prepared to identify patients who might benefit from a more targeted approach.
The Novartis team moved forward with their trial despite the challenge. Now after another ten years of research and development, the compound is approved for certain breast cancer patients with a PIK3CA mutation.
“This could be progress toward a more personalized approach in breast cancer,” says Christine Fritsch, director of drug discovery biology at NIBR and a key member of the drug discovery team alongside scientist Michel Maira.
NIBR drug hunters and PI3K
When Novartis drug hunters were developing their first experimental PI3K inhibitors in the early 2000s, the PI3K pathway was on everyone’s radar. It acts as a signaling hub in cells and is known to be active in many forms of cancer. The pathway receives messages from outside the cell and turns them into cues that trigger the cell to proliferate.
By 2006, Novartis researchers had already discovered two compounds that helped to inhibit the PI3K pathway and had one other in the works. Tests of all three investigational compounds in patients would later reveal that they acted too broadly and caused unwanted side effects.
Meanwhile, research in the field had uncovered a cancer-related gene mutation in PIK3CA, the gene that contains the instructions for building PI3K-alpha, one of four sub forms of the PI3K protein. PI3K-alpha regulates glucose metabolism, a process that turns sugar into energy.
The mutation flips the protein machinery on and drives cancer by giving cells a steady influx of fuel. “It becomes an accelerator of pro-survival, pro-growth signaling,” says Francesco Hofmann, Global Head of Oncology Drug Discovery at NIBR.
In response to this new information, the Novartis researchers started a new hunt, this time for a compound that would predominantly inhibit PI3K-alpha. “We were constantly integrating what we were learning and informing the next wave of drug discovery,” says Fritsch.
Advanced clinical trials
The Novartis team synthesized and studied approximately 600 compounds that inhibited PI3K-alpha before homing in on one potential drug candidate. Fritsch and her colleagues tested that investigational PI3K-alpha inhibitor using the Cancer Cell Line Encyclopedia, a collection of patient-derived cancer cell lines that had been genetically sequenced and categorized by Novartis and the Broad Institute of MIT and Harvard as part of a joint research program.
Tests against about 500 cell lines revealed that those most likely to die or stop growing when treated with the new compound had PIK3CA mutations.
It was this evidence that inspired the researchers to design a clinical trial to test the compound in patients with the PIK3CA mutation. The only way to do this was to sequence the tumor genes of every patient wishing to enroll.
To get the trial going, the team worked with cancer hospitals that were already testing patients for gene mutations. Later, they set up a centralized screening solution so that they could include more patients from a wider variety of locations.
That early-stage trial revealed that patients with a few types of cancer, including breast cancer, responded to the drug. Other evidence, such as the Cancer Cell Line Encyclopedia tests, had also pointed to responses in breast cancer.
More cancer treatment findings for PI3K
Given the data from this study, the team felt they had enough evidence to invest in a late-stage trial of their investigational PI3K-alpha inhibitor in breast cancer patients with the mutation. At this point, however, the organization already had terminated development of three other investigational PI3K inhibitors.
“You can imagine that the organization was feeling some fatigue and skepticism,” says Hofmann.
The team found additional instructive evidence in an unexpected place: an earlier failed Novartis trial that had run prior to discovery of the PIK3CA mutation. A close look at the data from that trial, which had tested an earlier investigational PI3K inhibitor in breast cancer patients, also showed a higher concentration of responses among patients with breast cancer with the mutation.
“You have to keep learning,” says Hofmann. “Persistence and continuous learning are the keys to drug discovery.”
The team zoomed in on patients with hormone receptor-positive, human epidermal growth factor receptor 2-negative (HR+/HER2-) advanced breast cancer. Approximately 40% of patients with HR+/HER2- breast cancer have the PIK3CA mutation. Patients with the PIK3CA mutation may develop resistance to endocrine therapies. “There was an unmet medical need for HR+/HER2- advanced breast cancer patients with a PIK3CA mutation,” says Fritsch.
The evidence taken all together allowed Novartis drug developers to design a clinical trial, which launched in 2015. US regulators recently approved the medicine, alpelisib, for use in combination with fulvestrant for the treatment of postmenopausal women, and men, with HR+/HER2- advanced or metastatic breast cancer with a PIK3CA mutation, as detected by an FDA-approved test after disease progression following an endocrine-based regimen.