NEW YORK (GenomeWeb) – Researchers with the I-SPY 2 TRIAL have determined that a pair of phosphoproteins could identify triple-negative breast cancer (TNBC) patients likely to respond to the tyrosine kinase inhibitor neratinib.
In a paper published last month in JCO Precision Oncology, the I-SPY 2 (Investigation of Serial Studies to Predict Your Therapeutic Response With Imaging and Molecular Analysis 2) researchers found that phosphorylation levels of EGFR and HER2 were associated with a positive response to neratinib (marketed by Puma Biotechnology as Nerlynx) in TNBC patients.
In addition to identifying a specific subset of patients who may respond to treatment with neratinib, the results indicate more generally that protein phosphorylation levels could identify patients likely to respond to targeted treatments despite lacking established genomic, transcriptomic, or protein markers, suggested Emanuel Petricoin, co-director of the Center for Applied Proteomics and Molecular Medicine (CAPMM) at George Mason University and senior author on the study.
This is of particular note in a disease like TNBC, which is challenging to treat due in part to a lack of targeted treatment options.
"We saw a very strong response rate in these triple-negative patients, who are ostensibly negative for the drug target [HER2]," he said. "And you wouldn't see it any other way except by measuring the [HER2 and EGFR] phosphorylation states."
The work presented in the JCO study stemmed from the identification in the I-SPY 1 TRIAL of a patient subpopulation that was HER2-negative based on standard pathology approaches but who had HER2 phosphorylation levels similar to that of HER2-positive patients. These HER2-negative, phosphoHER2-positive patients also showed heightened EGFR phosphorylation.
Based on those findings, the researchers decided to explore whether neratinib, which inhibits HER family kinases, would be effective in HER2-negative patients with phosphorylated HER2 and EGFR.
The I-SPY 2 TRIAL enrolled a total of 193 patients with locally advanced breast cancer determined to be at high risk for recurrence based on their Mammaprint scores. The goal of the trial was to identify markers, including imaging and molecular markers, for predicting the success of targeted treatments in different breast cancer subtypes.
Patients enrolled in the trial underwent pretreatment DNA sequencing, transcriptomic analysis, and expression and phosphorylation analysis of HER signaling proteins. All subjects received standard chemotherapy, with patients in the experimental arm also receiving neratinib. The endpoint for the trial was complete pathological response (pCR), meaning no cancer cells were detected in biopsies taken after treatment.
The JCO study focused on the TNBC subset of I-SPY 2 patients. Of these patients, 11 who were HER2- and HR-negative but had elevated phosphorylation of HER2 and EGFR received neratinib, while 11 other TNBC patients with elevated HER2 and EGFR phosphorylation were in the control arm. There were also 30 TNBC patients without elevated phosphorylation levels, with 20 in the experimental arm and 10 in the control arm.
Of the 11 with elevated levels treated with neratinib, nine (82 percent) achieved pCR. Of the 11 in the control arm, four (36 percent) achieved pCR. Among the TNBC patients without elevated phosphorylation levels, three of the 20 in the neratinib arm (15 percent), and two of 10 (20 percent) in the control arm achieved pCR.
These results indicate that TNBC patients with elevated HER2 and EGFR phosphorylation levels could be good candidates for treatment with kinase inhibitors targeting HER signaling, Petricoin said.
"Nearly 50 percent of the triple-negative patients [in the trial] had this phosphorylation signature that would be missed by every other way of measuring," he said. "There's a whole subset of patients that a drug like Neratinib could actually work very well in, and the only way to find those patients is with a phosphoprotein test."
He noted that while I-SPY 2 looked at neratinib, he believes the findings will prove generalizable to other drugs targeting this pathway and added that he and his colleagues are looking at other HER2-directed therapies.
Petricoin has long been a proponent of exploring protein phosphorylation signatures linked to cancer outcome and treatment response. He also is one of the inventors of the reverse phase protein array technology used in the I-SPY 2 TRIAL to measure protein phosphorylation levels.
RPPA uses cell lysates spotted in array formats that can then be probed with antibodies to proteins of interest. The assays can measure several hundred proteins in a sample of interest and have been useful in clinical cancer research due to their ability to work with small sample volumes.
Petricoin is also a co-founder and investor in Theranostics Health, which uses RPPA-based protein phosphorylation measurements to assess cancer signaling pathways and guide therapy. Avant Diagnostics acquired Theranostics in 2016.
Additionally, he is an inventor on patents filed by GMU on using phosphor HER2 and EGFR for predicting response to drugs targeting HER signaling.
More broadly, phosphorylation is a major area of interest in cancer research and protein research generally as it is key to protein signaling and cellular communication. Kinase inhibitors, which target the enzymes responsible for phosphorylating proteins, have emerged in recent decades as a major area of drug development.
Last week, in work unrelated to the I-SPY 2 TRIAL, researchers from the Spanish National Cancer Research Center and Utrecht University identified a set of six kinases whose activation levels appeared useful for predicting the likelihood of relapse and guiding therapy in TNBC. In that study, the researchers found that while TNBC was highly heterogeneous at the genetic level, with few highly penetrant mutations, information from these heterogeneous genetic alterations was integrated at the phosphoprotein level by a relatively small number of kinases, which could prove useful as biomarkers or therapeutic targets.
Regarding the I-SPY 2 TNBC findings, Petricoin noted that caution was warranted given the study's small sample size and additional validation in larger independent cohorts was needed. He said he and his colleagues are currently in discussions with Puma and other pharma companies with drugs that might be used to target this patient population, though they do not as of yet have any formal plans in place for an additional study.
"It's a surprising finding where a pharma company may not have been considering this as part of their strategic opportunity," Petricoin said, "because if you're developing a HER2 inhibitor, you're not going to be thinking about HER2-negative patients as being the patient population you're going after."