Envision this possible future clinical scenario: a breast cancer patient and her physicians are deciding on the best possible treatment. Their decision is informed by a comprehensive molecular profile of the patient’s cancer samples that predicts the most likely response of the cancer to treatment.

If the profile predicts a high likelihood of a complete positive response and long-term freedom from relapse, then this treatment would be the preferred choice. But if the profile predicts that the tumor would likely be resistant to treatment, alternative treatments must be implemented.

Although this situation is not yet a reality, a team led by researchers at Baylor College of Medicine and the Broad Institute of Massachusetts Institute of Technology and Harvard has taken significant steps in that direction. They report in Cell Reports Medicine that conducting an integrated proteogenomic profiling of cancer cells, which combines the analysis of DNA, RNA, protein and phosphoprotein data, revealed two novel indicators of tumor response to treatment and alternative therapeutic targets for treatment-resistant HER2+ breast cancer.