Serum biomarkers to predict immune related adverse events and benefit from single agent pembrolizumab therapy in early stage triple negative breast cancer

Abstract Breast cancer is the most diagnosed cancer and the second leading cause of cancer death in women in the USA. Immune checkpoint therapy (ICI) is revolutionizing the therapy of a number of malignancies, including triple negative breast cancer (TNBC). Therapeutic blockade of immune checkpoints, such as by anti-PD-1,

removes the tumor-initiated suppression of the immune system and unleashes prolonged anti-tumor immunity. Despite the encouraging success, many patients develop severe and sometimes life-threating adverse effects, or many also fail to benefit from immunotherapy. Existing immune therapy response predictive markers have

only modest positive predictive values and there are no clinically useful markers of toxicity. Our proposed study will focus on comprehensive evaluation of serological auto-antibodies (AAb) as potential predictors of immune related adverse event (irAE) and benefit from therapy. Serum based biomarkers exploit easy sample

accessibility and directly measure immune responses. Our platform can be rapidly adopted for clinical use. Our study leverages collaboration between experts on immunoproteomics and biomarker discovery and physician scientists specializing in breast cancer. Our study will analyze more than 3000 longitudinal serum

samples collected from 1,195 patients enrolled in a randomized phase III trial (SWOG S1418) that tests the efficacy of one year of single agent adjuvant pembrolizumab (anti-PD-1 antibody) therapy compared to observation in high risk TNBC. Serum samples were collected at baseline and at 13 and 55 weeks after

starting therapy, all samples are annotated with detailed toxicity and outcome information that were collected during this FDA registration trial. We will employ two complementary high-throughput antibody profiling technologies including Nucleic Acid Programmable Protein Array (NAPPA) and Multiple In Solution Antibody

Assay (MISPA) that we developed. NAPPA allows the detection of antibodies against tens of thousands freshly produced full length proteins in hundreds of samples while MISPA enables more precise quantification of hundreds of antibodies in thousands of samples and could be scaled for clinical use. Our approach involves (i)

a discovery step using the NAPPA arrays that will interrogate serum samples for AAbs against 18,000 human proteins in the discovery cohort, (ii) a verification step of identified outcome-predictive AAb using the MISPA platform using the discovery samples to select the final set of candidate markers, (iii) and blinded validation of

candidate AAb using MISPA on the held out validation set. Identification of biomarkers that can predict clinically-relevant immune-related adverse events or recurrence, and hence inefficacy of therapy, would help better estimate the risk benefit ratio of these very expensive and potentially toxic therapies. Predictors of

adverse events could also influence patient monitoring and allow earlier therapeutic intervention. The lessons learned from this proposed study on TNBC will likely impact a broad spectrum of other cancers since adverse events are not cancer type dependent.