Abstract LB-C05: Early exosome mRNA changes are associated with improved progression free survival of metastatic melanoma patents on ipilimumab: Identification of a novel exosome mRNA signature of ipilimumab response
Authors: Coticchia Christine M. , Sullivan Ryan J. , Flaherty Keith T. , Hurley James D. , Hu Lan , Blackmon Shauna M. , Brock Graham , O'Neill Vincent T. , Skog Johan 
Published: May 2016

Abstract
Background: The recent approval of several new targeted therapies for metastatic melanoma (including ipilimumab, an anti-CTLA-4 therapy) has introduced a new challenge for physicians to determine which drug(s) provide the most benefit to an individual patient. More effective strategies using blood or tissue biomarkers to identify patients who are responding (or not responding) to a particular therapy are needed.
Exosomes are abundantly released from tumors into biofluids such as plasma and carry nucleic acids and proteins from the cell of origin. This enables a non-invasive way to monitor a patient's tumor status in real-time. However, despite the many advantages of a liquid biopsy over traditional and invasive biopsy of primary tumors, there are challenges. Specifically, a biofluid-based cancer test for a tumor-specific exosome signature must be identified against a background of exosomes originating from non-malignant cells.
Here we set out to identify early changes in exosome mRNA that predict six month progression free survival (PFS) of metastatic melanoma patients treated with ipilimumab. To facilitate the identification of gene changes related to ipilimumab treatment, we examined exosome mRNA from patient plasma with and without exclusion of non-tumor exosomes. We predicted that depletion of normal reticulocyte exosomes using an anti-glycophorin A platform would enrich tumor-derived exosomes in plasma and reveal rapid exosome mRNA changes between baseline and week 2 or week 4 of treatment.
Methods: Plasma was obtained from 17 patients with metastatic melanoma before receiving ipilimumab (baseline) and longitudinally throughout treatment. Response to therapy was determined by RECIST. Patients who achieved at least six months PFS from start of ipilimumab (n = 7) were compared to patients with progressed disease (PD) on ipilimumab (n = 10).
Matched patient plasma samples at baseline and week 2 or week 4 were analyzed. The plasma exosome mRNA signature using the glycophorin A exclusion method was compared with total plasma exosome mRNA from the same patient samples. Analysis of exosomal mRNA utilized the OpenArray® Human Inflammation Panel. Fold change in gene expression between baseline and week 2 or 4 was calculated.
Results: Targeting glycophorin A to remove normal reticulocyte exosomes from plasma enriched the RNA profile compared to total exosome profiling. Of the 587 genes examined, the exclusion platform revealed 28 genes that were significantly increased between baseline and 2-4 weeks in the majority of patients who went on to achieve 6 month PFS, and decreased in patients with PD. This signature included immune-related genes such as CCR5, INFAR1, LTB, MALT1 and TNFSF8. In contrast, the exosome mRNA signature without the exclusion platform revealed only four genes that changed between baseline and week 2 or 4: A2M, CD163, TLR1 and TNFSF10.
Conclusions: We have developed a platform to exclude normal exosomes from plasma which increases the power to discriminate early exosome mRNA changes associated with improved progression free survival in metastatic melanoma patients in response to ipilimumab. Future work will focus on refining and validating the mRNA signature.
Citation Format: Christine M. Coticchia, Ryan J. Sullivan, Keith T. Flaherty, James D. Hurley, Lan Hu, Shauna M. Blackmon, Graham Brock, Vincent T. O'Neill, Johan Skog. Early exosome mRNA changes are associated with improved progression free survival of metastatic melanoma patents on ipilimumab: Identification of a novel exosome mRNA signature of ipilimumab response. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-C05.