Abstract 2500: Predictive biomarker discovery in sunitinib treated renal cancer patients: A non-hypothesis driven proteomic approach
Authors: Shreeve Rebecca L. , Vasudev Naveen , Zougman Alexandre , Selby Peter , Banks Roz 
Published: May 2015

Abstract
Introduction
Kidney cancer is one of the ten most common adult cancers, the majority of which (90%) represent renal cell carcinomas (RCC). Over 50% of patients develop metastases, for which the standard of care is vascular endothelial growth factor (VEGF)-targeted tyrosine kinase inhibitors (TKIs), such as sunitinib. Unfortunately, not all patients respond to these agents, toxicity is frequent and the treatment is expensive. The identification of biomarkers would have a significant impact on patient care, but unlike many targeted therapies in other cancers, no markers have yet been reliably found to predict response in this setting. Previous studies have mostly adopted a hypothesis-driven approach. Here, we use a global discovery approach, which may provide novel insights into response and resistance to these drugs.
Methods
Formalin fixed-paraffin embedded primary renal tissues, taken at nephrectomy from clear cell RCC patients subsequently starting sunitinib between 2008 and 2012 for metastatic disease, were employed in the study. Patient samples were identified from our large-scale research tissue bank. Tumors with intrinsic resistance versus those with prolonged sensitivity to drug were compared. Sixteen patients were selected based on best radiological response and duration on sunitinib; eight patients with partial response as best response and &gt;500 days on treatment, versus eight patients who had radiological disease progression within 200 days. Groups were matched by sex, age and grade, and pathological review was performed on all sections to avoid areas of necrosis and inflammation. Proteins were extracted, digested with trypsin and analyzed by liquid chromatography-tandem mass spectrometry with a Thermo Orbitrap Velos, using label free quantitation. Data were analyzed using the MaxQuant software suite, searched against the human UniProt database and statistical comparisons were performed in the R environment.
Results
In total, 4510 proteins were identified. Pairwise comparisons between the two groups revealed significant differences in 240 proteins (P&lt;0.05), of which 19 demonstrated a &gt;10 fold change between the total number of peptides identified. Proteins upregulated in the resistant group included those involved in proliferation, invasion and inflammation, whereas proteins upregulated in the sensitive group included those involved in immunogenicity and promotion of apoptosis.
Conclusion
We have identified a number of protein targets that have not previously been implicated in response / resistance to anti-VEGF TKIs, and which may provide novel insights into the biology governing this. Further work will focus both on verification of findings in additional clinical samples and functional characterization of proteins of interest. Preliminary verification of the results using Western blot and immunohistochemistry will be presented.
Citation Format: Rebecca L. Shreeve, Naveen Vasudev, Alexandre Zougman, Peter Selby, Roz Banks. Predictive biomarker discovery in sunitinib treated renal cancer patients: A non-hypothesis driven proteomic approach. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2500. doi:10.1158/1538-7445.AM2014-2500