Abstract A38: Comprehensive kinome activity mapping of triple-negative breast cancer
Authors: Koemans Nina M. , Borden Carolien L. Van Der , Mori Miki , Pan Bo , Wang Changjun , Veer Laura J. Van ‘t , Coppé Jean-Philippe 
Published: August 2018

Triple-negative breast cancer (TNBC) accounts for around 15% of all breast cancer, with over 35,000 newly diagnosed women per year in the US. TNBC patients are at highest risk for recurrence, and neoadjuvant standard chemotherapy gives pathologic complete response in about 30% of these patients. Currently, no targeted therapy has been conclusively established to improve the outcome of TNBC patients, though successful phase II studies have been completed (1, 2). Identification of mechanisms that are targetable is of great importance to improve the management of TNBC significantly. The aim of this study is to validate the accuracy and determine kinome interconnectivity of our enlarged peptide library used for a newly developed high-throughput kinase activity-mapping (HT-KAM) assay.

The HT-KAM assay is our new screening technology to assess the catalytic activity of many kinases in parallel, which relies on collections of peptide probes that are used as combinatorial sensors to measure the phospho-catalytic activity of kinases in large-scale high-throughput ATP-consumption assays (3). The HT-KAM system provides access to a new, untapped, and large resource of biologically meaningful measurements, both as a means to map the entire cancer kinome and as a means to convert global phospho-signatures into functional patterns of kinase activity signatures. Kinome maps represent how kinase-signaling networks are rewired by overactive kinases, or drugs/targeted therapies in the context of different cellular backgrounds and exogenously mutated proteins/pathways, and provide insight into potentially targetable kinases. We previously established PhosphoAtlas, a heavily curated, comprehensive catalog database of 1,733 functionally interconnected proteins comprising the human phospho-reactome, including 4,748 unique edges that connect kinases to a target (776 kinase genes, 1,276 substrate protein genes, 2,492 heptameric peptide sequences [HPS]) (4).

Previously, the HT-KAM assay with our initial set of 225 peptide probe sensors measuring the phosphorylating activity of &gt;50 kinases, such as kinases belonging to EGFR/HER, MAPK, and RAF kinase families, was applied to explore mechanisms driving the unresponsiveness of colorectal and melanoma cancers to anti-BRAFV600E therapy in cell culture and patient-derived xenografts (PDX) (3). This successfully produced the predictive oncogenic kinome of melanoma tissues from patients suffering from fatal metastatic disease and, more importantly, identified new kinases/nodes that could be targeted to overcome drug resistance (3). Now, we made a selection of 640 peptide probe sensors, capturing the functionality of &gt;110 kinases over &gt;900 kinase-substrate nodes directly relevant to tumor biology that represent the majority of the curated interconnected proteins, from our PhosphoAtlas (4).

In this HT-KAM study, we assessed the catalytic activity of selected purified recombinant kinases and 10 TNBC cell lines (BT-549, HCC1143, HCC1395, HCC1937, HCC38, HCC70, HS578T, MDA-MB-231, MDA-MB-436, MDA-MB-468) to investigate whether our enlarged peptide library provides insight into further interconnectivity.

We anticipate that expanding our peptide library is key to the comprehensive exploration of cancer kinome, and in particular for complex conditions such as TNBC.

References:

1. Engebraaten O, Vollan HKM, Børresen-Dale A-L. Triple-negative breast cancer and the need for new therapeutic targets. Am J Pathol 2013;183(4):1064-74. http://www.sciencedirect.com/science/article/pii/S0002944013004616.

2. Rugo HS, Olopade OI, DeMichele A, et al. Adaptive randomization of veliparib-carboplatin treatment in breast cancer. N Engl J Med 2016;375:23-34. PMID: 27406347.

3. Coppé JP, Mori M, Pan B, et al. Functional detection of phospho-catalytic circuits identifies new vulnerabilities of cancer. Submitted.

4. Olow A, Chen Z, Niedner RH, et al. An atlas of the human kinome reveals the mutational landscape underlying dysregulated phosphorylation cascades in cancer. Cancer Res 2016;76:1733-45. PMID: 26921330.

Citation Format: Nina M. Koemans, Carolien L. Van Der Borden, Miki Mori, Bo Pan, Changjun Wang, Laura J. Van ‘t Veer, Jean-Philippe Coppé. Comprehensive kinome activity mapping of triple-negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Breast Cancer Research; 2017 Oct 7-10; Hollywood, CA. Philadelphia (PA): AACR; Mol Cancer Res 2018;16(8_Suppl):Abstract nr A38.