Abstract 5511: Direct effect of regorafenib on tyrosine kinase activities in treatment naive colorectal cancer (CRC) primary tumor tissue

Background:

Regorafenib (BAY 73-4506) is the first small molecule tyrosine kinase inhibitor that has been approved for treatment of advanced CRC. In the Correct trial*, 1% of the participants showed a partial response and 42.8 % had stable disease. KRAS wild type and mutants showed equal response rates.

Regorafenib is a multityrosine kinase inhibitor with nM IC50's against CRAF, VEGFR2, KIT and RET and is about tenfold less potent for BRAF, BRAFV600E, PDGFRβ and VEGFR1 and 3. We tested the effect of regorafenib and other angiogenic inhibitors on patient-derived kinases in treatment naive primary colon tumor samples for potency and selectivity of inhibition.

Method:

Colon tumor tissue from patients who had given informed consent was fresh frozen after surgical resection. All tumor specimens were analysed for BRAF and KRAS mutation status. Tissue cryosections were lysed in buffer with phosphatase and protease inhibitors. Phosphotyrosine kinase (PTK) and serine/threonine kinase (STK) activity profiles of tumour tissue were generated on PamChip® peptide microarrays comprising hundreds of peptide sequences derived from known human phosphorylation sites. The ex vivo effect of kinase inhibitors on these kinase activity profiles was determined. Peptide phosphorylation was monitored using fluorescently labelled antibodies. Data were analysed with Bionavigator software.

Result:

Kinase activity profiles were obtained from 16 CRC patient tumors for both tyrosine as well as serine/threonine specific peptide phosphorylations. Direct enzymatic inhibition of tumor-derived PTK activity was observed in all 16 samples at low micromolar concentrations (3 µM) of spiked-in regorafenib. For the serine/threonine kinase activity, spiking in of a high concentration of regorafenib (50 µM) resulted in only low levels of inhibition of phosphorylations on a subset of peptides, including BRAF substrate peptides. No difference in inhibition was observed between KRAS and BRAF mutants and wild type tumors. Furthermore the non-inhibited kinase activity profiles did not correlate to mutation status either.

Conclusion:

For the first time the direct biochemical effect of regorafenib has been tested on primary tumor tissue from CRC patients. These data support previous findings suggesting that regorafenib, besides its angiogenic activity on vasothelial cells, can inhibit oncogenic tyrosine kinases in the tumor. These results will be a basis for biomarker analysis by correlating on-chip drug effects to clinical responses.

*Grothey et al, Lancet 2013 381(9863):303-312

Citation Format: Maria H. Hilhorst, Rosanne van den Oord, Hans Pruijt, Adriaan van den Brule, Peet Nooijen, Rik de Wijn, Liesbeth Houkes. Direct effect of regorafenib on tyrosine kinase activities in treatment naive colorectal cancer (CRC) primary tumor tissue. [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 5511. doi:10.1158/1538-7445.AM2014-5511

Peptide microarrays for profiling of serine/threonine kinase activity of recombinant kinases and lysates of cells and tissue samples

Peptide microarray technology can be used to identify substrates for recombinant kinases, to measure kinase activity and changes thereof in cell lysates and lysates from fresh frozen (tumor) tissue. The effect of kinase inhibitors on the kinase activities in relevant tissues can be investigated as well. The method for performing experiments on dynamic peptide microarrays with real-time readout is described, as well as the influence of assay parameters and suggestions for optimization of experiments.

Abstract 4113: Kinase activity based biomarkers: Identification of prognostic and erlotinib response prediction markers in NSCLC patients

Background: Reliable diagnostic tests are needed to identify early stage non-small cell lung carcinoma (NSCLC) patients with poor prognosis. Concomitantly there is a clear need for tests that enable the selection of patients who will benefit from targeted therapy with kinase inhibitors. We evaluated kinase activity profiles in two groups of early stage NSCLC patients, either for prognosis of long- or short-term survival, or for predicting erlotinib drug response.

Method: Retrospective studies were performed on fresh frozen resection material of two groups of early stage NSCLC patients. The first group consisted of 48 short- and long-term survivors who underwent a complete surgical resection (5+ years follow-up). The second group consisted of 14 NSCLC patients who received 3 weeks of neo-adjuvant treatment with erlotinib prior to complete surgical resection. Response evaluation to neo-adjuvant treatment was based on histopathological examination of the surgical specimens. For both studies, kinase activity profiles of lysed cryosections of tumour tissues were generated in the presence and absence of protein tyrosine kinase inhibitors on PamChip® peptide micro-arrays, comprising 144 tyrosine containing peptides, derived from known phosphorylation sites of human proteins. Partial least square discriminant analysis was used to construct prediction models. ClustalW alignment algorithms were used to investigate the most informative phosphorylation sites.

Results: Kinase activity profiles obtained in the absence of inhibitor did not distinguish between subgroups (long- versus short-term survival, responder or non-responder to TKI), whereas ratios of inhibited versus non-inhibited signals resulted in distinct classifiers predicting survival for the first group, and response for the second group. Multivariate unsupervised analysis with leave-one-out cross-validation resulted in an error rate for survival prediction of 29%. In the drug response prediction 13 out of 14 patients were correctly classified.

Conclusion: This is the first study to show that kinase activity profiles of tumour tissue exposed to a kinase inhibitor can be used to identify NSCLC patients likely to respond to erlotinib treatment. Furthermore, based on kinase activity profiles of early stage NSCLC tumours, a prognostic classifier, for a set of 48 patients, was obtained.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4113. doi:10.1158/1538-7445.AM2011-4113

Abstract 4046: Direct detection of AKT/PKB activity in a Pten knock out mouse model using dynamic peptide microarrays

Background. In many cancers, deregulation of kinases or phosphatases leads to activation of the AKT/PKB pathway. This pathway regulates many cellular processes including metabolism, differentiation, translation, proliferation and apoptosis, so is central in determining cell fate. Several kinase inhibitors that influence AKT activity are investigated in the context of new pharmacotherapies in cancer. However, often a fraction of patients responds and it is not possible to identify those patients up front. It would be a major leap forward if response to therapy could be determined in an in vitro assay prior to the onset of therapy. Methods to directly measure this activity do not exist.

In this study, we explored:

1) Whether it is feasible to determine AKT activity profiles in lysates of hyperplastic prostates of PSA-Cre;Pten-loxP/loxP mice.

2) Whether addition of AKT inhibitors affects the phosphorylation profiles in an inhibitor specific way.

Methods. The PSA-Cre;Pten-loxP/loxP mouse prostate cancer model was described in Ma et al, 2005 Cancer Res 65 5730 and Korsten et al, 2009 PLoS ONE 4(5) e5662. Prostate tissues of three 4 months old PSA-Cre;Pten-loxP/loxP mice and three wt mice were lysed in buffer with protease and phosphatase inhibitors. Lysates and recombinant AKT were incubated in triplicate on PamChip® peptide micro-arrays (Folkvord et al. Int J Radiat Oncol Biol Phys. 2010 78:55) comprising 140 or 256 ser/thr containing peptides derived from known human phosphorylation sites. Peptide phosphorylation was monitored with anti- phosphoserine and anti-phosphothreonine antibodies. Incubations were performed in the presence and absence of AKT inhibitors MK2206 and AKT Inhibitor VIII. Western blotting was performed using standard methods. Blots were stained with anti-phospho-AKT antibodies and anti total AKT antibody.

Results. Phosphorylation activity profiles revealed differential activity between PSA-Cre;Pten-loxP/loxP and wt mouse prostate lysates, with the Pten negative lysate having increased activity. Addition of AKT inhibitors reduced signals on several of these peptides in the prostate lysates from targeted Pten knockout mice, but not in the lysates of the wt mice. Addition of non-AKT specific inhibitors like UCN-01 resulted in signal reduction in both lysates.

Western blots showed the presence of AKT in the wt lysate and in the Pten knockout lysate. Only the Pten knockout lysates contained AKT phosphorylated on S473 and T308.

Conclusion. In PSA-Cre;Pten-loxP/loxP mouse prostate tissue lysate, the activity of AKT is increased compared to wild type tissue levels. The activity profiles of the PTEN/AKT pathway will support the studies on the complicated regulation of AKT activity. Up to now these studies were limited to detection of phosphoprotein abundances. This new multiplex kinase activity assay will add a new dimension and a scope of applications like drug testing.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4046. doi:10.1158/1538-7445.AM2011-4046

Abstract 797: Kinase activity profiling of tumor tissues of different origin

Introduction:

Many new anti-cancer drugs target kinase activity. Unfortunately, methods to monitor the drug effects at the enzymatic level in patient derived tumor tissue are lacking. Here, a novel molecular profiling method for application in biomarker discovery is presented. This method is based on measuring kinase activities in tumor tissue extracts, and involves assessment of inhibition by a drug of interest. This ex vivo activity-based approach is enabled by dynamic peptide microarrays. These arrays comprise of peptides, which are known substrates for phosphorylation by protein kinases. Here we investigated the applicability of this approach in the classification of multiple tumors of different origin.

Method:

Patient-derived fresh frozen tissues of different tumor types (24 breast cancer (BC), 14 non-small cell lung cancer (NSCLC), 12 renal cell carcinomas (RCC)) were used for extraction of total protein in lysis buffer. Dependent on the tissue source, 6 slices of 10 µm were sufficient for 20-100 microarray analyses. Equal amounts of total protein were analyzed for kinase activity on dynamic PamChip peptide microarrays. These arrays comprised 144 or 256 different peptides. A PamChip96 plate format was used, enabling 96 microarray incubations per run. Protein amounts ranging from 1 − 5 µg were used per microarray analysis. Tumor extracts were analysed in the presence and absence of kinase inhibitor drugs (RCC: sorafenib and sunitinib, NSCLC: gefitinib).

Results:

We show here that from different tumors kinase activity profiles could be generated reproducibly (10-15% CV for selected peptides). Control experiments showed protein concentration and ATP dependency. In the RCC experiments different phosphorylation profiles were obtained when the non-tumor tissue was compared to tumor tissue derived from the same patient, showing higher kinase activities in the latter. In addition, inhibitor dependent modulation of the peptide phosphorylations was observed (sorafenib vs. sunitinib). Furthermore, differential kinase activity profiles were obtained that could be correlated to different patient subgroups (BC) or clinical data (long vs. short term survivors; NSCLC).

Conclusion:

A novel molecular profiling approach was successfully applied for classification of different tumors. This approach is based on detection of kinase activities as well as inhibition of kinase activity in tumor tissues. Application of this method in the discovery of biomarkers for diagnosis, prognosis or prediction of drug response is foreseen.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 797.