Background: Focal amplification of fibroblast growth factor receptor 1 (FGFR1) defines a subgroup of breast cancers with poor prognosis and high risk of recurrence. We sought to demonstrate the ...potential of circulating cell-free DNA (cfDNA) analysis to evaluate FGFR1 copy numbers from a cohort of 100 metastatic breast cancer (mBC) patients. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples were screened for FGFR1 amplification by FISH, and positive cases were confirmed with a microarray platform (OncoscanTM). Subsequently, cfDNA was evaluated by two approaches, i.e., mFAST-SeqS and shallow whole-genome sequencing (sWGS), to estimate the circulating tumor DNA (ctDNA) allele fraction (AF) and to evaluate the FGFR1 status. Results: Tissue-based analyses identified FGFR1 amplifications in 20/100 tumors. All cases with a ctDNA AF above 3% (n = 12) showed concordance for FGFR1 status between tissue and cfDNA. In one case, we were able to detect a high-level FGFR1 amplification, although the ctDNA AF was below 1%. Furthermore, high levels of ctDNA indicated an association with unfavorable prognosis based on overall survival. Conclusions: Screening for FGFR1 amplification in ctDNA might represent a viable strategy to identify patients eligible for treatment by FGFR inhibition, and mBC ctDNA levels might be used for the evaluation of prognosis in clinical drug trials.
► Study of an AMPA-receptor potentiator (S70340) using transcriptomics-based approach. ► (
S)-AMPA
+
S70340 activated genes involved in neuroprotective and cognitive effects. ► Functional pathway ...analyses suggested the activation of neuronal neurite outgrowth. ► In silico promoter analysis of time course regulated genes. ► Important role of CREB mediating gene regulation.
To improve our understanding of the molecular events underlying the effects of positive allosteric modulators of the alpha-amino-3-hydroxy-5-methyl-4-isoxazoleproprionic acid (
S)-AMPA-type glutamate receptors, gene expression profiles of primary cortical culture were measured by Agilent-Microarray technique under (
S)-AMPA (1
μM) stimulation for 0.5, 6, 24 and 48
h in the presence or absence of S70340 (30
μM), an allosteric potentiator of AMPA receptors. (
S)-AMPA and S70340 treatment alone have little effect on gene expression whereas as early as 6
h, their combination induced a large number of genes known to decrease apoptosis and mediate cell survival. Pathway analyses of (
S)-AMPA
+
S70340 treatment-mediated gene expression from 6 to 48
h further suggested the activation of cellular functions including neuron differentiation and neurite outgrowth. A proportion of genes implicated in these functions encode proteins involved in environmental cues and are expressed in growth cones, such as extracellular matrix component proteins and filopodia microfilament-associated proteins. Time course analysis of mRNA expression combined with in silico promoter analysis revealed an enrichment in the cAMP response element (CRE) among co-regulated genes. This study demonstrated that S70340-mediated AMPA potentialisation activated genes and functional processes involved in neuroprotective and cognitive effects and describes putative new functional biomarkers.
Rosiglitazone (RSG), developed for the treatment of type 2 diabetes mellitus, is known to have potent effects on carbohydrate and lipid metabolism leading to the improvement of insulin sensitivity in ...target tissues. To further assess the capacity of RSG to normalize gene expression in insulin-sensitive tissues, we compared groups of 18-day-treated db/db mice with increasing oral doses of RSG (10, 30, and 100 mg/kg/d) with untreated non-diabetic littermates (db/+). For this aim, transcriptional changes were measured in liver, inguinal adipose tissue (IAT) and soleus muscle using microarrays and real-time PCR. In parallel, targeted metabolomic assessment of lipids (triglycerides (TGs) and free fatty acids (FFAs)) in plasma and tissues was performed by UPLC-MS methods. Multivariate analyses revealed a relationship between the differential gene expressions in liver and liver trioleate content and between blood glucose levels and a combination of differentially expressed genes measured in liver, IAT, and muscle. In summary, we have integrated gene expression and targeted metabolomic data to present a comprehensive overview of RSG-induced changes in a diabetes mouse model and improved the molecular understanding of how RSG ameliorates diabetes through its effect on the major insulin-sensitive tissues.
Abstract
Aberrant activity of receptor tyrosine kinases (RTKs) has been associated with tumor progression in a wide variety of human malignancies, making them promising drug targets for cancer ...therapy. Although, in some instances, specific inhibition of just one of these RTKs suffices for inhibition of tumor progression, in the majority of cases, targeting more than one RTK could be required for therapeutic efficacy. Moreover, increased expression or activation of RTKs is often associated with resistance to standard chemotherapy agents or signal transduction modulators. S 49076 is a novel, potent, ATP-competitive tyrosine kinase inhibitor of the RTKs MET, AXL and FGFR. S 49076 blocks autophosphorylation of these RTKs and their downstream signaling in cells with IC50 values of less than 50 nM in the case of MET and AXL, and at below 200 nM for FGFR1/2/3. In vitro, S 49076 inhibits the proliferation of MET- and FGFR2- dependent gastric cancer cells, blocks MET-driven migration of lung carcinoma cells and inhibits colony formation of hepatocarcinoma cells overexpressing FGFR2 and AXL. In vivo, oral administration of S 49076 inhibits MET autophosphorylation and tumor growth in subcutaneous GTL-16 human gastric carcinoma and U87-MG human glioblastoma at 6 mg/kg/day. In FGFR2-dependent SNU-16 gastric tumors S 49076 inhibits FGFR2 autophosphorylation, downstream signaling and tumor growth at 25 mg/kg/day. In a panel of 53 patient-derived tumors and 14 cell lines of diverse origin growing in three-dimensional in vitro culture, twenty-five (37%) were found to be sensitive to S 49076 at 1 µM or less. In the majority of cases, analysis of the expression, activation and mutation status of MET, AXL, FGFR1/2/3 and other target kinases of S 49076 as well as that of major signaling proteins enabled hypotheses to be made concerning the sensitivity or resistance to S 49076. Moreover, in many of these resistant tumors, a rationale for association of S 49076 with other targeted therapies emerged. Examples of the efficacy of such combined therapies will be shown. Based on these preclinical studies showing a favorable and novel pharmacological profile of S 49076, a phase I study is currently underway in patients with advanced solid tumors.
Citation Format: {Authors}. {Abstract title} abstract. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 848. doi:1538-7445.AM2012-848
Abstract
Protein kinase inhibitors constitute a class of anticancer agents with demonstrated clinical efficacy. However, the clinical benefit of these agents is often limited to a subset of patients ...with specific genomic lesions in their tumor cells rendering them sensitive to inhibition of one or more target kinases. It is therefore becoming increasingly important to identify biomarkers of patient stratification to enable personalized care. For those inhibitors targeting just one kinase this stratification strategy is relatively straightforward, although the number of patients who will benefit from these highly selective inhibitors alone is in general severely limited. In the majority of cases, the simultaneous targeting of more than one kinase, possibly by the same drug, will be required for therapeutic efficacy. However, for multi-target kinase drugs, patient stratification is considerably more complex and is becoming a major challenge during clinical development.
S 49076 is a novel, potent, ATP-competitive tyrosine kinase inhibitor with activity demonstrated in cell and animal assays against the receptor tyrosine kinases MET, FGFR1/2/3 and AXL, all of which are associated with progression of a wide range of human malignancies. In kinase binding assays, S 49076 also binds to clinically-relevant MET mutated isoforms and 32 other kinases, many of which have also been implicated in cancer pathology. In the present study, the antitumor activity of S 49076 was assessed in a panel of 53 patient-derived tumors of diverse origin growing in three-dimensional in vitro culture. Sixteen (30%) of these tumors were sensitive to S 49076 at 1 μM or less. With the aim to define molecular signatures of sensitivity or resistance, all 53 tumors were characterized for expression, activation and mutation of all of the known target kinases using protein, mRNA and DNA analysis techniques. On an individual basis, no clear relationship between expression level or activity of each target kinase and sensitivity or resistance to S 49076 could be established. However, analysis of microarray data using z-score transformation enabled a clear link to emerge between the sum of the z-scores of all potential target kinases (z-score) and tumor response to S 49076. Moreover, when the presence of RAS or PIK3CA activating mutations was taken into account, the predictive power of the analysis (in particular the positive predictive value for sensitivity) was even more striking. Overall, 91% (29/32) of tumors with a z-score less than 0 were resistant to S 49076, whilst 85% (11/13) of tumors with a z-score greater than 0 and with no known mutations in RAS or PIK3CA were sensitive. Six out of the 8 tumors with a z-score greater than 0 but with mutations in RAS or PIK3CA were resistant. In vivo evaluation of the response to S 49076 of several of the sensitive tumors is in progress in xenograft studies.
Together, these data demonstrate the potential power of molecular profiling and, in particular, transcriptomic analyzes in the stratification of patient tumors for treatment with a multi-kinase inhibitor. It is hoped that similar analysis of patient tumors during clinical trials of S 49076 will ultimately contribute to the progress towards a more personalized approach to cancer patient care.
Citation Format: {Authors}. {Abstract title} abstract. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A240.
PDF
