Early2 factor (E2F) deregulation is a prognostic and predictive biomarker in lung adenocarcinoma

Clinicians routinely prescribe adjuvant chemotherapy (ACT) for resected non-small cell lung cancer patients. However, ACT only improves five-year disease-free survival in stage I-III non-small cell lung cancer by 5-15%, with most patients deriving no benefit. Herein, deregulation of the E2F pathway was explored as a biomarker in lung adenocarcinoma patients. An E2F pathway scoring system, based on 74 E2F-regulated genes, was trained for RNA from two platforms: fresh-frozen (FF) or formalin-fixed paraffin-embedded (FFPE) tissues. The E2F score was tested as a prognostic biomarker in five FF-based cohorts and two FFPE-based cohorts. The E2F score was tested as a predictive biomarker in two randomized clinical trials; JBR10 and the NATCH (Neo-Adjuvant Taxol-Carboplatin Hope) trial. The E2F score was prognostic in untreated patients in all seven datasets examined (p < 0.05). Stage-specific analysis of combined cohorts demonstrated that the E2F score was prognostic in stage I patients (p = 0.0495 to <0.001; hazard ratio, HR, =2.04- 2.22) with a similar trend in other stages. The E2F score was strongly predictive in stage II patients from the two combined randomized clinical trials with a significant differential treatment effect (p = 0.015). Specifically, ACT improved survival in stage II patients with high E2F (p = 0.01; HR= 0.21). The 5-year survival increased from 18% to 81%. In contrast, in patients with low E2F, 5-year survival was 57% in untreated patients and 41% in ACT-treated patients with a HR of 1.55 (p = 0.47). In summary, the E2F score provides valuable prognostic information for Stage I and predictive information for Stage II lung adenocarcinoma patients and should be further explored as a decision support tool for their treatment.

Abstract 914: Development of a prognostic and predictive E2F signature in formalin-fixed, paraffin-embedded early-stage non-small cell lung cancer samples

Lung cancer remains the leading cause of cancer-related death in the United States. The 5 year survival for stage I-IIIA lung cancer ranges from only 15-50%. For many in the early stages of the disease, especially stage II patients, adjuvant chemotherapy (ACT) following surgical resection is standard treatment. Still, it appears that the benefits for ACT have plateaued at 4%. With these marginal survival rates and the toxicities associated with chemotherapy, there is a need to develop a predictive tool to identify those patients with early-stage disease who would most benefit from receiving ACT. Previously, we developed an E2F-based gene expression signature derived from microarrays of two non-small cell lung cancer cell lines that were transfected with small interfering RNAs targeted against several members of the E2F pathway. This signature was then filtered for genes that were altered in cancer, but not in normal lung tissues, agreeing between two publicly-available lung tumor/adjacent normal datasets. Through principal component analysis (PCA), the E2F signature was shown to be prognostic in the Molecular Classification of Lung Adenocarcinoma (MCLA) from the Director's Challenge Consortium, as well as predictive of early-stage lung adenocarcinoma patients’ response to ACT in the JBR.10 clinical trial. In order to demonstrate efficacy of the signature in a typical clinical setting, we evaluated whether the NanoString platform (a method that involves the use of a novel “barcode” system to measure gene expression) would be as effective using RNA derived from formalin-fixed, paraffin-embedded (FFPE) tumor samples as compared to fresh frozen RNA. NanoString quantification of RNA from fresh frozen samples correlated very well to FFPE samples (average r=0.9070, median r=0.9290, SD=0.0859). Further, NanoString expression for 32 pairs of both the fresh frozen and FFPE RNA were compared to gene expression microarray readings of the genes in the signature. This analysis demonstrated that the NanoString readings corresponded well to microarray expression, regardless of the method of RNA extraction for NanoString (paired NanoString-frozen vs. microarray: average r=0.5585, median r=0.5608, SD=0.0718; paired NanoString-FFPE vs. microarray: average r=0.5384, median r=0.5401, SD=0.0891). Taken together, these results demonstrate that this E2F signature may be a useful tool for predicting which patients would best respond to adjuvant chemotherapy, and NanoString analysis may be a very effective means of applying this signature to patient samples.

Citation Format: Courtney A. Kurtyka, Lu Chen, Matthew B. Schabath, Dung-Tsa Chen, William Brazelle, Eric A. Welsh, Anders E. Berglund, Steven A. Eschrich, Jhanelle E. Gray, Eric B. Haura, W. Douglas Cress. Development of a prognostic and predictive E2F signature in formalin-fixed, paraffin-embedded early-stage non-small cell lung cancer samples. [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 914. doi:10.1158/1538-7445.AM2014-914

E2F inhibition synergizes with paclitaxel in lung cancer cell lines

The CDK/Rb/E2F pathway is commonly disrupted in lung cancer, and thus, it is predicted that blocking the E2F pathway would have therapeutic potential. To test this hypothesis, we have examined the activity of HLM006474 (a small molecule pan-E2F inhibitor) in lung cancer cell lines as a single agent and in combination with other compounds. HLM006474 reduces the viability of both SCLC and NSCLC lines with a biological IC₅₀ that varies between 15 and 75 µM, but with no significant difference between the groups. Combination of HLM006474 with cisplatin and gemcitabine demonstrate little synergy; however, HLM006474 synergizes with paclitaxel. Surprisingly, we discovered that brief treatment of cells with HLM006474 led to an increase of E2F3 protein levels (due to de-repression of these promoter sites). Since paclitaxel sensitivity has been shown to correlate with E2F3 levels, we hypothesized that HLM006474 synergy with paclitaxel may be mediated by transient induction of E2F3. To test this, H1299 cells were depleted of E2F3a and E2F3b with siRNA and treated with paclitaxel. Assays of proliferation showed that both siRNAs significantly reduced paclitaxel sensitivity, as expected. Taken together, these results suggest that HLM006474 may have efficacy in lung cancer and may be useful in combination with taxanes.

Abstract 2354: An E2F signature predicts benefit of adjuvant chemotherapy in early-stage non-small cell lung cancer

Early-stage non-small cell lung cancer (NSCLC) is primarily treated by surgical resection. Unfortunately, after resection, one-third to one-half of early-stage patients will die of metastatic recurrence. Adjuvant chemotherapy (ACT) improves the survival of patients with early-stage disease and has become the standard treatment for patients with resected stage II-III NSCLC. However, the five-year survival advantage of ACT is only 4%-15% suggesting that many patients do not benefit. Given the morbidity associated with ACT, it is imperative to develop new prognostic tools to identify those patients with a high probability of relapse. Toward this end, we have used small inhibitory RNAs targeting multiple E2F pathway components to derive an E2F gene expression signature in vitro. This signature was refined by filtering for its components that were altered in non-small cell lung cancers compared to normal tissue. Principle component analysis was then used to represent the signature which was tested for correlation to overall survival in two large cohorts. The first of the two cohorts was the Molecular Classification of Lung Adenocarcinoma (MCLA) from the Director's Challenge Consortium and the second was a novel database on 444 lung adenocarcinomas treated as a part of Moffitt's Total Cancer Care Network. The E2F signature is strongly prognostic in both cohorts with P values &lt;0.0001. Additionally, using data in the JBR.10 trial (GSE14814) for patients who either did or did not receive ACT we were able to determine that patients having a high E2F signature benefit from ACT (have increased overall survival), whereas patients with a low E2F signature do not. Overall, these results suggest that this approach could be optimized in the clinical setting to distinguish patients likely to benefit from ACT from those who will not.

Citation Format: Courtney A. Kurtyka, Dung-Tsa Chen, Lu Chen, William Brazelle, Eric A. Welsh, Anders E. Berglund, Steven A. Eschrich, Matthew B. Schabath, Eric B. Haura, W. Douglas Cress. An E2F signature predicts benefit of adjuvant chemotherapy in early-stage non-small cell lung cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2354. doi:10.1158/1538-7445.AM2013-2354

Abstract 2943: Targeting the E2F pathway in cancer chemotherapeutics

HLM006474 is a recently identified small molecule E2F inhibitor. Since E2F is known to drive expression of genes required for cell cycle progression, it is predicted that blocking the E2F pathway will slow proliferation and have anticancer activity. Microarray analysis demonstrates that HLM006474 treatment results in profound changes in the expression of genes involved in cell cycle progression and nucleotide biosynthesis. Flow cytometry reveals that treatment of A375 cells results in a cell cycle arrest, primarily in G2/M. As would be expected, cell lines deficient in Rb are more sensitive to E2F inhibition than are syngeneic lines expressing Rb. HLM006474 reduces the proliferation of a broad array of cell lines with a biological IC50 that varies between 5 and 70 μM. Combination of HLM006474 with common chemotherapeutic agents cisplatin and gemcitabine demonstrate little synergy; however HLM006474 synergizes with paclitaxel and a novel cdk inhibitor NSC11702. Interestingly, we discovered that paclitaxel sensitivity inversely correlated with E2F4 levels in a series of non-small cell lung cancer (NSCLC) lines, suggesting that synergy between HLM006474 and paclitaxel is due to HLM006474's inhibition of E2F4 activity and expression. To test this, H1299 cells which have high E2F4 levels and a high paclitaxel IC50 were depleted of E2F4 with siRNA and the IC50 determined. Taken together, these results suggest that HLM006474 may have efficacy against cancers in which E2F is deregulated and may be useful in combination with other drugs that target cell cycle components.

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 2943. doi:10.1158/1538-7445.AM2011-2943

A small-molecule E2F inhibitor blocks growth in a melanoma culture model

HLM006474 was identified using a computer-based virtual screen and the known crystal structure of the DNA-bound E2F4/DP2 heterodimer. Treatment of multiple cell lines with HLM006474 resulted in the loss of intracellular E2F4 DNA-binding activity as measured by electrophoretic mobility shift assay within hours. Overnight exposure to HLM006474 resulted in down-regulation of total E2F4 protein as well as known E2F targets. The effects of HLM006474 treatment on different cell lines varied but included a reduction in cell proliferation and an increase in apoptosis. HLM006474 induced apoptosis in a manner distinct from cisplatin and doxorubicin. E2F4-null mouse embryonic fibroblasts were less sensitive than wild-type counterparts to the apoptosis-inducing activity of the compound, revealing its biological specificity. A375 cells were extremely sensitive to the apoptosis-inducing activity of the compound in two-dimensional culture, and HLM006474 was a potent inhibitor of melanocytes proliferation and subsequent invasion in a three-dimensional tissue culture model system. Together, these results suggest that interference with E2F activity using small molecules may have clinical application in cancer therapy.