Immunohistochemical Ki67 after short-term hormone therapy identifies low-risk breast cancers as reliably as genomic markers

Background

The purpose of this study was to test whether immunohistochemical (IHC) Ki67 levels after short-term preoperative hormone therapy (post-Ki67) predict similar numbers of patients with favorable prognoses as genomic markers.

Results

Thirty paired cases (60 samples) were enrolled in this study. Post-Ki67 levels were significantly lower than pre-treatment Ki67 levels (P < 0.001). Post-Ki67 predicted more low-risk cases (83.3%, 25/30) than pre-genomic surrogate signature(GSS) (66.7%: 20/30), but the difference in predictive power was not significant (P = 0.233). Proliferation (MKI67, STK15, Survivin, CCNB1, and MYBL2) and estrogen (ER, PGR, BCL2, and SCUBE2) related signatures were significantly downregulated after therapy (P < 0.001 and 0.041, respectively).

Materials and Methods

Core needle biopsy specimens of primary breast cancer were collected at Okayama University Hospital from hormone receptor-positive and human epidermal growth factor 2-negative patients that subsequently received two weeks of neoadjuvant hormone therapy. Paired post-treatment specimens from surgical samples were also collected. IHC Ki67 levels and GSS were compared between pre- and post-hormone treatment samples. Changes of gene expression pattern in short-term hormone therapy were also assessed.

Conclusions

IHC based post-Ki67 levels may have distinct predictive power compared with the naïve IHC Ki67. Future studies with larger cohorts and longer follow-up periods may be needed to validate our results.

Immune gene signatures in triple-negative breast cancers characterized by varying levels of chromosomal instability

1096

Background: Triple-negative breast cancer (TNBC) is generally characterized by high levels of chromosomal instability (CIN) and an intense immune infiltration. However, the link between these two hallmarks and its implications for clinical practice has not been fully elucidated. Methods: We generated eight immune metagenes representing various immune components: natural killer [NK], dendritic cells [DC], T-cells [TC], B-cells [BC], cytotoxic T-cells [CT], interferon [IFN], nuclear factor-κB [NF-kB], and macrophages [M]. Publicly available gene expression data from forty-two data sets, including 862 TNBC samples, were collected. TNBC tumors were clustered in three main subgroups (Basal-Like [BL1/2], Immunomodulatory [IM], and Mesenchymal/Mesenchymal Stem-Like [MS]) using transcriptomic profiling. The CIN70 signature was used to stratify TNBC patients according to the levels of CIN. Statistical analyses were performed using Mann–Whitney U test and Kaplan-Meier analyses. Results: The majority of TNBC samples showed a high level of CIN (83%), and several immune modules were differentially expressed between CIN-high and CIN-low tumors. Specifically, CT, NK, DC, M, and NF-kB signatures were overexpressed in CIN-low TNBC ( p < 1.0E-04). We then evaluated the distribution of genomic instability among TNBC molecular subgroups. Noteworthy, the CIN-high group was composed by a comparable proportion of BL1/2 (39%) and MS (35%) tumors, while CIN-low TNBCs were consistently enriched for MS cancers (61%). Higher expression of the NK, M, and IFN metagenes lead to better survival in CIN-high tumors ( p = 1.9E-02, p = 2.1E-04, and p = 1.1E-03, respectively). Only IFN had the same correlation to survival in CIN-low ( p = 1.4E-02). Conclusions: TNBCs with low levels of CIN may principally enclose M/MSL tumors, which are characterized by an intense immune infiltration and overall good prognosis. Conversely, the TNBC CIN-high group is more heterogeneous in terms of both biological features and levels of immune infiltrates. Therapeutic strategies to promote and boost immune response in the genomically unstable TNBC subgroup warrant further investigation.

Propagation on Molecular Interaction Networks: Prediction of Effective Drug Combinations and Biomarkers in Cancer Treatment

BACKGROUND

Biomedical sciences use a variety of data sources on drug molecules, genes, proteins, diseases and scientific publications etc. This system can be best pictured as a giant data-network linked together by physical, functional, logical and similarity relationships. A new hypothesis or discovery can be considered as a new link that can be deduced from the existing connections. For instance, interactions of two pharmacons - if not already known - represent a testable novel hypothesis. Such implicit effects are especially important in complex diseases such as cancer.

METHODS

The method we applied was to test whether novel drug combinations or novel biomarkers can be predicted from a network of existing oncological databases. We start from the hypothesis that novel, implicit links can be discovered between the network neighborhoods of data items.

RESULTS

We showed that the overlap of network neighborhoods is strongly correlated with the pairwise interaction strength of two pharmacons used in cancer therapy, and it is also well correlated with clinical data. In a second case study we employed this strategy to the discovery of novel biomarkers based on text analysis. In 2012 we prioritized 10 potential biomarkers for ovarian cancers, 2 of which were in fact described as such in the subsequent years.

CONCLUSION

The strategy seems to hold promises for prioritizing new drug combinations or new biomarkers for experimental testing. Its use is naturally limited by the sparsity and the quality of experimental data, however both of these aspects are expected to improve given the development of current databases.

HOXC10 Expression Supports the Development of Chemotherapy Resistance by Fine Tuning DNA Repair in Breast Cancer Cells

Development of drug resistance is a major factor limiting the continued success of cancer chemotherapy. To overcome drug resistance, understanding the underlying mechanism(s) is essential. We found that HOXC10 is overexpressed in primary carcinomas of the breast, and even more significantly in distant metastasis arising after failed chemotherapy. High HOXC10 expression correlates with shorter recurrence-free and overall survival in patients with estrogen receptor-negative breast cancer undergoing chemotherapy. We found that HOXC10 promotes survival in cells treated with doxorubicin, paclitaxel, or carboplatin by suppressing apoptosis and upregulating NF-κB Overexpressed HOXC10 increases S-phase-specific DNA damage repair by homologous recombination (HR) and checkpoint recovery in cells at three important phases. For double-strand break repair, HOXC10 recruits HR proteins at sites of DNA damage. It enhances resection and lastly, it resolves stalled replication forks, leading to initiation of DNA replication following DNA damage. We show that HOXC10 facilitates, but is not directly involved in DNA damage repair mediated by HR. HOXC10 achieves integration of these functions by binding to, and activating cyclin-dependent kinase, CDK7, which regulates transcription by phosphorylating the carboxy-terminal domain of RNA polymerase II. Consistent with these findings, inhibitors of CDK7 reverse HOXC10-mediated drug resistance in cultured cells. Blocking HOXC10 function, therefore, presents a promising new strategy to overcome chemotherapy resistance in breast cancer. Cancer Res; 76(15); 4443-56. ©2016 AACR.

Abstract PD6-06: Somatic mutation patterns differentially affect survival in breast cancer molecular subtypes

Background: The prognostic effects of somatic gene mutations and correlated gene expression in breast cancer is argument of debate. In this study we analyzed the impact of specific mutations on gene expression and their relevance in the prognosis of breast cancer subtypes.

Materials and methods: Exome sequencing and RNA-seq data obtained from TCGA were analyzed. Data was processed using MuTect, MapSplice and RSEM. All together data from 757 patients (ER-/HER2- [n=143], HER2+ including ER positive and negative patients, [n=136], and ER+/HER2- [n=478]) were included. Univariate Receiver Operating Characteristic (ROC) analysis was performed for the top mutated genes (mutated in at least 5% of patients) using the ROC Bioconductor library in R to identify genes whose expression was significantly associated with a mutation. Then, the mean expression of the significant genes was designated as a metagene for each genotype. We assessed the correlation with survival for each metagene by Cox proportional hazards regression and by plotting Kaplan-Meier survival plots. A significance threshold of p&lt;1E-04 was set for each gene to be considered in the survival analysis, and only the top 100 genes were used when there were more than 100 genes significant.

Results: In the overall population only few mutated genes including TP53 (HR=1.66), CDH1 (HR=0.61), AKT1 (HR=0.54), ATM (HR=1.76), NF1 (HR=0.58), KMT2D (HR=2.32), and UBR5 (HR=1.94) were significantly associated with survival. In ER-/HER2- mutant samples the PIK3CA (HR=2.79) and MAP3K1 (HR=2.98), and in HER2+ mutant samples the ARID1A (HR=0.26) and PIK3CA (HR=0.27) metagenes were associated with survival, respectively. Overall, using the combined metagene the majority of the significant mutated genes retained their prognostic power. Mutations of specific genes impacted their own expression and prognosis. The expression of TP53 (AUC=0.609, p=2.60E-06), and MAP3K1 (AUC=0.617, p=6.07E-03) was higher in samples with a mutation while the expression of CDH1 (AUC=0.684, p=2.72E-07), PTEN (AUC=0.687, p=1.47E-04), and BRCA1 (AUC=0.608, p=2.24E-02) was lower.

Conclusions: Our finding support that specific mutated genes may differentially impact prognosis in breast cancer subtypes. Further efforts are required to understand the biological and prognostic role of specific activating and inactivating mutations across molecular breast cancer subtypes.

Citation Format: Gyorffy B, Pongor L, Szabo A, Bottai G, Pusztai L, Santarpia L. Somatic mutation patterns differentially affect survival in breast cancer molecular subtypes. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD6-06.

Abstract P5-04-10: Phosphodiesterase type 5 promotes the invasive potential of breast cancer cells through Rho GTPase activation

The impairment of cyclic guanosine monophosphate (cGMP) signaling by overexpression of PDE5 isoform has been recently described in multiple human carcinomas. In addition, accumulating evidences indicate that PDE5 inhibitors could have direct anti-cancer activities as well as they may enhance the sensitivity of certain types of cancer to standard chemotherapeutic drugs. However, despite these studies, neither the expression of PDE5 in breast cancer subtypes nor the underlying regulatory molecular mechanisms by which PDE5 expression may contribute to breast cancer progression have been deeply studied.

We demonstrated that PDE5 was expressed in different subtypes of breast cancer cell lines at higher levels than in non tumorogenic human epithelial breast cell lines. Increased levels were detected in more aggressive endocrine non responsive basal-like breast cancer cells. Interestingly, PDE5 was expressed at very low levels in luminal A-type breast cancer cell lines, which display low ki67 expression, weak invasive behavior and endocrine responsiveness (MCF-7 and T47D cells) compared to luminal B-like cells (such as ZR-75 cells). These results well correlated with data obtained in immunohistochemistry analyses of human breast cancer tissues, showing PDE5 expression in 30 of 35 tumor entities analyzed, with the highest intensity staining in high-grade tumors. Concomitantly, no cytoplasmic PDE5 staining was observed in non neoplastic tissues examined (n=5). In addition, retrospective analyses (n=1959, median follow-up time: 25 years) showed that high PDE5 expression in breast cancer patients was correlated with a statistically significant poorer survival compared to low PDE5-expressing patients. A more relevant discrimination is achieved in lymphnode-negative patients, suggesting a role of PDE5 for identifying early patients at high risk of rapid progression.

In order to better ascertain the role of PDE5 in breast tumorogenesis, we selected a breast tumor cell line that express low levels of this enzyme, MCF-7 and engineered stable clones for overexpression studies. Both vector- and PDE5-stable MCF-7 clones demonstrated comparable proliferation rates; whereas, cell motility and invasion were dramatically increased in PDE5-overexpressing cells. RNA sequencing to compare the transcriptomes of vector- and PDE5-overexpressing MCF-7 cells identified differential expression of genes involved in cell migration and invasion. Particularly, based on pathway analysis we found marked changes in the expression of Rho GTPase family members, proteins involved in cell cytoskeleton organization, migration, and metastasis dissemination (Rho A, cdc42 and Rac signaling, activation score= 1.9, 1.342, and 0.302, respectively). Indeed, Rho and cdc42 pull-down assays revealed increased Rho GTPase activity in cells overexpressing PDE5. Moreover, the selective ROCK inhibitor Y-27632 as well as the PDE5 inhibitor sildenafil were able to significantly reduce both migration and invasion of PDE5 clones.

Our data reveal that PDE5 expression enhances motility and invasiveness of breast cancer cells through the activation of the Rho family of GTPases, and highlight, for the first time, a novel role for PDE5 as a marker of poor outcome in breast cancer patients.

Citation Format: Barone I, Campana A, Giordano C, Tarallo R, Rinaldi A, Bruno G, Gyorffy B, Lanzino M, Bonofiglio D, Catalano S, Ando' S. Phosphodiesterase type 5 promotes the invasive potential of breast cancer cells through Rho GTPase activation. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-04-10.

Abstract P6-08-31: Linking genotype to clinical outcome in breast cancer by combining NGS and gene chip data

Introduction: Next generation sequencing (NGS) provides the possibility to measure mutational status for any part of any gene. However, because of scarce data available to date, linking these mutations to relevant clinical outcome in a large number of patients is not possible.

Aim: Our goal was to combine available genotype data generated by using NGS with gene expression data generated by gene chips to establish a framework to assess the effect of genotype on clinical outcome.

Methods: NGS data generated by the TCGA consortia and publicly available gene chip data obtained from the GEO and EGA repositories were utilized. NGS data was processed using MuTect, SNPeff, GRCh37 and R. RNA-seq data was normalized using DEseq. Gene chip data was MAS5 normalized. Generation of the transcriptomic fingerprint for mutation status was computed by ROC utilizing the RNA-seq data. In the gene chip data, the average expression of significant genes identified was designated as a metagene for the given genotype. Correlation to survival for this metagene was assessed by computing Cox regression and plotting Kaplan-Meier survival plots. Finally, we have set up an online interface to enable running the analysis for any selected gene.

Results: The database contains 332 NGS samples containing mutational status for 22,938 genes and RNA-seq data for 10,987 genes. The gene chip database contains 5,934 patients with 10,987 genes plus detailed clinical characteristics and survival data. We evaluated correlation to outcome for previously identified genes harboring the ten most common somatic mutations in breast cancer. Of these, TP53 (n of mutations out of 332=93, hazard rate=0.51, p&lt;1E-16), AKT1 (n=18, HR=1.6, p=1.6E-15), PIK3CA (n=119, HR=1.5, p=8.5E-12), MAP3K1 (n=20, HR=1.4, p=1.3E-08), CDH1 (n=34, HR=1.3, p=4.4E-07), and RB1 (n=21, HR=1.3, p=7E-06) reached statistical significance while PI3K, PTEN, CDKN1B and GATA3 were not significant or had insufficient number of mutated samples.

Discussion: By connecting genotype to gene expression signature and employing this signature for survival analysis we have set up a pipeline enabling the functional validation of a discovered mutation for any gene in a large breast cancer cohort.

Citation Format: Balazs Gyorffy, Lorinc Pongor, Mate Kormos. Linking genotype to clinical outcome in breast cancer by combining NGS and gene chip data [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-08-31.

Abstract P6-01-22: PDE5 as a novel biomarker and a potential therapeutic target for breast cancer

Background: Phosphodiesterases are enzymes responsible for regulating second messenger signaling by hydrolyzing 3’-5’ cyclic guanosine monophosphate (cGMP), that activates specific pathways resulting in protein phosphorylation, ion fluxes, or cyclic nucleotide hydrolysis to affect gene expression or other aspects of cellular activity. Previous studies have reported increased PDE5 expression in multiple human carcinomas, including bladder, colon, lung and breast cancers, suggesting a role for PDE5 in tumorigenesis. In addition, several in vitro observations have shown antiproliferative and proapoptotic effects of sildenafil and other PDE5 inhibitors in cancer cell lines. However, very little is known about PDE5 expression in human breast tumours and its potential role in breast cancer initiation and progression. We therefore propose to determine whether PDE5 expression may be predictor of outcome in breast cancer patients, and examine PDE5 impact on breast cancer phenotype in vitro.

Methods: We employed MCF-10A normal breast epithelial cells, estrogen receptor (ER) α-positive (MCF-7/ZR-75/T-47D) and ERα-negative (BT-20/MDA-MB-468/SKBR-3/MDA-MB-435) breast cancer cells. We used RT-PCR, immunoblotting and immunofluorescence analyses for evaluating PDE5 expression. To examine PDE5 impact on breast cancer phenotype, MCF-7 cells were engineered to stably express PDE5 and four clones were selected. Cell proliferation was assessed by MTT and anchorage-independent assays, motility and invasion by wound-healing, transmigration and matrigel-based invasion assays. Retrospective analysis using 1959 breast cancer patients of the Metabric Project was performed to evaluate relationship between PDE5 expression and overall survival by Cox proportional hazard regression.

Results: PDE5 mRNA and protein were constitutively expressed at high levels in all the examined tumor cell lines compared to normal breast cells, except for the less motile and non-invasive MCF-7 cells. Interestingly, higher PDE5 expression was found in more aggressive ER-negative cells. Stable overexpression of PDE5 did not affect proliferation of MCF-7 cells, while it significantly increased motility and invasion of all the stable PDE5-transfected clones tested. Patients having high PDE5 expression had a statistically significant poorer survival compared to patients with low PDE5 expression (p=0.014, HR= 1.2). A more relevant discrimination was achieved in lymph node-negative patients (p=0.0015, HR= 1.6), suggesting that assessing PDE5 levels may be helpful to identify a subgroup of early-stage breast cancer patients who are most likely at the highest risk of progression.

Conclusions: PDE5 expression may enhance cancer cell invasive potential, thereby representing prospectively a potential molecular candidate as prognostic marker and target for breast cancer therapy.

Citation Format: Ines Barone, Antonella Campana, Cinzia Giordano, Marilena Lanzino, Daniela Bonofiglio, Balazs Gyorffy, Stefania Catalano, Sebastiano Andò. PDE5 as a novel biomarker and a potential therapeutic target for breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-01-22.

Abstract P4-15-13: CDK8 inhibition potentiates anti-ER and anti-HER2 therapies in breast cancer

CDK8, along with its paralog CDK19, is a cyclin dependent kinase which, in contrast to other members of the CDK family does not regulate cell cycle progression. CDK8 acts as a pleiotropic transcription regulator potentiating the induction of transcription by several transcription factors. Immunohistochemical staining of breast tissue arrays and bioinformatics analysis of gene expression microarray data of breast cancer patients revealed that CDK8 is overexpressed in breast cancer and that higher CDK8 expression correlates with the failure of systemic therapy. Small-molecule selective inhibitors of CDK8 and CDK19 (Senexin A and Senexin B) inhibited the mitogenic effects of estrogen and estrogen-dependent transcription in estrogen receptor (ER)+ breast cancer cell lines. CDK8/19 inhibitors had a cytostatic effect on different ER+ cell lines, and this growth inhibition was synergistic with the effect of the anti-estrogen fulvestrant, particularly in ER+ cell lines resistant to estrogen deprivation. Some of the ER+ cell lines sensitive to CDK8/19 inhibition also express HER2, and therefore we tested CDK8/19 inhibitors in combination with the HER2 and EGFR tyrosine kinase inhibitor lapatinib and an anti-HER2 monoclonal antibody, a biosimilar of trastuzumab. CDK8/19 inhibition produced a synergistic decrease in cell growth with both HER2 inhibitors; this effect was especially pronounced with a trastuzumab biosimilar. Surprisingly, the synergistic effect with HER2 inhibitors was observed in both ER+ HER2+ and ER-HER2+ cell lines, suggesting an effect on a HER2-complementing molecular target other than ER. Interestingly, CDK8/19 inhibition also synergized with trastuzumab biosimilar in a breast cancer cell line that exhibits innate resistance to trastuzumab, suggesting that CDK8/19 inhibition can overcome trastuzumab resistance in breast cancer. These results suggest that combining anti-estrogen and anti-CDK8 therapy may be more effective than conventional hormone therapy for ER positive breast cancer and that combining anti-HER2 and anti-CDK8 therapy is a rational potential treatment for HER2+ breast cancer, regardless of ER status or sensitivity to trastuzumab.

Citation Format: Martina S McDermott, Chang-uk Lim, Mengqian Chen, Alexander Chumanevich, James F Catroppo, Balazs Gyorffy, David Oliver, Igor B Roninson, Eugenia V Broude. CDK8 inhibition potentiates anti-ER and anti-HER2 therapies in breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-15-13.

Abstract P4-07-02: A large integrated-gene profiling analysis identifies prognostic microRNAs and correlated DNA repair genes in estrogen receptor positive and negative breast cancers

Background: MicroRNAs (miRNAs) are small non-coding RNAs involved in the pathogenesis of breast cancer (BC). Estrogen receptor (ER) is one of the most important factors influencing BC outcome. In this study we aim to assess the prognostic value in a cross-project analysis for all known miRNAs in ER-positive (ER+) and ER-negative (ER-) BC separately.

Materials and Methods: We assessed the prognostic value of miRNA expression in three independent BC datasets: TCGA (n=782), Metabric [M] (n=1,293) and GSE40267 (n=181) including 472, 853, and 475 miRNAs, respectively. Overall survival (OS) data was available for all patients. Statistical analysis was performed with R software. Survival analysis was performed using Cox proportional hazards regression in each dataset separately. To define an mRNA expression fingerprint for each miRNA, correlation between miRNA and mRNA expressions was computed using Spearman rank correlation in the Metabric dataset. Subsequently, specific metagenes were established using significant correlated mRNAs ("Metabric mRNA", M-mRNA) for each miRNA. Metagenes were also used in the Cox regression analysis. The entire analysis was performed for each miRNA in ER-positive and ER-negative BCs separately.

Results: In the ER+ BC, 283 miRNAs reached statistical significance in at least one dataset. The best performing and significant miRNAs in all datasets were miR-195 (M: HR=1.73, p=3.5E-06; TCGA: HR=2.17, p=3.5E-06, M-mRNA: HR=0.54, p=2.0E-10), miR-199b (M: HR=1.74, p=3.8E-06; TCGA: HR=0.46, p=0.028, M-mRNA: HR=0.56, p=2.8E-09), and miR-210 (M: HR=0.7, p=0.003; TCGA: HR=0.45, p=0.014, Metabric mRNA: HR=1.34, p=0.002). These 3 miRNAs retained their prognostic significance also in a multivariate analysis paired with HER2 status, lymph node status, size, grade and MKI67 expression. In the ER- group 73 significant miRNAs were identified. The best performing miRNAs in at least two datasets were miR-155 (GSE40267: HR=2.21, p=0.034, M: HR=1.67, p=0.008) and miR-381 (GSE40267: HR=0.41, p=0.026; M: HR=0.67, p=0.038). However, the miRNAs in ER- BC in a multivariate analysis were not independent from tumor size. The metagenes identified were significantly enriched in DNA repair genes (e.g. AURKB, TEK) and exhibited an inverse correlation to survival as compared to miRNA expression.

Conclusions: This is the first large-scale miRNA expression analysis demonstrating different prognostic miRNAs in ER+ and ER- BCs. Correlated miRNA-metagenes are involved in the regulation of DNA repair and genomic stability.

Citation Format: Balazs Gyorffy, Mate Kormos, Giulia Bottai, Kristine Kleivi, George A Calin, Anne-Lise Borresen-Dale, Libero Santarpia. A large integrated-gene profiling analysis identifies prognostic microRNAs and correlated DNA repair genes in estrogen receptor positive and negative breast cancers [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-07-02.

Abstract PR06: Impact of RAL signal transduction on genetic program and growth control in KRAS- and BRAF-mutated colorectal cells and prognostic potential of pathway-responsive genes in cancer patients

The EGFR/RAS signaling system plays an imperative role in tumor pathogenesis and therapy response. Downstream effects of the EGFR/RAS signaling axis are mediated by three major pathway branches: the RAF/MAPK, PI3K and RALA pathways. While the RAF/MAPK and PI3K pathways have been extensively characterized in mechanistic, preclinical and clinical studies, the RAL pathway is less well understood.

Here we compared RALGTPase activities in three colorectal cancer cell lines by active GTPase pull-down assay and analyzed the effects of transient silencing of RALA expression by siRNA. RALA activity was highest in SW480 [KRAS codon 12 mutation] and HCT116 cells [KRAS codon 13 mutation] and also detectable in HT29 colorectal cancer cells [KRAS wild-type, BRAF V600E mutation]. Silencing of RALA expression strongly diminished the active GTP-bound form of the protein in all cell lines. The proliferation of the two KRAS mutated cell lines was significantly reduced. BRAF mutated cells showed a slight increase in cell death only. Next we interrogated microarrays using RNA prepared from the cell lines treated with siRNA and controls. We identified 550 common genes the expression of which was up-regulated or down-regulated after RALA knock-down (“RALA pathway-responsive genes”). None of them were affected when the RAF/MAPK or PI3K pathways were blocked.

To investigate the potential clinical relevance of transcriptional targets regulated by the RALA pathway, we performed a meta-analysis utilizing expression profiles of 1,424 colorectal cancers documented in 8 independent publicly available data sets comprising information on patient survival. Of 19 RALA pathway-responsive genes correlated with progression-free survival, IQGAP1 (IQ-motif containing GTPase-activating protein 1), TOP1 (topoisomerase 1), LGALS1 (lectin galactoside-binding soluble 1), FILIP1L (filamin A-interacting protein 1-like) and TCF4 (transcription factor 4) were identified as the most important RALA pathway targets capable of predicting survival.

In conclusion, the RALA pathway impinges on the transcription of a distinct subset of target genes in colorectal cancer cells independent of the KRAS and BRAF mutational status. RALA pathway-responsive genes were unaffected by RAF/MAPK and PI3K signaling. These findings support the concept of a pathway-sensitive modular organization of the transcriptome. In view of the correlation of RAL pathway-responsive genes and patient survival, further investigations of the diagnostic impact in prospective trials and exploitation of therapeutic approaches are warranted.

This abstract is also presented as Poster B32.

Citation Format: Balazs Gyorffy, Iwona Stelniec-Klotz, Christian Sigler, Attila Szijarto, Yu Qian, Reinhold Schäfer. Impact of RAL signal transduction on genetic program and growth control in KRAS- and BRAF-mutated colorectal cells and prognostic potential of pathway-responsive genes in cancer patients. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr PR06. doi: 10.1158/1557-3125.RASONC14-PR06

Biomedical hypothesis generation by text mining and gene prioritization

Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes. Previously, we developed a rare-term model called RaJoLink (Petric et al, J. Biomed. Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain. Since many current medical hypotheses are formulated in terms of molecular entities and molecular mechanisms, here we extend the methodology to proteins and genes, using a standardized vocabulary as well as a gene/protein network model. The proposed enhanced RaJoLink rare-term model combines text mining and gene prioritization approaches. Its utility is illustrated by finding known as well as potential gene-disease associations in ovarian cancer using MEDLINE abstracts and the STRING database.

Correlations of differentially expressed gap junction connexins Cx26, Cx30, Cx32, Cx43 and Cx46 with breast cancer progression and prognosis

BACKGROUND AND AIMS

Connexins and their cell membrane channels contribute to the control of cell proliferation and compartmental functions in breast glands and their deregulation is linked to breast carcinogenesis. Our aim was to correlate connexin expression with tumor progression and prognosis in primary breast cancers.

MATERIALS AND METHODS

Meta-analysis of connexin isotype expression data of 1809 and 1899 breast cancers from the Affymetrix and Illumina array platforms, respectively, was performed. Expressed connexins were also monitored at the protein level in tissue microarrays of 127 patients equally representing all tumor grades, using immunofluorescence and multilayer, multichannel digital microscopy. Prognostic correlations were plotted in Kaplan-Meier curves and tested using the log-rank test and cox-regression analysis in univariate and multivariate models.

RESULTS

The expression of GJA1/Cx43, GJA3/Cx46 and GJB2/Cx26 and, for the first time, GJA6/Cx30 and GJB1/Cx32 was revealed both in normal human mammary glands and breast carcinomas. Within their subfamilies these connexins can form homo- and heterocellular epithelial channels. In cancer, the array datasets cross-validated each other's prognostic results. In line with the significant correlations found at mRNA level, elevated Cx43 protein levels were linked with significantly improved breast cancer outcome, offering Cx43 protein detection as an independent prognostic marker stronger than vascular invasion or necrosis. As a contrary, elevated Cx30 mRNA and protein levels were associated with a reduced disease outcome offering Cx30 protein detection as an independent prognostic marker outperforming mitotic index and necrosis. Elevated versus low Cx43 protein levels allowed the stratification of grade 2 tumors into good and poor relapse free survival subgroups, respectively. Also, elevated versus low Cx30 levels stratified grade 3 patients into poor and good overall survival subgroups, respectively.

CONCLUSION

Differential expression of Cx43 and Cx30 may serve as potential positive and negative prognostic markers, respectively, for a clinically relevant stratification of breast cancers.

Abstract 2101: Role of CDK8 in estrogen receptor signaling in breast cancers

The majority of breast cancers (BrCa) overexpress estrogen receptor (ER)α, which regulates transcription and drives estrogen-stimulated proliferation of ER+ tumor cells. ER+ patients usually receive adjuvant anti-estrogen therapy based on ER modification, downregulation, or estrogen depletion. Tumors frequently develop resistance to anti-estrogen therapy through various mechanisms, which may involve stimulation of ER itself or of downstream mediators of ER-driven transcription, as well as activation of alternative proliferation pathways, in particular those driven by HER2/EGFR. The treatment efficacy of hormone-resistant BrCa could be greatly augmented by targeting new druggable mediators of ER activity. We have now identified a transcription-regulating oncogenic kinase CDK8 as a potentiator of ER signaling and ER-driven BrCa cell proliferation. Immunohistochemical staining of breast tissue arrays and bioinformatics analysis of gene expression microarray data of breast cancer patients revealed that CDK8 is overexpressed in BrCa and that higher CDK8 expression correlates with the failure of systemic therapy. Among systemically untreated patients, higher CDK8 expression was correlated with shorter relapse-free survival in a subset of ER+ tumors that expressed the lowest levels of ERα. This correlation suggested that CDK8 could play a role in the progression of ER+ breast cancers with reduced levels of ER, possibly by stimulating the mitogenic effects of ER-mediated transcription. Indeed, a selective small-molecule CDK8 inhibitor (Senexin A) decreased estrogen-induced ER-dependent transcription and inhibited estrogen-stimulated proliferation of ER+ BrCa cell lines. Microarray analysis revealed that CDK8 inhibition diminished the induction of genes that show rapid and sustained activation by estrogen in ER+ cells. CDK8 inhibition had an additive effect in combination with anti-estrogens in ER+ BrCa and a synergistic effect with fulvestrant in BrCa cells resistant to estrogen deprivation. Some of these cell lines also express HER2/EGFR, and CDK8 inhibition in combination with a HER2/EGFR inhibitor lapatinib synergistically inhibited the growth of these cells. These results suggest that combining anti-estrogen and anti-CDK8 therapy may be more effective than conventional hormone therapy for ER+ BrCa.

Citation Format: Martina McDermott, Balazs Gyorffy, Chang-uk Lim, Alexander Chumanevich, Zhengguan Yang, Mengqian Chen, James F. Catroppo, Igor Roninson, Eugenia V. Broude. Role of CDK8 in estrogen receptor signaling in breast cancers. [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 2101. doi:10.1158/1538-7445.AM2014-2101