Deregulation Of Oncogenic Pathways Research Articles

Metabolic dysregulation of tricarboxylic acid cycle and oxidative phosphorylation in glioblastoma.

Glioblastoma multiforme (GBM) exhibits genetic alterations that induce the deregulation of oncogenic pathways, thus promoting metabolic adaptation. The modulation of metabolic enzyme activities is necessary to generate nucleotides, amino acids, and fatty acids, which provide energy and metabolic intermediates essential for fulfilling the biosynthetic needs of glioma cells. Moreover, the TCA cycle produces intermediates that play important roles in the metabolism of glucose, fatty acids, or non-essential amino acids, and act as signaling molecules associated withthe activation of oncogenic pathways, transcriptional changes, and epigenetic modifications. In this review, we aim to explore how dysregulated metabolic enzymes from the TCA cycle and oxidative phosphorylation, along with their metabolites, modulate both catabolic and anabolic metabolic pathways, as well as pro-oncogenic signaling pathways, transcriptional changes, and epigenetic modifications in GBM cells, contributing to the formation, survival, growth, and invasion of glioma cells. Additionally, we discuss promising therapeutic strategies targeting key players in metabolic regulation. Therefore, understanding metabolic reprogramming is necessary to fully comprehend the biology of malignant gliomas and significantly improve patient survival.

Impact of R-loops on oncogene-induced replication stress in cancer cells.

Replication stress is an alteration in the progression of replication forks caused by a variety of events of endogenous or exogenous origin. In precancerous lesions, this stress is exacerbated by the deregulation of oncogenic pathways, which notably disrupts the coordination between replication and transcription, and leads to genetic instability and cancer development. It is now well established that transcription can interfere with genome replication in different ways, such as head-on collisions between polymerases, accumulation of positive DNA supercoils or formation of R-loops. These structures form during transcription when nascent RNA reanneals with DNA behind the RNA polymerase, forming a stable DNA:RNA hybrid. In this review, we discuss how these different cotranscriptional processes disrupt the progression of replication forks and how they contribute to genetic instability in cancer cells.

BIOM-09. GUIDING PRECISION THERAPEUTICS THROUGH INTERROGATING ONCOGENIC PATHWAY ACTIVATION

Abstract The deregulation of canonical oncogenic pathways are largely responsible for driving pediatric cancers and can be targeted for therapeutics. Currently, we interrogate these pathways clinically by looking for gene mutations, but these are not found in all cases, and in others multiple genes are. We hypothesized that assessing transcriptomic and proteomic-based pathway activation will allow a better understanding of the most active oncogenic pathways and help guide therapy. To do this, we developed and validated a nanostring based assay that interrogates 4 key actionable pathways (MAPK, PI3K-AKT-mTOR, JAK-STAT, and NFkB) including RNA, protein and phosphoprotein expression. The assay was clinically validated using isogenic cell lines and a cohort of 40 gliomas with previous RNAseq. We then interrogated over 400 tumor samples, including 15 ependymomas, 11 medulloblastomas, 250 low grade gliomas (LGG), 145 high grade gliomas and 10 control normal brain specimens. Interestingly, although pediatric LGG exhibited higher MAPK activation than control tissue and other tumor types, a subset of these tumors have increased activity in PI3K , JAK and NFKB pathways. Furthermore, high PI3K activation score was correlated with worse PFS in a subset of pediatric LGGs that required adjuvant chemotherapy (p=0.018). To further explore the therapeutic implication of the assay, we analyzed a cohort of patients treated with MEK inhibitors (n=20). Strikingly, on top of universal RAS/MAPK activation, crosstalk between additional activated pathways such as PI3K and JAK-STAT may contribute to lack of response. In particular, pre-treatment and post-progression PLGG who failed therapy, revealed mild reduction in MAPK signature accompanied by increased PI3K phospho-proteins (p-S6/p-4EBP1,p-AKT)(p< 0.01). We conclude that assessing oncogenic pathway activation can add to DNA sequencing to predict different outcome and response to targeted therapies in childhood brain tumors. This can inform future therapeutic strategies including the identification of potential responders and combination strategies for non-responders.

Complex Structural Variation Associated with Enhancer Hijacking and Loss of Tumor Suppressors in Mantle Cell Lymphoma

Mantle cell lymphoma (MCL) is a rare, incurable mature B-cell lymphoma that can have either an aggressive or indolent clinical course. The hallmark aberration of MCL is the t(11;14)(q13;q32) translocation that places CCND1 under control of the immunoglobulin heavy chain (IGH) locus resulting in its constitutive expression. CCND1/IGH translocation occurs in nearly all MCL cases and arises during VDJ recombination. Whole genome sequencing (WGS) of MCLs has shown the prevalence of additional structural variations (SV), particularly in tumors with poor outcome. Complex rearrangements, such as chromothripsis and chromoplexy have been observed in MCL but their role in lymphomagenesis has not been determined. We hypothesized that some of these complex rearrangements afford a selective advantage to the tumor by disrupting tumor suppressor genes or by placing oncogenes in proximity to regulatory elements in cis, thereby resulting in ectopic expression.We performed WGS on tumor DNA extracted from 106 RCHOP-treated MCL patients. Matching ribosomal-depleted RNA-seq data was available for all tumor samples. Gene expression count values were obtained using Salmon and counts were normalized using the DESeq2 method. Structural variants were identified using a consensus between GRIDSS and Manta and these were analyzed to identify the topology of complex rearrangements using JaBbA. This allows the annotation of rearrangements such as chromothripsis and chromoplexy and enables the detection of genes near new regulatory elements through complex (multi-breakpoint) rearrangements. We supplemented this analysis by including 57 published classical and non-nodal leukemic MCL genomes.Chromothripsis and chromoplexy were observed in 8 and 12 tumors, respectively. The majority of the genomes were associated with isolated structural variations such as large deletions, inversions and reciprocal translocations were more common. Six genes (BCL10, TRAF6, TRAF3, MAP3K7, BTK, RELB) coding for canonical and non-canonical NFκB signaling proteins were found rearranged to within 1Mbp of a naïve B-cell super-enhancer region. The TRAF6 rearrangement was part of a chromothripsis and chromoplexy event involving both chr9 and chr11. A separate chromothripsis example involving chr1 placed each of BCL10 and NOTCH2 within 100-200kbp of super-enhancers. A 1Mbp region containing RELB was amplified and inserted into chr19p approximately 150kbp downstream a super-enhancer. An 800kbp deletion brought MAP3K7 to within 400kbp of a super-enhancer. DAZAP1, a gene known to be recurrently mutated in MCL, was translocated upstream to within 300kbp of a super-enhancer by t(5;19)(p13.3;p15.33). TRAF3 was translocated 400kbp upstream a super-enhancer by t(14;20)(q32.32;q13.13). None of the aforementioned SVs were associated with a detectable increase in expression of the affected gene. In contrast, we identified one genome in which the MYC oncogene was relocated 500kbp upstream of a super-enhancer via an unbalanced t(4;8)(q21.23;q24.21) translocation. In this case, MYC expression was in the 95 th percentile of MYC expression across the cohort. Focal deletions and amplifications were also found affecting lymphoma driver genes. Focal amplifications affecting 3q (34 tumors) and 5p (9 tumors), were among the most common recurrent events. These respectively affect the TERC and TERT genes, both involved in telomerase function. All tumors with TERT amplifications also showed TERC amplifications. TERC and TERT were expressed higher on average in amplified tumors than in unamplified tumors. Two tumors showed focal deletions affecting the 3‘ end of BIRC3. The focal deletion in one tumor was found to span to the 3‘ end of BIRC2 resulting in a BIRC2/BIRC3 fusion. Aberrant splicing across the two genes was evident in matching tumor RNA-seq data.Complex rearrangements in MCL have been found to link distant super-enhancer elements with a variety of lymphoma oncogenes. We noted a recurrence of such events affecting known regulators of NFκB signaling. We are using nanopore-based long-read PromethION sequencing to validate the structure of the derivative chromosome in these cases. Although these genes were not detectably overexpressed, deregulation of genes may be occurring by other means. The full extent of deregulation of NFκB and other oncogenic pathways will be revealed as complex rearrangements are studied in additional MCL tumors. DisclosuresCoyle: Allakos, Inc.: Consultancy. Melnick: Epizyme: Consultancy; Daiichi Sankyo: Research Funding; Sanofi: Research Funding; Janssen Pharmaceuticals: Research Funding; Constellation: Consultancy; KDAC Pharma: Membership on an entity's Board of Directors or advisory committees. Scott: BC Cancer: Patents & Royalties: Patent describing assigning DLBCL COO by gene expression profiling–licensed to NanoString Technologies. Patent describing measuring the proliferation signature in MCL using gene expression profiling. ; AstraZeneca: Consultancy; Abbvie: Consultancy; NanoString Technologies: Patents & Royalties: Patent describing measuring the proliferation signature in MCL using gene expression profiling.; Rich/Genentech: Research Funding; Celgene: Consultancy; Incyte: Consultancy; Janssen: Consultancy, Research Funding. Morin: Epizyme: Patents & Royalties; Celgene: Consultancy; Foundation for Burkitt Lymphoma Research: Membership on an entity's Board of Directors or advisory committees.

Inhibition of STAT3 enhances sensitivity to tamoxifen in tamoxifen-resistant breast cancer cells

BackgroundThe mechanisms of endocrine resistance are complex, and deregulation of several oncogenic signalling pathways has been proposed. We aimed to investigate the role of the EGFR and Src-mediated STAT3 signalling pathway in tamoxifen-resistant breast cancer cells.MethodsThe ER-positive luminal breast cancer cell lines, MCF-7 and T47D, were used. We have established an MCF-7-derived tamoxifen-resistant cell line (TamR) by long-term culture of MCF-7 cells with 4-hydroxytamoxifen. Cell viability was determined using an MTT assay, and protein expression levels were determined using western blot. Cell cycle and annexin V staining were analysed using flow cytometry.ResultsTamR cells showed decreased expression of estrogen receptor and increased expression of EGFR. TamR cells showed an acceleration of the G1 to S phase transition. The protein expression levels of phosphorylated Src, EGFR (Y845), and STAT3 was increased in TamR cells, while phosphorylated Akt was decreased. The expression of p-STAT3 was enhanced according to exposure time of tamoxifen in T47D cells, suggesting that activation of STAT3 can cause tamoxifen resistance in ER-positive breast cancer cells. Both dasatinib (Src inhibitor) and stattic (STAT3 inhibitor) inhibited cell proliferation and induced apoptosis in TamR cells. However, stattic showed a much stronger effect than dasatinib. Knockdown of STAT3 expression by siRNA had no effect on sensitivity to tamoxifen in MCF-7 cells, while that enhanced sensitivity to tamoxifen in TamR cells. There was not a significant synergistic effect of dasatinib and stattic on cell survival. TamR cells have low nuclear p21(Cip1) expression compared to MCF-7 cells and inhibition of STAT3 increased the expression of nuclear p21(Cip1) in TamR cells.ConclusionsThe EGFR and Src-mediated STAT3 signalling pathway is activated in TamR cells, and inhibition of STAT3 may be a potential target in tamoxifen-resistant breast cancer. An increase in nuclear p21(Cip1) may be a key step in STAT3 inhibitor-induced cell death in TamR cells.

Oncogenic Mutations in Tumorigenesis and Targeted Therapy in Breast Cancer

Breast cancer is the most frequently identified cancer and the leading cause of women death from cancer worldwide. Although, based on the molecular classification, various therapeutic interventions are available for this deadly disease. However, increasing evidence suggests existence of differential mutation patterns in various cellular pathways crucial for the regulation of tumor microenvironment, cellular plasticity, and genomic instability. Genomic instability leads to the deregulation of oncogenic signaling pathways and makes it harder to find specific target in order to apply an effective therapy. Additionally, the deregulated oncogenic pathways acquire the gain of functions which makes the tumor more resilient to the available therapeutic intervention. These oncogenic mutations are also responsible for aiding up to tumor heterogeneity. Tumor heterogeneity in turn increases the intra-tumor diversity and the existence of various clonal population complicates the tumor diagnostic which leads to therapeutic challenges. In this review, we talked about the need of further molecular stratification of breast cancer to better understand the targetable mutation pattern and to design the effective outcome of treatment. Tumor heterogeneity has a serious clinical consequence for the breast cancer patients. However, there are no known ways to target the tumor heterogeneity yet. Although, we think that the future is in the hand of personalized medication in order to target the tumor heterogeneity, which still has a long way to go. Current treatment choices are mostly based on the molecular classification such as status of hormone receptors estrogen receptor, progesterone receptor, and HER2 expressions. The advancement in the global sequencing devices has given great advantages in understanding the tumor heterogeneity and identification of additional mutation patterns, which are being targeted in combination with available treatments for the better outcome of the patient’s survival. We summarize the clinical challenges and opportunities for better management of breast cancer patients and treatment choices. Investigating the mutational signatures and their associated mechanisms responsible for cancer could be a new evolving target and thus improve the opportunities for therapy.

The Potential Role of Selected miRNA in Uveal Melanoma Primary Tumors as Early Biomarkers of Disease Progression.

Uveal melanoma (UM) is the most common primary tumor of the eye diagnosed in adults, associated with a high risk of metastasis and thereby, poor prognosis. Among known risk factors for the development of metastatic disease is the loss of BAP1 expression and chromosome 3 monosomy in the primary tumor. However, the expression levels of specific micro RNAs (miRNA) in tumor tissue may also serve as a valuable marker for determining the risk of metastatic disease in patients with primary uveal melanoma. In our study, we analyzed the miRNA expression data of cases selected from The Cancer Genome Atlas study on uveal melanoma, and determined a panel of 15 miRNAs differentially expressed between patients with primary and metastatic disease. Next, 6 miRNAs were validated on a group of 46 tumor samples from primary and metastatic patients. We have shown, that expression of hsa-miR-592, hsa-miR-346, and hsa-miR-1247 was significantly increased, while hsa-miR-506 and hsa-miR-513c were decreased in the tumors of patients with metastatic disease. Hsa-miR-196b expression did not differ between the two subgroups, however, we showed significant correlation with BAP1 expression. Moreover, hsa-miR-592 also showed correlation with monosomy 3 tumors. Gene ontology analysis revealed involvement of those miRNAs with cellular processes mediating the metastatic process. Our results showed that miRNAs play an important role in the deregulation of several oncogenic pathways in UM and can, thereby, promote metastatic spread to distant organs. Moreover, differentially expressed miRNAs may be used as an interesting biomarker for the assessment of metastatic risk in uveal melanoma patients.

Systems analysis of key genes and pathways in the progression of hepatocellular carcinoma

The carcinogenesis of hepatocellular carcinoma (HCC) is a complex process, starting from a chronically altered hepatic microenvironment due to liver cirrhosis and ultimately progressing to HCC. However, the sequential molecular alterations driving the malignant transformation in liver cirrhosis are not clearly defined.In this study, we obtained gene expression profiles of HCC, including 268 tumor tissues, 243 adjacent tumor tissues, and 40 cirrhotic tissues (GSE25097) from Gene Expression Omnibus (GEO), to comprehensively define changes in the transcriptome of HCC during the sequential evolution of liver cirrhosis into HCC.We showed that changes in the molecular profiles of cirrhotic and adjacent tumor samples were small and quite uniform, whereas there was a striking increase in the heterogeneity of tumors in HCC tissues at the mRNA level. A massive deregulation of key oncogenic molecules and pathways was observed from cirrhosis to HCC tumors. In addition, we focused on FOXO1 and DCN, 2 critical tumor suppressor genes that play an important role in liver cirrhosis and HCC development. FOXO1 and DCN expression levels were significantly reduced in tumor tissues compared with adjacent tumor tissues in HCC. Kaplan-Meier analysis revealed that FOXO1 and DCN expression was positively correlated with overall survival, defining FOXO1 and DCN as adverse prognostic biomarkers for HCC.This system-level research provided new insights into the molecular mechanisms of HCC carcinogenesis. FOXO1 and DCN may be applied as potential targets for HCC treatment in the future.

Identification of COX5B as a novel biomarker in high-grade glioma patients.

BackgroundMalignant glioma is the second leading cause of cancer-related death worldwide, and is known to exhibit a high degree of heterogeneity in its deregulation of different oncogenic pathways. The molecular subclasses of human glioma are not well known. Thus, it is crucial to identify vital oncogenic pathways in glioma with significant relationships to patient survival.MethodsIn this study, we devised a bioinformatics strategy to map patterns of oncogenic pathway activation in glioma, from the Gene Expression Omnibus (GEO). Bioinformatics analysis revealed that 749 genes were differentially expressed and classified into different glioma grades.ResultsUsing gene expression signatures, we identified three oncogenic pathways (MAPK signaling pathway, Wnt signaling pathway, and ErbB signaling pathway) deregulated in the majority of human glioma. Following gene microarray analysis, the gene expression profile in the differential grade glioma was further validated by bioinformatic analyses, with coexpression network construction. Furthermore, we found that cytochrome c oxidase subunit Vb (COX5B), the terminal enzyme of the electron transport chain, was the central gene in a coexpression network that transfers electrons from reduced cytochrome c to oxygen and, in the process, generates an electrochemical gradient across the mitochondrial inner membrane. The expression level of COX5B was then detected in 87 glioma tissues as well as adjacent normal tissues using immunohistochemistry. We found that COX5B was significantly upregulated in 67 of 87 (77.0%) glioma and glioblastoma tissues, compared with adjacent tissue (p<0.01). Furthermore, statistical analysis showed the COX5B expression level was significantly associated with clinical stage and lymph node status, while there were no correlations between COX5B expression and age or tumor size.ConclusionThese data indicate that COX5B may be implicated in glioma pathogenesis and as a biomarker for identification of the pathological grade of glioma.

Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways.

Transcriptional deregulation of oncogenic pathways is a hallmark of cancer and can be due to epigenetic alterations. 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC-enriched loci with hmC-seal was conducted in a cohort of low-passage pancreatic cancer cell lines, primary patient-derived xenografts, and pancreatic controls and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected known regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers. Furthermore, base pair resolution analysis of cytosine methylation and hydroxymethylation with oxidative bisulfite sequencing was conducted and correlated with chromatin accessibility by ATAC-seq and gene expression by RNA-seq in pancreatic cancer and control samples. 5-hmC was specifically enriched at open regions of chromatin, and gain of 5-hmC was correlated with up-regulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia, such as MYC, KRAS, VEGFA, and BRD4. Specifically, BRD4 was overexpressed and acquired 5-hmC at enhancer regions in the majority of neoplastic samples. Functionally, acquisition of 5-hmC at BRD4 promoter was associated with increase in transcript expression in reporter assays and primary samples. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human pancreatic cancer.

Insights into the Regulation of Survivin Expression in Tumors

Survivin, an anti-apoptotic protein was found to be expressed in tumors, whereas in normal tissues the expression of this protein was shown to be absent or extremely low. Survivin exhibits multifunctional activity in tumor cells. Survivin is the smallest member of the inhibitor of apoptosis protein family and was demonstrated to have key roles in regulating cell division and inhibiting apoptosis. The cancer protein survivin was shown to be associated with tumor cell progression, invasiveness, resistance to therapeutics and poor prognosis. Its level in tumors is associated with deregulation of several oncogenic pathways. In this review, a delineation of survivin expression and progress in understanding the survivin transcriptional regulation with the emphasis of augmented apoptosis in cancer and its link to the Hedgehog pathway and cancer stem cells is discussed.

Chromatin-Remodeling-Factor ARID1B Represses Wnt/β-Catenin Signaling

The link of chromatin remodeling to both neurodevelopment and cancer has recently been highlighted by the identification of mutations affecting BAF chromatin-remodeling components, such as ARID1B, in individuals with intellectual disability and cancer. However, the underlying molecular mechanism(s) remains unknown. Here, we show that ARID1B is a repressor of Wnt/β-catenin signaling. Through whole-transcriptome analysis, we find that in individuals with intellectual disability and ARID1B loss-of-function mutations, Wnt/β-catenin target genes are upregulated. Using cellular models of low and high Wnt/β-catenin activity, we demonstrate that knockdown of ARID1B activates Wnt/β-catenin target genes and Wnt/β-catenin-dependent transcriptional reporters in a β-catenin-dependent manner. Reciprocally, forced expression of ARID1B inhibits Wnt/β-catenin signaling downstream of the β-catenin destruction complex. Both endogenous and exogenous ARID1B associate with β-catenin and repress Wnt/β-catenin-mediated transcription through the BAF core subunit BRG1. Accordingly, mutations in ARID1B leading to partial or complete deletion of its BRG1-binding domain, as is often observed in intellectual disability and cancers, compromise association with β-catenin, and the resultant ARID1B mutant proteins fail to suppress Wnt/β-catenin signaling. Finally, knockdown of ARID1B in mouse neuroblastoma cells leads to neurite outgrowth through β-catenin. The data suggest that aberrations in chromatin-remodeling factors, such as ARID1B, might contribute to neurodevelopmental abnormalities and cancer through deregulation of developmental and oncogenic pathways, such as the Wnt/β-catenin signaling pathway.

The “Macro” World of microRNAs in Hepatocellular Carcinoma

Hepatotropic viruses such as hepatitis B virus (HBV) and hepatitis C virus (HCV) are the major etiological agents associated with development of hepatocellular carcinoma (HCC). Progression of HCC is a multistep process that requires sequential or parallel deregulation of oncogenic and tumor suppressive pathways leading to chromosomal instability and neoplastic phenotype. In the recent years, microRNAs (miRNAs) have carved their own niche alongside oncogenes and tumor suppressors, owing to their innate ability to receive and relay multiple signals. Not surprisingly, miRNAs are fast emerging as central player in myriads of malignancies including HCC. miRNAs are reported to participate in initiation and progression of HCC, and have also been clinically correlated with risk assessment, disease grade, aggressiveness, and prognosis. Despite extensive data available on the role of miRNAs in HCC, there is a pressing need to integrate and evaluate these datasets to find its correlation, if any, with causal agents in order to devise novel interventional modalities. Through this review, we attempt to bridge the gap by consolidating the current knowledge and concepts in the field of HCC-related miRNAs with special emphasis on HBV and HCV. Further, we assess the potential of common as well as unique signatures that may be useful in developing novel biomarkers and therapeutics.

Abstract 1152: Gene profiling of multiple myeloma: MAPK pathway deregulation, which is regulated by PIM-1 and MOS, is associated with relapse within 6 months after autoSCT in MM patients

Abstract Substantial advances have been made in understanding the biology of multiple myeloma (MM) through the study of the bone marrow (BM) microenvironment. Dynamic interplay between bone marrow stromal cells (BMSCs) and MM cells regulated the relapsed MM after autologous bone marrow transplantation (ABMT). In this study, we performed gene expression profiling with microarray data to better dissect the molecular phenotypes and prognoses of relapsed multiple myeloma (MM). Using gene expression and clinical data, we applied gene expression signatures reflecting deregulation of oncogenic pathways to highlight molecular changes in bone marrow aspirate from 28 patients with relapsed MM. The patient subgroups were defined according to relapse-free interval, within 6 months versus more than 6 months. The microarray results revealed that dyregulation of MAPK pathway was associated with relapse within 6 months after ABMT. Among them, the expression of PIM-1 gene and MOS gene was higher in samples from patients with relapsed MM than MM cell lines (p=0.0037; p=0.0021). Also, IL-6, sIL-6R, and HGF expression in patients who relapsed within 6 months after ABMT was higher than the patients whose relapse-free interval were longer than 6 months. Treatment of shRNA PIM-1 gene and shRNA MOS gene in U266 and MOLP8 dramatically led to decreasing IL-6/sIL-6R mediated ERK phosphorylation and HGF-mediated MET phosphorylation. Similar results were noted for cluster genes for PIM-1/MOS. Especially, functional analysis of PIM-1 leads to inactivate the MAPK pathway through regulating p38 mediated signaling and Wnt/β-catenin pathway. Recent studies suggested that p38 activity in myeloma inhibits osteoblast differentiation and bone formation, but also enhances osteoclast maturation and bone resorption. p38 regulated the expression and secretion of the Wnt pathway antagonist DKK-1 and the monocyte chemoattractant MCP-1. Conclusionally, Our analysis suggested that MOS gene and PIM-1, which regulates MAPK pathway, is a noble prognostic marker for relapse of MM. The importance of the PIM-1-MOS-MAPK pathway as a prognostic marker in relapsed MM should be reassessed in the novel therapeutic agent era. Citation Format: Woo June Jung, Kwang-Sung Ahn, Chansu Lee, Youngil Koh, Hyun Jung Lee, Hyo Jung Kim, Hwi-Joong Yoon, Sung-Soo Yoon. Gene profiling of multiple myeloma: MAPK pathway deregulation, which is regulated by PIM-1 and MOS, is associated with relapse within 6 months after autoSCT in MM patients. [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 1152. doi:10.1158/1538-7445.AM2014-1152

Evaluating oncogenic pathway dysregulation in adolescents and young adults with acute myeloid leukemia.

7107 Background: Adolescent and young adults (AYAs) with Acute Myeloid Leukemia (AML) have been shown to have better outcomes with induction chemotherapy when compared to older young adults (OYAs). Multiple psychosocial, treatment, and host-related factors unique to AYAs have been identified but the contribution of disease biology to these outcomes has not yet been fully characterized. The purpose of this study was to evaluate disease biology as it relates to age-specific differences in outcomes for AYAs with AML. Methods: Clinically annotated, microarray data from 425 patients with newly diagnosed AML from two publicly available datasets: GSE1159; and GSE12417 were analyzed. Age-specific cohorts (AYAs ≤ 30 years; n = 58 and OYAs &gt;30 but ≤ 60 years; n=276) were prospectively identified. Patients in GSE1159 were treated according to protocols of the Dutch–Belgian Hematology–Oncology Cooperative group and included 111 patients who ultimately underwent stem-cell transplantation. Patients in GSE12417 were treated per the AMLCG-1999 protocol. Gene expression analysis was conducted by applying previously defined and tested signature profiles reflecting deregulation of oncogenic signaling pathways and altered tumor environment. All statistical analysis was performed using S-plus and survival analysis by Cox proportional-hazards regression was used to assess differences in overall survival (OS) between age-specified study cohorts and a one-sided p-value ≤ 0.05 was considered statistically significant. Results: AYA patients had a significantly better OS (median survival 24.1 months vs. 13.0 months in OYAs; p=0.0285), but there was no difference in Event Free Survival (p=0.23). Analysis of oncogenic pathways revealed that AYA patients likely had better OS because of lower TNF (p=0.03) and higher myc (p=0.02) pathway activation. Conclusions: AML arising in AYAs may represent a distinct biologic entity characterized by unique patterns of deregulated signaling pathways that contributes to OS. We hope these findings will enable clinically meaningful adjustments of treatment strategies in the AYA AML patient population.

Targeting the Akt Kinase to Modulate Survival, Invasiveness and Drug Resistance of Cancer Cells

The deregulation of oncogenic signaling pathways which provide survival advantages to tumor cells is mediated by multiple cellular networks. Among them, the PI3K-Akt-mTOR axis, in particular the serine/threonine kinase Akt, is recognized as a key player. The kinase is hyperactivated due to a variety of mechanisms including loss of PTEN, mutations in the PI3K catalytic subunit, receptor tyrosine kinase and Ras activation. Indeed, inappropriate activation of the Akt kinase is a common event in human tumors and Akt appears to be a critical player in cell survival that may also account for the therapeutic resistance and the invasive phenotype of tumors. Inhibition of Akt signalling results in apoptosis and growth inhibition of tumour cells with elevated Akt activity. A functional role in drug resistance is supported by evidence that tumor cells with acquired resistance to antitumor agents may display increased Akt activation and that treatment with molecularly targeted agents can activate feed-back loops involving Akt. This serine/threonine kinase may therefore represent an amenable target for modulation of sensitivity to compounds with different molecular features due to its pleiotropic role in cell survival. Different types of Akt inhibitors [i.e., ATP mimetics and pleckstrin-homology (PH) domain binders] have been generated and some of them have reached the clinical setting. The present review focuses on the i) mechanisms implicating Akt in increased survival and invasive potential of tumor cells of different tumor types and ii) on the development of Akt inhibitors as modulators of drug resistance.

A molecular profile of colorectal cancer to guide prognosis and therapy after resection of primary or metastatic disease.

339 Background: Biomarkers used to identify patients at high risk for recurrence after surgical resection of colorectal cancer (CRC) lack predictive capacity and are applicable only to localized disease. As the use of adjuvant therapy in this setting can be controversial, the development of a biomarker that is prognostic, predictive, and applicable after resection of primary or metastatic disease may dramatically improve patient outcomes. Methods: We compiled microarray data from 850 patients with predominantly primary CRC from four publically available datasets to predict activity of 19 oncogenic pathways to generate patterns of pathway deregulation for each patient tumor. Mixture modeling was applied to the samples using affinity propagation to subgroup tumors bearing unique patterns of pathway deregulation. The model was then applied to a dataset of 133 predominantly metastatic CRC samples from patients undergoing curative surgical resection at the Duke University Medical Center. Results: Mixture modeling resulted in the identification of 6 distinct molecular subgroups of CRC (MSCC) based on pathway deregulation for both primary and metastatic CRC. Kaplan-Meier analysis of the primary data set revealed differences in recurrence free survival among the 6 MSCC (p=0.0004) with patients assigned to MSCC3 having the poorest prognosis and patients assigned to MSCC4 having the best prognosis. A similar result was obtained when the model was applied to the metastatic data set (p&lt;0.05). Comprehensive analysis of 41 oncogenes showed that no specific mutations were associated with the any of the subgroups. Finally, we observed that MSCCs demonstrate differential sensitivity to specific targeted agents such as MSCCs 1, 2 and 3 to inhibition of Her2 by Lapatinib and EGFR by erlotinib (p&lt;0.05). Conclusions: Prediction of oncogenic signaling pathway deregulation is a powerful tool that may be used to molecularly sub-classify CRCs into clinically relevant subgroups. These subgroups have prognostic implications for recurrence following surgical resection and may help to identify therapies in the adjuvant setting after resection of either primary or metastatic disease.

Genomic Loss of Tumor Suppressor miRNA-204 Promotes Cancer Cell Migration and Invasion by Activating AKT/mTOR/Rac1 Signaling and Actin Reorganization

Increasing evidence suggests that chromosomal regions containing microRNAs are functionally important in cancers. Here, we show that genomic loci encoding miR-204 are frequently lost in multiple cancers, including ovarian cancers, pediatric renal tumors, and breast cancers. MiR-204 shows drastically reduced expression in several cancers and acts as a potent tumor suppressor, inhibiting tumor metastasis in vivo when systemically delivered. We demonstrated that miR-204 exerts its function by targeting genes involved in tumorigenesis including brain-derived neurotrophic factor (BDNF), a neurotrophin family member which is known to promote tumor angiogenesis and invasiveness. Analysis of primary tumors shows that increased expression of BDNF or its receptor tropomyosin-related kinase B (TrkB) parallel a markedly reduced expression of miR-204. Our results reveal that loss of miR-204 results in BDNF overexpression and subsequent activation of the small GTPase Rac1 and actin reorganization through the AKT/mTOR signaling pathway leading to cancer cell migration and invasion. These results suggest that microdeletion of genomic loci containing miR-204 is directly linked with the deregulation of key oncogenic pathways that provide crucial stimulus for tumor growth and metastasis. Our findings provide a strong rationale for manipulating miR-204 levels therapeutically to suppress tumor metastasis.

Use of gene expression profiling to determine prognosis and therapeutic targets for patients with appendiceal carcinoma.

418 Background: Appendiceal carcinomas are rare neoplasms that often present as peritoneal surface malignancies. The tumors are treated similarly to primary colorectal metastases, despite having different biological environments. The aim of this study is to utilize genomic analyses to understand the underlying biology of appendiceal carcinoma in order to better guide prognosis and therapy. Methods: Forty-one metastatic human tumors to the peritoneum (26 appendiceal carcinoma, 15 colorectal carcinoma) were subjected to global gene expression analysis. Unsupervised hierarchical clustering was used to differentiate phenotypes based on differential gene expression. Phenotypes were further analyzed to find differences in oncogenic pathway deregulation and findings were validated using gene specific inhibitors in vitro. Results: Unsupervised hierarchical clustering revealed three distinct phenotypes, two consisting of predominantly low grade appendiceal samples (Cluster 1 and Cluster 2) and one consisting of predominantly colorectal samples (Cluster 3). Cluster 1 consisted of patients with good prognosis and Cluster 2 consisted of patients with poor prognosis (p = 0.046). Further characterization of Cluster 1 and Cluster 2 with oncogenic pathway signatures identified increased deregulation of the EGFR pathway in the poor prognosis cluster. Similarly, colon cancer cell lines with the poor prognosis phenotype were found to be more sensitive to gefitinib (EGFR inhibitor) (p = 0.038). Conclusions: The use of geneexpression profiling can be used to identify prognosis and novel therapeutic targets for patients with appendiceal carcinoma. These methods can serve as models to understand the biology of appendiceal carcinoma and to assist in the design of future trials for patients with appendiceal cancer. No significant financial relationships to disclose.

MicroRNA-221/222 confers breast cancer fulvestrant resistance by regulating multiple signaling pathways

Fulvestrant is a selective estrogen receptor downregulator (SERD) and highly effective antagonist to hormone-sensitive breast cancers following failure of previous tamoxifen or aromatase inhibitor therapies. However, after prolonged fulvestrant therapy, acquired resistance eventually occurs in the majority of breast cancer patients, due to poorly understood mechanisms. To examine a possible role(s) of aberrantly expressed microRNAs (miRNAs) in acquired fulvestrant resistance, we compared antiestrogen-resistant and -sensitive breast cancer cells, revealing the overexpression of miR-221/222 in the SERD-resistant cell lines. Fulvestrant treatment of estradiol (E2)- and fulvestrant-sensitive MCF7 cells resulted in increased expression of endogenous miR-221/222. Ectopic upregulation of miR-221/222 in estrogen receptor-α (ERα)-positive cell lines counteracted the effects of E2 depletion or fulvestrant-induced cell death, thus also conferring hormone-independent growth and fulvestrant resistance. In cells with acquired resistance to fulvestrant, miR-221/222 expression was essential for cell growth and cell cycle progression. To identify possible miR-221/222 targets, miR-221- or miR-222- induced alterations in global gene expression profiles and target gene expression at distinct time points were determined, revealing that miR-221/222 overexpression resulted in deregulation of multiple oncogenic signaling pathways previously associated with drug resistance. Activation of β-catenin by miR-221/222 contributed to estrogen-independent growth and fulvestrant resistance, whereas TGF-β-mediated growth inhibition was repressed by the two miRNAs. This first in-depth investigation into the role of miR-221/222 in acquired fulvestrant resistance, a clinically important problem, demonstrates that these two 'oncomirs' may represent promising therapeutic targets for treating hormone-independent, SERD-resistant breast cancer.