bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1961: Characterization of MicroRNA Expression during the Development of Resistance to a mTOR-Inhibitor in renal cell carcinoma
Authors: Heinzelmann Joana , Bauer Franziska , Unteregger Gerhard , Schendel Darja , Weiland Anne , Stöckle Michael , Junker Kerstin 
Published: July 2016

Abstract
Introduction:
Second line therapy of metastatic renal cell carcinoma (RCC) using the mTOR inhibitor RAD001 (everolimus) is hampered by the appearance of drug resistance. The cellular mechanisms leading to drug resistance are not yet clarified. Although the influence of miRNAs is proven for other systemic treatments, their impact on mTOR inhibitors is not investigated. Therefore, we analyzed miRNA alterations in correlation to development of resistance to RAD001 in RCC cell culture models.
Material and Methods:
The RCC cell line 786-O was treated with 1μM RAD001 for up to 20 passages after developing sunitinib resistance. TotalRNA was isolated at defined intervals. Resistance-development as well as drug efficacy during the treatment was monitored by proliferation assays. MiRNA Microarrays (Agilent Technologies) were performed using RAD001 sensitive and RAD001 resistant cells to identify differently expressed miRNAs. Results were validated by qRT PCR. Functional analyses are performed after transfection of RAD001 sensitive cells with miRNA candidates.
Results:
The Microarray analyses revealed a miRNA signature including 9 differently expressed miRNAs in RAD001 resistant cells compared to sensitive cells. QRT-PCR results showed that especially miR-302e was strongly up-regulated by the factor of four. At present, functional analyses of miR-302e are ongoing.
Conclusion:
To our knowledge this is the first study analyzing miRNA alterations during the development of resistance to mTOR inhibitors. We have shown that miR-302e expression is associated with RAD001 resistance in RCC cells. Since miR-302e is a known tumor suppressor modulating radio sensitivity and drug sensitivity in several tumors we are proving now if miR-302e can regulate the mTOR inhibitor resistance of RCC.
Citation Format: Joana Heinzelmann, Franziska Bauer, Gerhard Unteregger, Darja Schendel, Anne Weiland, Michael Stöckle, Kerstin Junker. Characterization of MicroRNA Expression during the Development of Resistance to a mTOR-Inhibitor in renal cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1961.
Abstract 1969: miRNA expression as potential biomarker for leiomyosarcoma and undifferentiated pleomorphic sarcoma
Authors: Pazzaglia Laura , Novello Chiara , Conti Amalia , Quattrini Irene , Pollino Serena , Picci Piero , Benassi Maria Serena 
Published: July 2016

Abstract
Rare and highly aggressive adult soft tissue sarcomas (STS), leiomyosarcoma (LMS) and undifferentiated pleomorphic sarcoma (UPS), have complex genomics characterized by a multitude of rearrangements, amplifications and deletions. Our previous data (Guled et al., Genes Chromosomes Cancer, 2014) showed 21 common differentially expressed miRNAs in UPS and LMS samples when compared to mesenchymal stem cells. On the base of these results, we performed target analysis by using bioinformatic tools (Diana-microt v3.0, Targetscan Vert release 5.2 and Pictar-Vert) and we identified 12 miRNAs potentially implicated in tumor development and progression.
The expression of the selected miRNAs was evaluated by TaqMan microRNA Array in 59 high grade STS primary samples (27 LMS and 32 UPS) stored at Rizzoli biobank. Ten tissues from non oncologic patients were used as control. Our results showed a significant lower expression of miR-1, miR-133b and miR-152 (respectively p = 0.0045, p = 0.0027 and p = 0.0016) in tumors when compared to nontumor tissue. Three different target prediction databases (miRBase, TargetScan, miRanda) recognized MET as common target gene of miR-1, mir-133b and miR-152 and KIT as target of miR-152. MET and KIT gene expression was validated in our series of STS by RT-PCR by using 2−ΔΔCT comparative method. The data demonstrated higher mean expression levels in STS than in control (respectively 2.08 and 0.15 for KIT; 18527.9 and 2324.9 for MET) without significant differences between two histotypes.
Our preliminary results confirmed MET and KIT as miRNA targets. Correlation with clinical data and in vitro studies with miRNA precursor transfected cell lines are on-going to better investigate their role as potential prognostic and therapeutic markers.
Citation Format: Laura Pazzaglia, Chiara Novello, Amalia Conti, Irene Quattrini, Serena Pollino, Piero Picci, Maria Serena Benassi. miRNA expression as potential biomarker for leiomyosarcoma and undifferentiated pleomorphic sarcoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1969.
Abstract 1972: Changes in the architecture, interactions and chromatin remodeling of SWI/SNF due to loss of Snf5
Authors: Bartholomew Blaine , Persinger Jim , Sen Payel , Dechassa Lemma Mekonnen , Luo Jie , Ranish Jeff 
Published: July 2016

Abstract
The mammalian SWI/SNF complex is a family of an estimated ∼100 complexes, each with different combinations of related subunits. Efforts in sequencing many cancer genomes has revealed that mammalian SWI/SNF complexes is one of the most frequently mutated epigenetic factors found in a broad range of cancers. In order to understand more about the subunit organization of SWI/SNF and because yeast and mammalian SWI/SNF complexes share many conserved subunits and domains; we have studied the role of the Snf5 subunit in the yeast SWI/SNF to better understand the role of the mammalian homolog SNF5 that is a known tumor suppressor gene. The basis for the loss of mammalian SNF5 being a driver mutation in pediatric rhabdoid tumors is currently not well understood or how the loss of SNF5 effects the composition, recruitment and nucleosome remodeling activity of the SWI/SNF complex. We have assessed the effects on deletion of Snf5 on the compositional integrity of SWI/SNF and have evidence for Snf5 forming a sub-complex with two other highly conserved subunits of SWI/SNF that are lost from the complex when Snf5 is deleted. In addition we have mapped the inter-subunit and intra-subunit interactions of the yeast SWI/SNF complex with lysine specific homo bi-functional crosslinkers and mass spectrometry. These data confirm the formation of a tri-subunit Snf5 sub-complex and show that this module uniquely interacts with the ATPase domain of the catalytic subunit of SWI/SNF (Snf2). These observations lead to a further investigation into the regulation of the remodeling activity of SWI/SNF by the Snf5 subunit. We have found that Snf5 is required for the ATPase domain to make stable interactions with nucleosomal DNA. And the loss of these interactions in turn also causes a reduction in the remodeling efficiency of the SWI/SNF complex. We have done additional mapping of the interactions of Snf5 as part of the SWI/SNF complex and find that the highly conserved region of yeast Snf5 corresponding to the human SNF5 protein associates with the surface of the nucleosome near the histone H2A-H2B dimer. We will discuss the relevance of these findings in highlighting how an aberrant form of SWI/SNF could be created by loss of Snf5 and provide an example of how it alters the normal function and structure of SWI/SNF.
Citation Format: Blaine Bartholomew, Jim Persinger, Payel Sen, Mekonnen Dechassa Lemma, Jie Luo, Jeff Ranish. Changes in the architecture, interactions and chromatin remodeling of SWI/SNF due to loss of Snf5. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1972.
Abstract 1987: Recurrent chromosomal translocations mediate reprogramming of Myb dependent regulatory networks in adenoid cystic carcinoma
Authors: Brayer Kathryn , Ness Scott A. 
Published: July 2016

Abstract
Adenoid Cystic Carcinoma (ACC), the second most common malignancy of salivary glands, is a rare tumor with bleak prognosis for which therapeutic targets are unavailable. Recently, we used RNA-sequencing (RNA-Seq) to analyze low-quality RNA from archival, formaldehyde-fixed, paraffin-embedded samples (1). In addition to detecting the most common ACC translocation, t(6;9) fusing the MYB proto-oncogene to NFIB, we also detected previously unknown t(8;9) and t(8;14) translocations fusing the MYBL1 gene to the NFIB and RAD51B genes, respectively. Mutated versions of c-Myb are potent oncoproteins, and Myb proteins are over- or highly-expressed in a wide variety of human tumors. Interestingly, ACC tumors with MYB and MYBL1 translocations displayed similar gene expression profiles, and the combined MYB and MYBL1 expression correlated with outcome, suggesting that the related Myb proteins are interchangeable oncogenic drivers in ACC.
While RNA-Seq provides information about gene fusions, alternative RNA splicing and gene expression signatures, this type of data does not address how translocations alter transcription factor function. Previous studies in our lab, and others, have demonstrated that Myb proteins contain C-terminal regulatory domains and are known to interact with several proteins via C-terminal motifs (2). These regulatory and interaction sites are lost upon chromosomal translocation in ACC; however, the downstream affect of this loss is not understood. Do the translocations merely relieve Myb transcription factors of repressive regulatory signals, thereby globally increasing Myb-dependent gene expression or, does the altered protein allow novel protein-protein interactions which re-target Myb transcription factors? Furthermore, the most frequent translocations involve the relocation of a large enhancer regions. What role does the recruitment of novel enhancer regions play in up-regulating Myb protein expression? Using a combination of ChIP-Seq and digital genomic footprinting, we are attempting to understand the mechanism of regulatory rewiring observed in ACC tumors.
References
1. Brayer et al. Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor-Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma. Cancer Discovery. In press.
2. George and Ness (2014) Situational Awareness: Regulation of the Myb Transcription Factor in Differentiation, the Cell Cycle and Oncogenesis. Cancers: 6, 2049-2071.
Citation Format: Kathryn Brayer, Scott A. Ness. Recurrent chromosomal translocations mediate reprogramming of Myb dependent regulatory networks in adenoid cystic carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1987.
Abstract 1989: Multiple functional implications of MYB in ovarian cancer
Authors: Srivastava Sanjeev Kumar , Singh Seema , Bhardwaj Arun , Carter James E. , Rocconi Rodney P. , Scalici Jennifer , Singh Ajay P. 
Published: July 2016

Abstract
Ovarian cancer (OC) is the most common and deadliest gynecologic malignancies in the United States, with an estimated 21,290 new cases and 14,180 deaths in 2015. Therefore, it is highly imperative to identify novel molecular targets driving OC progression, so that an effective treatment strategy can be developed against this devastating disease. In the present study, we investigated the role of MYB in OC pathogenesis. MYB/c-MYB is a cellular progenitor of v-MYB oncogenes, which encodes for a transcription factor, and confers its oncogenic activity by regulating the expression of several target genes. First, we examined the expression of MYB in clinical specimens and OC cell lines by immunohistochemical and immunoblot analysis, respectively. We observed intense staining of MYB in the tissues of all the subtypes of OC, while no or negligible staining was observed in normal ovarian tissues. Moreover, we found MYB to be expressed in all the OC cell lines examined, with its heightened expression in highly aggressive (TOV112D, SKOV3-ip) and chemo-resistant (A2780-Cip) OC cell lines. To examine the pathological significance of MYB in OC, we silenced its expression in TOV112D, SKOV3-ip and A2780-Cip OC cell lines. Functional studies demonstrate that silencing of MYB led to decrease in growth and clonogenic ability in TOV112D, SKOV3-ip and A2780-Cip cells, as compared to their scrambled sequence-transfected (Scr) control cells. Furthermore, MYB-silencing reduced motility and invasion, as well as resulted in the loss of mesenchymal and gain of epithelial markers. In addition, our data showed that TOV112D-shMYB, SKOV3-ip-shMYB and A2780-Cip-shMYB were more sensitive to cisplatin-cytotoxicity as compared to their respective controls. Altogether, our studies provide the first experimental evidence for a functional role of MYB in altered growth, malignant behavior and chemoresistance of ovarian cancer.
Citation Format: Sanjeev Kumar Srivastava, Seema Singh, Arun Bhardwaj, James E. Carter, Rodney P. Rocconi, Jennifer Scalici, Ajay P. Singh. Multiple functional implications of MYB in ovarian cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1989.
Abstract 1998: Alternative polyadenylation of eukaryotic initiation factor 5A-2 (eIF5A-2) mRNAs examined by quadruplex single molecule RNA fluorescence in situ hybridization (smRNA-FISH)
Authors: Johansson Hans E. , Yin Raymund H. , Mandal Swati , Park Myung-Hee 
Published: July 2016

Abstract
Normal expression of the minor oncogene EIF5A2 in the hypusine pathway is restricted to brain and testis. However aberrant expression has been noted in multiple cancers, including ovarian gastric, colorectal and pancreatic, and artificial overexpression causes tumor growth in naked mice. Unlike cDNAs from the homologous gene EIF5A1, which are readily translated into protein upon transient transfection, EIF5A2-mRNAs only associate with monosomes without production of eIF5A-2 protein.
Here we present data from multiple EIF5A2-positive cell lines on the steady state levels of the four different EIF5A2-mRNAs that arise through differential polyadenylation. While considering qPCR and RNA-Seq, we chose to apply Stellaris single molecule RNA fluorescence in situ hybridization with four unique probe sets, each reporting on the dependent A, B, C, or D segments. The probe sets were designed with multiple tiled singly labeled 18-22-mer oligonucleotides with balanced GC content, and hence similar hybridization characteristics, which in turn enabled the simultaneous quadruplex smRNA FISH.
Stellaris RNA FISH leaves the cell intact, and also does not require RNA isolation or nucleic acid amplification that may introduce an otherwise hidden experimental bias. The single molecule spots revealed by widefield microscopy and subsequent image analysis co-localized with a high degree of confidence. Taking advantage of the added spatial dimension that RNA FISH affords, we also determined the localization of each mRNA variant and recorded the cell-to-cell variability and the actual range of mRNA copy numbers per cell.
Our data is consistent with previous gene expression analysis data, but also provide actual counts of each mRNA variant.
The results presented here have direct applications for the expression of the minor oncogene EIF5A2, and the regulated protein synthesis of its mRNAs, as well as of other mRNAs in polyamine and hypusine pathways. Further, the techniques and probes developed here can be directly transferred to the analysis of other mRNA variants that may arise through alternative transcription start site use, alternative splicing or alternative 3’ end processing in normal and aberrant cells.
Citation Format: Hans E. Johansson, Raymund H. Yin, Swati Mandal, Myung-Hee Park. Alternative polyadenylation of eukaryotic initiation factor 5A-2 (eIF5A-2) mRNAs examined by quadruplex single molecule RNA fluorescence in situ hybridization (smRNA-FISH). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1998.
Abstract 20: Outlier overexpression of genes involved in fatty acid metabolism and processing define two aggressive prostate cancer phenotypes
Authors: Gaston Sandra M. , Dehimer Kerry , Kearns James , Chinsky Kyle-Ravi , Otali Dennis , Oelschlager Denise , Rais-Bahrami Soroush , Nix Jeffrey W. , Kolettis Peter , Adams George W. , Grizzle William E. 
Published: July 2016

Abstract
Major shifts in fatty acid metabolism are part of the malignant phenotype of many types of cancer, including prostate cancer. We have used a biopsy based approach to characterize high grade prostate cancers in both African American and European American patients. This approach allows us to analyze prostate cancers from patients whose disease is too advanced for radical prostatectomy and who are thus not represented in the study specimens available from conventional biorepositories. mRNA gene expression profiling of high grade prostate cancers from biopsies revealed cancer subtypes with very high (&gt;10 fold) levels of overexpression of fatty acid binding protein 5 (FABP5) and fatty acid synthase (FASN). Interestingly, these prostate cancer subtypes showed an either-or phenotype, with “super-overexpression” of either FABP5 or FASN but not both. These findings suggest two “outlier” prostate cancer subtypes with striking differences in the pathways that drive a shift in tumor fatty acid metabolism; one is a fatty acid synthase (FASN) dominant phenotype and the other a previously unrecognized fatty acid binding protein (FABP5) dominant phenotype. In contrast, prostate cancers with lower levels of FABP5 and/or FASN overexpression (2-4 fold) often co-overexpressed both of these genes. Immunohistochemical analyses confirmed prostate cancer FABP5 and FASN overexpression; both showed strong cytoplasmic staining. FABP5 also showed robust nuclear staining consistent with its proposed role in regulating fatty acid mediated gene expression. At both the mRNA and protein levels, the high grade prostate cancers with the highest levels of FABP5 over-expression were more common in African Americans, while the highest levels FASN overexpression were more common in prostate cancers from European Americans. These findings may provide the basis for more effective dietary interventions and targeted therapies for African American and European American patients with these two different subtypes of high grade prostate cancer.
Citation Format: Sandra M. Gaston, Kerry Dehimer, James Kearns, Kyle-Ravi Chinsky, Dennis Otali, Denise Oelschlager, Soroush Rais-Bahrami, Jeffrey W. Nix, Peter Kolettis, George W. Adams, William E. Grizzle. Outlier overexpression of genes involved in fatty acid metabolism and processing define two aggressive prostate cancer phenotypes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 20.
Abstract 200: PDLIM2 phosphorylation in determining breast cancer phenotype
Authors: Cox Orla T. , Berghoff Janina , Buckley Deirdre A. , O’Connor Rosemary 
Published: July 2016

Abstract
Several genes that are involved in cancer progression are induced by Insulin-like Growth Factor-1 (IGF-1). One of them encodes the PDZ-LIM protein PDLIM2, which is localized at the cytoskeleton and nucleus in epithelial and hematopoietic cells. PDLIM2 is repressed in certain cancers including breast cancers, but it is highly expressed in invasive cancer cells in triple negative breast cancer (TNBC), where it has also been associated with poor survival. PDLIM2 regulates the stability and activity of transcription factors including beta catenin, STATs, NFκB and IRFs and has been associated with ubiquitination and destabilization of proteins such as NF-κB, E-cadherin, and p27KIP1. However, PDLIM2 itself is also regulated by posttranslational modifications, but how this controls PDLIM2 activity is still largely unclear.
Therefore, this study aimed to investigate PDLIM2 phosphorylation and its effect on PDLIM2 sub-cellular location and function in transcription factor regulation. The PDLIM2 protein sequence includes multiple potential phosphorylation sites and it migrates as several distinct phosphatase-sensitive species in SDS PAGE and 2D electrophoresis, indicating phosphorylation at several residues. Using cellular fractionation and immunofluorescence we show that PDLIM2 accumulates in the nucleus in response to cell stimulation with IGF-1 or TGFβ. Moreover, we show that inhibitors of Rho Kinases suppress PDLIM2 phosphorylation in response to these stimuli. In addition, we demonstrate that mutation of the predicted Rho Kinase phosphorylation sites in PDLIM2 reduce protein stability, an effect that can be reversed by application of proteasomal inhibitor.
Overall, our results indicate that phosphorylation by Rho kinases plays an important role in the subcellular location and regulation of PDLIM2 function, which opens a new avenue in targeting PDLIM2 activity in invasive cancer cells.
Citation Format: Orla T. Cox, Janina Berghoff, Deirdre A. Buckley, Rosemary O’Connor. PDLIM2 phosphorylation in determining breast cancer phenotype. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 200.