bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1966: Automated miRNA purification without the use of organic solvents
Authors: English Jami D. , Horejsh Doug , Moreland Chris , Urh Marjeta 
Published: July 2016

Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNAs 18-24 nucleotides in size that play important roles involving gene regulation associated with cancer, disease control and gene silencing. Because of the impact on disease progression, miRNA research is rapidly shifting towards biomarker discovery. Many of the commercially available miRNA purification methods involve organic extraction during pre-processing. Here, we describe a novel chemistry that enables total RNA purification including smaller RNA such as miRNA. This chemistry offers significant advantages with a simple automated workflow, no organic extraction and minimal pre-processing.
In this study, we successfully show purification of miRNAs from a range of solid and liquid sample types including frozen tissue, whole blood, plasma, exosomes, mammalian cell lines, saliva, bone and FFPE samples. Absorbance yield, absorbance ratios, RINs, and amplification of miRNA show equivalence with organic solvent-based purification methods. The miRNA studied included miR-21, let-7a, miR-141, and miR-125b, depending on starting sample type. Next generation sequencing (NGS) analysis shows equivalent sequence diversity when compared pairwise with a manual, organic pre-processing method.
This novel chemistry and method enables purification of small and large RNA from a range of sample types. The purified RNA has little or no detectable DNA contamination and does not require phenol extraction, thus improving safety. Also, the automation of this workflow decreases manual hands on time, saving scientist time and reducing the risk of RNase contamination.
Citation Format: Jami D. English, Doug Horejsh, Chris Moreland, Marjeta Urh. Automated miRNA purification without the use of organic solvents. [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 1966.
Abstract 1970: miRNA differential profiling between fibroblasts originated from breast cancer and normal adjacent tissue from benign disease
Authors: Rozenchan Patricia Bortman , de Carvalho Cristina V. , Bonetti Tatiana , Melo Carina , Brentani M Mitzi , Girão Manoel JBC 
Published: July 2016

Abstract
The importance of tumor-stromal cells interactions in breast tumor progression and invasion has been recognized; therefore, modifications in the stromal fibroblasts can play a significant role in overall cancer development and progression. Accumulating evidence indicates that epigenetic phenomena such as microRNAs are extremely important and were already recognized as key regulators of gene expression, as well as expression of these small RNAs has been linked to human disease, including those related to estrogen-dependent disorders and in cancer homeostasis. So, deciphering molecular alterations in breast tumor microenvironment such as miRNAs differential expression could lead not solely to target for therapeutic intervention as well as to novel early diagnosis markers. Stromal fibroblasts were isolated from four invasive breast carcinoma samples (CAFs) and from five women with benign breast disorders (NAFs). RNA was extracted from low-passage cultures and transformed into cDNA and used for the Human Breast Cancer miScript® miRNA PCR Array expression analysis on StepOne Plus Real Time. This Array profiles the expression of 84 mirRNAs known or predicted to alter their expression during breast cancer initiation or progression. We could find 05 differentially expressed miRNAs in CAFs in comparison to NAFs; 04 down-regulated: mir107 (fold: -1,56, p = 0,04), miR-125b-1 (fold:-1,83, p = 0,03), miR-200b (fold: -2, p = 0,02), miR-93 (fold: -2,25, p = 0,02) and 01 up-regulated: miR-424 (fold: 5,73, p = 0,01). After bioinformatics analysis, these miRNAs were predicted to regulate genes involved in important cancer related pathways like, Cyclins and Cell Cycle Regulation; EGF Signaling Pathway; MAPKinase Signaling Pathway and Apoptotic Signaling in Response to DNA Damage. All together, our results showed that there are important differences regarding miRNAs expression profiling between CAFs and NAFs that could be determinant for breast cancer tumorigenesis.
Citation Format: Patricia Bortman Rozenchan, Cristina V. de Carvalho, Tatiana Bonetti, Carina Melo, M Mitzi Brentani, Manoel JBC Girão. miRNA differential profiling between fibroblasts originated from breast cancer and normal adjacent tissue from benign disease. [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 1970.
Abstract 1975: The 3D chromatin structure of the PTHLH region comprises a dynamic hierarchical looping complex that approximates the protein-coding genes and facilitates promoter and enhancer promiscuity
Authors: Freeman Adam N. , Henderson Michael A. , Kapuscinski Miroslaw K. , Hopper John , Martin T John 
Published: July 2016

Abstract
Parathyroid Hormone-Like Hormone (PTHLH) is an important regulatory gene encoding the product Parathyroid Hormone-related Protein (PTHrP). Among many biological roles, it has been demonstrated to be essential to the development of multiple tissue-types, the regulation of foetal calcium levels, and the metastasis of breast cancer to bone. Its region has GWAS associations with breast cancer, breast size, height, type 2 diabetes mellitis, neural development, cardiac arrest, and several immunological phenotypes. They extend both up- and down-stream of PTHLH, however their driving molecular mechanisms remain obscure.
Analysis of datasets including Hi-C, ChIA-PET, IM-PET and ChIP-seq suggests PTHLH sits within a 1.3Mb Topologically Associating Domain (TAD) containing 4 other protein-coding genes (pc-genes) CCDC91, MRPS35, MANSC4 and KLHL42. PTHLH itself rests between two 220kb inducible sub-TADs that likely comprise regulatory archipelagos directed primarily at its regulation. There are several other inducible loops in the TAD.
All protein-coding genes within the TAD feature an Activated Chromatin Hub (ACH) nearby their 5’. The 3D-structure of the TAD appears to be supported by a system of permanent and dynamic tether points producing primary and inducible chromatin loops. These result in all pc-genes’ ACHs being 30 to 60kb from each other. RNA Pol II (RNAPII) ChIA-PET data suggests there is an inclusive hierarchical regulatory structure within the TAD, with substantial interaction between the ACHs of respective pc-genes that is likely facilitated by the 3D conformation.
Citation Format: Adam N. Freeman, Michael A. Henderson, Miroslaw K. Kapuscinski, John Hopper, T John Martin. The 3D chromatin structure of the PTHLH region comprises a dynamic hierarchical looping complex that approximates the protein-coding genes and facilitates promoter and enhancer promiscuity. [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 1975.
Abstract 1988: MYB overexpression is associated with castration-resistance in prostate cancer
Authors: Srivastava Sanjeev K. , Bhardwaj Arun , Singh Seema , Arora Sumit , Tyagi Nikhil , Carter James E. , Singh Ajay P. 
Published: July 2016

Abstract
Clinical progression of prostate cancer (PCa) is characterized by a transition from castration-sensitive (CS) to castration-resistant (CR) phenotype. We previously demonstrated that MYB overexpression sustained the growth of PCa cells in androgen-depleted growth environment as well as promoted aggressive tumor phenotypes. Here, we examined its role in PCa progression and castration-resistance using appropriate mouse models and delineated underlying molecular mechanisms. Luciferase-tagged MYB-overexpressing (LNCaP-MYB) or -silenced (C4-2-shMYB) PCa cell lines along with their respective control sublines (LNCaP-Neo and C4-2-NTScr) were orthotopically implanted in nude mice and tumor growth was monitored by non-invasive bioluminescence imaging using Xenogen-IVIS optical system. Our data demonstrated significantly enhanced tumor growth in mice implanted with high MYB expressing (LNCaP-MYB and C4-2-NTScr) PCa cells as compared to low MYB expressing (LNCaP-Neo and C4-2-shMYB) cells. To study the role of MYB in castration-resistance, we castrated the mice after tumors from all groups reached comparable size as determined by in vivo imaging. Tumors in LNCaP-Neo and C4-2-shMYB groups exhibited drastic regression following castration. In contrast, only slight initial reduction in the tumor growth was reported in mice from LNCaP-MYB and C4-2-NTScr groups following castration, and they later regained tumor growth. Furthermore, Kaplan-Meier survival analysis revealed that the median survival of testis-intact (non-castrated) animals of LNCaP-Neo and C4-2-shMYB groups was significantly lower than that of castrated group mice. However, castration in high MYB-expressing tumor bearing mice could barely improve their median survival. Interestingly, MYB expression levels in orthotopic tumors correlated with serum PSA levels. Furthermore, castration of mice in LNCaP-Neo and C4-2-shMYB groups resulted in a rapid reduction in serum PSA levels; while it sustained and continued to rise in MYB overexpressing groups. In additional studies, we demonstrated that MYB interacts with androgen-receptor (AR) in prostate cancer cells, and facilitates the nuclear localization of AR in a ligand-independent manner. In essence, these results suggest a critical role of MYB in the CR progression of PCa.
Citation Format: Sanjeev K. Srivastava, Arun Bhardwaj, Seema Singh, Sumit Arora, Nikhil Tyagi, James E. Carter, Ajay P. Singh. MYB overexpression is associated with castration-resistance in prostate 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 1988.
Abstract 199: Evaluation of multiple EGFR tyrosine kinase inhibitors against clinically relevant EGFR mutants using in vitro modeling
Authors: Hasegawa Hanako 
Published: July 2016

Abstract
Purpose:
We are able to use multiple EGFR-TKIs to treat patients with lung cancer harboring EGFR mutations. However, there is no clear guideline regarding which EGFR-TKIs should be used for which mutations. The purpose of this study is to establish an in vitro model to determine the “therapeutic window” of EGFR-TKIs against various types of EGFR mutations, including several EGFR exon 20 insertion mutations.
Experimental design:
We evaluated drug sensitivity and downstream signaling of human lung cancer cell lines harboring EGFR mutations (PC9, H3255, PC9-ER, BID007 and H1975) and Ba/F3 cells exogenously expressing mutated or wild type EGFR for the 1st (erlotinib), 2nd (afatinib), and 3rd (osimertinib and rociletinib) generation EGFR-TKIs using MTS assay, apoptosis assay and western blotting, simultaneously.
An in vitro model of mutation specificity was created by calculating the ratio of IC50 values between mutated and wild type EGFRs.
Results:
The model of mutation specificity identified wide therapeutic windows of afatinib for exon 19 deletions and L858R and those of osimertinib and rociletinib for T790M positive mutations in human cell lines and Ba/F3 cells. In human cell lines and Ba/F3 cells harboring exon 19 deletions or L858R, afatinib showed the lowest IC50 and most potently inhibited the phosphorylation of EGFR, AKT, and ERK. Afatinib and 3rd generation EGFR-TKIs (osimertinib and rociletinib), effectively inhibited the cell growth and the phosphorylation of downstream signaling of EGFR in T790M positive cells. For EGFR exon 20 insertion mutations, osimertinib was potent and presented the most wide therapeutic window.
Conclusion:
This model will provide a preclinical rationale for proper selection of EGFR-TKIs against clinically-relevant EGFR mutations including EGFR exon 20 insertions.
Citation Format: Hanako Hasegawa. Evaluation of multiple EGFR tyrosine kinase inhibitors against clinically relevant EGFR mutants using in vitro modeling. [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 199.
Abstract 1990: Unique in vitro transcriptional activities of oncogenic Myb fusions identified in salivary gland adenoid cystic carcinoma
Authors: Frerich Candace A. , Ness Scott A. 
Published: July 2016

Abstract
Chromosomal translocations involving the MYB and NFIB (t(6;9)) genes are the sole recurrent cytogenetic aberration in Adenoid Cystic Carcinoma (ACC), a rare cancer that frequently manifests as salivary gland tumors. Since ACC has poor prognosis and treatment is accompanied by high morbidity, there is a need for additional investigation of this cancer with the goal of improving patient outcomes. Recurrent translocations create fusions involving the N-terminus of MYB, located on chromosome 6, and the C-terminus of NFIB, located on chromosome 9. Our lab also recently identified translocations involving the related MYBL1 gene fusing it to NFIB t(8;9) and RAD51B t(8;14) genes. Further, recent work in our lab demonstrated tumors with MYB or MYBL1 translocations have similar gene expression (1). The presence of recurrent translocations involving both the MYB proto-oncogene and the related MYBL1 gene suggests that the resulting novel fusion proteins are likely oncogenic drivers in these tumors. In order to directly address the transcriptional activities of the resulting fusion proteins MYB and MYBL1 fusion genes, identified in primary ACC tumors, were cloned and expressed in vitro. The fusion proteins transcriptional activities were examined using reporter gene assays and trancriptomics. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed to interrogate promoters bound by these proteins. Reporter genes specific for normal vs. oncogenic MYB variants have been constructed. These data demonstrate that the proteins predicted to be produced by MYB fusion genes after chromosomal translocation are transcriptionally active. Further, Myb fusion proteins bind and activate gene sets distinct from their wild type c-Myb and A-Myb counterparts. These data indicate Myb fusion proteins have unique transcriptional activities, perhaps underlying their ability to drive tumorigensis in ACC.
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.
Citation Format: Candace A. Frerich, Scott A. Ness. Unique in vitro transcriptional activities of oncogenic Myb fusions identified in salivary gland 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 1990.
Abstract 1991: Mutant GATA3 actively promotes the growth of normal and malignant mammary cells
Authors: Chandiramani Natasha , Peterson Esther , Kenny Paraic A. 
Published: July 2016

Abstract
GATA3 is a transcription factor expressed in luminal breast epithelial cells and is required for mammary gland development. Analysis of TCGA data reveals that somatic heterozygous mutations in GATA3 occur in up to 15% of estrogen receptor positive breast tumors, and that these tumors are diagnosed a median of eight years earlier than other estrogen receptor positive tumors, suggesting a more aggressive phenotype. These mutants have been proposed to be null alleles resulting in haploinsufficiency, however the mutation spectrum of GATA3 in breast cancer is in sharp contrast to that found in HDR syndrome, a true GATA3 haploinsufficiency disease. Based on this disparity, we propose that there is a selective pressure to mutate and retain a portion of the GATA3 in breast cancer. Here we focus on the GATA3 mutants which lack the second zinc finger which is responsible for GATA motif binding. Expression of these mutants accelerated xenograft tumor growth by ZR751 cells, and transgenic expression in mouse mammary glands promoted precocious lobuloalveolar development. We have used integrated gene expression and ChIP-Seq profiling to demonstrate that these zinc-finger deleted proteins retain the ability to associate with the genome by tethering to complexes associated with FOXA1 and AP-2gamma recognition motifs, where they modulate the expression of adjacent genes. These data support a model in which the GATA3 mutations recently observed in breast cancer encode for active transcription factors which elicit proliferative phenotypes in normal mammary epithelium and promote the growth of estrogen receptor positive breast cancer cell lines.
Citation Format: Natasha Chandiramani, Esther Peterson, Paraic A. Kenny. Mutant GATA3 actively promotes the growth of normal and malignant mammary cells. [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 1991.
Abstract 1992: Exploring target genes of eukaryotic initiation factor 5A in cancer using RNA sequence analysis
Authors: Muramatsu Tomoki , Tanimoto Kousuke , Inazawa Johji 
Published: July 2016

Abstract
Protein synthesis has a key role of maintaining cellular homeostasis such as growth and metabolism. However, dysregulation of translational process is a frequent feature of cancer and contributes to cancer progression. Since oncogenes and tumor suppressor genes are regulated by the translation machinery, therapeutic drugs which target the translation machinery have the possibility for overcoming cancer. We then focused on the hypusine cascade which is related to translational process. In our previous study, we showed that overexpression of the deoxyhypusine synthase (DHPS), an enzyme contained in the hypusine cascade, promoted cancer progression such as migration and invasion ability through RhoA signaling pathway. A DHPS inhibitor, GC7, showed significant decrease in the tumor formation in vivo. In particular, eukaryoutec initiation factor 5A (eIF5A) which is activated by hypusination has important roles of the translational regulation such as initiation and elongation of protein synthesis and nucleocytoplasmic transport of mRNA. We tried to identify the target genes of eIF5A by combining RNA-ChIP method with RNA sequencing analysis. As a result, candidate genes which bound to eIF5A were extracted by bioinformatics analysis, and redundant binding motifs for eIF5A in mRNAs emerged. These findings and future analyses would reveal the regulation of translational machinery by eIF5A which could be an important target for cancer therapy.
Citation Format: Tomoki Muramatsu, Kousuke Tanimoto, Johji Inazawa. Exploring target genes of eukaryotic initiation factor 5A in cancer using RNA sequence analysis. [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 1992.
Abstract 1994: Post-translational regulation of the cleaved fragment of Par-4 in ovarian and endometrial cancer cells
Authors: Brasseur Kevin , Adam Pascal , Tardif Laurence , Fabi François , Parent Sophie , Asselin Éric 
Published: July 2016

Abstract
Prostate Apoptosis Response-4 (Par-4) is a tumor suppressor protein whose expression level in cancer is frequently decreased; however, it is rarely mutated nor suppressed. Par-4 is not only regulated at the expression level, but also post-translationally. Most recently, we reported the cisplatin-induced caspase3-dependent cleavage of Par-4 resulting in the accumulation of a 25kd cleaved-Par-4 (cl-Par-4) fragment. In the present study, we investigated the mechanisms regulating this fragment using cl-Par-4-expressing stable clones derived from ovarian and endometrial cancer cell lines.
Briefly, we used cancer cell lines in which we produced stable clones expressing the cleaved form of PAR-4 (cl.PAR-4) using lentiviral particles. Using these models, we studied the regulation of cl.PAR-4 at the protein level using Western blots.
Intriguingly, cl-Par-4 protein was weakly expressed in all stable clones despite constitutive transgene expression. However, upon cisplatin treatment, cl-Par-4 levels increased up to 50-fold relative to baseline conditions. We assessed the subcellular localization of cl-Par-4 in baseline and cisplatin-treated conditions using cytoplasmic/nuclear fractionation. Results showed that cl-Par-4 is localized in both the cytoplasm and nucleus compartments, but cisplatin treatment did not alter its localization. Treatment of stable clones with proteasome and translation inhibitors revealed that cisplatin exposure may in fact protect cl-Par-4 from proteasome-dependent degradation. To confirm proteasome involvement in this process, potential ubiquitination sites were predicted using bioinformatic tools. Interestingly, we showed that PI3K and MAPK pathways are also implicated in this post-translational regulation, as evidenced by an increase of cl-Par-4 in the presence of PI3K inhibitors (Wortmannin and NVP-BEZ235) and a decrease of cl-Par-4 using MAPK inhibitors (U0126 and PD98059). Finally using bioinformatics resources, we found diverse datasets showing similar results to those we observed with the proteasome and cl-Par-4. Indeed, we have showed, using data from a published study, that the use of Bortezomib (a potent proteasome inhibitor) significantly increased Par-4 expression in MCF7 cancer cells.
These new findings add to the complex mechanisms regulating Par-4 expression and activity, and justify further studies addressing the biological significance of this phenomenon in gynecological cancer cells.
Citation Format: Kevin Brasseur, Pascal Adam, Laurence Tardif, François Fabi, Sophie Parent, Éric Asselin. Post-translational regulation of the cleaved fragment of Par-4 in ovarian and endometrial cancer cells. [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 1994.