bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3561: Whole transcriptome analysis of testicular germ cell tumors
Authors: Degoricija Lovorka , Lee Kathy Y. , Patel Sunali , Chu Shirley , Gillis Ad J.M. , Rijlaarsdam Martin , Dorssers Lambert C.J. , Looijenga Leendert 
Published: May 2015

Abstract
Next generation sequencing of the whole transcriptome enables high resolution measurement of gene expression activity in different tissue and cell types. This methodology provides an in depth study of known transcripts and depending on the data analysis, allows identification of additional transcript types such as transcript variants, fusion transcripts, and small and long ncRNAs. In this study we performed RNA-Seq using the Ion Torrent sequencing platform to compare the expression profile of testicular germ cell tumors (seminoma type, n=3) and normal testis (n=3). Using Partek Flow and Star or TopHat aligners, we aligned the reads to the human genome and mapped sequences to the RefSeq database. We identified a large number of genes that were up and down regulated with high degree of significance p&lt;0.01, &gt;2X FC). These included genes related to testicular tissue type, stem cell pleuripotency (NANOG; POU5F1) and proliferation (KRAS, CCND2). In addition, a number of differentially expressed noncoding RNAs were identified (SNORD12B, XIST). The method was validated on a small set of genes (&gt;20) using qPCR (TaqMan Assays). We used the Open Array platform to quantitatively screen a larger number of differentially expressed genes (224) across a number of different testicular germ cell tumor types (non-seminoma).
Citation Format: Lovorka Degoricija, Kathy Y. Lee, Sunali Patel, Shirley Chu, Ad J.M. Gillis, Martin Rijlaarsdam, Lambert C.J. Dorssers, Leendert Looijenga. Whole transcriptome analysis of testicular germ cell tumors. [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 3561. doi:10.1158/1538-7445.AM2014-3561
Abstract 3574: Analysis of whole genome and transcriptome sequencing in single cell
Authors: Kwon Nak-Jung , Lee Woo Chung , Kim Jiwoong , Kim Hyeri , Seong Ahreum , Kim Bong Cho , Park Doo Hyun , Yang Kap-Seok 
Published: May 2015

Abstract
The rapid advancement in Next Generation Sequencing (NGS) technology has allowed extensive genetic profiling and analysis of tumor tissues. While accurate tumor characterization is crucial for cancer therapy, current sequencing methods are unable to resolve the genetic differences between the heterogeneous cell populations within tumor. By profiling specific subpopulations of cells from a larger heterogeneous population, single cell sequencing can improve the efficiency of cancer treatments through early detection of rare tumor cells, monitoring of circulating tumor cells, and accurate profiling of intra-tumor heterogeneity. In this study, we compared commercially available single cell amplification methods and sequencing platforms for whole genome and whole transcriptome sequencing. We isolated single cells from a human breast cancer cell line, MCF7, and human embryonic kidney cell line, HEK293, by micromanipulation, and their whole genome and transcriptome were sequenced. For whole genome sequencing, the performance of Repli-g (Qiagen), Ampli1 (Slicon Biosystems) and WGA4 (Sigma) were assessed for whole genome amplification. Next, we used TruSeq DNA Library Kit and Ion Plus Fragment Library Kit for library preparation, and whole genome sequencing was performed on HiSeq2000 and Proton. The sequencing data were analyzed by SAMtools/GATK and tmap-f3. For whole transcriptome sequencing, cDNA was synthesized from single cells using SMARTer ultra low input RNA kit (Clontech), and the cDNA library was prepared with Nextera XT library prep kit (Illumina) and Ion Total RNA-Seq Kit v2 (Life Technologies). Sequencing was performed on HiSeq2000 and Proton, and analyzed with Tophat and Cufflink. We show that the percentage of mappable reads and regions with more than 1X coverage in whole genome sequencing were similar to that of the genomic DNA data, but the coverage rate of regions with more than 10X was lower in single cell data on both NGS platforms. In the RNA-Seq, the gene detection rate in single cell and more than 100 cells were about 65% and 85% compare to total RNA, respectively.
Citation Format: Nak-Jung Kwon, Woo Chung Lee, Jiwoong Kim, Hyeri Kim, Ahreum Seong, Bong Cho Kim, Doo Hyun Park, Kap-Seok Yang. Analysis of whole genome and transcriptome sequencing in single cell. [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 3574. doi:10.1158/1538-7445.AM2014-3574
Abstract 3580: Hotspot mutation and fusion transcript detection from the same non-small lung adenocarcinoma sample
Authors: Cheng Angie , Bagai Varun , Cienfuegos Joey , Hernandez Natalie , Li Mu , Schageman Jeff , Fekete Richard , Petraroli Rosella , Vlassov Alexander , Magdaleno Susan 
Published: May 2015

Abstract
The presence of certain chromosomal rearrangements and the subsequent fusion gene derived from translocations has been implicated in a number of cancers. Hundreds of translocations have been described in the literature recently but the need to efficiently detect and further characterize these chromosomal translocations is growing exponentially. The two main methods to identify and monitor translocations, fluorescent in situ hybridization (FISH) and comparative genomic hybridization (CGH) are challenging, labor intensive, the information obtained is limited, and sensitivity is rather low. Common sample types for these analyses are biopsies or small tumors, which are very limited in material making the downstream measurement of more than one analyte rather difficult; obtaining another biopsy, using a different section or splitting the sample can raise issues of tumor heterogeneity. The ability to study mutation status as well as measuring fusion transcript expression from the same sample is powerful because you're maximizing the information obtained from a single precious sample and eliminating any sample to sample variation. Here we describe the efficient isolation of two valuable analytes, RNA and DNA, from the same starting sample without splitting, followed by versatile and informative downstream analysis. This methodology was applied to FFPE and degraded samples as well as fresh tissues and cells. DNA and RNA were recovered from the same non-small lung adenocarcinoma sample and both mutation analysis, as well as fusion transcript detection was performed using the Ion Torrent PGM™ platform on the same Ion 318™ chip. Using 10ng of DNA and 10ng of RNA input, we applied the Ion AmpliSeq™ Colon and Lung Cancer panel to analyze over 500 COSMIC mutations in 22 genes and the Ion AmpliSeq™ RNA Lung Fusion panel to detect 40 different fusion transcripts.
Citation Format: Angie Cheng, Varun Bagai, Joey Cienfuegos, Natalie Hernandez, Mu Li, Jeff Schageman, Richard Fekete, Rosella Petraroli, Alexander Vlassov, Susan Magdaleno. Hotspot mutation and fusion transcript detection from the same non-small lung adenocarcinoma sample. [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 3580. doi:10.1158/1538-7445.AM2014-3580
Abstract 3582: A simple multiplex PCR approach for target enrichment in next-gen sequencing
Authors: Zhou Xiaochuan , Zhu Qi , Hebel Chris 
Published: May 2015

Abstract
Multiplexing PCR is a simple way to extract genomic regions of interest for various medical and genetic tests. Somatic mutations lead to various diseases including cancer. These mutations are unlikely to be best detected using regular whole genome sequencing. Clinical samples often consist of disease cells, e.g. cancer cells, surrounded by normal cells. Thus, deep sequencing of hundreds to thousands fold coverage is required to detect the mutations. In clinical research many doctors are interested in specific genes or genomic regions and they want to extract the regions from genomic DNA or RNA before sequencing. Many current clinical, forensic, and heretical genetic test workflows start with multiplexing PCR to extract genetic marker carrying regions from whole genomes before running hybridization, sequencing, or electrophoresis tests to identify the markers. Personal medicine and prognosis mostly involve examining sequence variations of a number of targeted genes and metabolic pathway genes so as to predict drug efficacies and drug toxicities.
We have developed a new multiplexing PCR approach with a significantly simplified workflow and significantly improved robustness. When applied to sequencing target enrichment application, the workflow for producing amplified targets involves only one hands-on step and one PCR run. The approach is designed to require low sample input and to produce superior amplicon uniformity and sequence specificity. The approach involves a novel primer design and a proprietary reaction composition. A PCR run consists of two functionally separated reaction phases, namely target capture and library amplification, without any hands-on step in between. The performance of the new approach will be demonstrated by a caner panel data.
Citation Format: Xiaochuan Zhou, Qi Zhu, Chris Hebel. A simple multiplex PCR approach for target enrichment in next-gen sequencing. [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 3582. doi:10.1158/1538-7445.AM2014-3582
Abstract 3584: Analysis of colorectal intratumoral genetic heterogeneity by high efficiency and rapid deep targeted sequencing
Authors: Hopmans Erik S. , Lee Hojoon , Miotke Laura , Rumma Rowza Tur , Grimes Sue , Bell John M. , Ji Hanlee P. 
Published: May 2015

Abstract
Metastasis is the most frequent cause of morbidity and mortality in cancer. Metastatic disease lethality is often the result of cancer progression despite treatment. Therapeutic resistance is seen nearly in all cases of metastatic cancer. Genetic studies relying on deep sequencing have shown that many cancers are genetically heterogeneous as a result of diverse clonal populations with delineating and unique set of mutations. Several studies suggest that resistance mutations are present in tumors before the start of treatment and via evolution, clonal populations expand under therapeutic selection. However, these minor allelic mutations that define clonal populations are not typically detectable with typical sequencing coverage (20-50X) employed in whole genome approaches.
Relying on an innovative programmable targeting method that enables us to rapidly configure nearly any region of the human genome and efficiently sequence cancer genomes, we are determining the extent of intratumoral genetic heterogeneity and clonal diversity in colorectal cancer. Our study involves over 120 patients with available clinical data and a subset of matched tumors indicative of tumor progression (e.g. tumor-normal, premalignant-malignant, malignant-metastasis). Via an integrative analysis of TCGA, COSMIC and other genomic data sets of colorectal cancer, we identified the top ranking 53 cancer genes prone to mutation and associated with advanced colorectal cancer by. These top genes are found in known cancer pathways such as the WNT and RAS/RAF pathway and we are analyzing the exons of these genes for mutations, insertions and deletions with a sequencing depth of at least 1000x. Preliminary results have shown that we can readily reach sequencing depths of 7000x with our automated targeting approach and that a minimal sequencing depth of 1000x will enable detection of aberrations present in the sample below 1%. Samples are being analyzed for the overall level of heterogeneity and correlation of clonal mutations to clinical outcome.
For optimal personalized treatment of cancer patients, the analysis of intratumoral genetic heterogeneity may be useful in predicting treatment response and metastatic potential of any given primary colorectal cancer.
Citation Format: Erik S. Hopmans, Hojoon Lee, Laura Miotke, Rowza Tur Rumma, Sue Grimes, John M. Bell, Hanlee P. Ji. Analysis of colorectal intratumoral genetic heterogeneity by high efficiency and rapid deep targeted sequencing. [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 3584. doi:10.1158/1538-7445.AM2014-3584
Abstract 3591: 15-Deoxy-Δ12,14-prostaglandin J2-induced epithelial-to-mesenchymal transition in human breast cancer cells promotes fibroblast activation
Authors: Kim Do-Hee , Choi Jeehye , Suh Jin-Young , Na Hye-Kyung , Surh Young-Joon 
Published: May 2015

Abstract
In inflammation-associated carcinogenesis, cyclooxygenase-2 (COX-2) is markedly overexpressed, resulting in accumulation of various prostaglandins. 15-Deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) and prostahlandin E2 (PGE2) are the predominant COX-2-derived prostaglandins (PGs) with oncogenic potential. In the present study, we examined the effects of these to PGs on epithelial-to-mesenchymal transition (EMT), a process by which epithelial cells lose their cell polarity and cell-cell adhesion, and gain migratory and invasive properties. 15d-PGJ2 induced EMT to a greater than PGE2 in human breast cancer (MCF-7) cells. Snail and ZEB1 are known to bind to the E-boxes present in the E-cadherin promoter, thereby repressing E-cadherin transcription. Treatment of MCF-7 cells with 30 μM of 15d-PGJ2 increased the expression of Snail and ZEB1, followed by the down-regulation of E-cadherin. Nuclear extract from 15d-PGJ2-treated MCF-7 cells showed the binding of Snail and ZEB1 to E-box sequences in the E-cadherin promoter. In addition, among various cytokines/chemokines examined, the mRNA level of interleukin-8 (CXCL8) was highly elevated in 15d-PGJ2-stimulated MCF-7 cells. 15d-PGJ2-induced up-regulation of CXCL8 expression was abrogated by the introduction of Snail short interfering RNA. These findings suggest that CXCL8 may function as a positive regulator of EMT in 15d-PGJ2-treated MCF-7 cells. Moreover, the addition of conditioned medium of MCF-7 cells undergoing EMT activates normal fibroblast cells to cancer-associated fibroblasts (CAFs). Co-culture of normal fibroblasts with 15d-PGJ2-treaed-MCF-7 cells also induced the expression of α-SMA and FAPα, representative markers of CAFs. As a corresponding receptor of CXCL8, CXCR2 was overexpressed in activated fibroblasts co-cultured with 15d-PGJ2-treated MCF-7 cells. Unlike 15d-PGJ2, its non-electrophilic analogue 9,10-dihydro-15d-PGJ2 failed to induce EMT, suggesting that the α,β-unsaturated carbonyl group located in the cyclopentenone ring of 15d-PGJ2 is essential for EMT induction. Notably, activation of Rho kinase through direct binding of ArhGEF5, a guanine nucleotide exchange factor, with 15d-PGJ2 seems to contribute to the EMT induction. Taken together, above findings suggest that 15d-PGJ2 induces EMT through up-regulation of Snail expression and subsequent production of CXCL8 which may contribute to increased EMT of human breast cancer cells.
Citation Format: Do-Hee Kim, Jeehye Choi, Jin-Young Suh, Hye-Kyung Na, Young-Joon Surh. 15-Deoxy-Δ12,14-prostaglandin J2-induced epithelial-to-mesenchymal transition in human breast cancer cells promotes fibroblast activation. [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 3591. doi:10.1158/1538-7445.AM2014-3591
Abstract 3593: Examining the role of tumor cell secreted factors in intravasation and enhancing paracrine loop invasion
Authors: Cabrera Ramon M. , Zhou Zhen N. , Roh-Johnson Minna , Condeelis John , Cox Dianne , Segall Jeffrey E. 
Published: May 2015

Abstract
The interaction of breast cancer cells with other cells in the tumor microenvironment plays an important role in metastasis. Invasion and intravasation, two critical steps in the metastatic process, are thought to be influenced by these interactions in addition to their intrinsic invasive properties. Macrophages are of particular interest when it comes to studying tumor cell invasiveness. Previous studies have shown that there is paracrine loop signaling between breast cancer cells and macrophages in which colony stimulating factor 1 (CSF-1) produced by tumor cells stimulates epidermal growth factor (EGF) production by macrophages. This EGF, in turn, stimulates invasion of the tumor cells. In addition to the classically described paracrine loop, it has been seen that tumor cell expression of ErbB3, a member of the EGFR family of receptor tyrosine kinases, may play a role in facilitating tumor cell intravasation. Overexpression of ErbB3 in breast cancer patients correlates with decreased survival. We show that using a blocking antibody against ErbB3 results in a significant decrease in macrophage-induced transendothelial migration of breast cancer cells. Tumor cell secretion of Neuregulin 1 (NRG1), a ligand of the ErbB3 receptor, may also play a role in the tumor cell- macrophage paracrine interaction. We show that stimulation of macrophages with NRG1 upregulates mRNA expression of JAG1, a ligand of the Notch receptor. Activation of the Notch receptor pathway has been shown to be involved in the process of tumor cell invasion. Overall, our studies look to examine this interaction between tumor cells and macrophages and these observations indicate that ErbB3, NRG1, and JAG1 could serve as novel targets in metastasis and the tumor microenvironment.
Citation Format: Ramon M. Cabrera, Zhen N. Zhou, Minna Roh-Johnson, John Condeelis, Dianne Cox, Jeffrey E. Segall. Examining the role of tumor cell secreted factors in intravasation and enhancing paracrine loop invasion. [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 3593. doi:10.1158/1538-7445.AM2014-3593
Abstract 3594: Tumor microenvironment derived exosomes regulate prostate cancer metabolism
Authors: Zhao Hongyun , Yang Lifeng , Achreja Abhinav , Marini Juan , Peehl Donna , Nagrath Deepak 
Published: May 2015

Abstract
Tumor microenvironment is composed of myofibroblasts, extracellular matrix, and many other cells. There are many ways for tumor to communicate with its microenvironment, such as growth factors, cytokines, chemokines and so on. Recent research has indicated that exosomes may serve an important role in communication between tumor and its microenvironment. Exosomes are nanosized particles secreted by cells and contain microRNA, metabolic enzymes, biomarker proteins, and some other functional components. We show a novel regulatory mechanism for modulating metabolism in prostate cancer cells by stromal cells. We found that exosomes from stromal fibroblast cells are uptaken by prostate cancer cells and they release RNAs, enzymes to regulate cancer cells metabolism. Our result shows that exosomes from patient derived fibroblasts enhance glucose uptake, lactate production and pyruvate uptake in prostate cancer cells. We further performed 13C based isotope labeling experiments using glucose and glutamine labeling to study metabolic rewiring induced in cancer cells by stromal exosomes. We found that exosomes downregulated mitochondria metabolism in prostate cancer cells. In summary, stroma derived exosomes enhanced Warburg effect in prostate cancer cells. Our findings can lead to the development of new therapeutics integrating tumor microenvironment and metabolic pathways in tumor cells.
Citation Format: Hongyun Zhao, Lifeng Yang, Abhinav Achreja, Juan Marini, Donna Peehl, Deepak Nagrath. Tumor microenvironment derived exosomes regulate prostate cancer metabolism. [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 3594. doi:10.1158/1538-7445.AM2014-3594
Abstract 3596: The role of PIM1 kinase in the prostate tumor microenvironment
Authors: Zemskova Marina , Kraft Andrew S. 
Published: May 2015

Abstract
Prostate cancer (PCa) remains the second leading cause of cancer-related deaths in men. The prostate is a tubulo-alveolar gland composed of epithelial tissues embedded in stromal components. PCa includes reactive stroma which consists of myofibroblasts and extracellular matrix (ECM) remodeling. Increasing evidence suggests that myofibroblasts may refine the prognostic assessment of tumors. The PIM1 serine/threonine protein kinase is a true oncogene and has been implicated in the initiation and progression of multiple cancer types including PCa. The level of PIM1 correlates with the disease state and Gleason grade and has been shown to stimulate growth of murine prostate cancer. The role of PIM1 in prostate stromal cells has never been investigated. Using human prostate tissue microarray analysis we now demonstrate that (1) the PIM1 protein is detected in human stroma adjacent to cancer tissue; (2) stromal cells isolated from PIM1 knockout mice contain a decreased number of myofibroblasts and expose slow growth rate when compared with wild type control, suggesting that kinase expression can alter stromal cell composition and proliferation; (3) elevated level of PIM1 kinase in human benign prostate stromal cells increases migration and growth of prostate epithelial cells and this effect can be reversed by PIM inhibitors; (4) PIM1 over-expressing stromal cells increase epithelial cell growth in tissue regeneration model; (5) stromal cells with elevated level of PIM1 expose increased number of myofibroblasts when co-cultivated with prostate epithelial cells. These data suggest that PIM1 kinase may contribute in formation of a “reactive stroma” phenotype. We used the conditioning media analysis to decipher the PIM1 specific signal transduction pathways that may lead to stroma activation and drive prostate cancer growth. Using cytokine/chemokine arrays and ECM protein analysis we found that overexpression of PIM1 kinase in stromal cells is associated with elevated level of CCL5 chemokine and increased secretion of collagen1. Examination of the pathways involved in formation of myofibroblasts revealed that PIM1 can modulate activation of PDGFRβ leading to the increased CCL5 expression. We are suggesting that PIM1 is a modulator of stromal cells response to the stimuli produced by prostate epithelial cells through increase of matrix stiffness, receptor activation and accumulation of myofibroblasts which induce further ECM remodeling and expression of the growth factors leading to epithelial cells transformation and cancer propagation.
Citation Format: Marina Zemskova, Andrew S. Kraft. The role of PIM1 kinase in the prostate tumor microenvironment. [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 3596. doi:10.1158/1538-7445.AM2014-3596