bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4738: Maximize recovery of quality nucleic acid from formalin-fixed paraffin-embedded tissue samples using a novel, flexible purification technology
Authors: Wieczorek Doug , Hook Brad , Vincent Eric , Schagat Trista 
Published: August 2015

Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples are a valuable source of genetic information for gene expression and clinical research. Extraction of nucleic acid (NA) from FFPE tissues is a challenge because the fixation process results in cross-linking between proteins and nucleic acid, as well as between different strands of DNA or RNA molecules. Recent advances in sample preparation enables access to the valuable information contained within these difficult samples. We use a novel purification technology that does not rely on use of any harsh organic solvents and concentrates the NA for low volume elution on a specially designed spin column, thus maximizing concentration. Using this technology, we examined several aspects of the purification protocol for flexibility and adaptability: effect of de-crosslinking time on the quality and length of nucleic acids released from diverse FFPE tissues, effect of overnight storage between lysis and extraction steps, and whether the technology could be adapted to extract both DNA and RNA from the same FFPE tissue sample. Yield and quality of isolated nucleic acids were examined by absorbance, fluorescent binding dye, and real-time qPCR and
RT-qPCR. We demonstrate that amplification-based quantitation gave the best indication of the quality of NA recovered. We found that a short decrosslinking time gave significant yields, but only with longer decrosslinking, times were amplifiable yields maximized for many of the tissue types tested. Preprocessing conditions were determined that allow release of both DNA and RNA for subsequent capture and elution in separate spin columns, enabling recovery of high quality DNA and RNA from the same sample in separate tubes.
In this study, we demonstrate that de-crosslinking conditions can affect the recovery of amplifiable nucleic acid from FFPE samples and that RNA and DNA can be recovered from the same FFPE sample using an optimized protocol.
Citation Format: Doug Wieczorek, Brad Hook, Eric Vincent, Trista Schagat. Maximize recovery of quality nucleic acid from formalin-fixed paraffin-embedded tissue samples using a novel, flexible purification technology. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4738. doi:10.1158/1538-7445.AM2015-4738
Abstract 474: Regulation of epithelial plasticity of cancer cells by tumor-associated macrophages
Authors: LEE CHIH-CHAN , Yang Muh-Hwa 
Published: August 2015

Abstract
Epithelial plasticity of cancer cells is considered to be critical for the metastatic process of cancer cells. Epithelial-mesenchymal transition (EMT) has been proved to associate with cancer metastatic dissemination from primary tumor site to distal metastatic organ. In contrast, accumulated evidence showed that the reversal process of EMT, i.e., mesenchymal-epithelial transition (MET), is critical for metastatic colonization. However, the mechanism for controlling the epithelial plasticity during metastatic process is unclear. Tumor-associated macrophages (TAMs) are the most abundant host immune cells in tumor microenvironments. TAMs have been shown to modulate cancer progression through regulating cancer cell growth and metastasis, and remodeling extracellular matrix. However, it is still unclear about the roles of TAMs in regulating epithelial plasticity during cancer metastasis. Here, we demonstrate the distinct characteristics of that the TAMs in primary and metastatic tumors. The TAMs in metastatic tumors carry a M2-like phenotype; in contrast, the TAMs in primary tumors are composed of heterogeneous population containing both M1-like and M2-like cells. Furthermore, we polarize human monocytes into M1-like and M2-like macrophages and treat cancer cells with M1 and M2 macrophages conditioned medium. We find that different macrophage subtypes have a distinct effect in modulating epithelial plasticity of cancer cells. Interestingly, polarized macrophages regulate cancer cell morphological changes through epigenetic regulation. Therefore, we propose that TAMs in tumor microenvironment may polarize into different subtypes and facilitate cancer metastatic dissemination. These findings have implications for designing alternative strategies aimed at preventing and inhibiting cancer metastasis.
Citation Format: CHIH-CHAN LEE, Muh-Hwa Yang. Regulation of epithelial plasticity of cancer cells by tumor-associated macrophages. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 474. doi:10.1158/1538-7445.AM2015-474
Abstract 4750: Transcriptome sequencing of the Reed-Sternberg cells of classical Hodgkin lymphoma
Authors: Reichel Jonathan , Brody Joshua , Elemento Olivier , Rabadan Raul , Cesarman Ethel 
Published: August 2015

Abstract
Introduction: Most genomic studies of classical Hodgkin lymphoma (cHL) have been confined to cell lines due to the difficulty of isolating sparsely distributed Hodgkin and Reed-Sternberg (HRS) cells from reactive background tissue. One approach to evaluate primary cases has been to microdissect HRS cells from fresh-frozen tissue biopsies, which has been used for gene expression profiling and array comparative genomic hybridization to assess copy number alterations. However, laser capture microdissection is technically challenging, does not provide a pure tumor cell population, and yields very small amounts of degraded nucleic acids that may not be adequate for whole-transcriptome level RNA sequencing.
Methods: We used a flow cytometric cell isolation method, which has enabled rapid isolation of thousands of viable HRS cells from primary cHL tumors (Fromm, et al., Am J Clin Pathol 126, 2006). Here we combined flow cytometry using CD64, CD95, CD30, CD5, CD20, CD15, CD40, and CD45, with the Arcturus PicoPure RNA Isolation kit to isolate high quality RNA from viable HRS cells and intratumor B cells from nine primary cases of CHL respectively. We applied the Clontech SMARTer Ultra Low Input RNA Kit followed by Kapa Library Preparation kit to generate what is to our knowledge the first full transcriptome RNA sequence data from primary cases of cHL. Four cell lines were sequenced using the same methodology. We performed differential expression and gene fusion analyses, and conducted a search for activated pathways.
Results: We report the expression signature of purified primary HRS cells. PCA analysis showed that these segregate from HRS cell lines and primary B cells. We confirmed at the RNA level overexpression of relevant amplified genes for which inhibitors are available (AURKA and EZH2), and underexpression of transcripts encoded by genes previously found to be deleted (for example ATM). Pathway analysis revealed extensive downregulation of antigen presentation, consistent with our previous exome sequence analysis showing mutations in beta-2 microglobulin as the most common genetic alteration. Results of the mutational and transcriptional landscape of the HRS cells will be presented.
Conclusions: Transcriptome-level analysis of flow-sorted HRS cells allows for expanded study of CHL pathogenesis, new target identification based on altered signaling pathways and potentially individualized approaches to CHL therapy.
Citation Format: Jonathan Reichel, Joshua Brody, Olivier Elemento, Raul Rabadan, Ethel Cesarman. Transcriptome sequencing of the Reed-Sternberg cells of classical Hodgkin lymphoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4750. doi:10.1158/1538-7445.AM2015-4750
Abstract 4751: Simple modifications in Ion Torrent Variant Caller (TVC) parameters improve somatic variant detection from circulating tumor cells and cell free DNA to 1% allele frequency
Authors: Davidson Colin , Sun Yongming , Davies Christopher , Parikh Chaitali , Tom Warren , Hyland Fiona , Scafe Charles , Dhingra Dalia 
Published: August 2015

Abstract
By increasing quality-associated parameters and lowering sensitivity thresholds, a significant improvement in low frequency allele detection was achieved. The approach described was optimized using a dilution series of synthetic spike-ins (the AcroMetrix® Oncology Hotspot Control), and a titrated range of tumor cell lines in a normal background. The optimized variant calling approach was then applied to the analysis of somatic variants in circulating tumor cell (CTC) samples and associated cell-free DNA (cfDNA) using next-generation sequencing (NGS). Libraries were produced using the Ion AmpliSeq™ Cancer Hotspot Panel v2 for coverage of 50 cancer-associated genes and 2,800 COSMIC mutations. Using the above samples, the improved somatic variant detection workflow demonstrated analytical sensitivity down to 1% allele ratio in the observed sequence reads.
Citation Format: Colin Davidson, Yongming Sun, Christopher Davies, Chaitali Parikh, Warren Tom, Fiona Hyland, Charles Scafe, Dalia Dhingra. Simple modifications in Ion Torrent Variant Caller (TVC) parameters improve somatic variant detection from circulating tumor cells and cell free DNA to 1% allele frequency. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4751. doi:10.1158/1538-7445.AM2015-4751
Abstract 4753: An effective detection method for the EGFR single mutation T790M using BNA-NC clamping real-time PCR
Authors: Kim Sung-Kun , Liu Xiaoyun , Castro Aaron , Loredo Leticia , Castro Miguel 
Published: August 2015

Abstract
Mutations on epidermal growth factor receptor (EGFR) cause a variety of cancers including breast and lung cancers. The single mutation T790M on tyrosine kinase domain of EGFR signifies the response to the popular cancer drug gefitinib, which leads to the development of resistance to gefitinib. Detecting the mutation thus guide effective therapeutical options for patients who are in need of cancer drug treatments. We sought to develop a rapid, reliable detection method for the T790M mutation using bridged nucleic acids (BNA), which has been known to enhance the hybridization affinity of oligonucleotides that contain BNA bases. Oligonucleotides containing BNA bases designed to block PCR reaction against wild-type genes, called BNA-clamp, were used to discriminate the presence of mutant genes mixed with a large number of wild-type genes. Real-time PCR in conjugation with BNA-clamping allows us to view the different levels of PCR amplifications in the degree of mixture of wild-type and mutant genes. In an effort to explore this possibility, 13mer long clamps were prepared with various numbers of BNA bases. The clamps containing 9 BNA bases appear to be most effective in blocking the PCR reactions at an optimized concentration to distinguish the mutant from the wild-type genes. In addition to PCR results, the difference in the Tm values for the 7 BNA bases in the 13mer was the largest among differently designed clamps, which is consistent with the results obtained by real-time PCR. We also examined the degree of sensitivity using the clamp containing 9 BNA bases, revealing that the clamp has the ability to determine the level of mutation as low as 1% mixture of the mutant and wild-type gene. The effectiveness of blocking the PCR reaction with only 13mers containing BNA bases allowed us to detect a single mutation, and thus, this BNA-clamping real time PCR technology may offer a promising, new avenue to detect clinically important mutations in the future.
Citation Format: Sung-Kun Kim, Xiaoyun Liu, Aaron Castro, Leticia Loredo, Miguel Castro. An effective detection method for the EGFR single mutation T790M using BNA-NC clamping real-time PCR. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4753. doi:10.1158/1538-7445.AM2015-4753
Abstract 4755: Maximize genomic analysis through dual recovery of DNA and RNA from the same clinical sample
Authors: Cheng Angie , Hernandez Natalie , Li Mu , San Jose Hinahon Charmaine , Magdaleno Susan 
Published: August 2015

Abstract
DNA and RNA provide valuable information in order to detect differences such as chromosomal mutations and imbalances in gene expression. Common sample types for these analyses include surgical and needle biopsies, 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. Even adjacent areas of the same tumor tissue can result in a different profile so the ability to isolate multiple analytes from the same sample offer a number of benefits, which include preserving small samples and data consistency eliminating any sample to sample variation. Here we describe the efficient isolation of RNA and DNA from the same starting sample without splitting using the RecoverAll™ Multi-Sample RNA/DNA workflow, followed by versatile and informative downstream analysis. This workflow was applied to FFPE tissue samples, fine needle aspirates, degraded samples as well as fresh cultured cells from a number of different cancer types. As an example, we have shown that DNA and RNA can be isolated from the same non-small cell lung adenocarcinoma FFPE tumor sample and with the recovered analytes, both mutation analysis and fusion transcript detection can be performed by either qPCR or next-generation sequencing (NGS).
Citation Format: Angie Cheng, Natalie Hernandez, Mu Li, Charmaine San Jose Hinahon, Susan Magdaleno. Maximize genomic analysis through dual recovery of DNA and RNA from the same clinical sample. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4755. doi:10.1158/1538-7445.AM2015-4755
Abstract 4758: Genomic profiling of prostate cancer in Korean population
Authors: Park Ha Young , Kim Jong-il , Park Weon Seo , Lee Kang Hyun 
Published: August 2015

Abstract
Prostate cancer is one of the most common cancers for male population in the world. The search for accurate biomarkers in prostate cancer is critical for evolution of accurate management of prostate cancer. Previous studies have identified that several genomic alterations in prostate cancer including TMPRSS2-ERG fusion, PTEN deletion and SPOP single nucleotide variants (SNVs), the majority of which are from western population. To characterize the somatic mutations of prostate cancer in Korean, we sequenced the whole exome of 49 prostate cancer patient tissues and matched normal tissues. A total of 738 somatic non-silent variants affecting 692 distinct genes were identified. In addition to already known genes (SPOP, FOXA1 and PTEN), we also found previously uncharacterized genes such as GRIN2A, LRP1, LRP1B and KRT1. Of the 40 mutated genes across multiple cases, missense SNVs of SPOP (5/49 cases, 10.2%) were the most frequent, followed by missense and splice-site SNVs of GRIN2A (4/49 cases, 8.2%). Mutations in low density lipoprotein-related protein encoded by LRP1 and LRP1B affected considerable portion of all cases (7/49, 14.3%), describe the probable relation between lipid metabolism and prostate cancer. As a results, we suggested the distinct patterns of genetic variations involved in prostate cancer of Korean population.
Note: This abstract was not presented at the meeting.
Citation Format: Ha Young Park, Jong-il Kim, Weon Seo Park, Kang Hyun Lee. Genomic profiling of prostate cancer in Korean population. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4758. doi:10.1158/1538-7445.AM2015-4758
Abstract 4760: Stromal contribution to the colorectal cancer transcriptome
Authors: Isella Claudio , Terrasi Andrea , Bellomo Sara E. , Petti Consalvo , Muratore Andrea , Mellano Alfredo , De Ridder Mark , Cassoni Paola , Storme Guy , Bertotti Andrea , Medico Enzo 
Published: August 2015

Abstract
Recent studies have identified a stem/serrated/mesenchymal (SSM) molecular subtype of colorectal cancer (CRC) that is associated with poor prognosis. We noted that genes upregulated in this subtype are also prominently expressed by stromal cells. This led us to hypothesize that the SSM transcripts could derive from the tumor microenvironment, rather than being intrinsic to cancer cells. To test this hypothesis, we analyzed microarray and RNAseq expression data from patient-derived xenografts (PDXs) of CRC, where human cancer cells are supported by murine stroma. Species-specific expression analysis revealed that mRNA levels of SSM genes are mostly due to stromal expression. Considering only genes exclusively expressed by stromal cells in PDXs, We then built three expression signatures specifically reporting the abundance of cancer-associated fibroblasts (CAFs), leucocytes or endothelial cells. In human CRC samples, all stromal signatures were strongly associated with the SSM subtype. A high CAF signature was associated with poor prognosis in untreated CRC patients, while in rectal cancer high stromal signatures jointly predicted radioresistance. These data show that the distinctive transcriptional and clinical features of the SSM subtype can be ascribed to its particularly abundant stroma.
Citation Format: Claudio Isella, Andrea Terrasi, Sara E. Bellomo, Consalvo Petti, Andrea Muratore, Alfredo Mellano, Mark De Ridder, Paola Cassoni, Guy Storme, Andrea Bertotti, Enzo Medico. Stromal contribution to the colorectal cancer transcriptome. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4760. doi:10.1158/1538-7445.AM2015-4760
Abstract 4770: Levels of 5-methyl-cytosine and 5-hydroxymethyl-cytosine in hepatocellular carcinoma prognosis
Authors: Delgado-Cruzata Lissette , Wu Hui Chen , Thomas Tiffany , Siegel Abby B. , Shen Jing , Zhang Yu-Jing , Goyal Abhishek , Hsu Christine C. , Remotti Helen , Santella Regina M. 
Published: August 2015

Abstract
Hepatocellular carcinoma (HCC) is the third most common cause of cancer death in the world. The US incidence of HCC has tripled between 1975 and 2005 and has been accompanied by improved long term survival rates, but as a result of HCC ‘s poor prognosis, 1-year survival remains lower than fifty percent. Therefore, a better understanding of the molecular mechanisms underlying the disease process is currently needed. Epigenetic alterations have been linked to HCC and global genomic hypomethylation is a well known hallmark of the disease. Less is understood about the role hydroxymethylation plays in HCC carcinogenesis. Here, we conducted a study to determine 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels by UPLC/MS/MS in HCC tumor (T) and non-tumor (NT) adjacent tissue DNAs of sixty six individuals treated at Columbia Presbyterian Medical Center in New York. We analyzed the association between demographic and clinicopathological characteristics and 5mC and 5hmC levels, as well as performed a Cox-survival analysis to determine which factors better predicted survival. Mean levels of 5mC (5mCT = 3.15±0.49% vs.5mCNT = 3.80±0.12% (p&lt;0.0001) and 5hmC (5hmCT = 0.11±0.04% vs. 5hmCNT = 0.23±0.07%, p&lt;0.0001) in tumor tissues were statistically significantly lower than in non-tumor tissues. Older age was associated with lower 5mC content (5mC&lt;60y = 3.32±0.43% vs. 5mC≥60y = 3.00±0.50%, p = 0.001), while tumor DNA of transplant (LT) patients had higher 5hmC levels compared to surgical resection (LR) patients (5hmCLR = 0.10±0.04% vs. 5hmCLT = 30.13±0.04%, p = 0.0053). However, survival was predicted by whether transplant or resection were performed (Hazard ratio LT vs. LR, 3.54 (95% confidence interval:1.34-9.29), p = 0.01). Our study had a limited sample size, but suggests that future studies of 5hmC might be informative concerning HCC prognosis.
Citation Format: Lissette Delgado-Cruzata, Hui Chen Wu, Tiffany Thomas, Abby B. Siegel, Jing Shen, Yu-Jing Zhang, Abhishek Goyal, Christine C. Hsu, Helen Remotti, Regina M. Santella. Levels of 5-methyl-cytosine and 5-hydroxymethyl-cytosine in hepatocellular carcinoma prognosis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4770. doi:10.1158/1538-7445.AM2015-4770
Abstract 4772: Aberrantly hypermethylated Homeobox A2 derepresses metalloproteinase-9 through TBP and promotes invasion in nasopharyngeal carcinoma
Authors: PENG CHEN-CHING 
Published: August 2015

Abstract
Nasopharyngeal carcinoma (NPC) is notorious for its high invasiveness and metastatic ability. In this study, we identified a differential hypermethylated transcription repressor, Homeobox A2 (HOXA2), which helps explain such observation. Aberrant hypermethylation of HOXA2 led to low RNA expression in NPC tumors and cells. Addition of methylation inhibitor 5′Aza restored HOXA2 RNA expression in NPC cells. Methylated HOXA2 promoter reduces the binding affinity of the transcriptional co-activator p300, causing transcriptional repression of HOXA2. In NPC cells, re-expression of ectopic HOXA2 was correlated with decreased invasive ability and reduced metalloproteinase MMP-9 RNA and protein expression. Promoter, ChIP and DNA-pull down assays indicated that HOXA2 competes with the transcription activator, TATA-box binding protein (TBP) for a recognition sequence near the MMP-9 transcription start site, and suppresses MMP-9 transcription. Our results reveal a novel mechanism wherein HOXA2 acts as a suppressor or TBP-antagonist to inhibit MMP-9 expression; while methylation-mediated inactivation of HOXA2 in NPC derepresses MMP-9 production and increases invasion of NPC cells. In NPC plasma samples, increased plasma EBV copy number was correlated with increased in cell-free HOXA2 hypermethylation and elevated MMP-9 levels. Plasma EBV DNA and methylated cell-free HOXA2 may use as biomarkers for monitoring NPC treatment.
Citation Format: CHEN-CHING PENG. Aberrantly hypermethylated Homeobox A2 derepresses metalloproteinase-9 through TBP and promotes invasion in nasopharyngeal carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4772. doi:10.1158/1538-7445.AM2015-4772