bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3333: The receptor tyrosine kinase AXL mediates nuclear translocation of the epidermal growth factor receptor
Authors: Brand Toni M. , Iida Mari , Corrigan Kelsey L. , Braverman Cara M. , Coan John P. , Flanigan Bailey G. , Stein Andrew P. , Salgia Ravi , Rolff Jana , Kimple Randall J. , Wheeler Deric L. 
Published: July 2017

Abstract
The epidermal growth factor receptor (EGFR) is an important therapeutic target in patients with various cancers. Unfortunately, resistance to anti-EGFR therapeutics is common. Previous studies in our laboratory identified two mechanisms of resistance to the EGFR monoclonal antibody cetuximab: First, the nuclear translocation of EGFR bypasses the inhibitory effects of cetuximab; and second, the receptor tyrosine kinase AXL mediates cetuximab resistance by maintaining EGFR activation and downstream signaling. On the basis of these findings, we hypothesized that AXL could mediate the nuclear translocation of EGFR in the setting of cetuximab resistance. We found that NSCLC cetuximab-resistant clones and patient-derived xenografts (PDXs) had increased abundance of nuclear EGFR (nEGFR) and AXL. Cellular fractionation techniques, super resolution microscopy, and electron microcopy revealed that genetic loss of AXL diminished the nuclear translocation and accumulation of EGFR. Building on previous studies indicating that SRC family kinases (SFKs) and HER family ligands mediate the nuclear translocation of EGFR, we found that AXL knockdown down-regulated the expression of the SFKs YES and LYN, and the ligand neuregulin-1 (NRG1). Furthermore, AXL knockdown decreased the interaction between EGFR and HER3 and the nuclear abundance of HER3. Nuclear localization of EGFR could be rescued only upon simultaneous overexpression of Lyn and NRG1 in cells depleted of AXL. Collectively, these data uncover a previously unrecognized role for AXL in regulating the nuclear translocation of EGFR and suggest that AXL-mediated SFK activation and NRG1 expression are necessary and sufficient to regulate this process.
Citation Format: Toni M. Brand, Mari Iida, Kelsey L. Corrigan, Cara M. Braverman, John P. Coan, Bailey G. Flanigan, Andrew P. Stein, Ravi Salgia, Jana Rolff, Randall J. Kimple, Deric L. Wheeler. The receptor tyrosine kinase AXL mediates nuclear translocation of the epidermal growth factor receptor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3333. doi:10.1158/1538-7445.AM2017-3333
Abstract 3353: An epigenetic biomarker panel in HPV related oropharyngeal squamous cell carcinoma
Authors: Ren Shuling , Gaykalova Daria A. , Guo Theresa , Khan Zubair , Ando Mizuo , Haft Sunny , Califano Joseph A. 
Published: July 2017

Abstract
HPV related head and neck squamous cell carcinoma (HNSCC) is known to occur in a separate patient population in comparison to tobacco related HNSCC, and also exhibits less mutational, genetic, and chromosomal alterations, and a different composition of epigenetic alterations. In particular, HPV is present in up to 70% of oropharyngeal squamous cell carcinoma (OPSCC), and is driving the increase in incidence rates of OPSCC. Given the precedent for successful screening for cervical cancer, it is attractive to consider similar population based screening for HPV related OPSCC. Here, we developed an epigenetic biomarker panel that can be combined with high risk HPV DNA detection with potential utility in screening. We performed high throughput qMBD-seq analysis on 50 primary HPV positive OPSCC samples and 25 UPPP normal samples. Subsequently, we performed an outlier analysis and ranking strategy of 100 bp segmented regions within this discovery cohort and defined 20 differentially methylated regions to be used as biomarkers for detection. Simultaneously, we validated these 20 biomarker candidates using TCGA methylation array dataset and found that the methylation levels of these 20 candidates in HPV positive OPSCC were significantly higher than those in normal samples. Moreover, we created QMSP assays for these genes, and validated EMBP1 and KCNA3 in a separate validation cohort including tissue and saliva from 46 HPV related OPSCC and 25 normal controls. The sensitivity and specificity values for EMBP1, KCNA3 or both in tissue and saliva are shown. EMBP1 has a high sensitivity in tissue and a high specificity in saliva, while KCNA3 has a high specificity in both tissue and saliva. A panel including both genes has an extremely high sensitivity. Ultimately, we defined a panel of two differentially methylation regions that has a high sensitivity in tissue. This study might serve as a diagnostic biomarker development trial for HPV OPSCC detection with potential application for development of a population based screening test.
Sensitivity and specificity for HPV related OPSCC in tissue and salivaTissueTissueSalivaSalivaGeneSensitivitySpecificitySensitivitySpecificityEMBP197.7%83.3%13.3%94.7%KCNA376.7%92.0%13.3%94.7%EMBP1& KCNA3100.0%84.0%13.0%84.2%
Citation Format: Shuling Ren, Daria A. Gaykalova, Theresa Guo, Zubair Khan, Mizuo Ando, Sunny Haft, Joseph A. Califano. An epigenetic biomarker panel in HPV related oropharyngeal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3353. doi:10.1158/1538-7445.AM2017-3353
Abstract 3357: Heritable methylation marks associated with breast cancer risk
Authors: Southey Melissa C. , Joo Jihoon E. , Dowty James G. , Milne Roger L. , Wong EE Ming , Dugué Pierre-Antoine , English Dallas , Hopper John L. , Goldgar Daivd E. , Giles Graham G. 
Published: July 2017

Abstract
While most epigenetic marks are reprogrammed during early embryogenesis, some studies have reported Mendelian-like inheritance of germline DNA methylation in particular cancer susceptibility genes. We aimed to identify heritable methylation marks associated with breast cancer susceptibility by studying 25 Australian multi-generational families with multiple cases of breast cancer who were not known to carry mutations in breast cancer susceptibility genes. Peripheral blood DNA methylation was measured at approximately 480,000 genetic loci (methylation sites) for 210 members of these families using the Infinium HumanMethylation450 BeadArray. We developed and applied a new statistical method to identify heritable methylation marks based on complex segregation analysis. Carrier probabilities were estimated for the 1000 most heritable methylation marks, based on family structure but not disease status, and Cox proportional hazards survival analysis was used to test for associations between these carrier probabilities and breast cancer. After correcting for multiple testing, we identified 11 methylation marks whose corresponding carriers probabilities were significantly associated with breast cancer. Three marks clustered within 200 base pairs of the noncoding RNA miR886. We found evidence for these marks to be associated with aggressive (but not non-aggressive) prostate cancer risk in a population-based prostate cancer study. The association with breast cancer risk was replicated for three of the eleven marks in an independent population-based breast cancer study. Our work demonstrates the efficacy of our novel approach for identifying heritable methylation marks associated with breast cancer. This methodology may provide insights into other disease settings where known lifestyle exposures and genetic risk variants do not fully explain the familial relative risk.
Citation Format: Melissa C. Southey, Jihoon E. Joo, James G. Dowty, Roger L. Milne, EE Ming Wong, Pierre-Antoine Dugué, Dallas English, John L. Hopper, Daivd E. Goldgar, Graham G. Giles. Heritable methylation marks associated with breast cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3357. doi:10.1158/1538-7445.AM2017-3357
Abstract 3361: Methylome differences in differentiated thyroid cancers and benign adenomas
Authors: Stephen Josena K. , Chen Kang Mei , Merritt Jason , Datta Indrani , Chitale Dhananjay , Divine George , Worsham Maria J. 
Published: July 2017

Abstract
Many recent studies examining aberrant DNA methylation in thyroid cancer are restricted to either candidate genes or genome-wide methylation in specific thyroid tumor subtypes. The goal of this study was to identify differentially methylated genes globally and their association with molecular pathways and signaling networks. Common mutations in papillary thyroid cancer (PTC), follicular thyroid cancer (FTC), follicular adenoma (FA) and normal thyroid were also examined. Genome-wide methylation profiling using the Infinium HumanMethylation450FFPE (formalin fixed paraffin embedded) BeadChip Array was performed on 24 thyroid cases (8 PTC, 8 FTC, 4 FA and 4 normal thyroid). Ingenuity Pathway Analysis (IPA) was utilized to assess the roles of significantly differentially methylated genes in biological functions, signaling/metabolic pathways, and networks. Common mutations in 4 genes (BRAF, NRAS, HRAS, and KRAS) were assessed using TaqMan Mutation Detection assay. Twelve genes were significantly differentially methylated among 4 comparison groups: cancer vs normal, cancer vs adenoma, PTC vs normal, and PTC follicular variant (PTC-FV) vs PTC-Classic. CTU1 and HLA-DPB1 were significantly hypermethylated and AARS2, TMSB10, RNF216L, KIF15, KIAA1143, and SLC2A13 were significantly hypomethylated between cancer and normal. Significant differential hypermethylation was noted for PNPLA7 and NPC1L1 in cancer vs adenoma and SNX6 in PTC-FV vs PTC-Classic. NT5C1B was hypermethylated and AARS2 was hypomethylated in PTC vs normal. IPA identified 2 gene networks, involving 11/12 genes, characterized by 1) Cellular development, Cellular growth and proliferation, Connective tissue development and function and 2) Drug metabolism, Cell-mediated immune response, Cellular development. NT5C1B was involved in all 4 highly ranked canonical nucleotide degradation pathways. Several significant bio-functions involved NPC1L1. Mutations of NRAS codon 61 were identified in 1 sample each of FTC-Classic, PTC-FV and FA and BRAF V600E in one PTC-Classic sample. Differential methylation of AARS2, CTU1, HLA-DPB1, SLC2A13, PNPLA7, NPC1L1, NT5C1B and SNX6 suggest potential markers for discriminating thyroid cancers from adenomas and normal. NT5C1B was noted in highly ranked canonical pathways, suggesting a role in nucleotide degradation. Pathway analysis of differentially methylated genes support important biological processes in thyroid cancer pathogenesis. Supported by JFCI/CRAG A20038
Citation Format: Josena K. Stephen, Kang Mei Chen, Jason Merritt, Indrani Datta, Dhananjay Chitale, George Divine, Maria J. Worsham. Methylome differences in differentiated thyroid cancers and benign adenomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3361. doi:10.1158/1538-7445.AM2017-3361
Abstract 3362: PBRM1 regulates the transcription of cell adhesion genes in ccRCC
Authors: Chowdhury Basudev 
Published: July 2017

Abstract
Advances in parallel sequencing have facilitated the recent identification of Polybromo-1 (PBRM1), a component of the PBAF (Polybromo-associated-BRG1- or BRM-associated factors) chromatin remodeling complex, as the second most frequently mutated gene in clear-cell renal cell Carcinoma (ccRCC). While several studies have described the diversity of PBRM1 mutations in ccRCC and established the mutation of PBRM1 as a “driver” of ccRCC carcinogenesis, little is known about the biological significance of PBRM1. With the intent of shedding light on the mechanistic roles of PBRM1, we have employed Next Generation Sequencing to delineate the transcriptional profile of cellular models of ccRCC with or without PBRM1 expression and identified genes associated with cell adhesion to be regulated by PBRM1 in 2D monolayer cultures. Since 2D cultures lack the architectural complexities to support studies pertaining to cellular adhesion, we evaluated the role of PBRM1 in 3D culture on Basement Membrane Matrix to provide a physiologically relevant analysis of gene expression and the resulting cellular phenotype. The results showed that of the 97 cell adhesion genes identified to be upregulated by PBRM1 in 2D cultures, 45 were also upregulated in 3D cultures and a subset of 32/45 genes underwent increased gene expression in 3D with respect to 2D cultures. The gene expression profile of candidate genes were verified by qPCR and Western Blotting. Mining The Cancer Genome Atlas (TCGA) publicly available data, we were able to correlate the gene expression profiles of cell adhesion genes identified in 3D cultures with those of ccRCC patients bearing at least 1 copy of the PBRM1 gene. Furthermore, we performed a PBRM1-ChIP-seq to map the genome-wide targets of PBRM1 and revealed the association of PBRM1 occupancy at proximal regulatory regions of 8/45 cell adhesion genes. All of these taken together, indicate a role for PBRM1 in regulating the gene expression of cell adhesion genes which act as important players in cellular morphogenesis and responsiveness to changes in the external environment. Disruption of cell adhesion is believed to affect signal transduction and pave the way facilitating metastasis in neoplastic cells. Currently we are investigating the effect of loss-of-PBRM1 on Epithelial to Mesenchymal Transition (EMT) and metastasis in ccRCC.
Note: This abstract was not presented at the meeting.
Citation Format: Basudev Chowdhury. PBRM1 regulates the transcription of cell adhesion genes in ccRCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3362. doi:10.1158/1538-7445.AM2017-3362
Abstract 3368: Omics data integration analysis in high grade serous ovarian cancer: results from three studies
Authors: Natanzon Yanina , Earp Madalene , Cunningham Julie M. , Kalli Kimberly R. , Winham Stacey J. , Armasu Sebastian M. , Larson Melissa C. , Wang Chen , Bowtell David D. , Garsed Dale W. , Goode Ellen 
Published: July 2017

Abstract
High grade serous ovarian cancer (HGSOC) is a complex disease in which initiation and progression have been associated with gene mutation, DNA methylation changes, genetic variation, and epigenetic processes. Variation in several susceptibility regions and cancer-typical global methylation patterns have been observed in HGSOC; however, this knowledge has not been compelling in understanding HGSOC intiation or progression. As ingetration of genomic, epigenomic, and transcriptomic data has increased mechanistic understanding in other cancers, we hypothesized that tumor methylation alone or in combination with germline genetic variation influences tumor gene expression in HGSOC. We examined three nested models using an Elastnic Net (ENET) penalized regression method while adjusting for somatic copy number (CNV): a) germline genotype and tumor DNA methylation (full model), b) genotype only, and c) DNA methylation only. We included 339 cases from The Cancer Genome Atlas (TCGA), 54 cases from Mayo Clinic, and 78 cases from the Australian Ovarian Cancer Study (AOCS). Genotyping and copy number calls on germline DNA, expression, methylation and copy number on somatic samples were collected and analyzed on different platforms separately at each study site. We excluded genes with low overall expression and thus analyzed a total of 11,922 genes available in three datasets ( Ensembl IDs, 500kb window up- and downstream). In general, combining genomic data in HGSOC did not reveal a role for germline genetic variation in altering gene expression. However, in methylation only models 79 genes were associated with differential expression in the TCGA cases (permutation multiple testing adjusted p-val &lt;0.05), in the Mayo cases (unadjusted p-val &lt;0.05) and AOCS cases (unadjusted p-val &lt;0.05). A known tummor suppressor (FBXW7) was associated with differential expression in the three datasets at p-val &lt;0.01. This work demonstrates the feasibility, utility, and statistical power of ENET gene-level analyses incoporating maximal genomic information.
Citation Format: Yanina Natanzon, Madalene Earp, Julie M. Cunningham, Kimberly R. Kalli, Stacey J. Winham, Sebastian M. Armasu, Melissa C. Larson, Chen Wang, David D. Bowtell, Dale W. Garsed, Ellen Goode. Omics data integration analysis in high grade serous ovarian cancer: results from three studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3368. doi:10.1158/1538-7445.AM2017-3368
Abstract 3373: The use of long-read sequencing to determine the structure of the Her2 amplicon in breast cancer
Authors: Rosenfeld Jeffrey , Goodwin Sara , Ganesan Shridar 
Published: July 2017

Abstract
HER2 amplification is present in ~15% of breast cancers, and is present in small subsets of other cancer types including gastric and lung cancers. Therapy targeting HER2 is now routinely used in treatment of HER2-amplificed breast cancer and has changed the natural history of this disease. The region of chromosome 17q12 containing Her2 contains many genes, and little is known about the actual genomic alterations that underlie the amplification event. While it is known that parts of the amplicon exist in multiple copies in a tumor, the exact structure of the duplicated region is not known and their relative orientation and positions in the genome is not clear. There is the potential for rearrangements between the genes and for different segments of the amplicon to exist and varied copy numbers. There is no clear way to assemble the complete structure of this region using short reads, as they cannot resolve repetitive regions and identify junction reads. Long read sequencing has the potential to overcome these limitations, however the sequencing depth is limited and difficult to apply to large genomes. To apply long read sequencing to a limited part of the cancer genome, we have used Nimblegen target enrichment coupled with Oxford Nanopore and Pacific Bioscience sequencing in an attempt to sequence and assemble the Her2 amplicon. The error rate of the sequencers are not of concern since we are not looking at base-pair level variation. Instead, our need is for long reads that can span the gene boundaries and repetitive elements to give complete structure of the amplicon. Nimblegen custom capture probes were designed for the 2mb chromosomal region containing Her2. DNA was extracted from 3 breast cancer cell lines and enriched using the Nimblegen kit. This DNA was then sequenced with long reads on the MinIon and the PacBio to allow for complete assembly of the region. The DNA was assembled to determine the structure of the HER2 amplicon in each cell line. These results may give new insight into the molecular events that led to formation of the HER2 amplicon.
Citation Format: Jeffrey Rosenfeld, Sara Goodwin, Shridar Ganesan. The use of long-read sequencing to determine the structure of the Her2 amplicon in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3373. doi:10.1158/1538-7445.AM2017-3373
Abstract 3374: APA isoform diversity in triple negative breast cancers
Authors: Erson-Bensan Ayse Elif , Akman Begum H. , Oyken Merve , Agus Hizlan H. , Yavuz Esra , Erdem Murat , Can Tolga 
Published: July 2017

Abstract
Alternative polyadenylation (APA) plays a role in gene expression regulation generally by shortening of 3'UTRs and relieving microRNA-mediated repression. Therefore, APA is gaining increased attention as a potential mechanism to activate oncogenes. Owing to high proliferative indices of triple negative breast cancers (TNBCs), we hypothesized APA to cause 3'UTR length changes in this aggressive subgroup of breast cancers. Our probe-based meta-analysis approach identified 3'UTR length alterations where the significant majority was shortening events (70%, 113 of 165) of mostly proliferation-related transcripts in over 500 TNBC patients compared with normal breast tissue. Representative shortening events correlated with increased protein levels and relapse free survival of patients, suggesting functional significance of isoform variability. To begin addressing the underlying mechanisms of 3’UTR shortening, we turned to APA machinery proteins. We detected variable expression of APA machinery proteins in different breast cancer subtypes but CSTF2 (cleavage stimulation factor 2) has the most prominent overexpression in breast cancer cells. Therefore, among potential regulators of 3’UTR shortening, we further investigated the role of CSTF2 in proximal polyA signal selection. Because some of the TNBC patients are EGFR positive, we found EGF treatment to cause increased CSTF2 levels. Higher CSTF2 levels indeed correlated with further shortening of the 3'UTRs. Accordingly, RNAi-induced silencing of CSTF2 decreased the proliferative rate of cancer cells. Therefore, our integrated approach revealed a pattern of 3'UTR length changes in TNBC patients and a potential link between APA and EGF signaling. Further studies are underway to investigate the mechanistic link between EGF signaling and regulation of 3’UTR lengths. (This work is funded by TUBITAK 112S478 and 114Z884)
Citation Format: Ayse Elif Erson-Bensan, Begum H. Akman, Merve Oyken, Hizlan H. Agus, Esra Yavuz, Murat Erdem, Tolga Can. APA isoform diversity in triple negative breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3374. doi:10.1158/1538-7445.AM2017-3374