bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5377: Intragenic DNA methylation and increased gene expression: New directions from pan-cancer analysis
Authors: McGuire Michael H. , Herbrich Shelley , Wu Sherry , Wang Ying , Rupaimoole Rajesha , Yao Hui , Gharpure Kshipra , Lopez-Berestein Gabriel , Baggerly Keith , Sood Anil 
Published: July 2017

Abstract
Purpose: While the impact of DNA methylation at the promoter region as a repressive influence is well-known, the vast majority of DNA methylation actually occurs outside of the promoter region. The function of intragenic DNA methylation remains incompletely understood. Here, we investigate how intragenic DNA methylation impacts gene expression, and how these modifications differ between normal and corresponding cancer tissues.
Methods: A pan-cancer analysis of gene expression array data was integrated with Illumina 450k methylation array data across ten tumor types to produce correlation values between DNA methylation and gene expression at distinct loci on a genome-wide basis. The probes exhibiting a significant correlation between gene expression and DNA methylation were selected for further analysis.
Results: We uncovered robust positive correlations between gene expression and 3’ methylation in 3,200 genes, with 590 genes in bladder cancer, and 256 genes in squamous cell lung carcinoma displaying a correlation coefficient of &gt;0.5. Furthermore, we observed 44 genes with a correlation coefficient of &gt;0.7 in at least two tissue types. The majority of genes with the strongest correlations are transcription factors known to play roles in differentiation and development, with an enrichment of zinc finger and homeobox-containing genes. Further analysis of these genes exhibit divergent 3’
methylation when comparing normal and tumor tissues. Importantly, the extent of 3’ methylation of these genes is associated with patient overall survival in 5 of the 10 tumor types analyzed, strongly suggesting that this process plays a role in cancer pathogenesis.
Conclusion: DNA methylation of the 3’ region is a functionally and clinically relevant epigenetic modification, and may serve as a novel target for inhibiting tumorigenesis and tumor progression.
Citation Format: Michael H. McGuire, Shelley Herbrich, Sherry Wu, Ying Wang, Rajesha Rupaimoole, Hui Yao, Kshipra Gharpure, Gabriel Lopez-Berestein, Keith Baggerly, Anil Sood. Intragenic DNA methylation and increased gene expression: New directions from pan-cancer analysis [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 5377. doi:10.1158/1538-7445.AM2017-5377
Abstract 5380: Inactivation of endogenous genes in cancer cells using targeted promoter DNA methylation via CRISPR-DNMT3a fusion protein
Authors: Spivack Simon D. 
Published: July 2017

Abstract
Background: Developing technologies for precise manipulation of individual DNA methylation loci is an attractive challenge in cancer and lung biology, because aberrant expression via hyper- or hypo-methylation is so common. Projects such as ENCODE and the Roadmap Epigenetics Project, have identified thousands of epigenetic marks from human genome. However, the functional evaluation of these marks has been largely limited to determining their associations with gene expression. Technologies for targeting manipulation of epigenetic marks would allow direct experimental testing of the impact of DNA methylation at specific residues, mechanisms of gene regulation, and potential use as interventions, for example to silence constitutively active oncogenes.
Methods: Here, we developed a CRISPR Cas9-based tool for specific DNA methylation in which the catalytic domain of DNMT3a (DNMT3a-CD) is fused to the carboxy-terminus of Cas9 D10A-H840A mutant (dCas9). Both construct promoter strength and transfection strategies were optimized.
Results: We demonstrated targeted and consistent CpG methylation in 30~100bp regions downstream of the PAM (binding) site of the gRNA guided fusion protein in HEK293 cells. The multiple guide RNAs could target the dCas9-DNMT3A to multiple sites consistently. DNA methylation activity was specific for the targeted region and was heritable across cell divisions. We also found directed promoter DNA methylation of DAL1, GATA5 and C-MYC could decrease the corresponding mRNA expression by up to 80%; different DNA methylation positions had consequently different effects on gene expression. We have now performed C-MYC methylation-mediated knockdown in A549 lung cancer cells and are evaluating resulting cell cycle and apoptosis phenotypes.
Conclusion: We believe this new targeted epigenetic technology can be directed to cancer cells for the purpose of reprogramming lung cancer, and unregulated stromal and microenvironment cells, for preventive and therapeutic uses.
Note: This abstract was not presented at the meeting.
Citation Format: Simon D. Spivack. Inactivation of endogenous genes in cancer cells using targeted promoter DNA methylation via CRISPR-DNMT3a fusion protein [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 5380. doi:10.1158/1538-7445.AM2017-5380
Abstract 5385: Colorectal cancer methylome and laterality
Authors: Hirabayashi Sho , Hayashi Masamichi , Nakayama Goro , Kurimoto Keisuke , Tanabe Hiroshi , Kanda Mitsuro , Takami Hideki , Niwa Yukiko , Iwata Naoki , Kobayashi Daisuke , Tanaka Chie , Yamada Suguru , Sugimoto Hiroyuki , Koike Masahiko , Fujii Tsutomu , Fujiwara Michitaka , Kodera Yasuhiro 
Published: July 2017

Abstract
Background: Colorectal cancers are anatomically derived from Midgut area (from cecum to mid transverse colon) and Hindgut area (from mid transverse to anal canal). The laterality of colorectal cancers was reported as one of the prognosis markers of these cancers. Midgut originated cancers had statistically poorer overall survivals than Hind gut (Yahagi et al, J Gastrointest Surg, 2016). In addition to clinical reasons, for example its symptomless nature of the bowel obstruction on the right side, the difference of genetic and/or epigenetic profiles between both side colorectal cancers may exists.
Methods: Surgically resected 30 colorectal cancers (Midgut n=9, Hidgut n=21) were included. Any clinicopathological factors except for tumor site was not statistically different between 2 groups. We decided to focus on colon cancer methylome and laterality in this study. Two novel methylation markers of colon cancers (PAX5 and VGF) which were extracted from microarray analysis were used, and quantitative methylation-specific PCR (QMSP) assay was performed for each marker.Results: Both PAX5 and VGF methylations were extremely tumor-specific markers (P&lt;0.001 and P=0.011). Interestingly, Both markers tended to have high methylation frequency in Midgut derived cancers. High frequency of PAX5 promoter methylation was found in 9/9 cases (100%) of Midgut and 15/21 cases (71%) of Hindgut (P=0.141), while that of VGF was found in 6/9 cases (67%) of Midgut and 4/21 cases (19%) of Hindgut (P=0.030). In addition, three multiple colon cancers were found in the cohort. All of them were derived from Midgut area (T1/T1, T3/Tis and T3/Tis), and had high frequency of both PAX5 (2/3, 67%) and VGF (3/3, 100%) methylation.
Conclusion: Cancer methylome between Midgut and Hindgut seemed to be different, and it may affect tumor malignancy, plurality and chemotherapy sensitivity. Now we are in progress of increased colorectal cancer cases (over 100) and methylation markers.
Citation Format: Sho Hirabayashi, Masamichi Hayashi, Goro Nakayama, Keisuke Kurimoto, Hiroshi Tanabe, Mitsuro Kanda, Hideki Takami, Yukiko Niwa, Naoki Iwata, Daisuke Kobayashi, Chie Tanaka, Suguru Yamada, Hiroyuki Sugimoto, Masahiko Koike, Tsutomu Fujii, Michitaka Fujiwara, Yasuhiro Kodera. Colorectal cancer methylome and laterality [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 5385. doi:10.1158/1538-7445.AM2017-5385
Abstract 539: MAEL promotes colorectal cancer cell growth and migration by activating EGFR pathway
Authors: Liu Lulu , Tong Zhou , Jiang Weiqin , Zheng Yi , Zhao Peng , Fang Weijia 
Published: July 2017

Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors of the digestive system. It is generally accepted that CRC pathogenesis is a long-term process involving accumulation of multiple genetic alterations. Herein, we aim to explore the molecular biological mechanisms of CRC initiation and progression. We have been committed to investigating MAEL function in digestive neoplasms and have found MAEL is a new candidate oncogene. Previously, overexpression of MAEL was frequently detected in CRC tissues and significantly associated with poor 5-year outcome. By MTT assay and transwell assay, functional study demonstrated that overexpression of MAEL promoted cell growth and cell migration in DLD1 and THC8307 cell lines. Furthermore overexpression of MAEL in DLD1 cell line could promote tumor formation in nude mice. Further study found that MAEL overexpression in DLD1 and THC8307 elevated the protein expression of p-EGFR, p-Raf-1, p-ERK 1/2, p-PI3K and p-AKT. These data indicated that MAEL enhanced the activity of EGFR/Ras/Raf/MEK/ERK1/2 and EGFR/PI3K/Akt pathways. However, more effort is needed to investigate MAEL function and how MAEL activate EGFR pathways.
Citation Format: Lulu Liu, Zhou Tong, Weiqin Jiang, Yi Zheng, Peng Zhao, Weijia Fang. MAEL promotes colorectal cancer cell growth and migration by activating EGFR pathway [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 539. doi:10.1158/1538-7445.AM2017-539
Abstract 5390: Broad Genomics and Cancer Program development of comprehensive blood biopsy sequencing capabilities to support direct-to-patient cancer research initiatives
Authors: Cibulskis Carrie , Hollinger Andrew 
Published: July 2017

Abstract
Genomic profiling of cell free tumor DNA (Blood Biopsy) offers the potential to revolutionize cancer precision medicine. As a proxy for tumor tissue profiling, successful blood biopsy analysis can help select appropriate patients for clinical trials, provide useful data for treatment monitoring, and discover genomic mechanisms of disease resistance. Recognizing these potential benefits, we aim to enable large-scale genomic data generation and analysis of cfDNA samples to support the patient driven Metastatic Breast Cancer Project (mbcproject.org) and many other such efforts. The widespread adoption of cfDNA sequencing technology in clinical research will require low cost, efficient, and in some cases clinically-validated processes. Commercial offerings in this field are focused on analysis of small targeted hotspot panels due to the challenges of more complete sequencing approaches for cfDNA (e.g. variability in the fraction of tumor present and high false positive rates). Working in collaboration with the Broad Institute Cancer Program, we have developed a process to overcome these challenges and provide high quality comprehensive exome analysis of cfDNA. Our process includes screening samples using ultra low pass, UMI-enabled whole genome sequencing to quantify the % of tumor DNA available for sequencing. Qualified samples are then moved into automated processes for exome sequencing and somatic mutation detection. In our initial validation study of 23 breast and prostate cancer patients with matched cfDNA and tumor tissue sequencing, we are able to identify 90% of clonal and 45% of subclonal mutations found in the matched tumor biopsy. In our effort to scale this process, and fully characterize the benefits and limitations of this technology we will present additional validation analysis. We will evaluate the relative importance of using paired sample analysis (tumors and matched normals) with analysis of tumor sequencing alone and assess sensitivity and specificity of somatic alterations as a function of tumor fraction and sequencing depth.
Citation Format: Carrie Cibulskis, Andrew Hollinger. Broad Genomics and Cancer Program development of comprehensive blood biopsy sequencing capabilities to support direct-to-patient cancer research initiatives [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 5390. doi:10.1158/1538-7445.AM2017-5390
Abstract 5396: An NGS workflow to detect down to 0.1% allelic frequency in cfDNA for breast and colon cancers
Authors: Dhingra Dalia , Chien Richard , Gu Jian , Brinza Dumitru , Chaudhary Ruchi , Banjara Kunal , Li Yanchun , Ballesteros-Villagrana Efren , Bramlett Kelli 
Published: July 2017

Abstract
Noninvasive detection of rare mutations in blood could allow tumor monitoring for research purposes. Research studies have suggested that cfDNA contains DNA from tumor cells with somatic mutations that could inform on tumor progression and therapeutic resistance. Here, we demonstrate a complete workflow from a single tube of blood through data analysis for research samples down to a 0.1% allelic frequency.
The low abundance tumor mutations found in cfDNA requires sensitive and accurate mutation detection. We have developed two panels that utilize an amplification-based assay that generates tagged DNA copies, which allows detection of low abundance tumor mutations found in cfDNA. The two panels allow multiplex interrogation of primary driver and resistance mutations specific to ctDNA from breast and colon cancer. The Oncomine Colon cfDNA panel targets 236 hotspots within 14 genes while the Oncomine Breast cfDNA panel covers 157 hotspot mutations in 10 genes. This workflow was validated from matched single blood tubes, Streck and K2EDTA. Additionally, the utility for cancer research was demonstrated with concordance studies using matched FFPE and plasma from oncology samples.
To further characterize these panels we have developed an oncology control for cfDNA with nucleosome fragment sizing and minimal sonication damage. This engineered control contains SNPs and indels at 0.1% allelic frequencies, orthogonally confirmed with TaqMan based Rare Mutation assays. With this control, the Oncomine Breast cfDNA panel had over 81% sensitivity and 99.9% specificity. The Oncomine Colon cfDNA panel had over 85% sensitivity and 100% specificity. The Oncomine Breast cfDNA panel and Oncomine Colon cfDNA panel integrated into a complete workflow starting from a single tube of blood can advance oncology research with the ability to detect blood based cancer biomarkers present at 0.1%.
Citation Format: Dalia Dhingra, Richard Chien, Jian Gu, Dumitru Brinza, Ruchi Chaudhary, Kunal Banjara, Yanchun Li, Efren Ballesteros-Villagrana, Kelli Bramlett. An NGS workflow to detect down to 0.1% allelic frequency in cfDNA for breast and colon 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 5396. doi:10.1158/1538-7445.AM2017-5396
Abstract 5398: High-throughput clonal analysis of AML tumors with droplet microfluidics
Authors: Eastburn Dennis , Pellegrino Maurizio , Treusch Sebastian , Sciambi Adam , Hyun Bill , Yates Jamie 
Published: July 2017

Abstract
Single cell analysis tools are crucial to better understand the role that rare or heterogeneous cancer cells play in the evolution of tumor progression. Although, it is now feasible to perform single-cell RNA-Seq on thousands of, several challenges remain for high-throughput single-cell DNA sequencing. To address these challenges and enable the characterization of genetic diversity in cancer cell populations, we developed a novel approach that barcodes amplified genomic DNA of individual cells confined to microfluidic droplets. The barcodes are used to reassemble the genetic profiles of individual cells from next generation sequencing data. A key feature of our approach is the “two-step” microfluidic workflow that releases genomic DNA from cellular proteins prior to amplification. The microfluidic workflow first encapsulates individual cells in droplets, lyses the cells and prepares the lysate for genomic DNA amplification using proteases. Following this lysate preparation step, the proteases are inactivated and droplets containing the genomes of individual cells are then paired with molecular barcodes and PCR reagents. We demonstrate that the two-step microfluidic approach is vastly superior to workflows without the two-step process for efficient DNA amplification on tens of thousands of individual cells per run with high coverage uniformity and low allelic dropout of targeted genomic regions. To apply our single-cell sequencing technology to the study of acute myeloid leukemia (AML), we developed a targeted panel to sequence genes frequently mutated in AML including TP53, DNMT3A, FLT3, NPM1, NRAS, KRAS, JAK2, IDH1 and IDH2. Using this panel, we were able to identify clonal populations from AML research samples; moreover, the single-cell nature of our approach enabled the correlation of multiple mutations within subclones and determination of whether the mutations existed as as a homozygote or heterozygote. Collectively, our results show a greater degree of heterogeneity in AML tumor samples than is commonly appreciated with bulk sequencing methods.
Citation Format: Dennis Eastburn, Maurizio Pellegrino, Sebastian Treusch, Adam Sciambi, Bill Hyun, Jamie Yates. High-throughput clonal analysis of AML tumors with droplet microfluidics [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 5398. doi:10.1158/1538-7445.AM2017-5398
Abstract 54: The many faces of antibody in G protein-coupled receptor biology
Authors: Chen Lei , Cheung Wing-Tai 
Published: July 2017

Abstract
G protein-coupled receptors (GPCRs), the largest family of cell-surface receptor proteins mediating signal transmission, play a pivotal role in many physiological functions and are involved in multiple diseases. Although receptor activities of GPCRs are successfully modulated by many small molecules which represent 30% of all marketed drugs today, in fact only a few GPCR members are targeted and many more GPCRs of interest are intractable targets of small molecules, like orphan GPCRs and GPCRs with large binding sites. Besides, small molecule drugs rarely trigger GPCR-mediated apoptosis or induce direct cell killing, which is crucial for cancer therapies. Therefore, for these GPCRs, antibody-based drug would be a good alternative. Despite being eagerly sought for, the production of monoclonal antibody (mAb) targeting GPCR is hindered by the low expression of recombinant GPCR on cell surface, and relatively small exposed regions with glycosylation and conformational heterogeneity. Therefore those conventional methods that were well established for generation of mAbs targeting soluble proteins usually showed frustrating results in the case of GPCRs. To bypass the production and purification of recombinant GPCR proteins, we developed a novel approach of transplanting immunogenic conformational epitopes of GPCR into an antibody scaffold to make a water soluble surrogate antigen of GPCR, named as GPCR-antigenized antibody which can be easily and abundantly produced in bacteria for animal immunization. In coupled with phage display technology and cell panning strategy, which allow the retrieval of specific binders from a huge number of candidates, we have successfully isolated scFv antibodies for two human GPCRs, the MAS1 receptor and the chemokine receptor CXCR4. These antibodies showed good specificity in immunofluorescent staining, flow cytometry analysis, western protein immunoblot and immunoprecipitation assay. The results demonstrated this novel approach may offer a generic and effective method to generate specific monoclonal antibody targeting GPCR for diagnostic and therapeutic applications. [The project is partly funded by a CUHK direct grant (4054300)]
Citation Format: Lei Chen, Wing-Tai Cheung. The many faces of antibody in G protein-coupled receptor biology [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 54. doi:10.1158/1538-7445.AM2017-54
Abstract 5407: Integrated analysis of genome-wide microRNA and mRNA profiling reveals unregulated miR-125b associated with poor prognosis by reducing cell apoptosis in gastric cancer
Authors: Liu Ben , Yang Da , Song Fengju , Zhang Xining , Guo Yan , Zhao Yanrui , Zheng Hong , Zhang Wei , Chen Kexin 
Published: July 2017

Abstract
Background & Aims: In our prior study, an integrated analysis of microRNA and mRNA profiling of gastric cancer (GC) revealed a mRNA-regulatory network. It defined a GC microRNA subtype that was associated with poor survival in 90 GC cases. In this study, we further demonstrate that miR-125b, a key node in this microRNA regulatory network, is upregulated in GC and associated with poor overall survival by interfering in the apoptosis pathway.
Methods: To further investigate the role of miR-125b in GC, we conducted both an in vitro experiment and clinical study (cohort of 373 GC samples). miR-125b and targets in the network were validated through RT-PCR and tissue microarray GC cases. The miR-125b targeted gene and related pathway were identified by a gene expression profile analysis in miR-125b transfected GC cell lines. The Annexin V-FITC and TUNEL assay were used to assess apoptosis. MTT and flow cytometry were performed to detect the effect of miR-125b on proliferation and cell cycle. The wound healing test and transwell assay were used to analyze migration and invasion.
Results: The markly upregulated expression of miR-125b was validated in 373 GC samples.. Univariate and multivariate analyses find that the miR-125b was associated with poor prognosis (p=0. 011). Pathway analysis shows that the predicted targets of miR-125b are highly involved in apoptosis/program death pathway. The robust apoptosis genes, BIK and CASP6 are validated as the directed targets of miR-125b. miR-125b can suppress apoptosis and increas cell growth, migration and invasion in GC cell lines. Furthermore, low expression of BIK (p=0. 034) and CASP6 (p=0.048) in GC were associated with poor disease-free survival.
Conclusions: The apoptosis pathway was found to be dominant in the pathway construction based on target genes of miR-125b. Our findings suggest that miR-125b-regulated apoptosis pathway is important to GC progression and that the miR-125 may be an important clinical biomarker for GC survival and possible therapeutic target for GC treatment.
Citation Format: Ben Liu, Da Yang, Fengju Song, Xining Zhang, Yan Guo, Yanrui Zhao, Hong Zheng, Wei Zhang, Kexin Chen. Integrated analysis of genome-wide microRNA and mRNA profiling reveals unregulated miR-125b associated with poor prognosis by reducing cell apoptosis in gastric 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 5407. doi:10.1158/1538-7445.AM2017-5407