bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5335: A highly efficient targeted bisulfite sequencing method for accurate DNA methylation profiling
Authors: Peng Quan , Kim Daniel , Ranjbar Mohammad Nezami , Strauss Sascha , Winter Scott , Wang Yexun 
Published: August 2018

Abstract
Background DNA methylation plays an important role in gene regulation. Bisulfite sequencing (BS), in which unmethylated cytosines are converted to uracil while methylated cytosines remain intact, is considered as the gold standard for DNA methylation detection with single nucleotide resolution. Due to the high cost of whole genome BS and the low throughput of amplicon BS, there remains the need for new targeted bisulfite sequencing methods with high efficiency and flexibility.
Results We developed a targeted bisulfite sequencing method, by incorporating single primer enrichment (SPE) and molecular barcoding (UMI) technology. This enables flexible and scalable targeted DNA methylation analysis with high efficiency. We first studied the ability of our assay to detect CpG methylation at various levels in reference materials. We also evaluated its utility in profiling CpG methylation in different cell line DNA, and compared the results with published data from alternative technologies (WBS, RRBS and microarray).
Conclusions We demonstrated the successful implementation of SPE and UMI technology on bisulfite converted DNA with high enrichment specificity and low bias. We showed that our method accurately detected CpG methylation at different levels, in concordance with expected titration mixture or published datasets. Comparing to reported amplicon BS, our technology enables much higher multiplexing scale and much simpler workflow. Comparing to probe capture based enrichment, our technology enables much lower DNA input, much higher sequencing efficiency (on-target) and shorter turnaround time.
Citation Format: Quan Peng, Daniel Kim, Mohammad Nezami Ranjbar, Sascha Strauss, Scott Winter, Yexun Wang. A highly efficient targeted bisulfite sequencing method for accurate DNA methylation profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5335.
Abstract 5339: Epigenetic silencing of ANGPTL4 in tumor tissues and its overexpression in the urothelial carcinoma microenvironment
Authors: Chan Michael WY , Hsieh Hsiao-Yen , Jou Yeong-Chin , Tung Chun-Liang , Tsai Yuh-Shyan , Wang Yuan-Hung , Chi Chen-Lin , Lin Ru-Inn , Hung Shih-Kai , Chuang Yu-Ming , Wu Shu-Fen , Li Chin , Shen Cheng-Huang , Hsu Cheng-Da 
Published: August 2018

Abstract
Urothelial carcinoma (UC) carcinogenesis has been hypothesized to occur through epigenetic repression of tumor suppressor genes (TSGs). By qRT-PCR array, we found that one potential TSG, ANGPTL4, was expressed at very low levels in all UC cell lines we examined. Previous studies had demonstrated that ANGPTL4 is highly expressed in some cancers, but downregulated, by DNA methylation, in others. Consequently, due to these seemingly conflicting functions in distinct cancers, the precise role of ANGPTL4 in the etiology of UC remains unclear. In this study, using methylation-specific PCR and bisulfite pyrosequencing, we show that ANGPTL4 is transcriptionally repressed by promoter hypermethylation in UC cell lines and primary tumor samples, as compared to adjacent noncancerous bladder urothelium. Functional studies further demonstrated that ectopic expression of ANGPTL4 potently suppressed UC cell proliferation, monolayer colony formation in vitro, and invasion, migration, and xenograft formation in vivo. As ANGPTL4 is a secreted factor, we therefore examined the circulating ANGPTL4 (cir-ANGPTL4) level in UC patients. Surprisingly, cir-ANGPTL4 was significantly higher in plasma samples from UC patients than normal control, suggesting it might be secreted from other cell types. More importantly, exogenous c-terminal fragment of ANGPTL4 (cANGPTL4) could promote cell proliferation and cell migration via activation of signaling through the Erk/FAK axis. We further confirmed that mouse xenograft tumor growth could be promoted by administration of exogenous cANGPTL4. Finally, immunohistochemistry demonstrated that ANGPTL4 was downregulated in tumor cells but overexpressed in tumor-adjacent stromal tissues including muscle and macrophages of muscle-invasive UC tissue samples. In conclusion, our data supports dual roles for ANGPTL4 in urothelial carcinoma progression, either as a tumor suppressor or oncogene, in response to microenvironmental context.
Citation Format: Michael WY Chan, Hsiao-Yen Hsieh, Yeong-Chin Jou, Chun-Liang Tung, Yuh-Shyan Tsai, Yuan-Hung Wang, Chen-Lin Chi, Ru-Inn Lin, Shih-Kai Hung, Yu-Ming Chuang, Shu-Fen Wu, Chin Li, Cheng-Huang Shen, Cheng-Da Hsu. Epigenetic silencing of ANGPTL4 in tumor tissues and its overexpression in the urothelial carcinoma microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5339.
Abstract 5342: Somatic bi-allelic loss of TSC genes in eosinophilic solid and cystic renal cell carcinoma (ESC RCC)
Authors: Lee Nicole D. , Vats Pankaj , Cao Xuhong , Su Fengyun , Lonigro Robert , Premkumar Kumpati , Trpkov Kiril , McKenney Jesse K. , Mehra Rohit , Dhanasekaran Saravana M. , Chinnaiyan Arul M. 
Published: August 2018

Abstract
Renal cell carcinoma (RCC) subtypes with overlapping histomorphologic features pose diagnostic challenges. For instance, a unique category of sporadic renal tumors with eosinophilic cytoplasm and solid and cystic growth pattern (ESC RCC) may mimic a RCC subtype usually encountered in patients with germline aberrations of tuberous sclerosis complex (TSC) genes (TSC RCC). Here, we used next-generation sequencing (NGS) technology to interrogate the clinicopathologic and molecular profiles of ESC RCC tumors. Mutational and copy number analysis of NGS data from ESC RCC tumors revealed a somatic bi-allelic loss of TSC family genes, specifically TSC1 or TSC2, in six out of seven profiled cases. However, the corresponding background kidney showed only wild type alleles, thus excluding any germline involvement and differentiating ESC RCC from TSC RCC. Furthermore, bi-allelic loss of the TSC genes occurred in a mutually exclusively manner in this cohort. Our study clarifies the molecular identity of ESC RCC, and can thus guide future therapeutic strategies and provide a basis for the revision of current RCC classification.
Citation Format: Nicole D. Lee, Pankaj Vats, Xuhong Cao, Fengyun Su, Robert Lonigro, Kumpati Premkumar, Kiril Trpkov, Jesse K. McKenney, Rohit Mehra, Saravana M. Dhanasekaran, Arul M. Chinnaiyan. Somatic bi-allelic loss of TSC genes in eosinophilic solid and cystic renal cell carcinoma (ESC RCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5342.
Abstract 5343: Mutational signatures in EGFR sensitizing mutation positive lung adenocarcinoma
Authors: Kim Eun Young , Kim Arum , Chang Yoon Soo 
Published: August 2018

Abstract
Lung cancer has high mutational burden, which is featured by smoking signature. However, lung cancer with EGFR mutations is common in nonsmokers and women, which suggests that mutational stresses other than smoking are involved. We analyzed repeated deep sequencing data of EGFR sensitizing mutation positive lung adenocarcinoma tissue to identify characteristic mutational signatures, proposed by Alexandrov et al. Targeted next-generation sequencing was performed using Ion AmpliSeq Custom Panel of 0.6 Mb size containing 70 major genes including EGFR in 69 cases harboring sensitizing EGFR mutation. Publicly available data from EGFR sensitizing mutation were extracted from GDC data portal. Mutational signature was analyzed using maftools package. EGFR-TKI domain analysis revealed 53 mutations. C&gt; T mutation was found in 26.4%, but C&gt; T transition at CpG site that suggests aging effect was found in 2%, and C&gt; T or C&gt; G mutation in TCW motif reflecting APOBEC activity were found in 1.4%. C&gt; A transversion corresponding to Signature 4 was also found in only one case, suggesting that the possibility of EGFR mutation by smoking effect is very low. The T&gt; C substitution in ApT, indicating signature 5, was detected in 4%. The EGFR-TKI sensitizing mutation (E19del, L858R) has lower frequency of co-mutation while other EGFR-TKI domain mutations were frequently associated with multiple co-mutations. T&gt;G substitution, indicating signature 28 and commonly found in Korean gastric cancer, was found in 39.1%. When the mutational signatures of a total 70 genes were analyzed, the C&gt; T mutation was the most commonly detected (73.1%) and similarity with signature 5 was highest. These findings suggest that the mutational signature of EGFR sensitizing mutant lung cancer, which is frequent in Far East Asia, may be different from that of Western data. Additional data and analysis will be updated until the annual meeting.
Citation Format: Eun Young Kim, Arum Kim, Yoon Soo Chang. Mutational signatures in EGFR sensitizing mutation positive lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5343.
Abstract 5346: Recurrent genomic copy alterations deregulate the transcriptome and key signaling networks in head and neck cancer cell lines and tumors with worse prognosis
Authors: Cheng Hui , Yang Xinping , Si Han , Saleh Anthony , Xiao Wenming , Coupar Jamie , Gollin Susanne M. , Ferris Robert L. , Issaeva Natalia , Yarbrough Wendell G. , Prince Mark E. , Carey Thomas E. , Waes Carter Van , Chen Zhong 
Published: August 2018

Abstract
Human cancer cell lines have been important tools for biological and preclinical investigation, and establishing their relationship to genomic alterations and subtypes found in tumors could further accelerate functional and therapeutic discoveries. We conducted an integrated analysis of the genomic and transcriptomic profiles of 15 human papillomavirus negative (HPV−) and 11 HPV(+) head and neck squamous cell carcinoma (HNSCC) lines, to identify models of important molecular subtypes uncovered among 279 HNSCC tumors from The Cancer Genome Atlas (TCGA). We developed analytic approaches to detect copy number alterations (CNAs) driving altered expression and predict deleterious mutations in HNSCC lines for comparison with TCGA. Strikingly, HNSCC lines displayed recurrent amplifications on chromosomes 3q22-29, 5p15, 11q13/22, and 8p11 that drive increased expression of a cluster of ~100 mRNAs encoding multiple known and understudied candidate oncogenes. These CNAs, together with loss and under-expression or mutations of putative tumor suppressor genes, recapitulate genomic alterations found in more aggressive HNSCC tumor subtypes. Among these, concurrent 3q26.3 amplification and TP53 mutation in HPV(−) HNSCCs is associated with worse overall survival. Common and distinctive CNAs, transcriptome, and mutations converge on biologically and therapeutically important signal pathways and functions in HNSCCs differing in HPV status, including PI3K, Hippo, TGF-β, Wnt/β-catenin, TP63, TP53/death, cell cycle/mitosis, stemness/differentiation, chromatin remodelling/DNA replication, post-transcriptional regulation, and mitochondrial biosynthesis. Our findings elucidate and validate genomic alterations underpinning numerous discoveries made with historic and recently derived HNSCC lines, and provide valuable models for future preclinical and therapeutic studies in subsets of HNSCCs with worse prognosis.
Supported by NIDCD/NIH intramural projects ZIA-DC-000073, ZIA-DC-000074.
This work utilized the computational resources of the NIH HPC Biowulf cluster. (http://hpc.nih.gov)
Citation Format: Hui Cheng, Xinping Yang, Han Si, Anthony Saleh, Wenming Xiao, Jamie Coupar, Susanne M. Gollin, Robert L. Ferris, Natalia Issaeva, Wendell G. Yarbrough, Mark E. Prince, Thomas E. Carey, Carter Van Waes, Zhong Chen. Recurrent genomic copy alterations deregulate the transcriptome and key signaling networks in head and neck cancer cell lines and tumors with worse prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5346.
Abstract 535: The impact on transcriptome diversity after oncogenic transformation of human mammary epithelial cells
Authors: Tran Anthony 
Published: August 2018

Abstract
Breast cancer is a leading cause of cancer-related morbidity and mortality worldwide. In the USA, one out of eight women will be diagnosed with breast cancer over the course of their lifetime. A major obstacle hindering the treatment of breast cancers is intratumor heterogeneity since cytotoxic drug sensitivities among different clonal populations may vary. Previously, we have shown that cancer cells display an increased repertoire and abundance of all transcripts within a cell (termed transcriptome diversity) compared to normal cells. The driving mechanism(s) of cellular intratumor heterogeneity has yet to be fully elucidated. In this study, we utilize immortalized human mammary epithelial cells (MCF10A) transformed with an array of doxycycline-inducible lentiviral vectors encoding known genetic drivers of breast tumorigenesis (TP53 mutant, BRCA1 mutant, PIK3CA mutant, shPTEN and c-MYC) alone and in combination to determine their impact on transcriptome diversity based on RNA-seq. Our strategy enables strict temporal control and reversibility of gene expression alterations via the doxycycline-inducible promoter. Transcriptome diversity will also be interrogated using single-cell RNA sequencing to determine how individual cellular transcriptional profiles contribute to the overall population-based transcriptional landscape. These results will be compared to patient tumor samples' transcriptome diversity and correlated with their respective clinicopathologic characteristics. Advancing our understanding of cellular transcriptome diversity will enable new avenues of treatment for breast cancers resistant to current clinical interventions such as metastatic and triple negative breast cancers, both of which are characterized by high transcriptome diversity.
Citation Format: Anthony Tran. The impact on transcriptome diversity after oncogenic transformation of human mammary epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 535.
Abstract 5355: Multiple mutations to the same gene are selected for and cooperate to drive cancer
Authors: Gorelick Alexander N. , Reznik Ed , Cai Yanyan , Bielski Craig , Bandlamudi Chaitanya , Penson Alexander , Jonsson Philip , La Konnor , Scaltriti Maurizio , Schultz Nikolaus , Taylor Barry S. 
Published: August 2018

Abstract
Cancers accumulate oncogenic mutations whose biochemical impact depends upon other germline and somatic variants in the cell. It stands to reason that the consequence of a somatic mutation is mediated by the presence of additional genetic variants within the same gene, and by the allele on which they arise. We have undertaken integrative analyses of 27,534 human tumors, including 19,640 prospectively sequenced advanced and metastatic cancers, and revealed a startling rate of multiple non-synonymous somatic mutations in the same cancer gene and tumor, hereafter referred to as multiple mutations. Overall, 26% of primary and metastatic tumors had at least one cancer gene with two or more somatic mutations. A minority of multiple mutations arose from somatic hypermutation or as secondary mutations driving resistance to molecularly targeted therapy. Clonality analysis further indicated that the majority of multiple mutations were present in the same cell. Multiple cancer genes were enriched for a greater burden of multiple mutations than would be expected in the absence of selection, including APC, B2M, EGFR, and TERT. The allelic configuration of these mutations indicated that while multiple mutations in trans arose predominantly in tumor suppressor genes, consistent with the selective pressure for biallelic inactivation, the majority of phaseable mutations arose in cis in both tumor suppressors and oncogenes, implying a selective pressure exists for a biochemical function distinct from individual driver mutations in the same gene. Collectively, these data argue that multiple genetic variants within a gene and their allelic configurations can interact to drive cancers.
Citation Format: Alexander N. Gorelick, Ed Reznik, Yanyan Cai, Craig Bielski, Chaitanya Bandlamudi, Alexander Penson, Philip Jonsson, Konnor La, Maurizio Scaltriti, Nikolaus Schultz, Barry S. Taylor. Multiple mutations to the same gene are selected for and cooperate to drive cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5355.
Abstract 5356: Robust gene fusion detection in formalin-fixed tissue sample with QIAseq RNAscan Oncology Panel
Authors: Falk Jeffrey , Sitlani Parth , Orosco Claire , Panjikaran Maya , Weiner Dana , Tian Song , Samara Raed , DiCarlo John , Wang Yexun , Lader Eric , Reinecke Frank 
Published: August 2018

Abstract
Introduction: Gene fusions are frequently associated with tumorigenesismalignant tumors. Highly sensitive and reproducible detection of gene fusions in clinical samples, especially formalin-fixed paraffin-embedded (FFPE) specimens, is important for diagnosis, prognosis, and treatment guidance. Although many clinical tests utilize next-generation-sequencing (NGS) for detection of genetic alterations, reliable detection of gene fusions by NGS in FFPE samples remains a challenge.
Methods: Five FFPE non-small cell lung cancer samples confirmed by FISH to contain EML4-ALK or KIF5B-RET fusions were selected for testing along with the Seraseq™ FFPE Tumor Fusion RNA Reference Material, v1, which evaluates forcontains 12 known fusions. Four operators prepared NGS libraries for each sample (89-250ng input) using the commercially available QIAseq RNAscan Oncology Panel, which targets 223 fusion gene pairs or 576 unique breakpoints. The resulting libraries were sequenced on an Illumina® NextSeq 500 sequencer. Demultiplexed FASTQ files were analyzed using cloud-based QIAseq RNAscan Analysis pipeline v1.7.20.2. Detected fusions that are on the panel's target list were reported as curated gene fusions and assigned a score based on unique molecules supporting the transcript.
Results: For the Seraseq™ FFPE Tumor Fusion RNA Reference v1 sample, all 12 expectedknown fusions were detected in each of the libraries generated by four different operators. The analysis pipeline correctly called the expected fusion in all four replicates of the five clinical FFPE samples tested, which varied in both input quantityamount and quality. Reproducibility was evaluated by comparing the score values across replicate libraries for each sample; expected fusion detection was 100% consistent between users, and the average correlation coefficient for the fusion score was 0.995.
Conclusions: The commercially available QIAseq RNAscan Oncology panel is a highly sensitive and robust product for detection of gene fusions in FFPE samples. QIAseq RNAscan methodology provides a useful tool for studying gene fusions in tumor samples and with optimization, customization, and validation can further fit the specific needs for of clinical laboratories.
Citation Format: Jeffrey Falk, Parth Sitlani, Claire Orosco, Maya Panjikaran, Dana Weiner, Song Tian, Raed Samara, John DiCarlo, Yexun Wang, Eric Lader, Frank Reinecke. Robust gene fusion detection in formalin-fixed tissue sample with QIAseq RNAscan Oncology Panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5356.
Abstract 536: Targeting PRPK and TOPK for skin cancer prevention and therapy
Authors: Roh Eunmiri , Lee Mee-Hyun , Zykova Tatyana A. , Zhu Feng , Kim Hong-Gyum , Bae Ki Beom , Cho Yong Yeon , Bode Ann M. , Dong Zigang 
Published: August 2018

Abstract
Solar ultraviolet (sUV) irradiation is a major environmental carcinogen that can cause inflammation and skin cancer. The costs and morbidity associated with skin cancer are increasing, thus identifying molecules that can help prevent skin carcinogenesis is important. In this study, we identified the p53-related protein kinase (PRPK) as a novel oncogenic protein that is phosphorylated by the T-LAK cell-originated protein kinase (TOPK). Knockdown of TOPK inhibited PRPK phosphorylation and conferred resistance to solar simulated light (SSL)-induced skin carcinogenesis in mouse models. In the clinic, acute SSL irradiation significantly increased epidermal thickness as well as total protein and phosphorylation levels of TOPK and PRPK in human skin tissues. We identified two PRPK inhibitors, FDA-approved rocuronium bromide (Zemuron®) or betamethasone 17-valerate (Betaderm®) that could attenuate TOPK-dependent PRPK signaling. Importantly, topical application of either rocuronium or betamethasone attenuated SSL-induced epidermal hyperplasia, neovascularization and cutaneous squamous cell carcinoma (cSCC) development in SKH1 (Crl: SKH1-Hrhr) hairless mice by inhibiting PRPK activation, and also reduced expression of the proliferation and oncogenesis markers COX-2, cyclin D1 and MMP-9. This study is the first to demonstrate that PRPK- targeted therapy could be useful against sUV-induced cSCC.
Citation Format: Eunmiri Roh, Mee-Hyun Lee, Tatyana A. Zykova, Feng Zhu, Hong-Gyum Kim, Ki Beom Bae, Yong Yeon Cho, Ann M. Bode, Zigang Dong. Targeting PRPK and TOPK for skin cancer prevention and therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 536.