bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3232: Circulating sCD27 and sCD30 in samples collected fifteen years apart and non-Hodgkin lymphoma risk: Findings from the CLUE-I and CLUE-II cohorts
Authors: Purdue Mark P. , Lan Qing , Hoffman-Bolton Judith , Hildesheim Allan , Strickland Paul , Visvanathan Kala , Rothman Nathaniel
Published: August 2018

Elevated serum levels of the immune activation markers sCD27 and sCD30 have been consistently associated with increased future risk of non-Hodgkin lymphoma (NHL). However, past studies could not clarify patterns of these markers over time preceding diagnosis, given their use of a single banked sample per participant. To address this question, we conducted a nested case-control study within the CLUE-I and CLUE-II cohorts including 102 case-control matched pairs with two banked samples per participant, collected fifteen years apart. The CLUE-II sCD27 concentrations among cases were higher than in the earlier CLUE-I samples (P<0.0001), whereas no systematic difference was observed for controls (P=0.89). The sCD27 increase was greater for cases diagnosed less than 10 years vs. 10+ years after CLUE-II enrollment (P = 0.0007). For sCD30, an increase between samples was observed for both cases (P = 0.0002) and controls (P=0.02), and the magnitude of increase among cases did not significantly differ across the two follow-up periods (P = 0.12). In comparison to having low (below-median) sCD27 levels in both CLUE-I and CLUE-II samples, associations with NHL were observed for having low CLUE-I sCD27 and high CLUE-II sCD27 (“low / high”; odds ratio 2.4, 95% confidence interval 1.0-6.2) as well as having high sCD27 levels in both samples (“high / high”; 2.1, 1.0-4.4). For sCD30, only the “high-high” category was associated with NHL (2.1, 0.9-5.0). The “low-high” sCD27 association was apparent only for cases diagnosed less than 10 years after CLUE-II (4.1, 1.3-13.0), while the “high-high” associations were consistent across follow-up periods. Our findings suggest that multiple factors may underlie NHL associations with these markers; rising sCD27 closer to diagnosis is likely driven by occult disease, whereas associations with stable elevated analyte levels may reflect etiologically relevant effects.

Citation Format: Mark P. Purdue, Qing Lan, Judith Hoffman-Bolton, Allan Hildesheim, Paul Strickland, Kala Visvanathan, Nathaniel Rothman. Circulating sCD27 and sCD30 in samples collected fifteen years apart and non-Hodgkin lymphoma risk: Findings from the CLUE-I and CLUE-II cohorts [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 3232.
Abstract 3243: Associations of polyomavirus seroreactivity with AIDS-related non-Hodgkin's lymphoma
Authors: Song Minkyo , Bender Noemi , Goedert James J. , Winkler Cheryl A. , Brenner Nicole , Waterboer Tim , Rabkin Charles S.
Published: August 2018

Background: Human polyomaviruses have a suspected role in carcinogenesis. In the setting of human immunodeficiency virus (HIV) infection, coinfection with MCV polyomavirus is associated with high risk of Merkel cell carcinoma. A role in lymphomagenesis has also been suggested by studies in the general population, but there are no prior studies in individuals with the acquired immunodeficiency syndrome (AIDS).

Methods: We measured antibodies against 11 common polyomaviruses in archived serum and plasma samples from two prospective cohort studies of HIV infection. Patients with incident (n=28) and prevalent (n=38) AIDS-related non-Hodgkin lymphoma (NHL) were matched by age, sex, and CD4 count to 67 HIV-positive AIDS-free controls. Seroreactivity was measured by fluorescent bead-based multiplex serology, quantified as median fluorescence intensity (MFI). Logistic regression models were used to estimate adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) for NHL risk. Multinomial logistic regression compared incident and prevalent NHL cases to lymphoma-free controls and heterogeneity between case groups was evaluated by Wald tests. Differences in MFI were assessed by Kruskal-Wallis tests. Based on log-transformed MFI values for 15 masked duplicate samples, estimated coefficients of variation (CV) were <20% and intraclass correlation coefficients (ICC) were >90% for all antibodies except LPV (CV 29%, ICC 67%).

Results: Cases had significantly lower prevalence of antibodies to WU polyomavirus than lymphoma-free controls (64% vs. 85%), with OR 0.28 (95% CI 0.12-0.68). Cases had non-significantly lower prevalence of antibodies to JC, TSV, MCV and KI polyomaviruses (ORs 0.42-0.71); similar prevalence of antibodies to BK, HPyV6 and HPyV7 polyomaviruses (ORs 0.98-1.18); and non-significantly higher prevalence of antibodies to HPyV10, LPV and HPyV9 polyomaviruses (ORs 1.35-1.77). MFIs for anti-WU antibodies were also lower for cases (median 552.6, interquartile range [IQR] 140.3-1298.3) than controls (median 1096.3, IQR 410.3-2044.3; p-value 0.047). The association of anti-WU antibody with NHL was stronger in samples obtained post-diagnosis (OR 0.18, 95% CI 0.07-0.48) than pre-diagnosis (OR 0.66, 95% CI 0.19-2.31; p-heterogeneity=0.037).

Conclusion: Our data do not directly implicate known polyomaviruses as lymphomagenic in the setting of HIV-associated immunodeficiency. Nevertheless, impaired antibody response to WU may be a harbinger of AIDS-related lymphoma.

Citation Format: Minkyo Song, Noemi Bender, James J. Goedert, Cheryl A. Winkler, Nicole Brenner, Tim Waterboer, Charles S. Rabkin. Associations of polyomavirus seroreactivity with AIDS-related non-Hodgkin's lymphoma [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 3243.
Abstract 3251: TaqMan Advanced miRNA cDNA Synthesis Kit to simultaneously study expression of miRNA and mRNA and to detect somatic mutations by qPCR
Authors: Hayashibara Kathleen , Veereshlingam Harita , Buchholz Malte
Published: August 2018

MicroRNAs (miRNA) are a class of small non-coding RNAs (approximately 21 nt long) that bind complementary sequences in target mRNAs to specifically regulate gene expression. Aberrant regulation of miRNAs and their targets has been associated with several diseases including cancer. The relationship between miRNA and mRNA has been found to be important in cancer development and progression. Simultaneous expression studies of miRNA and mRNA and detection of mutations in mRNA transcripts can be valuable in understanding molecular mechanisms that have an underlying role in various diseases. We demonstrate the technical verification of a novel method to reverse-transcribe and pre-amplify miRNA and mRNA from sample-limiting serum research samples using the TaqMan® Advanced miRNA cDNA Synthesis Kit. Based on results from previous studies, a signature of 49 mRNA and 37 miRNA targets has been identified that may help distinguish between benign and malignant pancreatic tissues. In this study, these targets and an additional set of transcript mutations were analyzed in serum from normal and test samples. TaqMan assays for miRNA and mRNA targets and custom TaqMan Mutation Detection Assays were placed on TaqMan Array Cards to facilitate investigation of several samples in a single experiment. Results demonstrate that transcript mutations can be detected and miRNA and mRNA targets can be reliably quantified from a single reverse transcription reaction. (For research use only. Not for use in diagnostic purposes.)

Citation Format: Kathleen Hayashibara, Harita Veereshlingam, Malte Buchholz. TaqMan Advanced miRNA cDNA Synthesis Kit to simultaneously study expression of miRNA and mRNA and to detect somatic mutations by qPCR [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 3251.
Abstract 3255: The roles of ALDH2, ADH1B and ADH1C gene polymorphism in predicting upper digestive tract multiple primary malignancies in head and neck cancer patients
Authors: Huang Shiang-Fu , Chien Huei-Tzu , Cheng Sou-De , Liao Chun-Ta , Wang Hung-Ming
Published: August 2018

Head and neck cancer was closely related with habitual use of cigarette and alcohol. The genes involving in the metabolism of alcohol are reported to play roles in increasing risks of head and neck cancer. In this study, we investigated the single nucleotide polymorphisms (SNPs) of alcohol metabolizing enzymes (ALDH2, ADH1B and ADH1C) in their distributions among different tumor subsites and their risks of developing multiple primary cancers. We recruited 659 male head and neck cancer patients between Mar 1996 and Feb 2017. Four hundred and twenty-seven normal controls were also recruited. The SNPs in ALDH2 (rs671), ADH1B (rs1229984) and ADH1C (rs698) were analyzed by Taqman PCR primers and TaqMan probes synthesized by Applied Biosystems (Foster City, CA). Genotyping was performed using the Taqman-based allelic discrimination method on an Applied Biosystems 7500 Real-Time Polymerase Chain Reaction System (Applied Biosystems, Foster City, CA). The A allele carriers than G/G homozygotes in ALDH2 is significantly higher in oral cavity cancer (p = 0.016), oropharynx (p = 0.018) and hypopharynx cancer (p = 0.051) than normal population but not in tonsillar cancer (p = 0.099). In ADH1B, the G allele carriers is significantly higher than A/A homozygotes in oropharynx (p = 0.012), tonsillar cancer (p = 0.050) and hypopharynx cancer (p < 0.001) than normal population but not in oral cavity cancer (p = 0.406). We did not observe ADH1C (rs698) SNP significantly related with HNSCC tumor subsites (p > 0.05). For ALDH2 (A allele carriers vs G/G homozygotes) and ADH1B (G allele carriers vs A/A homozygotes), they significantly increased risks to develop multiple primary cancers in upper digestive tract (p < 0.001, OR [95% confidence interval, C.I.]: 5.358 [2.565-11.195]. and p < 0.001, OR [95% C.I.]: 2.907 [1.598 - 5.290]). Conclusion:ALDH2 (rs671) A allele carriers and ADH1B (rs1229984) G allele carriers had higher risks of developing multiple primary cancers in upper digestive tract. For those with high risk allele carriers, routine screening of upper digestive tract including laryngoscope and esophagoscope is suggested to detect new primaries early.

Citation Format: Shiang-Fu Huang, Huei-Tzu Chien, Sou-De Cheng, Chun-Ta Liao, Hung-Ming Wang. The roles of ALDH2, ADH1B and ADH1C gene polymorphism in predicting upper digestive tract multiple primary malignancies in head and neck cancer patients [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 3255.
Abstract 3279: Comprehensive analysis of small nucleolar RNAs across in human cancers
Authors: Gong Jing , Li Yajuan , Liu Chunjie , Xiang Yu , Guo An-yuan , Lin Chunru , Han Leng
Published: August 2018

Recent studies demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes. We further identified 46 clinically relevant snoRNAs and experimentally demonstrated functional roles of SNORD46 in promoting cell proliferation, migration, and invasion. We developed a user-friendly data portal, SNORic, to benefit the research community. Our study highlights the significant roles of snoRNAs in the development and implementation of biomarkers or therapeutic targets for cancer and provides a valuable resource for cancer research.

Citation Format: Jing Gong, Yajuan Li, Chunjie Liu, Yu Xiang, An-yuan Guo, Chunru Lin, Leng Han. Comprehensive analysis of small nucleolar RNAs across in human cancers [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 3279.
Abstract 3280: Utah somatic variant calling pipeline featuring multi-sample joint calling, variant-graph based accurate allele frequency estimation and subclone analysis
Authors: Qiao Yi , Huang Xiaomeng , Lee Dillon , Farrell Andrew , Nicholas Thomas , Pederson Brent , Quinlan Aaron , Marth Gabor
Published: August 2018

Current tumor variant detection software tools are focused on the identification of somatic mutations in a single tumor sample (e.g. the primary tumor) compared to normal control tissue, and are not adequate for studies where multiple samples from the same patient, either at consecutive time points or at different metastatic sites are collected. Here we present a software framework that facilitates simultaneous analysis of such multi-sample datasets.

Our framework utilizes our FreeBayes variant caller for jointly calling all tumor samples and normal controls from the patient. This ensures that even very low frequency mutations are called because read evidence is aggregated across all samples; and that allele frequency information for a called somatic variant is provided uniformly for all samples. Short and medium-length INDELs, and structural variants are identified by our RUFUS software, a new reference-free mutation calling algorithm for both germline and somatic mutation detection, with extremely high sensitivity and specificity. We use our Graphite tool, a graph-genome based read realignment algorithm, to eliminate false positive somatic calls i.e. inherited variants masquerading as somatic mutations, and to substantially increase accuracy of allele frequency estimation of the true somatic calls, a feature critical for downstream subclone analysis. In addition, we use the FACETS package for CNV and LOH analysis, also critical for downstream subclone analysis.

Finally, we utilize SubcloneSeeker, our algorithm to reconstruct the evolution of the cancer at the subclonal level from the somatic variant allele frequencies, to understand how the tumor evolved over time, in response to multiple courses of treatment, or over space, across multiple metastatic sites. We demonstrate the use of this pipeline in published and ongoing studies involving longitudinal and multi-site tumor sample datasets.

Citation Format: Yi Qiao, Xiaomeng Huang, Dillon Lee, Andrew Farrell, Thomas Nicholas, Brent Pederson, Aaron Quinlan, Gabor Marth. Utah somatic variant calling pipeline featuring multi-sample joint calling, variant-graph based accurate allele frequency estimation and subclone analysis [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 3280.
Abstract 3285: COSMIC-3D: Impacts of cancer mutations on protein structure, function, and druggability
Authors: Jubb Harry C. , Saini Harpreet K. , Verdonk Marcel L. , Forbes Simon A.
Published: August 2018

In recent years there has been an explosion in cancer genomic data that has enabled understanding of the incidence and patterns of mutations in cancer patients. The challenge is to translate this vast resource of genomic research and data into precision medicines that target specific mutations in patient populations and improve clinical outcomes. Delivering personalised cancer medicines requires greater understanding of how cancer mutations impact the structure, function, and druggability of known and potential protein drug targets.

In this study we annotate each missense mutation in COSMIC, via COSMIC-3D (http://cancer.sanger.ac.uk/cosmic3d), with protein structural features derived from the wwPDB, and rich functional features derived from the UniProt protein database. The structural features include small molecule binding sites (including drug binding sites), protein-protein interaction interfaces, protein-nucleic acid interactions, solvent inaccessible protein “core” versus solvent exposed areas, and predicted small-molecule druggability. The UniProt-derived functional features represent high quality functional site annotations, including post-translational modification sites, functional domains and motifs, and regions of biological interest.

In addition, we explore the relationship between mutation occurrence in protein structural and functional sites, and recurrence in cancer. We found that recurrent missense mutations are significantly enriched in specific structural and functional environments, including small-molecule binding sites and predicted druggable pockets. These results provide promising hypotheses that recurrent, cancer driving mutations may be targeted by small-molecule drugs. We posit that further characterisation of the structure-function implications of each mutation in COSMIC-3D will increasingly aid mutation-guided target discovery and drug design.

Citation Format: Harry C. Jubb, Harpreet K. Saini, Marcel L. Verdonk, Simon A. Forbes. COSMIC-3D: Impacts of cancer mutations on protein structure, function, and druggability [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 3285.
Abstract 3286: A prototype Cancer Publication Portal (CPP) for summarizing and accessing cancer genomic publications
Authors: Johnson Andrew , DePratti Roland , Dancik Garrett M.
Published: August 2018

A search of PubMed finds more than 71,000 publications with the keywords “cancer” and “gene” published since the beginning of 2015. This increasingly large volume of publications necessitates the development of text-mining tools to help cancer researchers navigate and summarize articles efficiently. Here, we present a prototype Cancer Publication Portal (CPP) that allows a user to search and summarize the biomedical literature for a gene of interest. CPP leverages the data generated by PubTator, a tool that uses robust text-mining methods and associates articles with gene names and Medical Subject Heading (MeSH) terms. Additionally, CPP associates articles with therapeutic agents and selected cancer-related terms from the NCI Thesaurus. To use CPP, the user selects a gene of interest, and is presented with a summary of MeSH terms, therapeutic agents, and cancer-related terms that are associated with the selected gene. Cancer-related terms are highlighted, so that, for example, a user can quickly ascertain the frequency of publications per cancer type, or how many articles are associated with “mutations” in the gene. The summaries are interactive, so that the user can click on a term of interest to filter the results, and update the summaries. The user can repeat this process to narrow in on a specific topic of interest. Following all searches and filters, relevant articles are listed and are linked back their PubMed entries so that the reference article can be accessed. CPP currently includes information for ~4 million publications associated with >10,000 human genes. The underlying data is stored in an Oracle database while R/Shiny is used to implement the web interface. CPP is available from the following link: https://gdancik.github.io/bioinformatics/

Citation Format: Andrew Johnson, Roland DePratti, Garrett M. Dancik. A prototype Cancer Publication Portal (CPP) for summarizing and accessing cancer genomic publications [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 3286.
Abstract 3294: Functional annotation for alternative splicing to investigate disrupted splicing in cancer
Authors: Hyung Daejin , Kim Jihyun , Cho Soo Young , Park Charny
Published: August 2018

Alternative splicing (AS) plays a key role to confer human genome complexity. The advent of mRNA high-throughput sequencing facilitates to identify precise differential alternative splicing analysis. Massive result estimated from RNA-Seq should be sorted out whether AS has functional impact or not. Previous studies investigated protein domain or nonsense-mediated decay of AS event region. However other functional sites on exon inclusion region also exist. For example, miRNA binding site, and post-translational modification of AS site already are reported to assign functional impact. Therefore we developed ASpedia (http://combio.snu.ac.kr/aspedia/) to annotation functional impact of AS event. AS events of our database were generated from human genome hg19 ENSEMBL and Refseq. ASpedia provides a database, explore system, and AS browser to annotate functional impact evidence encompassing DNA, RNA, and protein. The user could query multiple AS events from differential AS analysis result. Currently our system supports a jar execution file to convert input query file from MISO or rMATS result.

The variant of splicing factor (SF) disrupts normal splicing. It could be assumed that target genes of mutated SF could be transcribed to aberrant isoforms by changed splicing machinery. Therefore we investigated the comprehensive SF variant status from TCGA somatic mutation and copy number. SF3B1 (2% in BRCA) and U2AF1 (4% in AML, and 2% in LUAD) were shown to recurrent mutation including hotspot. ELAVL2 known dispensable splicing factor to brain tissue were highly recurrent in deletion (18% in GBM). In order to examine aberrant AS events caused SF variants, we estimated exon-inclusion proportion Percent-Spliced-In (PSI) values for identifiable AS events using TCGA RNA-Seq dataset. Using differentially AS event analysis, we identified AS events that were significantly differentially spliced in the presence of a U2AF S34F/Y mutation (119 in AML). And we purposed to finding In order to investigate functional site, the differentially spliced AS events were additionally annotated using ASpedia. Finally we identified the landscape of that AS events were altered by SF variants, and we proved that a part of the events was involved in cancer-associated functions.

Citation Format: Daejin Hyung, Jihyun Kim, Soo Young Cho, Charny Park. Functional annotation for alternative splicing to investigate disrupted splicing in 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 3294.
Abstract 3301: Using a novel single-cell lineage-tracing technique to uncover the mechanisms driving nongenetic cancer relapse
Authors: Oren Yaara , Regev Aviv , Brugge Joan
Published: August 2018

Despite favorable initial response to platinum chemotherapy, the majority of patients with ovarian cancer will develop recurrent disease and succumb to it within 5 years of diagnosis. Initial recurrence is frequently platinum-sensitive and women can respond to multiple lines of platinum-based chemotherapy before eventually developing platinum-refractory disease. The observation that the tumor cells that survive the initial therapy give rise to a chemosensitive progeny is inconsistent with a simple Darwinian model of selection of genetically resistant clones. Tumor dormancy, stochastic cell state shifts and stem cell-like populations are among the mechanisms hypothesized to mediate re-emergence of platinum-sensitive ovarian cancer. However, given the lack of high-throughput methods to simultaneously track cell state and lineage, it is not currently feasible to distinguish the relative contribution of each of these factors. To address this need, we generated a new lentiviral barcode library, termed Watermelon. Unlike existing barcoding libraries that enable the tracking of multiple cancer cells solely at the DNA level, the Watermelon library encodes transcribed barcodes, which allows one to map the lineage to the transcriptional profile of each individual cell. This unique barcoding scheme, which is coupled with a genetic H2B retention system, enables simultaneous tracing of lineage as well as the transcriptional and proliferative states of each cell in the population during drug treatment. We have established and characterized an in vitro platinum-sensitive relapse model and are applying the Watermelon system together with time-lapse imaging to study the mechanisms underlying time-to-relapse variation and cell-fate decisions. By broadening our knowledge of the cellular and molecular pathways that affect noninherited drug resistance, our work will facilitate the future development of novel therapies that delay or even prevent the emergence of platinum-refractory ovarian cancer.

Citation Format: Yaara Oren, Aviv Regev, Joan Brugge. Using a novel single-cell lineage-tracing technique to uncover the mechanisms driving nongenetic cancer relapse [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 3301.
Abstract 3305: Cell-of-origin differentiation stages define methylation-based subtypes of human colorectal adenomas and carcinomas
Authors: Bormann Felix , Rodríguez-Paredes Manuel , Lasitschka Felix , Edelmann Dominic , Benner Axel , Bergman Yehudit , Ball Claudia R. , Glimm Hanno , Linhart Heinz G. , Lyko Frank
Published: August 2018

Introduction: Colorectal adenomas are precursor lesions of colorectal cancers and represent clonal amplifications of single cells from colonic crypts. DNA methylation patterns specify cell-type identity during cellular differentiation and therefore provide novel opportunities for tumor subclassification and patient stratification.

Methods: Infinium 450k and EPIC data from of non-malignant colorectal adenomas was applied to a consensus clustering algorithm. This defined epigenetic subtypes that were subsequently tested for clinico-pathological features, such as morphology and mutation status. Additionally, the subtypes were compared with Infinium 450k data from colonic crypt sections and also colorectal cancer samples provided by The Cancer Genome Atlas. Finally, clinical significance was addressed by testing for subtype specific overall survival rates.

Results: The analysis of the adenoma dataset defined 3 distinct epigenetic subtypes of human premalignant lesions. These 3 subtypes also reflect 3 of 4 epigenetic subtypes identified in colorectal cancer. The fourth, cancer-specific subtype represents the previously known subclass defined by microsatellite instability phenotype and the CpG island methylator phenotype. Comparisons to Crypt section methylomes and to other reference methylomes revealed that the other 3 subtypes represent epigenetic programs reflecting various intestinal crypt cell differentiation stages. Patient survival correlated with the differentiation stages with a particular poor prognosis for patients with stem cell-related epigenetic signatures.

Conclusion: Our results establish a novel and clinically relevant approach for colorectal adenoma and cancer classification and illustrate how differences in the cell-type of origin shape the tumor methylome.

Citation Format: Felix Bormann, Manuel Rodríguez-Paredes, Felix Lasitschka, Dominic Edelmann, Axel Benner, Yehudit Bergman, Claudia R. Ball, Hanno Glimm, Heinz G. Linhart, Frank Lyko. Cell-of-origin differentiation stages define methylation-based subtypes of human colorectal adenomas and carcinomas [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 3305.
Abstract 3310: Non-invasive diagnosis of colorectal cancer via targeted high-throughput DNA methylation sequencing of circulating tumor DNA (ctDNA)
Authors: Wu Xianrui , Chuan Jiacheng , Hu Tuo , Peng Tingting , Yang Meng , Shen Hui , Laird Peter , Gao Yangbin , Cai Xuyu , Xu Weihong , Fan Jian-bing , Lan Ping
Published: August 2018

Colorectal cancer (CRC) commonly develops from precancerous polyps. Most polyps are benign. The current screening method involves stool tests and colonoscopy, which is an unpleasant procedure. Even though stool DNA-based approach has been developed, it is still a clinical challenge to differentiate benign complications and malignant CRC.

We took the approach of high-throughput DNA bisulfide sequencing of tissue samples to identify cancer-specific methylation signatures. We learned methylation patterns by in-depth data mining and then applied pattern recognition approach to classify plasma samples. From a cohort of 70 pairs of tumor-normal matched tissue samples, we identified 1062 differential methylation markers. Next, we applied a greedy optimization algorithm to build a malignancy classification model using a training set of 118 plasma samples (malignant CRC: 56, benign complications: 23, healthy subjects: 39). In the training set, we achieved an AUC of 91.9% (95%CI: 87.3-96.5%). In an independent test set of 150 plasma samples (malignant CRC: 56, benign complications: 23, healthy subjects: 71), we achieved an AUC of 92.9% (95%CI: 88.3%~97.5%). Specifically, the model had a sensitivity of 91.1% for the identification of malignant CRC, and a specificity of 84.5% and 78.3% for healthy subjects and benign complications respectively. Our assay was demonstrated to be very sensitive towards early-stage CRC detection, with a sensitivity of 76.5% and 95% for stage I and II CRC respectively. The performance of this assay still awaits further validation in a large-scale clinical trial.

In summary, we have developed a highly sensitive blood-based non-invasive diagnostic assay for the identification of malignant CRC, which can aid clinical decisions for doctors. This approach can also be extended to non-invasive early screening for various other cancer types.

Citation Format: Xianrui Wu, Jiacheng Chuan, Tuo Hu, Tingting Peng, Meng Yang, Hui Shen, Peter Laird, Yangbin Gao, Xuyu Cai, Weihong Xu, Jian-bing Fan, Ping Lan. Non-invasive diagnosis of colorectal cancer via targeted high-throughput DNA methylation sequencing of circulating tumor DNA (ctDNA) [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 3310.
Abstract 332: The BET bromodomain inhibitor JQ1 synergizes with WEE1 inhibitor AZD1775 by impairing non-homologous end joining and enhancing DNA damages in non-small cell lung cancer
Authors: Takashima Yuta , Kikuchi Eiki , Kikuchi Junko , Shoji Tetsuaki , Furuta Megumi , Kikuchi Hajime , Sakakibara-Konishi Jun , Kinoshita Ichiro , Dosaka-Akita Hirotoshi , Nishimura Masaharu
Published: August 2018

Background: The bromodomain and extraterminal domain (BET) inhibitors are broadly active in different cancer types, including non-small cell lung cancer (NSCLC). Although their activity on oncogene expression such as c-Myc has been addressed in many studies, the mechanism of BET inhibition on the cytotoxicity remain unknown. BET proteins have been also reported to interact with some DNA damage repair-related genes. AZD1775, a selective WEE1 G2 checkpoint kinase inhibitor, induces DNA damage and consequent apoptosis by abrogating G2 cell cycle arrest and inducing premature mitotic entry. We hypothesized that repression of BET activity would increase WEE1 inhibitor-induced cytotoxicity by impairing DNA damage repair. Here, we evaluate the efficacy and mechanistic rationale for combining AZD1775 and JQ1 as a potential therapy for NSCLC.

Methods: NSCLC cell lines (A549, H1299, H1975) and human embryonic kidney cells line (293T) were used in the present study. Anti-tumor activities of JQ1, AZD1775, or the combination were analyzed using MTT survival assay. Changes in protein expression were analyzed by Western Blot analysis. mRNA expressions were evaluated by quantitative rt-PCR. Cell cycle was analyzed by flow cytometry using PI staining. Activity of non-homologous end joining (NHEJ) was evaluated using NHEJ reporter plasmid.

Results: The combination of AZD1775 and JQ1 showed synergistic effects for NSCLC cell lines in vitro with combination indices of 0.1-0.5. The JQ1 monotherapy did not induce gamma-H2AX expression, but JQ1 increased and prolonged AZD1775-induced gamma-H2AX expression. The mRNA analysis showed that JQ1 significantly repressed NHEJ-related genes, such as XRCC4 and LIG4. Moreover, NHEJ reporter assay revealed JQ1 diminished NHEJ activity.

Conclusions: Our data demonstrate that the combination of JQ1 and AZD1775 has a synergistic effect against NSCLC cell lines via a mechanism of compromised DNA damage repair by JQ1. This combination therapy can be a novel therapeutic strategy for NSCLC.

Citation Format: Yuta Takashima, Eiki Kikuchi, Junko Kikuchi, Tetsuaki Shoji, Megumi Furuta, Hajime Kikuchi, Jun Sakakibara-Konishi, Ichiro Kinoshita, Hirotoshi Dosaka-Akita, Masaharu Nishimura. The BET bromodomain inhibitor JQ1 synergizes with WEE1 inhibitor AZD1775 by impairing non-homologous end joining and enhancing DNA damages in non-small cell lung 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 332.
Abstract 3324: Diagnosis and prognosis of hepatocellular carcinoma with ctDNA methylation markers
Authors: Zhang Kang
Published: August 2018

Abstract

An effective blood-based method for the diagnosis and prognosis of hepatocellular carcinoma (HCC) has not yet been developed. Circulating tumor DNA (ctDNA) carrying cancer-specific genetic and epigenetic aberrations may enable a noninvasive “liquid biopsy” for diagnosis and monitoring of cancer. Here, we identified an HCC-specific methylation markers by comparing HCC tissue and normal blood leukocytes and showed that methylation profiles of HCC tumor DNA and matched plasma ctDNA are highly correlated. Using cfDNA samples from a large cohort of 1098 HCC patients and 835 normal controls, we constructed a diagnostic prediction model that showed high diagnostic specificity and sensitivity (P<0.001) and was highly correlated with tumor burden, treatment response, and stage (P<0.001). Additionally, we constructed a prognostic prediction model that effectively predicted prognosis and survival (P<0.001). Together, these findings demonstrate in a large clinical cohort the utility of ctDNA methylation markers in the diagnosis, surveillance, and prognosis of HCC.

Citation Format: Kang Zhang. Diagnosis and prognosis of hepatocellular carcinoma with ctDNA methylation markers [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 3324.
Abstract 3333: Detection of IDH1 R132H mutation in situ in human astrocytoma and glioma FFPE samples
Authors: Li Na , Wang Mindy , Sun Hongzhe , Zhang Zhifu , Wang Xin , Park Emily , Ma Xiao-Jun , Monroe Robert
Published: August 2018

IDH1 and IDH2 mutations have been shown to be early events in gliomagenesis. IDH1 mutations are present in ~33% of gliomas and constitute ~90% of all IDH mutations. Approximately 88% of IDH1 mutations involve the substitution c.395G>A leading to the R132H amino acid change. IDH1 mutations, including R132H, are important to recognize clinically as they are more frequent in younger patients and confer a survival advantage. Patients with IDH1 mutations show lower expression of the prognostic markers p53 and Ki-67 and achieve greater benefit from maximal tumor resection. In addition to their prognostic utility, IDH mutations including IDH1 R132H can be useful as diagnostic markers for low-grade gliomas. In difficult to diagnose glial lesions, the presence of IDH mutations strongly favors a diagnosis of glioma versus reactive gliosis. Although PCR and DNA sequencing-based approaches can detect the IDH1 R132H mutation, these techniques require destruction of tissue for nucleic acid isolation and destroy the morphologic context, highlighting the need for a methodology that can be performed on formalin-fixed, paraffin-embedded (FFPE) tissues. In this study, we developed an assay to specifically detect the IDH1 R132H mutation in FFPE samples in expressed IDH1 mRNA transcripts using the novel BasescopeTM technology. IDH1 wild-type (WT) and IDH1 mutation (MT) probes were tested in 6 astrocytoma and 3 glioma FFPE specimens from unique clinical cases. All samples exhibited positivity with the IDH1 WT probe. Two of six astrocytomas and one of three gliomas showed positivity with the IDH1 R132H mutation probe. Among the three positive samples, one astrocytoma exhibited positive signals for the IDH1 R132H mutation in almost all tumor cells, whereas one astrocytoma and one glioma showed only scattered positive signals with the IDH1 R132H mutation probe in a subset of tumor cells. Our findings indicate that the BasescopeTM assay is a novel RNA in situ hybridization assay to visualize point mutations in a highly specific and sensitive manner within the morphologic tissue context. In this study, we demonstrate that the BasescopeTM IDH1 R132H assay is capable of detecting the IDH1 R132H mutation in routine FFPE clinical specimens for the purpose of assisting in the diagnosis of gliomas and providing prognostic information. The BasescopeTM technology also allows for correlation of the frequency and distribution of IDH1 R132H mutations in glial tumors with patient outcomes and overall survival.

Citation Format: Na Li, Mindy Wang, Hongzhe Sun, Zhifu Zhang, Xin Wang, Emily Park, Xiao-Jun Ma, Robert Monroe. Detection of IDH1 R132H mutation in situ in human astrocytoma and glioma FFPE samples [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 3333.
Abstract 334: Detection of BRCAness by a functional biomarker
Authors: Lee Chih-Ying , Ko Min-Yu , Lei Kai-Hang , Chi Peter
Published: August 2018

Homologous recombination (HR) is an error-free repair pathway to eliminate DNA double-strand breaks and cells with deficiency of HR repair are highly sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. Thus, targeting HR-defective cells becomes a new therapeutic approach for cancer patients. HR deficiency can be identified as BRCAness which may be due to mutations or epigenetic silencing in genes involved in HR, such as BRCA1 and BRCA2. Recent studies have developed several approaches to analyze HR status of cancer cells including RAD51 focus formation assay, large-scale mutational signatures analysis, and genome-wide transcriptome profiling. However, these assays provide an indirect estimation of HR status. We wish to directly measure HR rate in cancer cells. We have successfully developed two approaches, plasmid-based and virus-based functional assays, to directly quantify HR activity in cells and serve as a functional biomarker. Our results show that the signal of the functional biomarker specifically depends on the presence of the key enzyme, RAD51 recombinase, in HR. Finally, these functional assays can be utilized in different cancer cell types to determine the HR activity and can be a functional biomarker to evaluate the “BRCAness” status for the treatment of PARP inhibitors.

Citation Format: Chih-Ying Lee, Min-Yu Ko, Kai-Hang Lei, Peter Chi. Detection of BRCAness by a functional biomarker [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 334.
Abstract 3355: Clock genes DEC1 and BMAL1 regulate the expression of stem cell marker genes Sox2 and c-Myc in cervical cancer
Authors: Sato Fuyuki , Muragaki Yasueru
Published: August 2018

It has been reported that abnormalities of clock genes are associated with tumor progression. Clock genes CLOCK, BMAL1/2, Differentiated embryonic chondrocyte gene (DEC)1/2, PER1/2/3 and CRY1/2 play important roles in the regulation of cell proliferation, cell cycle, apoptosis, epithelial to mesenchymal transition (EMT) and metastasis. We have shown that DEC1 is highly expressed in pancreatic cancer and oral cancer cells compared with non-tumor cells. However, the expression of clock genes is not well understood in cervical cancer. In this study, we focused on the expression of DEC1, DEC2 and BMAL1 in human cervical cancer tissues, examining their expression in biopsy and surgical resection samples by immunohistochemistry. As a result, DEC1 was strongly positive in tumor cells compared with adjacent non-tumor cells. Especially, the positive cells were observed in the front lesions of the tumors, suggesting that DEC1 is associated with invasion. The positive staining of vimentin was also observed in the same lesions where DEC1 was positive. On the other hand, no obvious significant difference in DEC2 expression was observed between tumor cells and non-tumor cells. For BMAL1, we found a week staining in the tumor cells compared with non-tumor cells. In addition, we examined the expression of stem cell marker Sox2 and c-Myc in cancer tissues. They were highly expressed in tumor cells compared with the adjacent non-tumor cells. Furthermore, Sox2 was expressed in metastatic lesions higher than the primary sites. These results suggest that clock genes DEC1 and BMAL1 may promote progression of cervical cancer, regulating Sox2 and c-Myc expression.

Citation Format: Fuyuki Sato, Yasueru Muragaki. Clock genes DEC1 and BMAL1 regulate the expression of stem cell marker genes Sox2 and c-Myc in cervical 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 3355.
Abstract 3363: PUM3 is a triple-negative breast cancer dependency gene that functions in replication fork restart and repair
Authors: Weekes Daniel , Noel Elodie , Walker Callum , Balan Nick , Shah Vandna , Sidhu Bhavna , Pardix Anna , Pettitt Stephen , Lord Christopher J. , Grigoriadis Anita , Andrew Tutt N.
Published: August 2018

Triple-Negative Breast Cancers (TNBC) are characterized by high levels of structural chromosome alterations and harbor mutational scars of defects in homologous recombination. Importantly, by acting either as drivers, or as tumor specific dependencies mutated genes in these regions represent potential therapeutic targets

In search of such genes we identified that knockdown of the PUM3 gene, which is contained in a 9p24 recurrent ampliicon, impaired the growth of a subset of breast cancer but not mammary epithelial cell lines. Furthermore, the growth defects observed upon PUM3 knockdown in SUM149, a BRCA1 deficient cell line, were reversed by reactivation of BRCA1's function suggesting a BRCA1-deficiency associated dependency. PUM3 knockdown led to an increase in gH2Ax and 53BP1 nuclear foci, impaired restart of stalled replication forks, and decreased RAD51 mediated repair of collapsed replication forks. As a result PUM3 depleted cells have reduced DNA replication rate and slowed cell cycle progression. Knockdown of PUM3 also impaired replication stress induced PARylation and PAR foci formation and PUM3 and PARP1 knockdown showed phenotypic epistasis with respect to cell growth suggesting a potential mechanism for PUM3s replication fork related functions.

PUM3 forms a complex with gH2Ax and the replication stalling agent hyroxyurea and PARP-inhibitors increases the nuclear concentration of PUM3. Furthermore PUM3 knockdown increased the sensitivity of breast cancer cells to these agents indicating a role for PUM3 in the repair of lesions generating by these DNA damaging agents.

By studying PUM3 we have identified a novel player in replication fork restart and repair whose activity may be particularly relevant in homologous recombination deficient TNBCs. A greater understanding of PUM3's function and the pathways that regulate it may identify novel therapeutic targets for TNBCs. Importantly, direct or indirect modulation of PUM's functions may potentiate the effects of replication stress inducing therapies such as PARP-inhibitors.

Citation Format: Daniel Weekes, Elodie Noel, Callum Walker, Nick Balan, Vandna Shah, Bhavna Sidhu, Anna Pardix, Stephen Pettitt, Christopher J. Lord, Anita Grigoriadis, Tutt N. Andrew. PUM3 is a triple-negative breast cancer dependency gene that functions in replication fork restart and repair [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 3363.
Abstract 3373: Analysis of the “centrosome-ome” reveals potential causes of centrosome amplification in human cancer
Authors: Denu Ryan A. , Jagodinsky Justin C. , Burkard Mark E.
Published: August 2018

The centrosome is the microtubule organizing center of human cells and facilitates a myriad of cellular functions. This includes the organization of the mitotic spindle for faithful chromosome segregation during mitosis, cell polarization and migration, and primary cilia formation. A numerical increase in centrosomes, or centrosome amplification (CA), is common in cancer and correlates with aggressive clinical features and poor patient outcomes. CA is thought to arise by two major mechanisms: (1) centriole overduplication and (2) cell doubling events. To better assess the relative contributions of these two mechanisms, we analyzed 79 melanomas compared to 17 benign nevi and 60 prostate cancers compared to 20 benign prostate samples. We probed these samples for pericentrin (to mark all centrosomes) and CEP170 (to mark centrosomes with mature centrioles). CEP170 is expected on most or all amplified centrosomes with cell doubling, but not with overduplication (1 per cell expected). We find fewer CEP170-positive centrosomes in cancer samples compared to benign samples, indicating that centriole overduplication is the predominant mechanism leading to CA in human cancer. Given this finding, we next sought to identify the predominant molecular mechanisms leading to centriole overduplication. To address this question, we analyzed mutations, copy number alterations, and RNA expression data in the 366 proteins reported to localize to the centrosome using TCGA data. We identified a list of candidate centrosome proteins that are most frequently altered in cancer. Furthermore, given that cells with CA undergo cell cycle arrest unless other compensatory alterations are made, such as loss of p53, we ranked alterations in centrosome genes by the fold enrichment in p53 mutant versus p53 wild-type tumors. We identified the following candidates: CEP19, CEP72, NDRG1, PTK2, SPATC1, and TBCCD1 (gain-of-function mutations) and AKAP9, CEP76, CTNNB1, MCPH1, NEURL4, and NPM1 (loss-of-function mutations or deletion). In cellulo analysis of these candidates reveals that loss of MCPH1 (microcephalin) causes the most robust increase in centriole number. MCPH1 mutations are known to give rise to microcephaly and CA. MCPH1 gene deletions and/or mRNA downregulation (Z score < 2) are seen in 5-15% of human cancers, depending on the anatomic site of the tumor. We conclude that a myriad of different alterations in centrosome genes can give rise to CA in human cancer, and that loss of MCPH1 is a common and penetrant cause of CA in human cancer.

Citation Format: Ryan A. Denu, Justin C. Jagodinsky, Mark E. Burkard. Analysis of the “centrosome-ome” reveals potential causes of centrosome amplification in human 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 3373.