bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3245: The interplay between patient´s features and mutational processes in tobacco related cancers
Authors: Lima João Paulo da Silveira Nogueira , Drummond Rodrigo Couto Duarte , Santos Monize Nakamoto Provisor , Valieris Renan , Mitrowsky Rafael Andres Rosales , Lima Vladmir Cordeiro , Nunes Diana Noronha , Dias-Neto Emmanuel , Silva Israel Tojal da
Published: August 2018

Background: There is a complex interplay between smoking and patient demographics in the emergence and development of cancer. We vetted the possible relationship between gender, race and age with mutational processes operating on aerodigestive tract cancers, known to be highly associated to tobacco. Methods: We used an empirical Bayesian approach to identify genomic patterns that lead to mutational processes in head and neck, esophageal, and lung cancers from TCGA database followed by confirmation in independent cohorts (cBioPortal). Results: After confronting clinical information and smoking-habits to molecular findings in those cancers, we identified imprints of different mutational processes in a disease-, gender- and race-specific fashion. Black and female patients - despite their lower tobacco consumption in comparison to whites or males - had tumors with the highest enrichment for tobacco-induced DNA damage. The relevance of mutational signatures related to aging varied across race and gender and were independent from chronological age. The activity of smoking signature was different according to disease histotype, and stage. tumors of never-smoker lung cancer patients showed tobacco-specific mutational signatures, which could suggest the influence of second-hand smoking. Patients with tumors enriched for the smoking mutational signature presented longer survival, whereas those with ageing-enriched signature had poorer prognosis. Conclusions: Mutational processes may unravel connections between patient features and tumorigenesis, particular to race, gender, and tumor type. Therefore, it is paramount to assess those details with greater granularity in every effort of personalized medicine either in preventive or therapeutic approaches.

Citation Format: João Paulo da Silveira Nogueira Lima, Rodrigo Couto Duarte Drummond, Monize Nakamoto Provisor Santos, Renan Valieris, Rafael Andres Rosales Mitrowsky, Vladmir Cordeiro Lima, Diana Noronha Nunes, Emmanuel Dias-Neto, Israel Tojal da Silva. The interplay between patient´s features and mutational processes in tobacco related 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 3245.
Abstract 3269: Metformin to prevent metabolic syndrome associated with androgen deprivation therapy (ADT): Metabolic analysis from a placebo-controlled study of metformin in non-diabetic men initiating ADT for advanced prostate cancer (PCa)
Authors: Mahalingam Devalingam , Hanni Salih , Fountzilas Christos , Michalek Joel , Sarantopoulos John , Pillai Sureshkumar Mulampurath Achuthan , Kuhn John , Pollak Michael , Thompson Ian
Published: August 2018

Background: ADT results in metabolic syndrome, characterized by hyperinsulinemia, insulin resistance and obesity. The hyperinsulinemia may result in ADT resistance; therefore preventing metabolic syndrome could have a therapeutic impact on PCa. Metformin decreases glucose & insulin by inhibiting hepatic gluconeogenesis. There is preclinical evidence for additional antineoplastic activity due to mTOR inhibition secondary to AMPK activation. Methods: We analyzed serum and PBMC from a recently completed clinical study of men with advanced PCa on ADT that were randomized 1:1 to metformin at 500mg TID or color matched placebo. Subjects serum insulin/glucose, metformin levels, weight and waist circumference (WC) was assessed at baseline, week 12 and 28. The primary endpoint of study was the metabolic consequences of metformin vs placebo cohort. Secondary endpoints were PSA response and PBMC analysis of downstream target of mTOR, phospho-S6 kinase. Results: There were 36 evaluable men. The mean age on study was 68.4. Mean weight, WC and insulin at baseline in metformin cohort was 187 lbs, 41.14 cm and 10.03 mIU/L respectively, and 177.65 lbs, 40.52 cm and 8.02 mIU/L in placebo cohort. An increase in mean weight, WC and insulin levels was seen in both cohorts. At week 12 and 28, no statistical difference in weight, WC and insulin was observe in either cohort. Four men randomized to metformin had undetectable serum drug levels despite drug-diary suggesting compliance; excluding them did not result in significant metabolic change. Assessing efficacy, 50% in metformin and 53.3% in placebo cohort achieved undetectable PSA at week 28; difference not statistically significant. PBMC analysis demonstrated variable down-regulation of phospho-S6 kinase in the metformin cohort. Conclusion: This study detected no impact of MET addition to ADT on the risk of metabolic syndrome and no additional anti-tumor effects. Control of hyperinsulinemia related to diabetes by MET does not necessarily imply MET has a similar action on hyperinsulinemia due to ADT.

Citation Format: Devalingam Mahalingam, Salih Hanni, Christos Fountzilas, Joel Michalek, John Sarantopoulos, Sureshkumar Mulampurath Achuthan Pillai, John Kuhn, Michael Pollak, Ian Thompson. Metformin to prevent metabolic syndrome associated with androgen deprivation therapy (ADT): Metabolic analysis from a placebo-controlled study of metformin in non-diabetic men initiating ADT for advanced prostate cancer (PCa) [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 3269.
Abstract 3269A: 2-Hydroxyflavanone: A novel estrogen receptor alpha downregulator with potent antitumor effect in breast cancer
Authors: Singhal Sharad S. , Chikara Shireen , Nagaprashantha Lokesh , Singhal Jyotsana , Horne David , Awasthi Sanjay
Published: August 2018

Breast cancer (BC) remains one of the major causes of cancer deaths in women. 2Hydroxyflavanone (2HF), a constituent of citrus fruits, inhibits growth of human breast cancer cell lines in culture. The present study was undertaken to determine in vivo efficacy of 2HF against MDAMB231 human breast cancer xenografts. The 2HF administration retarded growth of MDAMB231 cells subcutaneously implanted in female nude mice without causing weight loss or any other side effects. The 2HF mediated suppression of MDAMB231 xenograft growth correlated with reduced cell proliferation as revealed by immunohistochemical analysis for Ki67 expression. Analysis of the vasculature in the tumors from 2HF treated mice indicated smaller vessel area compared with control tumors based on immunohistochemistry for angiogenesis marker CD31. The 2HF mediated inhibition of angiogenesis in vivo correlated with downregulation of vascular endothelial growth factor (VEGF) level in the tumor. Consistent with these results, 2HF treatment suppressed cell cycle regulators levels in cultured MDAMB231 cells. Moreover, the 2HF treated MDAMB231 cells exhibited reduced capacity for migration compared with vehicle-treated control cells. In addition, 2HF administration elicits apoptotic response as judged by annexin V and PI staining and TUNEL assay. 2HF treatment reduced the levels of ER alpha in ER positive MCF7 breast cancer cells. In conclusion, the present study demonstrates in vivo anticancer efficacy of 2HF against MDAMB231 xenografts in association with reduced cell proliferation and suppression of neovascularization. Our results indicate that 2HF is a promising anticancer agent for breast cancer due to its ability to collectively inhibit major regulators of breast cancer including RLIP76, ER alpha, and HER2. Interestingly, a spontaneously immortalized non-tumorigenic normal human mammary epithelial cell line (MCF10A) is significantly more resistant to 2HF mediated apoptosis compared with breast cancer cells, demonstrating selectivity of 2HF towards malignant breast cells. These preclinical observations merit clinical investigation to determine efficacy of 2HF against human breast cancers. (This work was supported in part by the Department of Defense grant W81XWH 16 1 0641. Funding from the Beckman Research Institute of City of Hope is also acknowledged).

Citation Format: Sharad S. Singhal, Shireen Chikara, Lokesh Nagaprashantha, Jyotsana Singhal, David Horne, Sanjay Awasthi. 2-Hydroxyflavanone: A novel estrogen receptor alpha downregulator with potent antitumor effect in breast 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 3269A.
Abstract 3283: NDEx, the Network Data Exchange: Collaboration, publication and data sharing for cancer pathways
Authors: Pratt Dexter R.
Published: August 2018

Computable network models of pathway mechanisms, molecular interactions, and cellular function are widely developed and used in cancer genome analysis. Dissemination and reuse of networks, however, needs common data standards, facile access by visualization and analysis applications, mechanisms for pre-publication collaboration, and integration with the publishing process. We present NDEx, the Network Data Exchange, an online resource (www.ndexbio.org) that addresses these needs by providing a framework in which users can store, share, access, and disseminate networks. These networks can range from small pathways to large interaction data or to hierarchical cell models. NDEx is user-driven, where every researcher can be an author, easily creating publicly available network resources with full control of the data content and organization. Networks can range from standard resources disseminated by organizations to novel, up-to-date content from individual scientists. Collaborators can privately share their networks for review and reference or for integration in analysis workflows across multiple scripts and applications. Access to NDEx by an extensive API and client libraries supports network-enabled application development. Published networks can go beyond diagrams and static supplemental data, becoming immediately accessible and interactive. Integration with academic publishing is underway, facilitated by features such as anonymous access by reviewers and minting of DOIs for networks. NDEx breaks down barriers to scientific discourse involving networks, fostering collaboration within and between communities.

Citation Format: Dexter R. Pratt. NDEx, the Network Data Exchange: Collaboration, publication and data sharing for cancer pathways [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 3283.
Abstract 3292: Revisiting TCGA data identifies key genes in lung adenocarcinoma
Authors: Shi Jianxiang , Xing Mengtao , Luo Chenglin , Wang Xiao , Dai Liping , Zhang Jianying
Published: August 2018

Although the incidence rate of lung cancer has declined over the past few years, it remains the leading cause of cancer death worldwide. The Cancer Genome Atlas has provided invaluable resources for cancer research. The development of next generation sequencing technology and evolution of data analysis tools make it possible to interpret the underlying mechanism of oncogenesis. In current study, normalized FPKM data from 572 samples derived from patients with lung adenocarcinoma (LUAD) from TCGA was used to do weighted gene co-expression network analysis (WGCNA) to identify gene modules associated with lung adenocarcinoma. Raw counts data was used to identify differentially expressed genes in LUAD by using DESeq2 in R (version 3.4.2). WGCNA results shows that magenta (r = 0.47, p <0.001)), black (r = 0.40, p <0.001)) and yellow (r = -0.88, p <0.001) modules are top 3 modules that associated with LUAD and cancer stage. Gene Ontology over-representation analysis shows that genes in magenta modules are involved with transcript elongation; genes in black modules are enriched in cell meiosis related biological processes, including chromosome segregation, nuclear division, DNA replication and mitotic nuclear division et al; genes in yellow module are enriched in angiogenesis, leukocyte migration and hemostasis. It is noteworthy that genes in magenta and black modules are upregulated and in yellow modules are downregulated. GOLM1 and MUC4 in magenta module play certain roles in cancer development. Several genes in MEGA family, including MAGEA3, MAGEA6, MEGEA16 and MEGEA1, and IGF2BP1 in black module have been reported to be overexpressed in various kinds of tumors. However, whether these in silicon discovered genes can be used to distinguish LUAD from controls still needs to be further evaluated.

Keywords: lung adenocarcinoma; TCGA; gene expression analysis; bioinformatics; cancer biomarker

Citation Format: Jianxiang Shi, Mengtao Xing, Chenglin Luo, Xiao Wang, Liping Dai, Jianying Zhang. Revisiting TCGA data identifies key genes in 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 3292.
Abstract 330: BRCA1 and BLM helicase compensate for replication fork defects in the absence of 53BP1 protein
Authors: Sybouts Erin H. , Tonapi Sonal S. , Bishop Alexander J.
Published: August 2018

53BP1 is well-known for its involvement in DNA double strand break (DSB) repair, binding DNA and influencing choice of DSB repair. In S/G2 phases of the cell cycle, 53BP1 accumulates at DSBs, but can be removed by BRCA1, allowing end-resection and homology-directed repair (HDR) to occur. Without BRCA1, HDR is defective unless 53BP1 is also lost, in which case HDR can proceed. Such secondary mutation is relevant as a mechanism of acquired chemoresistance in BRCA1 deficient tumors. BRCA1 is also important for maintaining replication fork stability, particular for blocking end resection by MRE11a at a collapsed fork. We therefore set out to ask whether 53BP1 also plays a role in maintenance of fork stability and how this role relates to the role of BRCA1 at a collapsed fork. 53BP1 has been indicated to co-localize with collapsed forks and indeed we find that in its absence fork stability is compromised in a DNA2, but not MRE11a, dependent manner. With decreased fork stability in the absence of 53BP1 we observe increased HDR, indicating a role for BRCA1 to compensate for the lack of 53BP1 by promoting HDR. However, if both 53BP1 and BRCA1 are both necessary for fork stability, then there must be additional compensating mechanisms providing fork stability when both are absent. In fact, absence of both 53BP1 and BRCA1 results in better replication progression than when either 53BP1 or BRCA1 alone are absent. A third mechanism of fork stabilization was identified involving BLM; a RecQ helicase involved in dissolving homologous recombination intermediates, can facilitate fork restart and reverse fork regression. Additionally, BLM has been shown to interact with both 53BP1 and BRCA1, is found at stalled replication forks, and promotes BRCA1 recruitment to sites of DNA damage. Targeting BLM in cells with impaired 53BP1 and BRCA1 increases chemosensitivity to DNA damaging agents, supporting the redundant nature of these three proteins at stalled replication forks. Our findings indicate that targeting BLM may be an effective treatment for HDR defective cancers that have developed chemoresistance; with applicability to BRCA1 and homologous recombination deficient cancers, such as breast, ovarian, and Ewing sarcoma.

Citation Format: Erin H. Sybouts, Sonal S. Tonapi, Alexander J. Bishop. BRCA1 and BLM helicase compensate for replication fork defects in the absence of 53BP1 protein [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 330.
Abstract 3300: Network analysis of the human protein-protein interactome: Tumorigenic signaling mechanisms
Authors: Murray Diana , Begum Kamrun N. , Califano Andrea , Honig Barry
Published: August 2018

The dysregulated signaling responsible for tumor cell state implementation and maintenance has been shown to be mediated by the concerted action of master regulator (MR) proteins. Highly connected MR protein modules serve as “tumor checkpoints” by translating upstream genetic alterations into aberrant protein activity that drives pathophysiological cellular phenotypes. Direct pathways for information flow among MR proteins, and between individual MR proteins and their upstream modulators and downstream effectors, are largely unknown. The Prediction of Protein-Protein Interactions (PrePPI) database contains 1.4M predictions for ~85% of the human proteome; of these, ~300K are predicted to be physical, i.e. direct one-to-one, interactions.We apply network analysis concepts, as implemented in the R package igraph, to the PrePPI interactome to predict structural mechanisms underlying tumorigenic signal transduction. Shortest path and random walk with restart algorithms elucidate 1) physical interactions between MR proteins, 2) physical interactions that connect MR proteins that do not directly bind to each other, 3) upstream signaling proteins with recurrent and patient-specific mutations that physically interact with MR proteins, and 4) downstream cofactors and transcription factors that may be involved in effecting a dysregulated phenotype.Our analysis predicts that physical interactions fully connect BACH2, BCL6, IRF8, and SPIB, established germinal center MR proteins. 1) BACH2 and BCL6 are predicted to interact directly through their BTB/POZ domains; BTB domains are known to mediate heterodimeric protein-protein interactions. 2) Additional proteins, including IBTK, ANFY1, PAX7, ZEB1, GABPB1/B2, connect SPIB to BACH2 and to BCL6, in some cases through ankyrin repeats, which are structural protein-protein interaction motifs. Several of the PrePPI-predicted proteins, e.g. IBTK, ZEB1, GABP, have previously been implicated in B-cell biology. The possible implications of our analyses for a wide range of MR proteins modules will be presented.The computational prediction of physical protein-protein interactions within the regulatory architecture of a tumor cell is a powerful approach to discovering novel tumorigenic signaling mechanisms, formulating specific experimentally testable hypotheses of function, including compound mechanisms of action, and prioritizing novel drug targets.

Citation Format: Diana Murray, Kamrun N. Begum, Andrea Califano, Barry Honig. Network analysis of the human protein-protein interactome: Tumorigenic signaling mechanisms [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 3300.
Abstract 331: Therapeutic co-targeting of WEE1 and ATM has synergistic effects and contributes to downregulation of PD-L1 expression in pancreatic cancer
Authors: Jin Meihua , Nam Ah-Rong , Park Ji Eun , Bang Ju Hee , Bang Yung-Jue , Oh Do-Youn
Published: August 2018

Background: Currently, targeting DNA damage response (DDR) is one of strategies for new cancer drug development. DDR pathway involves DNA damage repair, cell cycle progression, apoptosis, and regulate the immune system. In pancreatic cancer (PC), one of the most fatal disease, TP53 mutation was found in approximately 78% of cases and BRCA pathway alteration including BRCA1, BRCA2, the ataxia telangiectasia mutated (ATM) and PALB2 was observed in 5% (germline) and 12% (somatic) of patients. The purpose of this study is to evaluate the DDR-targeting strategy using Wee1 inhibitor and ATM inhibitor in PC.

Methods: Using a total of 11 kinds of PC cell lines (AsPC-1, Capan-1, Capan-2, MIA PaCa-2, PANC-1, SNU213, SNU324, SNU410, SNU2822, SNU2913, and SNU2918), AZD1775 (Wee1 inhibitor) and AZD0156 (ATM inhibitor) were tested.

Results: AZD1775 significantly inhibited cell proliferation in all of the PC cell lines. AZD1775 monotherapy induced apoptosis and S phase arrest, and decreased Wee1/ p-wee1/ p-CDC2 expression. An increase of rH2AX and caspase-7 cleavage were occurred by AZD1775. When the cells were treated with AZD1775, upregulation of p-ATM was observed.

The combination of AZD1775 and AZD0156, the synergism was found. P-wee1 and p-CDC2 were downregulated more obviously in co-treated cells compared with monotherapy.

In some cells, PD-L1 was increased after AZD1775 treatment. Interestingly the combination of AZD1775 and AZD0156 synergistically reduced PD-L1 protein level in the cancer cells, especially in SNU213 and SNU2913 cells.

Conclusion: Therapeutic WEE1 and ATM co-targeting strategy demonstrated promising anti-cancer effect in pancreatic cancer cells. Moreover, this co-treatment blocked PD-L1 expression. Taken together, this supports further clinical development of DDR targeting strategy in pancreatic cancer.

Citation Format: Meihua Jin, Ah-Rong Nam, Ji Eun Park, Ju Hee Bang, Yung-Jue Bang, Do-Youn Oh. Therapeutic co-targeting of WEE1 and ATM has synergistic effects and contributes to downregulation of PD-L1 expression in pancreatic 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 331.
Abstract 3317: Genes encoding neuropeptide receptors are epigenetic markers in patients with head and neck cancer: A site-specific analysis
Authors: Mochizuki Daiki , Misawa Kiyoshi , Imai Atsushi , Kanazawa Takeharu , Mineta Hiroyuki
Published: August 2018

Staging and pathological grading systems are useful but imperfect predictors of recurrence in head and neck squamous cell carcinoma (HNSCC). The aim of this study was to determine the methylation status of eight GPCR-encoding genes in HNSCCs and its relationship to recurrence, survival, and clinical characteristics (e.g., tumor location and lymph node metastasis). All eight genes (NPFFR1, NPFFR2, HCRTR1, HCRTR2, NPY1R, NPY2R, NPY4R, and NPY5R) encode neuropeptide receptors and are in the Class A β subgroup. This study is the first to implicate neuropeptide receptors in the genesis of HNSCC. To identify potential prognostic markers, we examined the methylation status of eight neuropeptide receptor gene promoters in 231 head and neck squamous cell carcinomas. The NPFFR1, NPFFR2, HCRTR1, HCRTR2, NPY1R, NPY2R, NPY4R, and NPY5R promoters were methylated in 80.5%, 79.2%, 67.1%, 73.2%, 35.1%, 36.4%, 38.5%, and 35.9% of the samples, respectively. In a multivariate Cox proportional hazards analysis, the odds ratio for recurrence was 2.044 (95% confidence interval [CI], 1.323-3.156; P = 0.001) when the NPY2R promoter was methylated. In patients without lymph node metastasis (n = 100), methylation of NPY2R (compared with methylation of the other seven genes) best correlated with poor disease-free survival (DFS) (odds ratio, 2.492; 95% CI, 1.190-5.215; P = 0.015). In patients with oral cancer (n = 69), methylated NPY1R and NPY2R were independent prognostic factors for poor DFS, both individually and, even more so, in combination (odds ratio, 3.90; 95% CI, 1.523-9.991; P = 0.005). Similar findings were observed for NPY2R and NPY4R in patients with oropharyngeal cancer (n = 162) (odds ratio, 5.663; 95% CI, 1.507- 21.28; P = 0.010). The present study suggests that the methylation status of the NPY1R, NPY2R, and NPY4R genes is an independent indicator of DFS in patients with oral and/or oropharyngeal cancers. Our findings support the use of methylation markers in patient selection for adjuvant therapy after initial surgical treatment and may aid oropharyngeal cancer screening and surveillance programs. However, they are preliminary and hence need to be validated in larger and more homogeneous HNSCC patient cohorts.

Citation Format: Daiki Mochizuki, Kiyoshi Misawa, Atsushi Imai, Takeharu Kanazawa, Hiroyuki Mineta. Genes encoding neuropeptide receptors are epigenetic markers in patients with head and neck cancer: A site-specific 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 3317.
Abstract 3327: Correlating blood-based DNA methylation markers and prostate cancer risk factors in African-American men
Authors: Kwabi-Addo Bernard , Moses-Fynn Emmauel , Tang Wei , Beyene Desta , Apprey Victor , Kanaan Yasmine
Published: August 2018

Background: Detection of prostate cancer at an early stage is key for successful treatment and improvement of outcome. However, the limitations of PSA screening are well recognized and therefore novel approaches to prostate cancer screening are necessary. We have investigated the clinical significance of DNA methylation in the blood serum of African-American men with prostate cancer.

Method: We used pyrosequencing to examine the promoter methylation for a panel of 8 genes in blood samples extracted from 91 prostate cancer cases and 91 noncancerous control cases.

Results: Seven of the 8-gene panel–RARβ2, TIMP3, SPARC, CDH13, LINE1, CYB5R2 and DRD2–tested achieved significant difference between the cancer cases when compared to control cases. The RARβ2 and TIMP3 demonstrated significant association of DNA methylation with age for all cases analyzed. Associations of methylation status and various clinicopathologic features and patient survival were evaluated: we observed significant inverse association of serum vitamin D levels in the cancer cases and DNA methylation of CDH13 and also an inverse correlation between TIMP3 and DRD2 methylation with supplementary vitamin D in the cancer cases. On the other hand, we observed a direct correlation between HIN1 methylation and serum vitamin D level. In addition, we observed a direct correlation between RARβ2 and Sparc methylation with PSA level in the control but not the cancer cases.

Conclusion: Promoter methylation occurred more frequently in the serum of patients with prostate cancer than noncancerous cases, suggesting that epigenetic markers in serum have potential for diagnosis of prostate cancer in AA men.

Citation Format: Bernard Kwabi-Addo, Emmauel Moses-Fynn, Wei Tang, Desta Beyene, Victor Apprey, Yasmine Kanaan. Correlating blood-based DNA methylation markers and prostate cancer risk factors in African-American men [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 3327.
Abstract 3329: A newly developed Septin9 gene methylation assay dectecting double DNA strands for screening of colorectal cancer
Authors: Liang Qiuju , Huang Zhengbin , Xu Qingwen , Xu Feipeng , Huang Wenwei , Xie Wenfang , Zeng Lei , Liu Jiasu , Yu De-Hua
Published: August 2018

Colorectal cancer (CRC) is one of the most common malignant tumors and places an enormous burden on society. The US FDA approved the application of Epi proColon on 12 April 2016, and permitted the application of the Septin9 gene methylation assay as a CRC screening test for average-risk population over 50 years old. The effectiveness of methylated Septin9 for CRC detection has been reviewed in the newly published recommendation statement by US Preventive Services Task Force (USPSTF). The Septin9 gene methylation assay is more cost efficient with higher compliance than the stool DNA test, and has been proven to be an accurate, reliable, fast, and convenient molecular test. However, the currently FDA approved Epi proColon assay needs to perform triplicated PCR reactions for each sample which leads to high cost. In order to improve the sensitivity and specificity, simplify the operational procesure, and reduce cost, we have developed an new Septin9 gene methylation assay in which the specific sequences of both methylated DNA strands and control gene could be amplificated and detected in one reaction. We evaluated sensitivity, specificity, and clinical performance using plasma samples from colonoscopy negative individuals and CRC patients. The preliminary data showed that the sensitivity and specificity for CRC detection was 77.4%(41/53) ,97.8%(90/92) respectively. A large scale clinical study with more than 1000 subjects is currently in progress. In conclusion, we have developed a new Septin9 gene methylation assay detecting double DNA strands, which demonstrated improved performance for early detection of CRC in clinical setting.

Citation Format: Qiuju Liang, Zhengbin Huang, Qingwen Xu, Feipeng Xu, Wenwei Huang, Wenfang Xie, Lei Zeng, Jiasu Liu, De-Hua Yu. A newly developed Septin9 gene methylation assay dectecting double DNA strands for screening of colorectal 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 3329.
Abstract 3374: CRISPR/Cas9 mediated genome editing induces exon skipping by alternative splicing or exon deletion
Authors: Mou Haiwei , Smith Jordan , Peng Lingtao , Yin Hao , Moore Jill , Zhang Xiao-Ou , Song Chunqing , Sheel Ankur , Wu Qiongqiong , Ozata Deniz , Li Yingxiang , Anderson Daniel , Emerson Charles , Moore Melissa , Weng Zhiping , Xue Wen
Published: August 2018

CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exons. For example, CRISPR-mediated editing of β-catenin exon 3, which encodes an autoinhibitory domain, induces partial skipping of the in-frame exon and nuclear accumulation of β-catenin. A single sgRNA can induce small insertions or deletions that partially alter splicing or unexpected larger deletions that remove exons. Exon skipping adds to the unexpected outcomes that must be accounted for, and perhaps taken advantage of, in CRISPR experiments.

Citation Format: Haiwei Mou, Jordan Smith, Lingtao Peng, Hao Yin, Jill Moore, Xiao-Ou Zhang, Chunqing Song, Ankur Sheel, Qiongqiong Wu, Deniz Ozata, Yingxiang Li, Daniel Anderson, Charles Emerson, Melissa Moore, Zhiping Weng, Wen Xue. CRISPR/Cas9 mediated genome editing induces exon skipping by alternative splicing or exon deletion [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 3374.
Abstract 3386: The oncogenic role of CD133 in hepatocellular carcinoma
Authors: Ching Yick Pang , Chan Wing Lim
Published: August 2018

Liver cancer (hepatocellular carcinoma, HCC) is one of the most prevalent malignancies worldwide. Because of the late diagnosis of the disease, the prognosis of HCC patient is often undesirable. Cancer Stem Cell (CSC), which represents a subpopulation of cancer cells with stem-like properties, plays a critical role in tumorigenesis and contributes significantly to the relapse and chemo-drug resistance of cancers. The cell surface marker, CD133/Prominin-1, has been identified as a biomarker for CSC in various cancers, including HCC. To understand the role of CD133 in hepatocarcinogenesis, we expressed CD133 in HCC cells and showed that CD133 significantly promoted cell growth. Interestingly, our data also indicated that expression of CD133 led to chromosomal instability indicated by elevation of aneuploidy population and centrosome numbers in CD133 expressing cells. To understand the molecular mechanism, we observed that a putative tumour suppressor in HCC, called TAX1-binding protein 2 (TAX1BP2), which functions as a centrosome over-duplication suppresser, was downregulated by CD133. Taken together, these data suggest that CD133 plays an oncogenic role in HCC and may downregulate TAX1BP2 to promote chromosome instability, centrosome duplication and hepatocarcinogenesis.

Citation Format: Yick Pang Ching, Wing Lim Chan. The oncogenic role of CD133 in hepatocellular carcinoma [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 3386.
Abstract 3390: Comprehensive analysis of tumor immunity by integrating transcriptome and methylome
Authors: Wang Xuefeng , Liang Cong
Published: August 2018

Immunotherapy has produced promising results in treating cancers. Further understanding of the crosstalk between tumor and its immune microenvironment is likely to have an immediate impact on therapeutic intervention as well as the development of markers of drug resistance. One main difficulty in quantifying the components of tumor microenvironment is that currently there are considerable technological and analytical barriers to assessing and measuring tumor immunity in situ. In this work, we propose to improve the prediction of cell mixtures by both gene expression and epigenetic information. The vast amount of DNA methylation data has been collected in public domain but remains under-analyzed and largely disconnected. No studies have yet investigated the value of using existing methylation panels for immune cell deconvolution in tumor tissues. In our preliminary data, we have observed a strong association between DNA methylation probes and immune signatures such as total TCR expression and tumor infiltrates estimation in melanoma and breast cancer. We have built a more rigorous prediction model based on methylation markers and to extend the analyses to all major cancer types. The results will be externally validated with pooled data from published studies with eligible methylation assay and immune signature measurements. We work closely with immunology scientists to perform a critical evaluation of the robustness and reproducibility of the predictive models. Results of the study, if validated, will have immediate clinical application in screening patient immunity, and will further support the hypothesis that the DNA methylome adds a new dimension to the pan-omic snapshot of cancer immunity and tumor microenvironment. Based on the proposed analytical framework, future prospective studies can be developed using newer methylation platforms—to compare patient groups with different immune conditions and patients in different stages of treatment.

Citation Format: Xuefeng Wang, Cong Liang. Comprehensive analysis of tumor immunity by integrating transcriptome and methylome [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 3390.
Abstract 3391: Comparison of gene copy number variations (CNV) in primary and metastatic lung cancers
Authors: Shi Yunfei , Mao Naiquan , Ding Xiao , Guo Jianji , Guo Gang , Chen Zheng , Gu Weiguang , Dai Lei , Wen Shiwang , Jia Hui , Tian Ziqiang , Shi Junping , Guo Taiyan , Yao Jicheng , Pang Fei , Chirn Gungwei , Yao Ming
Published: August 2018

Background: Characterization of genomic alterations that drive patient disease development is critical in cancer management. The genomic alteration and population characteristics between the primary tumors and metastases in patients with non-small cell lung cancer (NSCLC) is still unclear. Here we evaluated the frequency and distribution of all classes of genomic alterations in both primary and metastatic NSCLC by comprehensive genomic profiling approach.

Methods: FFPE tumor and matched blood samples of 1135 Chinese NSCLC patients (female:male is 670: 465), including 954 primary tumors and 181 metastases, were collected for next-generation sequencing (NGS) based panel assay. Gene copy number variations (CNV) including gene amplifications and deletions, short variants, and gene fusions were assessed.

Results: On average, 0.65 gene copy number variations were detected in the 181 metastatic lesions, which is higher than 0.43 CNVs per sample in the primary lesions (p value is 0.003). No significant difference was found in short variants (2.48 vs 2.31), fusions (0.27 vs 0.20) and germline mutations (0.26 vs 0.31) between the primary and metastatic NSCLC. In the top-ranked genes with copy number alterations, EGFR amplifications were detected in 11% of the primary and 15% in metastases. MET amplifications, CDKN2A/B deletions, and PMS2 deletions were more frequently found in metastatic lesions: MET (7.7% vs 1.7%, p=0.0001), CDKN2A (5.5% vs 1.5%, p=0.002), CDKN2B (5.0% vs 1.9%, p=0.0007), and PMS2 (3.9% vs 1.2%, p=0.016).

Conclusions: Copy number variations are common driver mutations in NSCLC. We reported here that the prevalence of copy number variations between primary and metastatic lung cancers was different, including driver genes MET, CDKN2A/B, and PMS2. No difference was observed in terms of frequency on short variants or gene fusions in NSCLC.

Citation Format: Yunfei Shi, Naiquan Mao, Xiao Ding, Jianji Guo, Gang Guo, Zheng Chen, Weiguang Gu, Lei Dai, Shiwang Wen, Hui Jia, Ziqiang Tian, Junping Shi, Taiyan Guo, Jicheng Yao, Fei Pang, Gungwei Chirn, Ming Yao. Comparison of gene copy number variations (CNV) in primary and metastatic lung 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 3391.
Abstract 3458: Neurotensin increases breast cancer proliferation through activation of AMPK
Authors: Johnson Jeremy , Li Jing , Evers B. Mark
Published: August 2018

Introduction. Neurotensin (NT), a thirteen amino acid peptide predominantly localized to enteroendocrine cells of the small intestine, is released after fat ingestion. While its major role involves regulating lipid metabolism and storage, NT, acting through its high-affinity receptor (NTR1), stimulates the growth and progression of a variety of NTR1-positive cancers. Proneurotensin—a stable precursor produced in equimolar amounts as NT—has been associated with breast cancer development in women, and prior work has implicated the NT/NTR1 axis in breast cancer progression; however, very little is known about the underlying NT signaling pathways that stimulate breast cancer growth. The purpose of this study is to elucidate mechanisms by which NT leads to increased proliferation and aggression of breast cancer—with particular emphasis placed on the role of AMP-activated protein kinase (AMPK). Methods. MCF-7 (estrogen-dependent) and MDA-MB-231 (triple negative) are breast cancer cell lines that express NTR1. (i) Proliferation assays were performed by treating both cell lines with NT (0 or 100 nM) in serum-free media for 24, 48, and 72 h and then counting the viable cells. (ii) Next, to assess signaling pathways mediating the effects of NT, both cell lines were treated with NT (0 or 100 nM) in serum-free media for 15 min, 30 min, 1 h, 6 h, 12 h, and 24 h; immunoblotting was performed for phosphorylated and total forms of AMPK and its downstream effector acetyl CoA carboxylase (ACC). Results. (i) Increased proliferation of MCF-7 cells treated with NT (100 nM) was observed after serum-starvation for 48 h. While MDA-MB-231 cells treated with NT demonstrated improved survival after serum-starvation for 48 h, the effects were not significantly different. (ii) NT induced activation of AMPK and ACC in MCF-7 cells after treatment for 6 and 12 h, but these effects were not observed in MDA-MB-231 cells. Conclusions. Our findings suggest a possible linkage between NT and increased proliferation of estrogen-dependent breast cancer cells through activation of AMPK and its downstream effector proteins. These effects were minimal in NTR1-expressing triple negative breast cancer cells, suggesting that the molecular classification of the tumor plays an important role in NT signaling and downstream effects. Further delineation of the differential effects of NT in specific breast cancer phenotypes has the potential to identify novel therapeutic targets in the treatment of this disease.

Citation Format: Jeremy Johnson, Jing Li, B. Mark Evers. Neurotensin increases breast cancer proliferation through activation of AMPK [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 3458.
Abstract 3493: Promoting role of AKR1B10 in HER2+ breast cancer at early stage
Authors: Khoshaba Ramina , Cao Deliang
Published: August 2018

Background:

Breast cancer is the second most common cause of female cancer-related death in the United States. Aldo-keto reductase 1B10 (AKR1B10) is a 35-kDa protein that is highly expressed in breast cancer in infiltrative and Ductal Carcinoma in Situ (DCIS) stages. Human epidermal growth factor receptor2 (HER2) is a tyrosine kinase receptor which is highly expressed in 15-20% of infiltrative breast cancer but over 60-70 % in DCIS.

Methods:

We targeted AKR1B10 and HER2 expression using AKR1B10 and HER2 expression lentiviruses in a panel of breast cancer cell lines that have different endogenous expression status of AKR1B10 or HER2, including MCF-7(AKR1B10-/HER2 low), ZR-75-1(AKR1B10-/HER2+), MDA-MB-468 (AKR1B10+/HER2-) and the normal human mammary cells MCF10A (AKR1B10-/HER2-). We investigated the effects of AKR1B10 or HER2 expression on cell proliferation, clonogenicity, adhesion, migration, and invasion. Western blots were performed to check integrin α5, δ-catenin expression and the phosphorylation of signaling proteins in Raf/MEK/ERK and AKT/P-mTOR pathways.

Results:

Our data showed that AKR1B10 promoted the proliferation of HER2+ human breast cancer cell. The results of colony forming and soft agar assays demonstrated that AKR1B10 stimulated clonogenic efficiency of HER2+ cells. Also, AKR1B10 promoted HER2+ cells adhesion to extracellular matrix, facilitated their migration and significantly increased their invasion capability. Moreover, it upregulated integrin α5, δ-catenin expression, and promoted HER2+ cells growth and invasiveness through the activation of AKT/mTOR and Raf/MEK/ERK pathways

Conclusion:

AKR1B10 promotes HER2+ human breast cancer cell proliferation and invasiveness.

Citation Format: Ramina Khoshaba, Deliang Cao. Promoting role of AKR1B10 in HER2+ breast cancer at early stage [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 3493.
Abstract 3497: Fibroblast growth factor receptor 3 (FGFR3) aberrations in muscle-invasive urothelial carcinoma
Authors: Kim Young Saing , Lee Soon Il , Park Se Hoon
Published: August 2018

Purpose: Muscle-invasive urothelial carcinoma (UC) has a poor prognosis and novel approaches to systemic therapy are required. Recent studies show that FGFR3 activation is an important contributor to tumor development and angiogenesis in UC. Therefore, FGFR3 is a potential therapeutic target in UC. The purpose of this study was to evaluate the rates and types of FGFR3 aberrations in invasive UC.

Methods: We analyzed primary tumor samples from 74 UC patients who had received radical cystectomy (n=40) or ureteronephrectomy (n=34). Ion AmpliSeq Cancer Hotspot Panel v2 and nCounter Copy Number Variation Assay were used to detect FGFR3 aberrations.

Results: Fifty-four patients (73%) had high-grade tumors, and 62% had lymph node involvement. Sixteen patients (22%) harbored FGFR3 alterations, the most common of which was FGFR3 mutations (n=13). These mutations included Y373C (n=3), N532D (n=3), R248C (n=2), S249C (n=2), G370C (n=1), A797P (n=1), and 746_747insG (n=1). In all three patients with FGFR3 rearrangement, the fusion partner was TACC3. The frequency of FGFR3 aberrations was higher in bladder UC (28%) than in UC of the renal pelvis and ureter (15%), but the difference was not statistically significant (P=0.183). Genes that were co-aberrant with FGFR3 included APC (88%), PDGFRA (81%), RET (69%), and TP53 (69%).

Conclusions: FGFR3 abnormalities are less frequently seen in upper tract UC than bladder UC. Patient selection could be critical in designing new approaches for anti-FGFR3 therapy in the perioperative setting.

Citation Format: Young Saing Kim, Soon Il Lee, Se Hoon Park. Fibroblast growth factor receptor 3 (FGFR3) aberrations in muscle-invasive urothelial carcinoma [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 3497.
Abstract 350: Che-1/aatf-induced transcriptionally active chromatin promotes cell growth in multiple myeloma
Authors: Bruno Tiziana , Nicola Francesca De , Goeman Frauke , Pallocca Matteo , Sorino Cristina , Catena Valeria , Bossi Gianluca , Amadio Bruno , Cigliana Giovanni , Spugnini Enrico , Ricciardi Maria Rosaria , Petrucci Maria Teresa , Baldi Alfonso , Cioce Mario , Cortese Giancarlo , Mattei Elisabetta , Merola Roberta , Gianelli Umberto , Pisani Francesco , Gumenyuk Svitlana , Mengarelli Andrea , Hopker Katja , Benzing Thomas , Floridi Aristide , Passananti Claudio , Blandino Giovanni , Iezzi Simona , Fanciulli Maurizio
Published: August 2018

Tumor transformation is the result of genetic and epigenetic modifications that alter gene transcription, consequently producing a specific oncogenic program. Multiple myeloma (MM) is a neoplasia characterized by the accumulation of proliferating antibodies producing plasma cells in the bone marrow. This disease is the second most frequent haematological malignancy in the US and Europe. In this study we demonstrate that Che-1 plays a crucial role in the control of transcription and cellular proliferation by regulating the state of the chromatin and by increasing its accessibility, highlighting Che-1 as an essential component of the transcription machinery in MM. Che-1 loss induces a global transcription shut-off, by reducing RNA Pol II recruitment onto the DNA. Most importantly, transcriptional inhibition in Che-1 depleted cells could already be detected at pre-mRNA levels, leading to the hypothesis that Che-1 could regulate RNA pol II activity directly. Our study shows that Che-1 is required for the maintenance of open chromatin in MM cells, and is involved in general histone acetylation. Morever, we found that Che-1 downregulation further sensitizes MM cells to bromodomain and extra-terminal (BET) inhibitors. Indeed Che-1 silencing increased JQ1 sensitivity of MM cells. In summary, our findings identify Che-1 as a key player for maintaining the open chromatin structure required for sustaining MM growth. These findings support Che-1 as a possible target for MM therapy, alone or in combination with BET inhibitors.

Citation Format: Tiziana Bruno, Francesca De Nicola, Frauke Goeman, Matteo Pallocca, Cristina Sorino, Valeria Catena, Gianluca Bossi, Bruno Amadio, Giovanni Cigliana, Enrico Spugnini, Maria Rosaria Ricciardi, Maria Teresa Petrucci, Alfonso Baldi, Mario Cioce, Giancarlo Cortese, Elisabetta Mattei, Roberta Merola, Umberto Gianelli, Francesco Pisani, Svitlana Gumenyuk, Andrea Mengarelli, Katja Hopker, Thomas Benzing, Aristide Floridi, Claudio Passananti, Giovanni Blandino, Simona Iezzi, Maurizio Fanciulli. Che-1/aatf-induced transcriptionally active chromatin promotes cell growth in multiple myeloma [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 350.