bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5300: smCounter2, a highly accurate UMI-aware variant caller and its applications in detecting 0.5-1% somatic mutations using targeted panel sequencing
Authors: Xu Chang , Gu Xiujing , Wu Zhong , DiCarlo John , Wang Yexun
Published: August 2018

We introduce smCounter2, our new version of low-frequency variant caller for targeted panel sequencing data. Upgraded from the previous version of smCounter (Xu et al, BMC Genomics, 2017), smCounter2 has a higher accuracy of detecting 0.5-1% variants and a more solid and scalable theoretical foundation. For 1% SNVs, smCounter2 achieved above 98% sensitivity and fewer than 10 false positives per megabase on a 680kb custom panel using a mixture of Genome in a Bottle reference samples. For 0.5% SNVs (including multi-allelic variants), smCounter2 achieved 87.5% sensitivity (7 out of 8) using a mixture of Horizon Tru-Q samples. We have also tested smCounter2 on other datasets with 5% and germline variants. On all these datasets except the germline variants, smCounter2 has demonstrated superior performance compared with other state-of-the-art UMI-aware variant calling algorithms. Currently, we are generating data on another custom panel (~900kb) to demonstrate the sensitivity and specificity of calling 0.5% variants.

smCounter2 models DNA polymerase errors for each substitution type, therefore more accurately distinguishes real variants from the first-cycle PCR errors, which cannot be corrected by UMIs. smCounter2 is equipped with model-based filters that can reduce false calls in repetitive regions such as homopolymers and micro-satellite sequences, where error rate is generally higher and UMIs tend to be less effective. These features, to some extent, overcome the intrinsic limitations of UMI-based variant calling and are essential to smCounter2's improved performance.

Citation Format: Chang Xu, Xiujing Gu, Zhong Wu, John DiCarlo, Yexun Wang. smCounter2, a highly accurate UMI-aware variant caller and its applications in detecting 0.5-1% somatic mutations using targeted panel sequencing [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 5300.
Abstract 5308: Using RNA expression data for splicing variant assessment and confirmation
Authors: Lund Jim , Bailey Shannon , Gujja Sharvari , Gulcher Jeffrey
Published: August 2018

Nine percent of disease-causing mutations classified in HGMD have the potential to impact RNA splicing. Splicing variants called from DNA sequence data, especially variants outside the canonical splice site, are difficult to evaluate clinically as they often have no effect on protein expression. A method to utilize RNA-Seq data for splice site variant classification was developed. RNA reads aligned to the region of a splice site variant are examined to determine if RNA read through is present which indicates normal splicing at the site is disrupted.

Thousands of paired tumor and normal TCGA DNA and RNA samples were used to evaluate the algorithm and rule out alternate splicing in the tissue as explanation for RNA read through. Splicing variants can also alter exon usage and RNA isoform expression, and this can be identified by examining RNA isoform expression. An analysis of splicing variants in the TCGA project datasets has generated sets of confirmed functional and non-disruptive splicing varaints. This splicing dataset can be used to test and refine splicing defect prediction algorithms.

Citation Format: Jim Lund, Shannon Bailey, Sharvari Gujja, Jeffrey Gulcher. Using RNA expression data for splicing variant assessment and confirmation [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 5308.
Abstract 5312: The effect of Dnmt1 overexpression on intestinal tumorigenesis
Authors: Schaaf Nicole A. Vander , Park JinA , Dina Oluwasei , Lee KwangHo , Laird Peter W.
Published: August 2018

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the United States. Strong genetic drivers of tumorigenesis, such as loss of function of the APC tumor-suppressor gene, have been well characterized, but the role of epigenetic alterations remains poorly understood. Upregulation of DNA methyltransferases (DNMTs), including DNMT1, has been reported in various human cancers, but its functional significance to cancer is unclear. Here we report a novel mouse model of inducible Dnmt1 upregulation, bypassing the embryonic lethality of Dnmt1 overexpression. We accomplish inducible control of Dnmt1 expression by targeting the tet transcriptional activator to the endogenous Dnmt1 promoter. We combine this model with the ApcMin allele to investigate the effect of Dnmt1 upregulation on intestinal tumorigenesis. Our preliminary data suggests that Dnmt1 overexpression increases the size and multiplicity of intestinal polyps in ApcMin/+ mice. Previous work in our lab showed that DNA methylation is critical for tumor formation, but it is not known which DNA methylation alterations have functional relevance. To investigate this, we will use the Dnmt1 overexpression model to identify DNA methylation events that are responsible for the observed phenotype in ApcMin/+ mice. In summary, we describe a novel mouse model of Dnmt1 overexpression and provide preliminary evidence to suggest that such upregulation exacerbates intestinal tumorigenesis. Our investigation may yield new insights into the role of epigenetics in CRC initiation and progression and into potential epigenetic therapies.

Citation Format: Nicole A. Vander Schaaf, JinA Park, Oluwasei Dina, KwangHo Lee, Peter W. Laird. The effect of Dnmt1 overexpression on intestinal tumorigenesis [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 5312.
Abstract 5319: Genetic regulation of DNA methylation in breast cancer
Authors: Lin Nan , Shendre Aditi , Liu JinPeng , Wang Chi , Liu Yunlong , He Chunyan
Published: August 2018

Aberrant DNA methylation plays an important role in breast cancer initiation and progression. It is believed that changes in DNA methylation occur early in breast cancer development or even in normal tissue before tumor occurrence, and these changes could be a useful source for early detection, prognosis, and targeted therapy. DNA methylation is tissue-specific and is influenced by inherited genetic variations in the human genome. Genome-wide association studies (GWAS) have identified more than 600 single nucleotide polymorphisms (SNPs) associated with breast cancer risk and outcome. However, how these germline genetic variants influence DNA methylation in breast tissue, especially in normal breast tissue, remains largely unknown. We performed a methylation quantitative trait loci (meQTL) analysis to examine the association between the GWAS identified breast cancer risk loci and DNA methylation in 48 women with paired blood and breast tissue samples. Genotyping of SNPs was performed using blood-derived DNA and the Illumina HumanOmni 2.5-4v1_D array chip. Genome-wide DNA methylation was measured using breast tissue derived genomic DNA and the new Illumina TruSeq Methyl Capture EPIC sequencing technology. We found that GWAS-identified breast cancer risk loci were associated with DNA methylation sites close to genes enriched in pathways related to cell differentiation and morphogenesis, DNA damage, cell movement, and hormonal signaling pathways. We identified more cis-acting than trans-acting meQTLs, and the peak enrichment for meQTLs was in close proximity to transcription start sites. We further compared our results with those from the meQTL studies conducted with lymphoblastoid cell lines and peripheral blood samples. We found more than 60% of the identified association between genetic variants and DNA methylation in our study are tissue-type specific. Our study may provide a post-GWAS functional characterization of breast cancer risk loci and shed light on epigenetic mechanisms that underlie the observed GWAS association.

Citation Format: Nan Lin, Aditi Shendre, JinPeng Liu, Chi Wang, Yunlong Liu, Chunyan He. Genetic regulation of DNA methylation 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 5319.
Abstract 5332: Prognostic value of aberrant promoter hypermethylation of tumor-related genes in early-stage head and neck cancer
Authors: Imai Atsushi , Misawa Kiyoshi , Mochizuki Daiki , Mineta Hiroyuki , Kanazawa Takeharu
Published: August 2018

Staging and pathological grading are useful, but imperfect predictors of recurrence in head and neck squamous cell carcinoma (HNSCC). Accordingly, molecular biomarkers that predict the risk of recurrence are necessary to improve clinical outcomes. The ability to distinguish between low- and high-risk HNSCCs at an early stage may reduce follow-up costs. We hypothesized that the quantitative methylation specific PCR (Q-MSP) assay could be used to define patterns of DNA methylation that differentiate low- and high-risk HNSCCs. The methylation statuses of the promoters of 11 tumor-related genes (p16, RASSF1A, E-cadherin, H-cadherin, MGMT, DAPK, DCC, COL1A2, TAC1, SST, and GALR1) were analyzed in 133 HNSCC cases using quantitative methylation-specific PCR. Frequent methylation of p16 (44%), RASSF1A (18%), E-cadherin (53%), H-cadherin (35%), MGMT (35%), DAPK (53%), DCC (42%), COL1A2 (44%), TAC1 (61%), SST (64%), and GALR1 (44%) in HNSCC were detected. Disease-free survival was lower in patients with 6-11 methylated genes than in those with 0-5 methylated genes (log-rank test, P = 0.001). In a multivariate Cox proportional hazards analysis, the methylation of E-cadherin, COL1A2, TAC1, and GALR1 was associated with poor survival, with hazard ratios of 4.474 (95% CI, 1.241-16.124). In a joint analysis of these four genes, patients with 2-4 methylated genes had a significantly lower survival rate than those with 0-1 methylated genes in early-stage HNSCC. Importantly, the methylation of some genes was closely related to poor prognosis in early-stage HNSCC, providing strong evidence that these hypermethylated genes are valuable biomarkers for prognostic evaluation. In conclusion, the methylation profiles of E-cadherin, COL1A2, TAC1, and GALR1 were the most powerful combination for predicting early-stage HNSCC. This demonstrates that molecular stratification may predict cancer progression. These findings can benefit HNSCC screening and surveillance algorithms. Although our study was retrospective, was conducted at a single institution, and the number of patients was small, it serves as a platform to establish optimal therapeutic strategies for early-stage HNSCC.

Citation Format: Atsushi Imai, Kiyoshi Misawa, Daiki Mochizuki, Hiroyuki Mineta, Takeharu Kanazawa. Prognostic value of aberrant promoter hypermethylation of tumor-related genes in early-stage head and neck 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 5332.
Abstract 5336: Methylation patterns in hepatoblastoma: A report from the Children's Oncology Group
Authors: Marcotte Erin , Spector Logan G. , Nelson Heather , Tomlinson Gail , Krailo Mark , Mills Lauren , Poynter Jenny
Published: August 2018

Introduction. Hepatoblastoma (HB) accounts for over 80% of all liver cancer diagnosed in children under 15 years of age in the United States. Aberrant DNA methylation has been implicated in the pathogenesis of multiple types of cancer, including HB. Global hypomethylation and DNA methylation in the promoter region of selected tumor suppressor genes, including RASSF1A, p16, SOCS1, CASP8, and MT1G, has been observed in previous studies of HB. Methods. A total of 47 flash-frozen samples of HB tumors were available for analysis. These tumors include 26 tumors from cases enrolled in Children's Oncology Group study AEPI04C1 (the HOPE study) and 21 tumors obtained as part of the Children's Oncology Group P9346 HB biology protocol. The Cooperative Human Tissue Network Pediatric Division (CHTN; Columbus, OH) provided 23 normal liver tissue samples from children ages 0—6 to serve as controls in this analysis. Initial multi-dimensional scaling (MDS) plots showed that 8 samples, 2 control and 6 patients, did not cluster with the other samples of the same group and were considered outliers. These 8 samples were removed from the study leaving a total of 62 samples, 21 control and 41 patients, remaining. Differentially methylated regions (DMR) were identified between control and patient samples using the bumphunter algorithm included in the minfi package. We used Ingenuity Pathway Analysis (IPA) to identify pathways that were enriched in the group of CpG with a change in methylation beta value of ≥39% between patients and controls. Results. We found 4833 DMR, which are associated with 3543 genes, when comparing HB patients and controls. Pathway analysis revealed 76 pathways enriched among the DMR. Conclusions. Identification of methylation patterns may elucidate the developmental stage at which HB arose and the at-risk period when environmental exposures could be most harmful. Further, understanding the relevant genetic pathways could lead to the development of new targets for therapy.

Citation Format: Erin Marcotte, Logan G. Spector, Heather Nelson, Gail Tomlinson, Mark Krailo, Lauren Mills, Jenny Poynter. Methylation patterns in hepatoblastoma: A report from the Children's Oncology Group [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 5336.
Abstract 537: CK1 delta as a therapeutic target in bladder cancer
Authors: Chen Chun-Han
Published: August 2018

Bladder cancer is a common malignancy worldwide, but targeted therapy is currently unavailable. Therefore, there is an unmet medical need for bladder cancer patients. Oncomine database revealed that gene expression of CK1 delta is higher in bladder cancer compared to normal tissue. The purpose of this study is to investigate the role of CK1 delta in the progression of bladder cancer, and the feasibility of CK1 delta as a therapeutic target. Lentiviral delivery of shRNA and CK1 delta inhibitors was used to modulate gene expression or kinase activity of CK1 delta in bladder cancer cell lines. Cell viability, cell cycle progression, apoptosis, migration and downstream signaling pathway were analyzed. The results showed that knocking down CK1 delta or treatment of CK1 delta inhibitors decreased cell viability and inhibited wnt/β-catenin pathway in bladder cancer cell lines. CK1 delta inhibitors increased the accumulation of sub-G1 phase by flow cytometry analysis, as well as the activation of caspase-3, 8, 9 and PARP cleavage by Western blot, indicating the promotion of cell apoptosis. Knocking down of CK1 delta and the treatment of CK1 delta inhibitors impaired cell migration activity, and altered protein expression of EMT markers, such as E-cadherin, vimentin, snail and slug. In conclusion, this study demonstrates that CK1 delta is a potential target for bladder cancer therapy.

Citation Format: Chun-Han Chen. CK1 delta as a therapeutic target in bladder 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 537.
Abstract 5375: Whole-genome sequencing reveals genomic signatures associated with the immunologic microenvironments in Chinese NSCLC patients
Authors: Wang Cheng , Dai Juncheng , Gu Yayun , Hu Zhibin , Shen Hongbing
Published: August 2018

Over the past decades, next-generation sequencing has accelerated the systematic characterization of genomic events, including single base substitutions and small insertions/deletions (indels), and has yielded substantial insights into the unique and shared genomic features of the two NSCLC subtypes. Genomic studies of lung cancer have mainly been conducted in patients from Western countries; however, Chinese lung cancer patients have distinct epidemiologic and genomic features, highlighting the presence of specific etiologic mechanisms in addition to smoking. To reveal the underlying mechanisms, we presented a comprehensive genomic landscape of 149 Non-Small Cell Lung Cancer (NSCLC) cases. We identified 15 potential driver genes and three mutational signatures, two of which have been connected with APOBEC enzymes and smoking. In addition, we revealed that Chinese patients are specially characterized by not only highly clustered and functional EGFR mutations but also a mutational signature, that is associated with inflammatory tumor-infiltrating lymphocytes (P = 0.001). The EGFR mutation rate is significantly increased with the proportion of the MS3 signature (P<0.001). As a classic tumor-enabling hallmark, inflammatory infiltration may contribute to the accumulation of EGFR mutations, especially in never-smokers. Additionally, patients with a higher proportion of the MS3 signature carried a higher contribution of characterized chromosomal rearrangements (P<0.001). The results revealed specific genomic features in the inflammatory microenvironments in Chinese patients with potential implications for understanding the etiology, prevention and therapy of NSCLC.

Citation Format: Cheng Wang, Juncheng Dai, Yayun Gu, Zhibin Hu, Hongbing Shen. Whole-genome sequencing reveals genomic signatures associated with the immunologic microenvironments in Chinese NSCLC 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 5375.
Abstract 5381: Understanding the genesis and oncogenic consequences of tandem duplicator phenotypes in human cancers
Authors: Menghi Francesca , Barthel Floris , Yadav Vinod , Tang Ming , Ji Bo , Carter Gregory , Jonkers Jos , Verhaak Roel , Scully Ralph , Liu Ed
Published: August 2018

Genome-scale instability configurations in cancer genomes are commonly found across different types of cancers. We and others have described an enrichment of head-to-tail somatic segmental tandem duplications (TDs) in primarily breast and ovarian cancers, a configuration known as the Tandem Duplicator Phenotype (TDP). Here, we perform a meta-analysis of 2,717 human cancer genomes, representing 30 different tumor types and refine the TDP classification based on the identification of highly specific and recurrent TD span profiles. Overall, we identify the TDP as a highly recurrent chromosomal instability configuration, occurring in 14% of the cancer genomes examined. The TDP is remarkably prevalent in triple negative breast cancer (50%), ovarian cancer (55%), and uterine cancers (45%), but is infrequent in most other cancer types. In TDP tumors, TD span sizes can be classified into three major discrete intervals with modal values of 10 Kb, 230 Kb, and 1.7 Mb. TDPs with a dominant TD modal span size of 10 Kb are strongly associated with conjoint TP53 mutations and BRCA1 deficiency across different tumor types. TDPs with larger span sizes (230 Kb and 1.7 Mb) are associated with CCNE1 pathway activation and CRKRS/CDK12 gene disruptions. We proved the driver role of the conjoint abrogation of the BRCA1 and TP53 genes for the induction of TDP cancers with the 10 Kb predominant span peak by generating mammary cancers with a Tandem Duplicator Phenotype of the ~10 Kb TD span configuration type in genetically modified mouse models harboring deleterious mutations in only these same two genes. Lastly, we describe how heterogeneous combinations of tumor suppressors and chromatin topologically associating domains are disrupted, and oncogene and tissue-specific super enhancers are duplicated as a consequence of TD formation in TDP tumors. In summary, our work unifies a number of observations around a specific cancer genomic signature, shows how a number of genetic drivers converge on creating the tandem duplicator phenotype, and how the downstream consequences of the TDs generate oncogenic diversity that allows for further formation of genetic subgroups. The implications of TDP-based stratification for therapy response are currently under investigation.

Citation Format: Francesca Menghi, Floris Barthel, Vinod Yadav, Ming Tang, Bo Ji, Gregory Carter, Jos Jonkers, Roel Verhaak, Ralph Scully, Ed Liu. Understanding the genesis and oncogenic consequences of tandem duplicator phenotypes 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 5381.
Abstract 5393: Exosomal microRNA profiles in peritoneal fluids as a therapeutic biomarker for peritoneal metastasis of gastric cancer
Authors: Ohzawa Hideyuki , Kumagai Yuko , Yamaguchi Hironori , Hosoya Yoshinori , Sata Naohiro , Kitayama Joji
Published: August 2018

Background: Repeated intraperitoneal chemotherapy (IPC) using taxane is highly effective for peritoneal metastasis. Peritoneal fluids are supposed to contain various factors derived from tumor cells seeded in peritoneal cavity. This study aimed to explore possible biomarkers for suitable IPC using exosomal miRNA profiles derived from malignant ascites or peritoneal lavages.

Methods: Peritoneal fluid samples were obtained from 11 patients with peritoneal metastasis (PM+) and 14 patients who received gastrectomy for early gastric cancer (PM-). Exosomal fractions were isolated using ultracentrifuge method and total RNAs were extracted. The pooled RNA samples in both groups were mixed and expression of miRNAs were analyzed using miRNome miScript miRNA PCR Array (QIAGEN). Based on these results, we constructed the custom miRNA PCR panel and evaluates expression of miRNAs in individual samples.

Results: The comprehensive PCR analysis showed that total of 56 and 54 miRNAs were strongly expressed in exosomes in PM+ and PM- peritoneal fluid sample, respectively. In analysis of individual samples, 7 upregulated miRNAs (miR-150-5p, miR-223-3p, miR-204-5p, miR-720, and miR-92a, miR-21-5p, miR-4301, and miR-342-3p) and 3 downregulated miRNAs (miR-29a-3p, miR-29b-3p, and miR-29c-3p) were identified in PM+ samples.

Conclusion: In patients who receive IPC, peritoneal fluids can be repeatedly obtained from peritoneal access port. Exosomal miRNA profiles of peritoneal fluid samples might be a useful biomarker to determine the therapeutic efficacy as well as to predict the outcome in those patients with peritoneal metastasis.

Citation Format: Hideyuki Ohzawa, Yuko Kumagai, Hironori Yamaguchi, Yoshinori Hosoya, Naohiro Sata, Joji Kitayama. Exosomal microRNA profiles in peritoneal fluids as a therapeutic biomarker for peritoneal metastasis of gastric 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 5393.
Abstract 5401: Dysregulated microRNAs in aflatoxin-induced hepatocellular carcinoma: Serum miR-182 as a potential predictive biomarker
Authors: Livingstone Merricka C. , Johnson Natalie M. , Roebuck Bill D. , Kensler Thomas W. , Groopman John D.
Published: August 2018

Hepatocellular carcinoma (HCC) continues to be a major cause of cancer death globally, with aflatoxin B1 (AFB1) as a prevalent risk factor in low- and middle-income countries. MicroRNAs have been shown to be differentially expressed in HCC and may serve as predictive biomarkers. In this study, we analyzed tumor and non-tumor tissue from rats dosed with AFB1 (200 µg/kg BW) for 28 consecutive days that received vehicle only or AFB1 plus the chemopreventive agent CDDO-Im (30 µmol), and control animals (Johnson et al., CaPR, 2014). Total RNA was isolated from tumor or non-tumor tissue at the time of sacrifice and sequenced. MicroRNA transcriptomic analysis revealed 17 miRNAs significantly upregulated (> 5 fold) in tumors compared to non-tumor tissue. The top ten dysregulated miRNAs determined by fold change and biological significance were selected for further investigation: rno-miR- 205, 200b-3p, 182, 429, 31a-5p, 10b-5p, 141-3p, 132-3p, 802-5p. Validation of sequencing results by quantitative PCR (qPCR) confirmed the upregulation of the majority of candidate miRNAs in tumors and rno-miR-224-5p as the most dysregulated miRNA (over 400 fold). We also examined the levels of these candidates in terminal sera of the same animals by qPCR. Circulating miRs-224-5p, 182, and 122-5p were increased (> 1.5 fold) in animals diagnosed with HCC compared to untreated animals and those previously dosed with AFB1 plus CDDO-Im. Analysis of tracking of serum miR-182 by generalized estimating equations (GEE) revealed significantly increased levels (5 fold; CI: 2.17- 2.50) in animals that developed HCC. This sustained increase in serum miR-182 is seen months before any tumors or other symptoms are present, and highlights this miRNA as a potential predictive biomarker in AFB1-induced HCC. Supported by T32ES007141-31A1 and CA197222.

Citation Format: Merricka C. Livingstone, Natalie M. Johnson, Bill D. Roebuck, Thomas W. Kensler, John D. Groopman. Dysregulated microRNAs in aflatoxin-induced hepatocellular carcinoma: Serum miR-182 as a potential predictive 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 5401.
Abstract 5408: Elevated level of serum miR-1290 is correlated with high-grade serous ovarian epithelial ovarian cancer and might be a potential biomarker
Authors: Kobayashi Masaki , Kenjiro Sawada , Akihiko Yoshimura , Mayuko Miyamoto , Erika Nakatsuka , Michiko Kodama , Kae Hashimoto , Seiji Mabuchi , Tadashi Kimura
Published: August 2018

Objective: There is a critical need for improved diagnostic markers to detect ovarian high grade serous ovarian cancer (HGSOC). MicroRNAs (miRNAs) stably exist in circulating blood, reflecting tissue or organ conditions and present in circulating microvesicles such as exosomes. Recent studies have confirmed the potential use of miRNAs profiling as a novel non-invasive biomarker for diagnosis of HGSOCs. The aim of this study is to identify which miRNAs are highly produced from HGSOCs and analyze whether serum miRNA can discriminate patients with HGSOC from healthy controls. Methods: Secreted exosomes from ovarian cancer cell lines were collected and exosomal miRNAs extracted. miRNA microarray was performed and several elevated miRNAs specific to HGSOCs were picked up. Among these, we focused on miR-1290. Serum from 71 pre-operative, 46 post-operative ovarian cancer patients and 13 healthy controls were gathered and its expression levels were detected by quantitative Real Time PCR. Results: In HGSOC patients, miR-1290 emerged overexpressed compared to healthy controls (3.52-fold). ROC analysis showed that at the cut-off of 1.61(healthy controls ; 1), the sensitivity and specificity were 63 % and 85 % respectively for detecting HGSOC (AUC = 0.71). The AUC of CA125 + miR-1290 combination was 1.00. Its expression singnificantly decreased after operation(5.87 → 1.17 ; P < 0.01). In advanced stage HGSOC patients, moreover, it expressed marginally higher than early stage ones(4.23 VS 1.58 ; P = 0.23). Conclusions: Serum miR-1290 can be a potential diagnostic biomarker for HGSOC.

Citation Format: Masaki Kobayashi, Sawada Kenjiro, Yoshimura Akihiko, Miyamoto Mayuko, Nakatsuka Erika, Kodama Michiko, Hashimoto Kae, Mabuchi Seiji, Kimura Tadashi. Elevated level of serum miR-1290 is correlated with high-grade serous ovarian epithelial ovarian cancer and might be a potential 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 5408.
Abstract 542: A disintergrin and metalloprotease (ADAM) 15 promotes non-small cell lung cancer (NSCLC) proliferation through cytosolic domain, not extra-cytosolic metalloprotease activity
Authors: Hou Hsin-Han
Published: August 2018

Emerging evidence indicates that proteins of a disintergrin and metalloprotease (ADAM) family contribute to cancer progression and metastasis. ADAM15 is up-regulated in multiple cancers and the enzymatic activities of its extracellular metalloprotrease domain promote cancer proliferation and migration by mediating the ErbB signaling pathway. In lung cancer, the enzymatic activity of ADAM15 extracellular domain is reported to be independent of ErbB signaling, indicating an alternative mechanism in promoting lung cancer progression. However, the role of ADAM15 in non-small cell lung cancer (NSCLC) and its correlation to patient prognosis is not well understood. This study demonstrated the longest ADAM15 isoforms, isoform 6 (i6), which contained the most cytoplasmic Src homology 3 (SH3) binding motifs, was significantly up-regulated in progressive NSCLC cell. Comparison of i6 and isoform 1 (i1) revealed that the cytoplasmic domain was essential for NSCLC cell proliferation and aggressiveness. ADAM15 i6, but not i1, mediated the activation the activation of the Src homolog 2 domain containing (Shc) through physical interaction with growth factor receptor-bound protein 2 (Grb2). ADAM15 i6 overexpression promoted NSCLC cell growth in a xenograft mouse model, while ADAM15 or Grb2 knockdown resulted in tumor shrinkage. ADAM15 was overexpressed in primary NSCLC tissues compared to adjacent normal tissues. Patients with ADAM15 i6 high-expressing lung tumors had shorter survival times. Thus, a novel mechanism of the ADAM15 cytoplasmic domain is identified in NSCLC tumor progression. This may help shed light on the molecular mechanisms of ADAM proteins and facilitate development of novel therapy for NSCLC.

Citation Format: Hsin-Han Hou. A disintergrin and metalloprotease (ADAM) 15 promotes non-small cell lung cancer (NSCLC) proliferation through cytosolic domain, not extra-cytosolic metalloprotease activity [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 542.
Abstract 5431: BRD4 regulates cellular senescence in gastric cancer cells via E2F/miR-106b/p21 axis
Authors: Dong Xingchen
Published: August 2018

Small molecules targeting bromodomains of BET proteins possess strong anti-tumor activities and have emerged as potential therapeutics for cancer. However, the underlying mechanisms for the anti-proliferative activity of these inhibitors are still not fully characterized. In this study, we demonstrated that BET inhibitor JQ1 suppressed the proliferation and invasiveness of gastric cancer cells by inducing cellular senescence. Depletion of BRD4, which was overexpressed in gastric cancer tissues, but not other BET proteins recapitulated JQ1-induced cellular senescence with increased cellular SA-β-Gal activity and elevated p21 levels. In addition, we showed that the levels of p21 were regulated at the post-transcriptional level by BRD4-dependent expression of miR-106b-5p, which targets the 3'-UTR of p21 mRNA. Overexpression of miR-106b-5p prevented JQ1-induced p21 expression and BRD4 inhibition-associated cellular senescence, whereas miR-106b-5p inhibitor up-regulated p21 and induced cellular senescence. Finally, we demonstrated that inhibition of E2F suppressed the binding of BRD4 to the promoter of miR-106b-5p and inhibited its transcription, leading to the increased p21 levels and cellular senescence in gastric cancer cells. Our results reveal a novel mechanism by which BRD4 regulates cancer cell proliferation by modulating the cellular senescence through E2F/miR-106b-5p/p21 axis and provide new insights into using BET inhibitors as potential anti-cancer drugs.

Citation Format: Xingchen Dong. BRD4 regulates cellular senescence in gastric cancer cells via E2F/miR-106b/p21 axis [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 5431.
Abstract 5432: Cancer-induced hypercalcemia promotes breast cancer progression via AP-1 transcription factor mediated upregulation of malignancy-associated genes
Authors: Beasley Heather K. , Widatalla Sarrah E. , Williams Stephen D. , Whalen Diva S. , Korolkova Olga Y. , Sakwe Amos M.
Published: August 2018

Cancer-induced hypercalcemia (CIH), is common in breast cancer patients with metastatic disease and in up to 30% of cases with solid tumors without evidence of metastasis. However, its role in the development of large and aggressive breast tumors remain poorly understood. In this study, we show that prolong exposure of triple negative breast cancer (TNBC) cells to high Ca2+ is accompanied by reduced sensitivity of the calcium sensing receptor to high Ca2+, increased growth and tumor cell motility. Gene expression profiling of TNBC cells cultured at high Ca2+ (5.0 mM) revealed that in addition to early response genes (FOS/FOSB), high extracellular Ca2+ also modulated the expression of MAGEC2/CT10 and PAI-2 and other malignancy associated genes (MAGs). To determine whether the expression of MAGs is regulated by FOS/FOSB we show that down regulation of FOSB strongly inhibited the high Ca2+-induced expression of MAGEC2 and that FOSB, as a component of the AP-1 transcription factor bound to the MAGEC2 promoter at high Ca2+. We also show that down regulation of MAGEC2 or FOSB affected the migration and proliferation of TNBC cells at high Ca2+. These data suggest that high Ca2+-induced expression of malignancy promoting genes such as MAGEC2/CT10 underlie the successful tumor cell survival, growth and/or motility in calcium-rich microenvironments and presumably, during the hypercalcemia prone late stages of the disease. This research is supported by NIH/NIGMS 5SC2 CA170244 and 1SC1 CA211030, NIH/NCI 2U54CA 163069-07

Citation Format: Heather K. Beasley, Sarrah E. Widatalla, Stephen D. Williams, Diva S. Whalen, Olga Y. Korolkova, Amos M. Sakwe. Cancer-induced hypercalcemia promotes breast cancer progression via AP-1 transcription factor mediated upregulation of malignancy-associated genes [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 5432.
Abstract 5434: Screen for immune-related transcriptional targets of the Hippo pathway in human breast cancer cells
Authors: Rensburg Helena J. Janse van , Azad Taha , Ling Min , Hao Yawei , Minassian Lori M. , Snetsinger Brooke , Khanal Prem , Rauh Michael J. , Graham Charles H. , Yang Xiaolong
Published: August 2018

The Hippo signaling pathway has recently emerged as a cellular network that is dysregulated in cancer. In breast cancer cells, aberrant activation of the Hippo transducers (and transcriptional co-activators) TAZ and YAP leads to altered expression of their downstream gene targets and endows cells with multiple “hallmarks of cancer”. While several transcriptional targets of TAZ and YAP underlying their pro-tumorigenic activity have been described (e.g. CTGF, CYR61), gene targets of TAZ and YAP that modulate immune cell behavior in the tumor microenvironment are poorly understood. We have performed a comprehensive screen for immune-related transcriptional targets of TAZ and YAP in human breast cells. We have identified many candidate genes that are potentially regulated by TAZ and YAP including the immune checkpoint molecules PD-L1 and PD-L2, the lymphocyte regulator S1PR1 and the inflammasome component NLRP3. We have further validated PD-L1 as a bona fide transcriptional target of TAZ and YAP. These findings reveal new functions for the Hippo pathway in modifying immune responses and implicate TAZ and YAP in cancer immune evasion.

Citation Format: Helena J. Janse van Rensburg, Taha Azad, Min Ling, Yawei Hao, Lori M. Minassian, Brooke Snetsinger, Prem Khanal, Michael J. Rauh, Charles H. Graham, Xiaolong Yang. Screen for immune-related transcriptional targets of the Hippo pathway in human breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5434.
Abstract 5453: Novel pan-PI3K inhibitor WX008 demonstrates significant antitumor efficacy in three xenograft tumor models
Authors: Yu Tao , Kong Lingwei , Wang Yong , Jiang Peipei , Rong Zhe min , Wang Chang jun , Huang Jing jie , Yao Dan , Qin Yu xin , Wu Cheng de , Chen Shu hui , Tian Xin , Liu Fei , Dong Ping , Chen Zhi Lin
Published: August 2018

Background: PI3K/Akt signaling pathway plays a key role in a series of cellular functions related to cell growth, proliferation, survival and differentiation. Dysregulation of the PI3K pathway is implicated in many human cancers. Thus we intended to discover novel pan-PI3K inhibitors to treat various solid tumors, such as colorectal cancer, gastric carcinoma, lung carcinoma and breast cancer, etc.

Methods: We explored SAR based on a PI3K/mTOR dual inhibitor series to selectively improve the PI3K activity over that of mTOR. PI3Kα/mTOR enzymatic activity assays, MCF-7 cellular (p-AktS473) activity assay and mouse in vivo pharmacokinetic analyses were used to direct compound optimization. Compounds with superior in vitro activity and in vivo pharmacokinetic properties were then tested for in vivo antitumor efficacy in patient derived xenograft (PDX) tumor models.

Results: WX008 was identified as a potent PI3K inhibitor with PI3Kα/mTOR IC50 of 0.07 nM/233 nM (selectivity 3328×) and superior MCF-7 cellular (p-AktS473) activity (IC50 of 5.91 nM). For its excellent pharmacokinetic properties WX008 was evaluated for in vivo antitumor efficacy. As results, WX008 displayed equivalent efficacy at much lower dose than BKM-120 in several PDX tumor models (Table 1).

Table 1 In vivo efficacy of BKM-120 and WX008

Cmpd_IDBKM-120WX008CO-04-0032 PDX72% TGI @30 mpk86% TGI @8 mpkST-02-0013 PDX50% TGI @8 mpk 77% TGI @15 mpk53% TGI @4 mpk 90% TGI @8 mpkLU-01-0010 PDX74% TGI @30 mpk74% TGI @8 mpk Conclusions: WX008 is a novel potent pan-PI3K inhibitor with high selectivity over mTOR and inhibits tumor growth in several PDX tumor models. Citation Format: Tao Yu, Lingwei Kong, Yong Wang, Peipei Jiang, Zhe min Rong, Chang jun Wang, Jing jie Huang, Dan Yao, Yu xin Qin, Cheng de Wu, Shu hui Chen, Xin Tian, Fei Liu, Ping Dong, Zhi Lin Chen. Novel pan-PI3K inhibitor WX008 demonstrates significant antitumor efficacy in three xenograft tumor models [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 5453.
Abstract 5454: New insights into the mode of action of cytotoxic alkyl-phospholipids
Authors: Argenzio Elisabetta , Moolenaar Wouter H. , Verheij Marcel
Published: August 2018

Background: Synthetic alkyl-phospholipid analogs (APLs), such as Edelfosine and Perifosine, are a class of anti-tumor agents that target cell membranes to induce growth arrest and apoptosis. In addition, APLs enhance the cytotoxic effect of radiation in preclinical models making these compounds attractive candidates as radiosensitizers. We previously found that different mechanisms determine ALP accumulation and consequent apoptotic toxicity in lymphoma versus carcinoma cells. Yet, despite decades of research, it is still unclear how ALPs are transported across the plasma membrane and how they affect, either positively or negatively, key intracellular signaling pathways to alter tumor cell behavior. Here we examine (i) the possible role of lipid flippases in mediating transbilayer transport of ALP-like lysophospholipids (notably lysoPC and lysoPE), and (ii) how Edelfosine affects gene expression in human breast cancer cells. Methods: The uptake of fluorescent lysophospholipids (TopFluor-LPC and -LPE) was monitored over time in wild-type HAP1 and CDC50A -/- cells using single-cell live-imaging. For RNA-seq analyses, MDA-MB-231 and Hs5788T triple-negative breast cancer (TNBC) cells were used. Results: Ad (i). Knockout of the flippase subunit CDC50a slows and attenuates the uptake of fluorescent lysoLPC and lyoPE. This suggests that CDC50a mediates, at least in large part, the active uptake of cytotoxic ALPs, similarly to natural lysophophoslipids.

Ad (ii). Whole genome RNA-seq analysis reveals that Edelfosine rapidly induces a unique gene expression program in breast cancer cells. When compared to bioactive lysoPA (LPA), Edelfosine upregulated about 25 genes after 4 hrs, whereas LPA upregulated about 300 genes under the same conditions. Strikingly, the Edelfosine- and LPA-induced early genes showed significant overlap, including transcription factors (FOS, EGR1, EGR3), CSF2 and the EGFR/HER2 inhibitor ERRFI1 (MIG6). Increased MIG6 expression by Edelfosine was confirmed by Western blot. Basal expression of MIG6 was high in MDA-MB-231 cells, but undetectable in Hs5788T TNBC cells. The latter cells were more sensitive than MDA-MB-231 cells to Edelfosine-induced apoptosis. Conclusions: We conclude that Edelfosine “hijacks” LPA receptor signaling pathways at early time points. Edelfosine-induced upregulation of the anti-proliferative gene MIG6, a negative regulator of the EGFR family, is of particular interest. Since MIG6 is induced by the G-actin-MAL transcriptional pathway, these results suggest that Edelfosine affects tumor cell behavior in part by influencing F-actin polymerization, a new scenario that warrants further studies.

Citation Format: Elisabetta Argenzio, Wouter H. Moolenaar, Marcel Verheij. New insights into the mode of action of cytotoxic alkyl-phospholipids [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 5454.
Abstract 5458: Antiproliferative activity of a novel 8-hydroxyquinoline ruthenium II complex against human breast cancer cell lines
Authors: Khalifa Amr M. , Sultan Ahmed S.
Published: August 2018

Ruthenium (Ru) complexes are recognized as the most perspective chemotherapeutic agents available, because of their low general toxicity and variety of modes of action. Ru(II)-based complexes show a higher tendency for ligand exchange reactions and therefore interact with target molecules more rapidly and there cytotoxicity often correlates with the DNA binding ability. The present study was aimed to test the anti-tumor effect of a new formulated ruthenium (II) complex Bis(quinolin-8-olato)bis(triphenylphosphine)ruthenium(II) complex (Ru(quin)2) that was prepared by reaction of the precursor RuCl2(PPh3)3 with Quinolin-8-ol on two human breast cancer cell lines, estrogen receptor-positive (ER+), T-47D, and MDA-MB-231, triple negative breast cancer cell line that display different phenotypic and differentiation patterns ranging from poor to high differentiation.

The two tested breast cancer cells showed a significant growth inhibition after 24 h of treatment, but the response of T47D cells to treatment was much higher than that of MDA-MB231 cells. In contrast, the near-normal mammary cell lines, MCF-10A, showed no response to Ru(quin)2 at higher doses. In tested cells, Ru(quin)2 significantly inhibited cells proliferation after 24 h treatment as evaluated by MTT assay, cell morphology alteration, and clonogenic assay. In addition, treated cells showed significant morphological and biochemical signs of apoptosis induction through releasing of histone protein, caspase-3 activation, and G2/M phase cell cycle arrest in a dose-dependent manner compared to control.

In T47D cells, Ru(quin)2 significantly downregulated protein expression of STAT3, and S6 kinase1 (S6K1) and significantly upregulated LC3B expression protein, a hallmark of autophagosomes formation, after 24 h of treatment as detected by western blot analysis and immunocytochemistry.

Furthermore, in established xenograft tumor model of MDA-MB231 cells in nude mice, the growth of MDA-MB231 tumors that treated with Ru(quin)2 was inhibited by 46.88% compared to the mock group (t=2.821, P<0.05) after three weeks of treatment. Besides, there was no cytotoxicity on both liver and kidney function tests. Collectively, our observations support the anticancer role of the novel Ru(II)- macrocyclic complex that might be through apoptosis and autophagy induction in human breast cancer cell lines.

Citation Format: Amr M. Khalifa, Ahmed S. Sultan. Antiproliferative activity of a novel 8-hydroxyquinoline ruthenium II complex against human breast cancer cell lines [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 5458.
Abstract 5468: Neratinib significantly inhibits responses to androgen in human prostate cancer cells
Authors: Dart Dafydd A. , Lalani Alshad S. , Avogadri-Connors Francesca , Bryce Richard , Jiang Wen G.
Published: August 2018

Background: Prostate cancer (PCa) is the most commonly diagnosed male cancer in the Western world. Tumor growth is initially androgen dependent - and driven by the androgen receptor (AR). The mainstays of prostate cancer treatment are androgen ablation and antiandrogen treatment, which block AR signalling. However, PCa often relapses to an androgen- independent disease. Androgens can transactivate genes directly via the AR-mediated transcription factor and indirectly via less well understood signal transduction pathways. These signal transduction pathways become increasingly relevant as prostate cancer cells progress to anti-androgen resistance, with HER2 being associated with higher relapse rates. Neratinib is an orally available tyrosine kinase inhibitor that irreversibly binds and inhibits EGFR, HER2 and HER4 receptor tyrosine kinases. This study aimed to examine the effect of neratinib on androgen signalling and on the expression of androgen-regulated genes in prostate cancer cells.

Methods: Changes in protein phosphorylation after androgen treatment of hormonally starved prostate cancer cells (LNCaP) was assessed using protein microarrays (Kinexus, Canada). Changes in gene expression after neratinib or androgen treatment were ascertained using AmpliSseq® technology or standard qPCR, and analysed via IPA Ingenuity software.

Results: Androgen treatment of hormonally starved prostate cancer cells (LNCaP) caused phosphorylation of several members of the signal transduction cascade including HER2 and Src within 2 hours, indicating a role for HER2 in rapid androgen signalling. Additionally, from over 1000 genes upregulated by androgen treatment (>2fold within 2 hours), 87% showed downregulation with neratinib treatment. Ingenuity pathway analysis indicated that STAT3, ETS-family and NF-κB transcription factors may be responsible for the rapid androgen-induced gene upregulation observed, and that these pathways were inhibited by neratinib treatment. Q-Quantitative PCR analysis of PSA expression in LNCaP cells stimulated with androgen in the presence of increasing concentrations of neratinib resulted in a dose-dependent inhibition of androgen activity.

Conclusions: These results show that neratinib is able to inhibit the responses of prostate cancer cells to androgens, and that a strong potential signaling cross-talk exists between the androgen receptor and the certain signal transduction pathways - pathways known to be involved in the progression of androgen-independent prostate cancer.

Citation Format: Dafydd A. Dart, Alshad S. Lalani, Francesca Avogadri-Connors, Richard Bryce, Wen G. Jiang. Neratinib significantly inhibits responses to androgen in human prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5468.