bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1169: Novel renal medullary carcinoma cell lines, UOK353 and UOK360, provide preclinical tools to identify new therapeutics
Authors: Wei Darmood , Yang Youfeng , Ricketts Christopher J. , Vocke Cathy D. , Ball Mark W. , Sourbier Carole , Wangsa Darawalee , Wangsa Danny , Guha Rajarshi , Zhang Xiaohu , Meltzer Paul , Reid Thomas , Thomas Craig J. , Merino Maria J. , Linehan W. Marston
Published: August 2018

Renal medullary carcinoma (RMC) is a rare and aggressive disease that predominantly afflicts individuals of African or Mediterranean descent with sickle cell trait. RMC comprises 1% of all renal cell carcinoma diagnoses, and the median overall survival for RMC patients is only 13 months. Patients are typically young (median age-22yo) and male (male:female ratio of 2:1). RMC was first characterized in 1995, and its hallmark SMARCB1 loss was identified in 2008. Due to the low incidence of RMC and the disease's aggressiveness, treatment decisions are often based on case reports. Thus, it is critical to develop preclinical models of RMC to both better understand the pathogenesis of this disease and identify an effective therapy. These RMC cell lines overexpress EZH2, relative to normal renal proximal tubule epithelium, thus making it an attractive druggable target. EZH2 inhibition in RMC tumor spheroids did not result in decreased viability. We have evaluated a potential clinical treatment (bortezomib) found in the literature and validate bortezomib's potency in vitro. Intriguingly, these cells lines not only lack NQO1, an antioxidant enzyme, but also the addition of N-acetyl cysteine, an antioxidant, has a protective effect against bortezomib. Together the data suggest that RMC are highly sensitive to oxidative stress. This evidence is consistent with case reports in the literature that found bortezomib treatment of RMC resulted in positive outcomes.

Citation Format: Darmood Wei, Youfeng Yang, Christopher J. Ricketts, Cathy D. Vocke, Mark W. Ball, Carole Sourbier, Darawalee Wangsa, Danny Wangsa, Rajarshi Guha, Xiaohu Zhang, Paul Meltzer, Thomas Reid, Craig J. Thomas, Maria J. Merino, W. Marston Linehan. Novel renal medullary carcinoma cell lines, UOK353 and UOK360, provide preclinical tools to identify new therapeutics [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 1169.
Abstract 117: Lysyl oxidase secreted by PTEN-deficient glioblastoma cells recruits macrophages and promotes malignant growth
Authors: Chen Peiwen , Wang Alan Y. , DePinho Ronald A.
Published: August 2018

Glioblastoma (GBM) is the most lethal form of brain cancer in adults. The median survival of GBM patients is only about one year after initial diagnosis. Genomic profiling has stratified GBM into various subgroups, which are driven by specific genetic alternations of core signaling pathways, including RTK/RAS/PI3K, P53 and RB pathways. Loss of PTEN, TP53 and CDKN2A tumor suppressors, and amplification of EGFR are frequently observed in GBM. However, targeted therapies, such as therapy against EGFR, have failed in the clinic, and no effective therapeutic drugs available to target tumor suppressors. The main reason for this failure is tumor-cell genetic heterogeneity, which induces aberrant activation of multiple signaling pathways. Stromal/immune cells in the tumor microenvironment (TME) are genetically stable, which not only play a pivotal role in GBM progression by affecting multiple cancer hallmarks, but can also be educated by cancer cells. However, whether and how the behavior and function of specific stromal/immune cells in the TME are regulated by cancer cell genetic alternations in GBM remain relatively undefined. Here, we show that PTEN deficiency in GBM specifically triggers immune response by promoting macrophage recruitment, while without affecting macroglia and other immune cells. Using unbiased transcriptome profiling, we identified that lysyl oxidase (LOX) is preferentially secreted by PTEN-deficient cancer cells, and is a potent macrophage chemoattractant. Transcriptome profiling following Gene Set Enrichment Analysis (GSEA) and functional validation demonstrated that activation of SRC and AKT signaling pathways drives LOX upregulation in PTEN-deficient cancer cells via the YAP1-TEAD complex. Upon the secretion from PTEN-deficient cancer cells, LOX can be uptaken by macrophages via integrin β1 signaling. Using the phospho-kinase antibody array, we identified PYK2 as the main downstream of LOX that is responsible for macrophage migration. Genetic and pharmacological inhibition of LOX in PTEN-deficient cancer cells does not affect tumor cell proliferation in vitro, but markedly inhibits macrophage density and tumor growth in vivo. Bioinformatics analysis in clinical samples demonstrated that PTEN-YAP1-LOX-integrin β1 axis is enriched in GBM patients with higher macrophage density, and that these patients show lower survival. Together, our findings highlight the significance of PTEN-YAP1-LOX-integrin β1 axis in macrophage infiltration in GBM, and demonstrate a possibility of improving GBM treatment by targeting this axis-mediated macrophage recruitment.

Citation Format: Peiwen Chen, Alan Y. Wang, Ronald A. DePinho. Lysyl oxidase secreted by PTEN-deficient glioblastoma cells recruits macrophages and promotes malignant growth [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 117.
Abstract 1170: NCI-H1975 L858R/T790M/C797S isogenic cell line for next-generation EGFR inhibitor screening
Authors: Hao Feng , He Feng , Zhang Wenna , Bai Zhaoshuai , Ning Jinying
Published: August 2018

Non-small-cell lung cancer (NSCLC) is the most common cause of cancer death. Over-activation of EGFR occurs in 13%~23% of NSCLC. The identification of EGFR as a cancer driver gene had led to rapid development of NSCLC targeted therapy, but the mutation of EGFR during treatment can cause drug resistance and cancer relapse. For example, T790M mutation causes resistance to the first generation of EGFR inhibitor Erlotinib and C797S mutation contributes to the resistance to the 3rd EGFR inhibitor AZD9291. There are several human cell lines for T790M mutation research, but there is not yet any primary human cancer cell line with C797S mutation. In the current study, a human isogenic EGFR C797S mutation cell line was generated through introducing nucleotide mutation into the EGFR gene in NCI-H1975 cell line using CRISRP technology, which originally bears L858R and T790M mutations of EGFR. First, the sgRNA sequence around the exon-20 of EGFR gene was screened using CRIPSR plasmid. Second, the donor plasmid with the homology arm containing exon-20 of EGFR and selecting marker was constructed and co-transfected into the parental cell line. Then, the NCI-H1975 C797S isogenic cell line was obtained and confirmed after screening over 100 single clones using the PCR method. The NCI-H1975 C797S isogenic cell line was resistant to AZD9291 but sensitive with EAI045 (the potential 4th generation EGFR inhibitor) combined with cetuximab. These data indicate that our NCI-H1975 L858R/T790M/C797S isogenic line is a useful model for next generation EGFR inhibitor study.

Citation Format: Feng Hao, Feng He, Wenna Zhang, Zhaoshuai Bai, Jinying Ning. NCI-H1975 L858R/T790M/C797S isogenic cell line for next-generation EGFR inhibitor screening [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 1170.
Abstract 1170A: Organoids: A new tool for the prediction of breast cancer patients' outcome
Authors: Roscigno Giuseppina , Cirella Assunta , Affinito Alessandra , Palma Francesco , Albero Maurizio , Messere Martina , Gelormini Martina , Cocca Lorenza , Thomas Renato , Condorelli Gerolama
Published: August 2018

Breast cancer is one of the leading causes of cancer mortality among women. The main causes of death are related to recurrence and metastasis. One major limitation in the breast cancer research field is that there are few in vitro models of breast cancer able to predict clinical patients' outcome. The main reason of this failure is that the present models do not take complexity or heterogeneity into account. Therefore, innovative models are now required to better represent tumor fidelity. To address this issue, we developed an in vitro 3D organoid culture system using primary human breast cancer tissue. Organoids are miniature forms of tissues that exhibit three-dimensional architecture and are able to maintain phenotypical properties cultured in a dish. Therefore, they could be used as models for diseases, including cancer. A major difficulty in the development of such models is to identify in vitro conditions that preserve the breast cancer phenotypes observed in vivo. For this reason, we isolated organoids from breast cancer patients and optimized the organoids growing conditions. We used a specialised medium and matrix (Cultrex Trevigen) required for supporting cell growth as it occurs in the human body. Then, we decided to test whether the obtained organoids could be used as an in vitro prediction tool. First, we performed immunofluorescence assay to assess the preservation of patient architecture (CK14, CK18 and E cadherin) and clinical phenotype (HER2, ER, PR). Then, we used an innovative chemotaxis assay in 3D collagen gels for analysing organoids cell invasion. It is based on a chamber in which a chemoattractant gradient is generated by diffusion through a porous membrane for mimicking blood microenvironment. Then we analysed the morphological changes after chemotherapeutics treatment to correlate the organoids response with patient tumor behaviour. Thus, organoids can be considered as a new tool for studying breast cancer and developing personalized medicine approaches for this disease.

Citation Format: Giuseppina Roscigno, Assunta Cirella, Alessandra Affinito, Francesco Palma, Maurizio Albero, Martina Messere, Martina Gelormini, Lorenza Cocca, Renato Thomas, Gerolama Condorelli. Organoids: A new tool for the prediction of breast cancer patients' outcome [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 1170A.
Abstract 118: Immuno-modulation of macrophages by ovarian cancer stem cells in an in vitro 3D spheroid platform
Authors: Raghavan Shreya , Mehta Geeta
Published: August 2018

The ascites microenvironment of ovarian cancers is enriched in ovarian cancer stem cells (OvCSCs) and macrophages (MPs). The immune system is complicit in the progression, chemoresistance and metastasis of ovarian cancer, yet little is known about the exact nature of interactions between OvCSCs and MPs, especially in the malignant ascites microenvironment. Here, we describe the use of the 3D in vitro hanging drop spheroid platform to study the reciprocal interactions between OvCSCs and MPs. Hetero-spheroids contained: i) monocyte-derived Macrophages (MP); and ii) OvCSCs (ALDH+ CD133+ OVCAR3). For immuno-modulation, we characterized MP polarization markers by flow cytometry and gene expression analysis. Using qPCR, we quantified changes in IL6, IL10, IL12, and Wnt7A, to understand signaling involved in OvCSC/MP hetero-spheroids. CD68 expression (~50%) was observed in OvCSC/MP hetero-spheroids, indicating the presence of MPs. OvCSCs drove higher CD206 expression in MPs (75%) when compared to unsorted ovarian cancer cells (OvCa; 40%). Even if MPs were pre-polarized to inflammatory M1 (HLA-DR+ CD206-), co-culture with OvCSCs reversed the M1 phenotype, and strongly induced CD206 expression. Pre-polarized M2 MPs resulted in 2-fold increase in ALDH+ cells in hetero-spheroids. Apart from CD206, MPs in hetero-spheroids also expressed iNOS, IFN-ϒ, and CD163. Gene expression analysis revealed increased immuno-suppressive IL10 in hetero-spheroids, with more IL10 in OvCSC/MP (3.5 fold) compared to OvCa/MP. OvCSC/MP and OvCa/MP spheroid also had consistently elevated (2-3 fold) increase in IL6 gene expression, consistent with the importance of the IL6/STAT3 axis in both cancer stem cell and macrophage signaling. Lastly, Wnt7A was significantly elevated in both differentiated MPs, and OvCSC/MP spheroids, indicating reciprocal trophic and immuno-suppressive signaling components at play. The 3D spheroid model can simulate biological interactions between OvCSCs and MPs within the malignant ascites. We describe that OvCSCs primarily polarize macrophages into a mixed phenotype that express both inflammatory and pro-tumoral markers. We believe that the putative involvement of Wnt7a in OvCSC/MP interactions drives this phenotype, and could have functional implications for tumorigenicity, response to chemotherapeutics and metastatic potential. This work was supported by the DOD OCRP W81XWH-13-1-0134, MIOCA, Rivkin Center for Ovarian Cancer and NIH T32DE00007057-41 and P30CA046592.

Citation Format: Shreya Raghavan, Geeta Mehta. Immuno-modulation of macrophages by ovarian cancer stem cells in an in vitro 3D spheroid platform [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 118.
Abstract 1182: Exploring longitudinal intra-tumor heterogeneity in cancer using whole genome sequencing and RNA rescue
Authors: Parulkar Rahul , Benz Steve , Vaske Charlie , Radenbaugh Amie , Szeto Christopher
Published: August 2018

We present a methodology for confidently characterizing subclonal exonic variants by pairing whole genome sequencing (WGS) with transcriptomics (RNAseq). We demonstrate the utility of this method by studying subclonal population changes in longitudinally collected samples.

Detection of variants specific to minority subclones has ordinarily only been achievable with very high-depth sequencing obtained by whole exome (WES) or targeted sequencing, and most available tools for studying subclonality require WES data as input. Although WGS provides more coverage breadth than WES, identifying subclonal mutations by WGS alone is difficult due to reduced read support for each variant. Detecting minority variants in WGS data is made especially difficult when tumor purity is low and subclonality is high. RNAseq is typically performed at high-depth and may be useful for replacing WES in detecting subclonal variants.

Our method has two steps: 1) Use WGS to establish a low-confidence preliminary set of variants present in the tumor, and 2) bolster the confidence in those variants by observing whether the variants are expressed in the RNAseq. We used this methodology to generate WES-like data from WGS+RNAseq in simulated data, and show that we can correctly identify subclonal populations using publicly available tools designed for WES data. Additionally, we demonstrate using this method to characterize the evolutionary lineage of the tumor population in a patient who was biopsied multiple times throughout several treatments, for whom only WGS and RNAseq data is available. Our proposed method resulted in 60% more confident variants than its WGS-only counterpart.

As tumor tissue availability is low and cost of sequencing is substantial, the choice of which molecular characterizations to perform is difficult. Here we show that paired WGS and RNAseq can be leveraged to infer information typically only obtained from WES, in addition to providing intergenic and expression information.

Citation Format: Rahul Parulkar, Steve Benz, Charlie Vaske, Amie Radenbaugh, Christopher Szeto. Exploring longitudinal intra-tumor heterogeneity in cancer using whole genome sequencing and RNA rescue [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 1182.
Abstract 119: Immunotherapy with dendritic cells inhibited tumor growth on an ID8 orthotropic mouse model of ovarian cancer
Authors: Kim Min-Je , Kim Joo-won , Kim Ju-hyun , Lee Young-Jae , Lee Shin-Wha , Kim Yong-Man
Published: August 2018

Background and Purpose: Ovarian cancer is the most frequent cause of death from gynecologic malignancy. Recently, immunotherapies have been suggested as ways to treat this malignancy. However, the ideal of immunotherapy has not been realized yet in ovarian cancer patients. Therefore, we investigated effects of monocyte-derived dendritic cells (mono DCs) and new-generation DCs subset (new DCs) on an ID8 orthotropic mouse model of ovarian cancer.

Methods: Mono DCs were prepared from bone marrow of C57BL/6 mice. We isolated monocyte from bone marrow by monocyte isolation kit. Isolated monocyte was incubated for 7 days with IL-4 and GM-CSF. In addition, monocytes were pulsed with LPS and ID8 tumor lysate while incubating. Likewise new DCs were isolated from bone marrow of C57BL/6 mice. We isolated lineage negative cells from bone marrow using lineage cell depletion kit. Isolated cells were incubated with IL-4 and GM-CSF; also the cells were pulsed by ID8 tumor lysate and Rg3, which is a ginsenoside. Orthotropic model of ID8 was made on C57BL/6 mice. We injected 5x106 cells into peritoneal cavity. 4 weeks after cell injection, mice were grouped into three groups, which were vehicle, mono DCs and new DCs. Mice were injected with mono DCs and new DCs. 5x106 cells of DCs were injected 1 time/week for three weeks. One week later, mice were sacrificed and organs were harvested such as peritoneum, phren, ovary and tumor mass for histologic analysis.

Results: DCs treated groups showed lower ascites formation than vehicle group. Ascites were fewest in new DCs group. Survival rate was lowest in vehicle group. Each survival rate is 0% in vehicle, 63% in new DCs and 80% in mono DCs. Also tumor growth at ovary was more decreased in mono DCs and new DCs group. In addition, mono DCs-treated mice showed low level of metastasis to other organs.

Conclusion: Immunotherapy with dendritic cells showed inhibition of tumor growth and metastasis on mouse ovarian cancer. These results indicated that DCs treatments are able to be a potential therapy for ovarian cancer. It also could have synergy with the combined treatment of existing anticancer drugs. However, there are several limitations such as a relatively high dose of DCs and the procedure of isolating DCs needed large amount of bone marrow. We will continue to study and improve these issues.

Citation Format: Min-Je Kim, Joo-won Kim, Ju-hyun Kim, Young-Jae Lee, Shin-Wha Lee, Yong-Man Kim. Immunotherapy with dendritic cells inhibited tumor growth on an ID8 orthotropic mouse model of ovarian 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 119.
Abstract 120: Local immune cytolytic activity stratifies clinical outcome and is linked to the immune microenvironment in breast cancer
Authors: Kawaguchi Tstutomu , Qi Qianya , Peng Xuan , McDonald Kerry-Ann , Narayanan Sumana , Young Jessica , Liu Song , Yan Li , Takabe Kazuaki
Published: August 2018

Purpose: Although a recent genomic landscape study identified molecular and genetic signatures of immune cytolytic activity (CYT) related to immune-mediated cancer elimination, less is known about the clinical relevance of CYT in the tumors linked to immune microenvironment in breast cancer. The aim of our study was to assess whether intratumor CYT associates with genetic alterations and tumor immune microenvironment, which impacts survival in breast cancer patients.

Experimental Design: We utilized genomic data from primary samples of 1,090 breast cancer patients with clinicopathologic information from The Cancer Genome Atlas (TCGA). We developed an immunogenomics pipeline that correlates CYT with clinical outcome and intratumor immune microenvironment, including infiltrating immune cell composition.

Results: Breast cancer displays a range of intratumor CYT. Patients with high CYT showed significantly better prognostic outcome, independent of age, hormonal status, and stage. CYT also has a strongly positive association with the expression of immune checkpoint genes such as PD1, PD-L1, and CTLA4, as well as regulatory T-cell (Treg) markers such as FOXP3 and CCR4. Enrichment of immune-response gene sets was observed in the high-CYT tumors. CYT was associated with higher composition of immune-elimination cells such as CD8+ T-cell, CD4+ T-cell, gamma delta T-cell, and M1 macrophage, as opposed to negatively associated with immunosuppressive cells, such as Treg and M2 macrophage. High CYT was also associated with improved survival in tumor-infiltrating lymphocyte (TIL)-positive breast cancer.

Conclusions: Patients with high CYT breast cancers show improved survival, likely due to high intratumor immunogenicity. CYT could also be used as a potential biomarker for immunologic response within tumors.

Citation Format: Tstutomu Kawaguchi, Qianya Qi, Xuan Peng, Kerry-Ann McDonald, Sumana Narayanan, Jessica Young, Song Liu, Li Yan, Kazuaki Takabe. Local immune cytolytic activity stratifies clinical outcome and is linked to the immune microenvironment 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 120.
Abstract 1205: Long-term survival of children with acute lymphoblastic leukemia, according to treatment regimen, in a regional French population
Authors: Gauthier Sophie , Mounier Morgane , Girard Stéphanie , Briandet Claire , Carli Paule Marie , Maynadie Marc
Published: August 2018

Acute Lymphoblastic Leukemia (ALL) is the main neoplastic disease in children. Treatment is based on chemotherapy associated or not to bone marrow transplantation. The 5-year survival rate in European children is reported as 86% but long term survival data are not available. We investigated the 20 year Overall Survival (OS) and Net survival (NS) of the patients diagnosed in the population of the Côte d'Or area in France. 162 cases were diagnosed in the population of the Côte d'Or area between 1970 and 2015. Cases diagnosed between 1970 and 1979 (n=29) were not formally registered in the registry database but data were available through the unique regional, reference hematology laboratory. All cases were followed until 01 01 2017. The treatment regimens that were used were as follows in chronological order (from the earliest to the most recent); LAL 76 and 80; the FRALLE 83, 87 and 89 until 1993; the FRALLE 93 from 1993 to 2001 and then the FRALLE 2000. The 20-y OS and NS of ALL was respectively 66% and 67%. It was 59% in boys but 75% in girls (p=0.04). No statistical difference was found according to age. According to lineage subtype, the 20-y NS was 82% in B-ALL, 65% in T-ALL and 34% in ALL, not otherwise specified (p<0.001). According to treatment regimen, the 20-y-NS was 51% before the use of the FRALLE 93, compared to 71% for cases treated by the FRALLE 93 regimen and 95% for those treated with the FRALLE 2000 regimen (p<0.001). The survival was 95% irrespective of the time of diagnosis following introduction of the FRALLE 2000 regimen. Data on long term survival of ALL in children are scarce. Our results show 1) a very high 20 year survival rate indicating the efficacy and safety of the treatment regimens used, 2) the utility of randomized clinical trials to define new standards of care.

Citation Format: Sophie Gauthier, Morgane Mounier, Stéphanie Girard, Claire Briandet, Paule Marie Carli, Marc Maynadie. Long-term survival of children with acute lymphoblastic leukemia, according to treatment regimen, in a regional French population [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 1205.
Abstract 1221: Chronic lymphocytic leukemia risk variants are associated with alteration of epigenetic states in regulatory regions
Authors: Yan Huihuang , Tian Shulan , Kleinstern Geffen , Slager Susan
Published: August 2018

Chronic lymphocytic leukemia risk variants are associated with alteration of epigenetic state in regulatory regions The vast majority of disease-associated single-nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWASs) reside in noncoding genomic regions. Functional impact of noncoding casual variants on target gene expression often involves regulatory mechanisms, typically through altering local chromatin accessibility, histone modifications, transcription factor (TF) binding affinity and chromatin interactions. In chronic lymphocytic leukemia (CLL), we and others have identified 41 GWAS risk variants, whose mechanism of action in CLL etiology remains largely unknown. In this study, we aim to decipher the regulatory potential of these variants and to better understand the mechanisms contributing to dysregulation of genes implicated in CLL pathogenesis. We performed ChIP-seq for H3K4me3, H3K4me1, H3K27ac and H3K27me3 in CLL. In addition, we also analyzed over 250 public ChIP-seq, ATAC-seq, DNase-seq, FAIRE-seq, and chromatin interaction data in CLL, B cells and/or lymphoblastoid cell lines. Comparing the 41 index SNPs and the nearby SNPs they associated with in linkage disequilibrium (R2 at least 0.5 in the EUR ethnic group in 1000 Genomes Project) to the above epigenetic data sets revealed overlaps with regulatory regions in 38 of the risk loci, with 28 of the loci overlapping super-enhancers. We used two approaches to elucidate the mechanisms of potential SNP causality. First, we used GATK UnifiedGenotyper to infer genotype for the SNPs that overlapped open chromatin regions and ChIP-seq peaks, by which evidence of imbalance between reference and alternative allele was identified at heterozygous sites. Second, for SNPs located within open chromatin regions or ChIP-seq peaks, we used FIMO program to scan the 100bp sequences centered on the SNPs for significant matches (p=1e-05) to the position weight matrices in five TF binding motif databases; SNPs that had TF motifs altered by the alternative alleles were retained. Together, these two approaches revealed evidence for allele imbalance or TF binding motif alterations at 36 of the 38 CLL risk loci, suggesting the generality of epigenetic regulation in CLL pathogenesis. Further analysis of chromatin interaction, gene expression and expression quantitative trait loci data will likely link the casual SNPs to their target genes.

Citation Format: Huihuang Yan, Shulan Tian, Geffen Kleinstern, Susan Slager. Chronic lymphocytic leukemia risk variants are associated with alteration of epigenetic states in regulatory regions [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 1221.
Abstract 1223: Significance of GSTM1 and GSTT1 gene polymorphism to breast cancer susceptibility in Nigerian women
Authors: Ogunlana Olubanke O. , Ortiseweyinmi Omaghomi , Ajoke Sadiq , Fatiregun Omolara , Rotimi Solomon O. , Adegboye Bose E. , Iweala Emeka E. , Igbinoba-Adebayo Angie O.
Published: August 2018

Human glutathione-S-transferases play a key role in the metabolism of drugs and environmental chemicals. There have been conflicting reports on the association of breast cancer susceptibility with null genotypes of glutathione-S-transferase (GST) classes of mu and theta (GSTM1 and GSTT1). However, this is the first report of the association of null genotypes of GSTs with breast cancer patients from Nigerian population. By multiplex PCR, we examined the null genotypes of GSTM1 and GSTT1 in relation to breast cancer risk in Nigerian women. The case-control study included 56 clinically diagnosed breast cancer patients and age-matched control participants. Odds ratio (OR) and 95% confidence interval (Cl) from conditional logistic regression model were used to estimate the association between GSTM1 and GSTT1 subtypes and breast cancer risk. The frequencies of GSTM1 and GSTT1 null genotypes in breast cancer (BC) patients differed from healthy controls (HC) (61% in BC vs. 39% in HC and 66% in BC vs. 34% in HC for GSTM1 and GSTT1 respectively). GSTM1 and GSTT1 null genotypes and their combinations were associated with increased breast cancer risk [OR = 3.06 (95% Cl 0.98-9.48)], [OR = 14.06 (95% Cl 3.02-70.6)] and [OR = 6.98 (95% Cl = 0.11-16.5)] respectively. The study showed an increased breast cancer risk in patients with GSTT1 homozygous gene deletions with relative risk (RR) value of 5.6 than those with GSTM1 (RR = 1.77). In conclusion, the data from our work provide evidence of increased risk of breast cancer associated with GSTM1 and GSTT1 homozygous gene deletions in women from Nigeria.

Citation Format: Olubanke O. Ogunlana, Omaghomi Ortiseweyinmi, Sadiq Ajoke, Omolara Fatiregun, Solomon O. Rotimi, Bose E. Adegboye, Emeka E. Iweala, Angie O. Igbinoba-Adebayo. Significance of GSTM1 and GSTT1 gene polymorphism to breast cancer susceptibility in Nigerian women [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 1223.
Abstract 1233: Reducing sequence artifact in clinical sequencing of treatment-naïve NSCLC patient using molecular barcoding system
Authors: Namba Kei , Tomida Shuta , Takahashi Yuta , Kurihara Eisuke , Ogoshi Yusuke , Yosioka Takahiro , Torigoe Hidejiro , Sato Hiroki , Shien Kazuhiko , Yamamoto Hiromasa , Soh Junichi , Toyooka Shinichi
Published: August 2018

Background: Recently the clinical significance of compound mutations in cancer relapse and/or acquired resistance has been reported. Amplicon-based deep sequence enables analysis of tiny amount of input DNA, however, a major problem of these high-throughput DNA sequencing is the high rate (~1%) of errors causing potential sequence artifact. Molecular barcoding system, which has been developed to reduce sequencing artifacts as well as to improve mutation detection accuracy, was applied to analyze the frequency of compound EGFR mutations in early stage non-small-cell lung cancer (NSCLC) patients who undergo surgical resection without any presurgical treatment is less described.

Materials and Methods: From 590 consecutive patients, 64 adenocarcinoma cases who underwent surgical resection for primary lung cancer were analyzed by using amplicon-based targeted sequencing method incorporating molecular barcodes in order to detect genetic alterations of 47 genes including EGFR.

Results: Out of 64 samples, EGFR common mutation profiles of 63 (98.4%) by molecular-barcode sequencing corresponded to those by clinical test. Uncommon EGFR mutations were detected in 7 cases (10.9%). Among the three types of EGFR major mutation, G719X (60%, 3/5) showed a significantly higher incidence of EGFR double mutations than L858R (9.5%, 4/42) or Ex19del (0%, 0/17) (p = 0.0052). Co-mutations of other genes were observed in 20 EGFR-mutated cases. TP53 mutations were frequently detected in younger age (p = 0.0066) and pStage II-III cases (p = 0.042).

Conclusion: Amplicon sequencing incorporating molecular barcoding system is a feasible approach to characterize predictive or prognostic mutations in early stage treatment naïve NSCLC patients, revealing those case who harbor EGFR G719X mutation have a significantly higher incidence of EGFR double mutations, likely to have worse prognosis.

Citation Format: Kei Namba, Shuta Tomida, Yuta Takahashi, Eisuke Kurihara, Yusuke Ogoshi, Takahiro Yosioka, Hidejiro Torigoe, Hiroki Sato, Kazuhiko Shien, Hiromasa Yamamoto, Junichi Soh, Shinichi Toyooka. Reducing sequence artifact in clinical sequencing of treatment-naïve NSCLC patient using molecular barcoding system [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 1233.
Abstract 1245: Identification of germline variants in cancer susceptibility genes in patients with hereditary breast and ovarian cancer syndrome by massive parallel sequencing in Argentinean population
Authors: Franco Alejandra , Orti Fernando , Perdomo Sandra , Riggi Cecilia , Frecha Cecilia , Oliver Javier
Published: August 2018

Breast cancer is the most frequent cancer and ovarian cancer the seventh most frequent cancer among females worldwide, representing approximately 25% and 4% of all cancers. In Argentina, breast cancer and Ovarian cancer cause 6163 and 1332 deaths per year, respectively. Both breast and ovarian cancers are heterogeneous diseases composed of different tumor types with distinctive features and behaviors. The main risk factors for breast and ovarian cancer include age, family history, and genetics.The genetic components of both of the diseases have been well established, contributing to up to 10% of all breast cancer cases and 15% of all ovarian cancer cases.The two major susceptibility genes for both diseases are BRCA1 and BRCA2, and several other susceptibility genes have been identified. However, in the majority of high-risk breast and/or ovarian cancer (HBOC) families, the genetic predisposition factors remain unidentified, making the genetic counseling of these families challenging. The aim of the current study is to utilize an NGS approach to identify genetic factors that predispose individuals to hereditary breast and/or ovarian cancer (HBOC) in the high-risk Argentinian BRCA1/2 mutation-negative HBOC patients.16 patients were analyzed, the DNA was extracted from a blood samples and was subjected to a targeted massively parallel sequencing platform comprising 141 cancer predisposition genes. We detected in these patient 6 pathogenic variants in SBDS, FANCA, MC1R, WRN, MSR1 and SDHD genes. The effect of these variants are of type: non-synonymous (67%) and stop codon gains (33%). We also found 6 variants of uncertain significance (VUS) in APC, RAD50, SDHB, FANCD2, MLH1 and CDH1 genes.In conclusion, the identification of new variants could help to discover new genes associated to HBOC in the population of Argentina.These findings provide an excellent premise for further studies and could be utilized in the design of more efficient clinical management strategies for HBOC.

Citation Format: Alejandra Franco, Fernando Orti, Sandra Perdomo, Cecilia Riggi, Cecilia Frecha, Javier Oliver. Identification of germline variants in cancer susceptibility genes in patients with hereditary breast and ovarian cancer syndrome by massive parallel sequencing in Argentinean population [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 1245.
Abstract 1256: Lynch syndrome premalignancy upregulates immune checkpoints independently from neoantigen and mutational rates
Authors: Chang Kyle
Published: August 2018

Colorectal carcinomas in Lynch syndrome (LS) patients arise in a background of mismatch repair deficiency that leads to the accumulation of high numbers of mutations and neoantigens, thus causing infiltration by abundant tumor-infiltrating lymphocytes, a unique immune profile with upregulation of immune checkpoints, and response to immunotherapy. However, there is still a knowledge gap with regards to the level of immune activation and the assessment of mutation and neoantigen rates in LS premalignancy. We performed whole transcriptomic analysis using next-generation sequencing in a total of 28 colorectal polyps (26 tubular adenomas and 2 hyperplastic polyps) from 21 patients diagnosed with LS (n=11) and FAP (n=10) as comparators and a model of mismatch repair proficient colorectal premalignancy.Overall, LS polyps presented with low mutational and neoantigen rates but displayed a strinking immune activation profile characterized by CD4 T-cells, proinflammatory (TNF, IL12) and checkpoint molecules (LAG-3 and PD-L1). This immune profile was independent of mutational rate, neoantigen formation, and MMR status. In addition, we identified a small subset of LS polyps with high mutational and neoantigen rates that were secondary to accumulation of indels enriched for deregulation of DNA damage repair pathways (ATM and BRCA1 signaling). Our findings challenge the canonical model, based on the observations made in carcinomas, that emphasizes a dependency of immune activation on the acquisition of high levels of mutations and neoantigens, thus opening the door to the implementation of immune checkpoint inhibitors and vaccines for cancer prevention in Lynch syndrome.

Citation Format: Kyle Chang. Lynch syndrome premalignancy upregulates immune checkpoints independently from neoantigen and mutational rates [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 1256.
Abstract 1263: TGF-ß inhibition as a novel strategy to prevent breast cancer brain metastases
Authors: Pinti Mark V.
Published: August 2018

Background: Incidence of breast cancer brain metastases (BCBM) is on the rise due to improved management of systemic disease and ranges from 15-20% in women with disseminated breast cancer. Common chemotherapeutic strategies have limited efficacy for brain metastases due to the presence of the blood brain barrier (BBB). Prevention of metastasis after diagnosis of primary breast tumors may lead to new treatment strategies. TGF-ß is a biomolecule in the metastatic pathway and inhibition of its expression can be achieved by treatment with the antihypertensive agent Losartan. Herein we hypothesized that treatment with Losartan will decrease metastatic burden and improve survival in a preclinical model BCBM.

Methods: Athymic female nude mice were separated into four groups as follows: Vehicle, (saline, 50µL/day), SB431542 (Inhibitor, 5mg/kg/day), Low Dose Losartan (10mg/kg/day) and High Dose Losartan (25mg/kg/day). On day 7 mice were intracardially injected with 175,000 cells of either JIMT-1-Br-LUC-GFP (HER2+) or MDA-MB-231Br-LUC (TNBC) breast cancer cell lines. Tumor burden was monitored once weekly utilizing bioluminescent imaging. Mice were allowed to progress until neurological symptoms arose. Following euthanasia, brains were extracted, sectioned and analyzed to determine number of metastatic lesions and size.

Results: With regard to survival, no significance was shown in the JIMT-1 (HER2+) metastatic model. The MDA-MB-231Br (TNBC) model demonstrated an increase in survival in all treatment groups compared to vehicle. End time-point analyses showed no difference in metastases number in either model, however, the low dose treatment group in the MDA-MB-231Br model had a smaller brain burden of metastases than high dose treatment as well as inhibitor treatment.

Conclusions: Losartan reduced metastatic seeding in the MDA-MB-231Br (TNBC) brain metastasis model, but had little to no effect in the JIMT-1 (HER2+) model.

Citation Format: Mark V. Pinti. TGF-ß inhibition as a novel strategy to prevent breast cancer brain metastases [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 1263.
Abstract 1271: Restricted feeding of a high-fat diet to the dark phase of the day attenuates mammary tumorigenesis in MMTV-PyMT mice
Authors: Sundaram Sneha , Yan Lin
Published: August 2018

Obesity is a risk factor for breast cancer. Chronic overeating during the rest phase of the day leads to metabolic dysfunction and obesity. Lifestyle changes including restriction of meal times may be successful weight loss strategies. In the present study, we tested the hypothesis that restricted feeding of a high-fat diet to the dark phase (the active phase) of the day reduces diet-enhanced mammary tumorigenesis in an MMTV-PyMT transgenic mouse model. Mice (female) were fed the AIN93G diet (16% of energy from soybean oil) or the high-fat diet (45% of energy from soybean oil) with or without restricted feeding to the dark phase (12 hours) over eight weeks of the study. The body fat mass of the restricted feeding group was lower than the high-fat group but similar to the AIN93G control group. The mammary tumor latency was 5.8, 7.0, and 6.4 weeks for the control, high-fat and high-fat restricted groups, respectively. Restricted feeding reduced mammary tumor progression by 58% compared to the unrestricted feeding of the high-fat diet. Compared to the AIN93 diet, the high-fat diet significantly increased plasma concentrations of plasminogen activator inhibitor-1, monocyte chemoattractant protein-1, resistin, leptin, insulin, angiopoietin-2, hepatocyte growth factor and vascular endothelial growth factor. The restricted feeding reduced concentrations of the aforementioned variables in plasma, except resistin, leptin, and insulin. In summary, restricted feeding of the high-fat diet to the dark phase reduces diet-enhanced mammary tumorigenesis. This protection of the restricted feeding against breast tumorigenesis may be associated with its actions in attenuating adipogenesis and production of related inflammatory cytokines and angiogenic factors.

Citation Format: Sneha Sundaram, Lin Yan. Restricted feeding of a high-fat diet to the dark phase of the day attenuates mammary tumorigenesis in MMTV-PyMT mice [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 1271.
Abstract 1275: A role for FGF2 in visceral adiposity-associated mammary epithelial transformation
Authors: Benham Vanessa , Chakraborty Debrup , Bullard Blair , Bernard Jamie J.
Published: August 2018

Obesity is a leading risk factor for post-menopausal breast cancer, and this is concerning as 38% of Americans are obese. Furthermore, 40% of cancer diagnoses in 2014 were associated with overweight/obesity. Despite the epidemiologic link between obesity and breast cancer risk, the underlying mechanism responsible is unknown. We recently published that VAT releases FGF2 and stimulates the transformation of skin epithelial cells. As obesity is differentially associated with many cancer types, this mechanistic link could be translational to other cancers. Specifically, FGF2 and FGFR1 are implicated in breast cancer progression, but their role in tumor formation is unknown. Therefore, I hypothesize that VAT-derived FGF2 plays a translational role in promoting mammary tumor formation.

Citation Format: Vanessa Benham, Debrup Chakraborty, Blair Bullard, Jamie J. Bernard. A role for FGF2 in visceral adiposity-associated mammary epithelial transformation [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 1275.
Abstract 1277: 3-Isothiocyanato-1-propene as biomodulatory agent in ameliorating phenobarbital induced alterations in profile of detoxifying enzymes in different metabolic sites of Wistar rats
Authors: Arora Saroj , Bhushan Sakshi , Vig Adarsh Pal , Kaur Pardeep , Shergill Robin
Published: August 2018

Backgound: Human exposure to xenobiotics is responsible for increased susceptibility to genetic and epigenetic changes. These changes are further accountable for disruption of pathways involved in cell proliferation, apoptosis, differentiation and senescence. Among array of plant products, that play an imperative role against such adverse catastrophes, the naturally occurring isothiocyanate known as 3-Isothiocyanato-1-propene (AITC) possesses abundant biological activities of therapeutic interest.

Purpose of the study: Hence, considering these facts, the present study was planned to analyse four metabolic sites viz., liver, kidneys, stomach and lungs for protective activities of AITC against phenobarbital induced damage in Wistar rats.

Methodology: The rats were divided into eight groups and treatments were given intraperitoneally for five days followed by sacrificing of animals on sixth day. The organs were homogenized and analysed for biochemical parameters and histopathology.

Results: AITC in all the metabolic sites attenuated the levels of cytochrome dependent oxygenases, phase II detoxifying enzymes (DT-diaphorase, γ-glutamyltranspeptidase and glutathione-S-transferase), cascade of antioxidant enzymes (superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase), membrane bound ATPases (Na+/K+-ATPase, Mg2+-ATPase, Ca2+-ATPase) and serum marker enzymes (SGOT, SGPT, direct bilirubin, indirect bilirubin, alkaline phosphastase, creatinine, blood urea nitrogen). Futhermore, the different doses of AITC (50, 100 and 150 µM/kg bw) resumed the necroinflammatory score by improving the piecemeal necrosis, focal lytic necrosis and portal inflammation.

Conclusion: The maximum efficacy of amelioration by AITC was observed in liver due to the fact that amount of these enzymes in metabolic sites other than liver is quantitatively low. Hence, AITC emerged as potent candidate for ameliorating the harmful effects of non genotoxic carcinogen (phenobarbital) by regulating its metabolism efficiently in rats. Owing to its useful functions, AITC can act as an important bioprotective agent.

Citation Format: Saroj Arora, Sakshi Bhushan, Adarsh Pal Vig, Pardeep Kaur, Robin Shergill. 3-Isothiocyanato-1-propene as biomodulatory agent in ameliorating phenobarbital induced alterations in profile of detoxifying enzymes in different metabolic sites of Wistar rats [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 1277.