bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2115: An authenticated in vitro model for prostate microenvironment studies utilizing prostate epithelial cells and stromal-derived cells
Authors: Rodriguez Luis G. , McDaniel Russell E. , Zhao Xiangshan , Zou Chaozhong
Published: August 2018

Prostate cancer remains one of the most common cancers diagnosed in men and one of the leading causes of cancer death in men. Tumor development and progression have been shown to be highly influenced not simply by the genetic makeup of a cell, but by its surrounding stroma, particularly fibroblasts. It has been demonstrated that prostate cancer-associated fibroblasts (CAFs, which are located marginal to the prostate tumor), differ from prostate normal-associated fibroblast (NAFs, which are located distal to the prostate tumor), on their contribution to tumor progression. However, human prostate cancer in-vitro model systems have focused largely on prostate cancer epithelial cells exclusively. A need exists for a more physiologically relevant human cell model system to study prostate cancer progression within the context of its tumor microenvironment. In this study, we utilized prostate cancer-associated fibroblasts (CAFs), prostate normal-associated fibroblasts (NAFs) and normal prostate epithelial (PrE) cells; all three lines were immortalized by hTERT (human telomerase reverse transcriptase) alone and they were continuously passaged for at least 15 passages without any indications of a decrease in growth rate. All cell lines express appropriate specific cell lineage markers for either fibroblasts or epithelial cells. Fibroblasts expressed TE7 and alpha smooth muscle actin (a-SMA), while prostate epithelial cells expressed cytokeratin 5, low levels of prostate specific antigen (PSA) and high levels of p63 throughout their continuous passage; all characteristics in accord with their primary cell counterparts. Next, cell proliferation was measured for various prostate-derived epithelial cells under the influence of CAFs and NAFs cells. Normal prostate epithelial cell proliferation was inhibited and produced a visible morphological change in the cells in the presence of CAFs or CAF-conditioned medium. Meanwhile, the effects of stromal cells on prostate cancer cells was cell line dependent, demonstrating both promotion and inhibition of growth of selected cancer cells. Surprisingly, both CAFs and NAFs promoted cancer cell growth, but CAFs promoted a greater increase in cell proliferation than NAFs in some cancer cell lines. This study demonstrates that these three hTERT immortalized cells from human prostate are a valuable model system for the study of prostate cancer cell progression and tumor micro environment studies.

Citation Format: Luis G. Rodriguez, Russell E. McDaniel, Xiangshan Zhao, Chaozhong Zou. An authenticated in vitro model for prostate microenvironment studies utilizing prostate epithelial cells and stromal-derived 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 2115.
Abstract 2123: Myeloma derived macrophage inhibitory factor regulates BMSC IL6/8 via cMYC
Authors: Piddock Rachel E. , Marlein Christopher R. , Abdul-Aziz Amina , Auger Martin J. , Bowles Kristian M. , Rushworth Stuart A.
Published: August 2018

Background

Multiple Myeloma (MM) is a plasma cell malignancy dependent on the bone marrow microenvironment. Macrophage inhibitory factor (MIF) acts directly on malignant plasma cells affecting homing and chemotherapy resistance, however the adaptive effect that MM derived MIF has on the tumor microenvironment is not yet defined. Here we investigate the function of MM derived MIF in the MM microenvironment by examining its effects on bone marrow mesenchymal stromal cells (BMSC).

Methods

Primary MM and BMSC were obtained from patient bone marrow. Proteome Profiler Human XL Cytokine Array was used. Inhibitors including JQ1 were

purchased from Merck. In-vivo experiments were performed using 8-10 week old NSG mice.

Results

First we injected 1 x 106 MM.1S MIF-knock down (KD) cells or MM.1S control-KD cells (containing the pCDH-luciferase-T2A-mCherry construct) into the tail vein of 6-8 week old NSG mice. MIF-KD in MM cells resulted in animals with significantly reduced tumor burden and improved overall survival. To further investigate the role of MIF in regulating the BM microenvironment we stimulated primary human BMSC with biologically appropriate doses of recombinant MIF and then used Human XL Cytokine Array and cytokine specific ELISA to assay the supernatant from these MIF stimulated BMSC. Results show that MIF induces IL-6 and IL-8 protein secretion from primary BMSC. To examine the mechanism of action of these observations we used a panel of inhibitors to screen for potential pathways responsible for MIF induced BMSC derived IL-6 and IL-8 expression. The c-Myc inhibitor JQ1 inhibited MIF induced IL-6 and IL-8 expression. Next, we looked at whether c-Myc regulates BMSC pro-tumoral interleukin production in-vivo. We injected NSG mice via the tail vein with human myeloma cell line U266 and then randomized animals to two groups; treating with either JQ1 (50mg/kg, IP) or alternatively vehicle control for 5 days, after which bloods were taken

to assess murine IL-6 levels (IL-8 is deleted from the mouse genome). Results show that murine IL-6 was significantly reduced in the JQ1 treated animals (carrying human MM) compared to vehicle control treated animals.

Summary

MM derived MIF is pro-tumoral through induction of c-Myc and downstream IL-6 and IL-8 in the BMSC of the tumor micro-environment. Identification of this novel pro-tumoral crosstalk mechanism which exists between MM and the bone marrow stroma provides scientific rationale for the clinical evaluation of new therapeutic targets in MM.

Citation Format: Rachel E. Piddock, Christopher R. Marlein, Amina Abdul-Aziz, Martin J. Auger, Kristian M. Bowles, Stuart A. Rushworth. Myeloma derived macrophage inhibitory factor regulates BMSC IL6/8 via cMYC [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 2123.
Abstract 215: Reconstructing the Barrett's-dysplasia-adenocarcinoma sequence from patient-matched stem cells
Authors: Xian Wa , Zhang Yanting , Duleba Marcin , Wang Shan , McKeon Frank
Published: August 2018

Introduction: Both esophageal and gastric adenocarcinoma (EAC; GAC) evolve from intestinal metaplasia (Barrett's and gastric IM, respectively) in a multi-decade and multi-step process involving transitions through low- and high-grade dysplasia often referred to as the “Correa Sequence”. In early stage EAC, each of these lesions can be seen co-existing in the 2-D topology of the distal esophagus. We have adapted methods we originally developed for cloning normal stem cells of the gastrointestinal tract to capturing stem cells of each of these lesions. We anticipate that a clonal analysis of these stem cells will reveal key steps in the evolution of highly lethal EAC.

Methods: Libraries of stem cell clones were generated from a series of patient-specific endoscopic biopsies derived from normal, Barrett's, dysplasia, and EAC. Single cell-derived clones were analyzed by in vitro differentiation, whole genome expression analysis, and SNP-based copy number variation.

Results: Highly undifferentiated, ground state stem cells were cloned from multiple endoscopic biopsies of patients with early EAC. Based on sampling site and adjacent biopsy histology, tissue corresponding to normal esophagus, gastric epithelia, Barrett's, and EAC were taken in these biopsies dissociated for stem cell cloning. All the clones derived showed unlimited proliferative potential and the ability to differentiate to normal or diseased epithelia in vitro. Thus the normal esophageal and gastric stem cells gave rise to squamous and gastric epithelia, the Barrett's stem cells yielded intestinal metaplasia, and dysplastic and EAC clones yielded highly proliferative and disordered epithelia marked by a loss of cell polarity. In contrast to the germline genotypes of the normal stem cells, those from Barrett's, dysplasia, and EAC sustained increasingly large numbers of copy number variation events, single nucleotide variations, and chromosomal aneuploidies. Significantly, all single cell-derived clones of EAC yielded “intestinal” adenocarcinoma following xenografting to immunodeficient mice. We are presently exploiting the genomic alterations present in hundreds of sample clones from each patient to reconstruct the evolutionary events that accompanied the progression to a highly lethal cancer.

Conclusions: Stem cells from all stages of lesions along to the path to epithelial cancers can be cloned and independently propagated to yield insights into the evolution of cancer. In addition, these cloned cells should enable insights into intratumor heterogeneity, therapy resistance, and drug discovery.

Citation Format: Wa Xian, Yanting Zhang, Marcin Duleba, Shan Wang, Frank McKeon. Reconstructing the Barrett's-dysplasia-adenocarcinoma sequence from patient-matched stem 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 215.
Abstract 2165: Mini-patient-derived xenograft sensitive assay: A rapid systemic detection method for assessment of cancer therapeutics
Authors: Pan Xiaoqing , Zhang Feifei , Long Yuan , Liu Hui , Guo Lin , Cheng Jijun , Wen Danyi
Published: August 2018

Patient-derived xenografts (PDX) have a high predictive power for efficacy of anticancer therapeutics. Limitations such as engraftment failure and time consuming for establishment and expansion of PDX models for drug efficacy testing need to be overcome for immediate application in patient decision-making for therapeutics. We developed a rapid in vivo drug sensitivity assay system so-called OncoVee® Mini-PDX, in which patient-derived tumor cells were arrayed within hollow fiber capsules in vivo over 7 days and screened against clinical relevant regimens. For validation study, the Mini-PDX was assessed by comparing the drug response in PDX tumor-bearing mice to response in Mini-PDX (capsule-containing) mice. The correlation between PDX tumorgrafts assay and Mini-PDX assay was evaluated using PDX models generated from 21 cancer patients. In the 21 cases, the overall predictive accuracy of the PDX assay for sensitivity was 69% and resistance was 88%, respectively. We also extended the approach to the patients with advanced malignancies. We report clinical cases in which Mini-PDX guided treatment improved the outcomes of treated cancer patients. In sum, Mini-PDX assay based on the capsule implantation was developed and optimized for quick assessment of the chemosensitivity of patients' cancers and found to be compatible with that of PDX tumorgrafts assay. This method hold promise for application of personalized chemotherapy for cancer patients.

Citation Format: Xiaoqing Pan, Feifei Zhang, Yuan Long, Hui Liu, Lin Guo, Jijun Cheng, Danyi Wen. Mini-patient-derived xenograft sensitive assay: A rapid systemic detection method for assessment of cancer 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 2165.
Abstract 2168: Anti-cancer drug sensitivity assay using in vitro primary culture cells
Authors: Fujino Shiki , Miyoshi Norikatsu , Ohue Masayuki , Saso Kazuhiro , Mizushima Tsunekazu , Doki Yuichiro , Mori Masaki
Published: August 2018

Primary culture of cancer cells derived from an individual patient's tumor provides important information regarding the tumor character. We established a novel culture method for primary colorectal cancer (CRC) with phenotypic heterogeneity as a human tumor model, named isolated tumor-derived cancer cells (iCCs). The success rate of iCC growth in vitro was 100%, passage was 90%, and establishment of a xenograft model from iCC was 80%. The gene expression of the cultured cells was similar to the clinical tumors, and exhibited a ductal structure of the tumor in the xenograft model even after several passages. The present in vitro analyses allow us to predict the clinical efficacy of chemotherapeutic drugs. For this purpose, we examined the sensitivities of iCCs isolated from patients. In this study four patients with distant metastasis received FOLFOX (folinic acid, 5-fluorouracil, and oxaliplatin) chemotherapy according to the treatment guidelines, and in vitro drug sensitivity was evaluated using the cultured cells, compared with each parental tumor in the individual clinical course. It is a model to predict the effect of chemotherapy to the individual tumor. Our results showed that the effect of chemotherapy was poor in three patients and good in one patient. In their clinical courses, the tumor size increased in two patients and decreased in two patients. In vitro drug sensitivity results reflected the clinical course in three of the four patients. In conclusion, our primary culture model is a novel tool for the prediction of anti-cancer drugs in the clinical courses.

Citation Format: Shiki Fujino, Norikatsu Miyoshi, Masayuki Ohue, Kazuhiro Saso, Tsunekazu Mizushima, Yuichiro Doki, Masaki Mori. Anti-cancer drug sensitivity assay using in vitro primary culture 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 2168.
Abstract 2172: Dying tumor cells (tumor debris) stimulate the growth of 4T1 breast cancer tumor in female athymic nude mice
Authors: Roomi M Waheed , Niedzwiecki Aleksandra , Rath Matthias
Published: August 2018

Current cancer therapies are based on chemotherapy and radiation. These therapeutic approaches can initially reduce the tumor mass or tumor burden by killing tumor cells. It has been postulated that the resulting dying tumor cells, or tumor debris, can act as sources of tumor stimulation on surviving cells leading to reappearance of the cancer, and thereby drastically reducing the survival rate. In our study we investigated whether 4T1 debris induced by chemotherapeutic agent docetaxel would affect breast tumor growth in female nude mice. Female athymic nude mice were divided into three groups: Group 1 was inoculated with 4T1 cells; Group 2 with 4T1 cells together with their debris and Group 3 with debris alone. All mice were fed a regular diet. After four weeks, the mice were sacrificed; tumors were excised, weighed and processed for histology and immunohistochemistry for inflammation parameters. Tumor weight significantly increased in Group 2 mice compared to the control Group 1. Group 3 mice developed no tumors. Although the tumor histology for both Groups 1 and 2 were similar, there were significant differences in inflammatory parameters in the two groups. Tumors developed in Group 2 mice had intense staining patterns for TNF-alpha, IL-6, Ki-67, i-Nos and VEGF compared to tumors in the control Group 1. Our results show that dying cells from docetaxel treatment, or tumor debris, had stimulatory effect on growth of breast cancer 4T1 cells in nude mice which was associated with increased inflammation. This study represents a novel method to evaluate the effects of chemotherapy or radiation on surviving tumor cells and to investigate the effect of various inhibitors on the growth recurrence.

Citation Format: M Waheed Roomi, Aleksandra Niedzwiecki, Matthias Rath. Dying tumor cells (tumor debris) stimulate the growth of 4T1 breast cancer tumor in female athymic nude 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 2172.
Abstract 2204: Influence of chronic comorbidities on colorectal cancer screening adherence in a population-based Canadian cohort
Authors: Bhatia Dominika , Sutradhar Rinku , Tinmouth Jill , Singh Simron , Lipscombe Lorraine
Published: August 2018

Background: Regular screening for colorectal cancer (CRC) is associated with a lower stage at diagnosis and improved survival. National guidelines recommend periodic screening for adults aged 50-74 years. Chronic diseases may distract from regular screening and increase CRC burden. We sought to determine whether having certain chronic conditions is associated with a lower rate of CRC screening adherence.

Methods: Using linked healthcare databases from Ontario, Canada, we assembled a population-based cohort of adults aged 50-74 years, who were eligible and overdue for routine CRC screening (fecal occult blood testing > 2 years, sigmoidoscopy > 5 years, or colonoscopy > 10 years) at any point between April 1, 2004 and March 31, 2016. We implemented Andersen-Gill extended Cox models for recurrent events using an age time scale to examine the impact of chronic conditions on the relative rate (RR, 95% confidence interval, CI) of becoming adherent with periodic CRC tests, adjusted for the relevant time-varying covariates.

Results: During the 12-year observation window, included individuals contributed a total of 19,818,050 person-years spent overdue for CRC tests. Over 70% of all CRC tests performed during the study period were fecal occult blood tests. At baseline, of the 4,642,422 individuals that met the inclusion criteria, 31% had hypertension, 12% had diabetes, 9% had chronic obstructive pulmonary disease (COPD), 7% had mental illness, 5% had cardiovascular disease (CVD), 1.6% had congestive heart failure (CHF), and 0.1% had end-stage renal disease (ESRD). After adjustment for sociodemographic and health system factors, the highest rates of nonadherence were observed for ESRD on dialysis (RR 0.66, CI 0.63-0.68), CHF (RR 0.75, CI 0.75-0.76), COPD (RR 0.84, CI 0.83-0.84), CVD (RR 0.85, CI 0.84-0.85), diabetes (RR 0.86, CI 0.86-0.87), and mental illness (RR 0.88, CI 0.87-0.88). Hypertension (RR 0.98, CI 0.97-0.98) and ESRD with kidney transplant (RR 1.00, CI 0.84-1.19) were associated with modest to no risk.

Conclusion: The presence of a major chronic condition is associated with lower adherence to CRC screening. Future studies should explore reasons for lower CRC screening adherence in individuals with chronic conditions and the appropriateness of secondary cancer prevention and early diagnosis in this population.

Citation Format: Dominika Bhatia, Rinku Sutradhar, Jill Tinmouth, Simron Singh, Lorraine Lipscombe. Influence of chronic comorbidities on colorectal cancer screening adherence in a population-based Canadian cohort [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 2204.
Abstract 2205: Prediction model of CA125 among premenopausal women
Authors: Sasamoto Naoko , Babic Ana , Rosner Bernard A. , Vitonis Allison F. , Cramer Daniel W. , Tworoger Shelley S. , Terry Kathryn L.
Published: August 2018

Background: Cancer antigen 125 (CA125) is a membrane-bound glycosylated mucin that has been reported to be the most promising biomarker for ovarian cancer screening, although results from two large randomized trials comparing screening using CA125 and transvaginal ultrasound to usual care have shown no clinically significant difference in ovarian cancer mortality. A major limitation of CA125 as an ovarian cancer screening biomarker has been low specificity and variation between individuals by personal characteristics. Identifying personal characteristics that influence CA125 levels could be used to create personalized thresholds for CA125 for each individual, thereby improving its performance as an ovarian cancer screening biomarker. However, reports on factors that influence CA125 among premenopausal women are limited.

Methods: We evaluated the association between reproductive and lifestyle factors and CA125 among 828 premenopausal population-based controls enrolled in the New England Case-Control study between 1992 and 2008. CA125 was measured using the CA125II assay at the CERLab at Boston Children's Hospital. We developed a prediction model of log-transformed CA125 using stepwise linear regression with <0.15 as significance level for entry and stay considering factors associated with CA125 in postmenopausal women and ovarian cancer risk factors, such as age, body mass index (BMI), race, smoking status, age at menarche, oral contraceptive use and its duration, parity, endometriosis, tubal ligation, unilateral oophorectomy, hysterectomy, family history of ovarian cancer, previous history of cancer, genital powder use, and caffeine intake as candidate predictors.

Results: In our univariate analyses, older age and endometriosis were associated with significantly higher CA125 while tubal ligation, hysterectomy, and time since last menstrual period were associated with significantly lower CA125 (p<0.05). Age, endometriosis, tubal ligation, hysterectomy, smoking status, caffeine intake, and interval days since last menstrual period were selected in our final prediction model, which explained 6% of the total variability of log-transformed CA125 levels.

Conclusion: Efforts to validate this CA125 prediction model in an independent cohort of premenopausal women and evaluate whether using the personalized CA125 cutoff based on this prediction model discriminates cases and controls better than the single 35 cutoff are ongoing.

Citation Format: Naoko Sasamoto, Ana Babic, Bernard A. Rosner, Allison F. Vitonis, Daniel W. Cramer, Shelley S. Tworoger, Kathryn L. Terry. Prediction model of CA125 among premenopausal 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 2205.
Abstract 2216: A novel prognostic model based on the tumor and its microenvironment in tongue squamous cell carcinoma
Authors: Yu Pei , Wang Weiwang , Zhuang Zehang , Xu Jieyun , Liu Xiqiang
Published: August 2018

Objective: Pathological factors of tumor including tumor budding, invasive type and invasive depth has been reported to predict survival in tongue squamous cell carcinoma (TSCC). However, their prognostic value remains inconclusive and the role of tumor microenvironment is unknown. In the current study, both parameters of tumor and its microenvironment were examined and a new grading system associated with high impact on patient outcome has been proposed. Methods: A total of 246 patients with TSCC were included in this retrospective study. Using H&E stained sections, factors including pathological differentiation, T classification, lymph node metastasis (LNM), intensity of tumor budding, invasive pattern, depth, inflammation response (KM grade), tumor stroma percentage (TSP) were evaluated; the prognostic models including BD model (combination of tumor budding and invasive depth) and GMS grade (combination of KM grade and TSP) were also scored. The associations between variables and the survival was examined. Results: High intensity of tumor budding was associated with increasing T classification and positive LNM. Deep invasive depth was correlated with poorly differentiation, high degree of T classification, positive LNM, late clinical stage, and recurrence. BD score had strong correlation with T classification, LNM and clinical stage. Low KM grade showed significant correlation with late clinical stage and high tumor budding. TSP is positively related to tumor budding. GMS grade had significant association with clinical stage. Cox's regression models indicated that both tumor budding and KM grade were independent variables for predicting overall survival (OS) and disease-free survival (DFS). BD score and GMS grade had significant prognostic impact on survival but showed inferior separation between score 0 and 1, score 1 and 2, respectively. The novel designed model based on the combination of the inflammatory infiltration (KM grade) and BD score, iBD model, was proved to be strongly correlated with T classification, LNM, clinical stage, and recurrence. Patients with high iBD score showed reduced OS and DFS with excellent separation of score 0, 1 and 2. Conclusion: iBD scoring model was a promising predictor of survival and strongly associated with lymph node metastasis and recurrence in TSCC.

Citation Format: Pei Yu, Weiwang Wang, Zehang Zhuang, Jieyun Xu, Xiqiang Liu. A novel prognostic model based on the tumor and its microenvironment in tongue squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2216.
Abstract 2231: Insulin and multi-system alterations in non-diabetic American adults: NHANES 1999-2016
Authors: Caporaso Neil E. , Jones Rena R. , Kahle Lisa L. , Graubard Barry I.
Published: August 2018

Epidemiological evidence for a relationship between insulin resistance and cancer is emerging, and insulins' complex actions suggest that its dysregulation results in multisystem alterations. Using cross-sectional demographic and laboratory data from the continuous NHANES conducted from 1999-2016. we surveyed the range of multisystem alterations observed in normal (not diabetic or prediabetic) adult subjects in relation to variation in insulin and glucose levels. The homeostatic model of insulin resistance (HOMA-IR) was used as the key outcome measure of insulin resistance. We examined cardiovascular (BP), respiratory (FEV1, FVC), renal (BUN, creatinine), inflammatory (C-reactive protein, fibrinogen), lipid (triglycerides, LDL, HLD), hematologic (WBC, hemoglobin, cell counts), and nutritional (vitamin levels) factors in relation to HOMA-IR, C-peptide, Hgb1Ac and fasting glucose levels after adjustment for demographic (age, gender, smoking, alcohol, race, SES) and anthropometric (BMI) factors. Every system exhibited highly significant associations with insulin/glucose measures. Strong correlations (p < 0.0001, Pearson, accounting for sample weights) of HOMA-IR were observed with waist size, systolic and diastolic blood pressure, triglycerides, HDL (inverse), LDL and inflammatory markers: fibrinogen, C-reactive protein, ferritin. Measured serum levels of vitamin C, vitamin D, and folate (RBC), were inversely associated with HOMA-IR. The relationship for selected variables, to HOMA-IR quartiles is shown below.

In a broad, representative sample of up to 9000 non-diabetic US subjects, we relate insulin resistance to adverse changes in anthropometric, cardiovascular, renal, metabolic, inflammatory and nutritional markers. Analyses accounting for NHANES sample design, confounding and potential interactions will be reported. Our preliminary results suggest that insulin resistance is linked to perturbations in normal function across numerous systems.

HOMA-IR Quartiles, adjusted (95% CI)1st2nd3rd4thFerritin79.1(71-87)75.9 (70-82)82.3 (76-89)96.2 (82-110)BP (d)69.7 (69-71)71.8 (70-73)71.4 (70-73)73.2 (72-75)HDL60.8 (60-62)56.3 (56-57)54.1 (53-55)51.3 (50-52)WBC6.37 (6.3-6.5)6.44 (6.3-6.6)6.68 (6.5-6.8)6.96 (6.8-7.1)

Citation Format: Neil E. Caporaso, Rena R. Jones, Lisa L. Kahle, Barry I. Graubard. Insulin and multi-system alterations in non-diabetic American adults: NHANES 1999-2016 [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 2231.
Abstract 2232: A high-sucrose diet does not enhance spontaneous metastases of Lewis lung carcinoma in mice
Authors: Yan Lin , Sundaram Sneha
Published: August 2018

Obesity is a risk factor for cancer, and high caloric intake contributes to obesity. We previously reported that a high-fat diet enhances metastasis in mice (Clin Exp Metastasis 2010). The purpose of this study was to determine the effects of a high-sucrose diet in comparison to a high-fat diet, on an isocaloric basis, on the spontaneous metastasis of Lewis lung carcinoma (LLC) in C57BL/6 mice. Mice (male) were fed a low-fat (AIN93G-based), a high-fat, or a high-sucrose diet for eight weeks before receiving a subcutaneous injection of 2.5x105 viable LLC cells. These diets contained 16% of energy from corn oil, 45% of energy from corn oil, or sucrose. The resulting primary tumor was resected 10 days later. The experiment was terminated 10 days after resection. There were no differences in caloric intake among the groups. The body fat mass of the high-sucrose group was lower than the high-fat group but higher than the low-fat group. The number and size of lung metastases were significantly higher in the high-fat group than in the low-fat group; however, they were similar between the high-sucrose and the low-fat groups. Compared to the low-fat diet, the high-fat diet, but not the high-sucrose diet, significantly increased plasma concentrations of insulin, inflammatory cytokines (leptin, plasminogen activator inhibitor-1, and monocyte chemotactic protein-1) and angiogenic factors (vascular endothelial growth factor and tissue inhibitor of metalloproteinase-1). These findings showed that the high-sucrose diet does not enhance metastasis in this LLC model. This null effect suggests that the high-sucrose diet, compared to the high-fat diet, is less capable of promoting adipogenesis and production of related inflammatory cytokines and angiogenic factors.

Citation Format: Lin Yan, Sneha Sundaram. A high-sucrose diet does not enhance spontaneous metastases of Lewis lung carcinoma in 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 2232.
Abstract 2244: Differential DNA methylation analysis of TCGA cholangiocarcinoma data
Authors: Mishra Nitish K. , Meng Niu , Guda Chittibabu
Published: August 2018

Cholangiocarcinoma (CCA), also known as bile duct cancer, is a rare malignancy that develops in bile duct, arising from the epithelial cells (cholangiocytes) lining the bile duct. CCA is the second most common type of primary liver cancer, and its incidence has been rising in the Unites States. Most of the patients with CCA are diagnosed at an advanced stage with a median survival of less than 1 year despite administering chemotherapy. In the current study, we analyze the global patterns of DNA methylation in CCA data from TCGA. Pathway and gene ontology (GO) enrichment analysis of differentially methylated genes (DMGs) enabled us to understand how changes in methylation and gene expression affect the biologic pathways involved in the progression of CCA. TCGA level-3 DNA methylation data were downloaded for 485,578 CpG sites with annotations. Further, we normalized β value by using Beta Mixed Integer-quantile normalization (BMIQ) to adjust type I and type II probes. For a CpG site to be considered differentially methylated, the difference in the median β value in primary tumor and normal samples should be at least 0.2 and the BH adjusted p-value should be less than 0.005 and AUC ≥ 0.7. A total of 12,259 differentially methylated (Δβ >) CpG were observed; out of these 9,534 are hypermethylated and 2,725 are hypomethylated. About 4,714 differentially methylated CpGs (dm-CpGs) were observed within 1.5Kb from the TSS of corresponding genes. Chromosome 1 has maximum number of dm-CpGs, while chromosome 18 has lowest number of dm-CpGs. Differential DNA methylation frequency per Mb was also calculated and it was observed that chromosome 17 has the highest differential methylation frequency (9.61 dm-CpGs/Mb) while chromosome 18 has the lowest (1.47 dm-CpG/Mb). KEGG pathway analysis of genes with differentially methylated CpGs (Δβ ≥ 0.2) observed the enrichment of cancer, cell division and differentiation, amino acid metabolism, xenobiotics degradation, and immune response pathways. Hippo signaling pathway also got affected by DNA methylation (FDR 3.70e-18), which also got affected by differential gene expression. Change in DNA methylation and gene expression level of hippo signaling pathway genes plays a vital role in CCA.

Citation Format: Nitish K. Mishra, Niu Meng, Chittibabu Guda. Differential DNA methylation analysis of TCGA cholangiocarcinoma data [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 2244.
Abstract 2252: Biomarkers for staging melanoma, a search at transcriptome level
Authors: Ortega-Bernal Daniel , Rangel-Escareño Claudia , Arechaga-Ocampo Elena , Rosa Claudia H. Gonzalez-De la
Published: August 2018

Background: Melanoma represents one of the most aggressive malignancies and has a high tendency to metastasize. Metastatic potential may not be predicted from the morphologic features alone, and the use of routine histologic prognostic factors is insufficient for melanoma staging. Because metastatic melanoma remains extremely difficult to cure, there has been an urgent need to find new markers to identify tumors capable of metastasizing. Here, we used a computational strategy based on transcriptome meta-analysis for melanoma staging. We aimed to identify biomarkers that differentiate between non-metastatic and metastatic melanomas.

Methods: Affymetrix HU 133A Plus 2.0 microarray data were obtained from the GEO database for the meta-analysis, representing benign nevi (N), stages I, II and III melanoma (EI-III), stage IV melanoma from primary site (EIV) and stage IV melanoma from metastatic site (Mm). Differential expression was analyzed using linear models (118 files) and time course (64 files). Transcripts with a log fold change of <-1/>1 and B-statistic >3 using linear models and evaluate by MB-statistic for Time Course were included in the study. The analysis focused on genes that encode secreted proteins, whose expression was upregulated throughout the progression of melanomas, starting at N and increasing gradually from EI-III to EIV and finally to Mm.

Results: We obtained 6137 differentially expressed genes with linear models (between EI-III vs. N, EIV vs. EI-III, Mm vs. EIV, EIV vs. N and Mm vs. N contrasts) and took the top 6137 genes ranked with Time Course. Our results show 17 possible biomarkers that grouped into three types: 1) genes capable of differentiating between EIV/Mm and EI-III/N (SPP1); 2) genes capable of differentiating between Mm and EIV/EI-III/N (CXCR4, FCGR1B, NGRN, PHTF1, RAB8B, ARHGEF2, ARMC9, BCL2A1, CALU, DLGAP5, DMXL2, FKBP11 and STARD3NL); and 3) genes capable of differentiating between Mm/EIV/EI-III and N (ADAM10, CLIC4 and STK36).

Conclusions: Our analyses, in agreement with previously reported results, identify SPP1 and CXCR4 as biomarkers of metastatic disease and poor clinical outcome, supporting the quality of our analysis. We also identified new biomarkers that may be used to predict undetectable metastasis. In order to provide a more precise evaluation, experimental validation or functional exploration of the reported gene expression differences is warranted.

Citation Format: Daniel Ortega-Bernal, Claudia Rangel-Escareño, Elena Arechaga-Ocampo, Claudia H. Gonzalez-De la Rosa. Biomarkers for staging melanoma, a search at transcriptome level [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 2252.
Abstract 2256: Efficient large-scale cell classification and analysis for MultiOmyxTMassays: A deep learning approach
Authors: Nagy Mate L. , Hanifi Arezoo , Tirupsur Ahalya , Wong Geoffrey , Fang Jun , Hoe Nicholas , Au Qingyan , Padmanabhan Raghav K.
Published: August 2018

Traditional immunohistochemistry (IHC) techniques utilize one slide per biomarker. When clinical samples are precious and the number of serial sections is limited, comprehensive biomarker profiling becomes difficult with IHC. MultiOmyx is a proprietary, multiplexing methodology capable of staining up to 60 biomarkers on the same slide. The output of the assay enables quantitative profiling of tissues at a single cell level. The assay generates data for millions of cells with billions of queryable data points. To detect and classify cells efficiently at this large scale, we developed an image analysis framework using Deep Learning. Our framework consists of seven major steps: (1) manual annotation of a small subset of the nuclear staining channel (DAPI); (2) training of a fully convolutional neural network [1] on this annotation-set to generate a feature map identifying cell centers; (3) application of the trained network in (2) on the nuclear stain (DAPI) of the entire dataset to delineate individual cells; (4) manual annotation of a small subset of each of the other biomarker channels; (5) training of a convolutional neural network on these annotation-sets for binary classification of each of the biomarkers; (6) application of these classifiers to the entire dataset; (7) combination of the binary classification results to identify phenotypes of interest. For our output, we provide both visual label maps and classification summary tables for individual and co-localized biomarkers at the region of interest level and the entire slide level. In addition, combining the phenotype and location information allows us to visualize complex spatial relationships in the tissue.

The benefits of using this Deep Learning framework are greatly felt through increased time efficiency without a loss in accuracy, when compared to more traditional computer vision methods requiring high levels of parameter fine-tuning. For future work, we plan on fully automating the approach as more manual annotation-sets are generated.

Citation Format: Mate L. Nagy, Arezoo Hanifi, Ahalya Tirupsur, Geoffrey Wong, Jun Fang, Nicholas Hoe, Qingyan Au, Raghav K. Padmanabhan. Efficient large-scale cell classification and analysis for MultiOmyxTMassays: A deep learning approach [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 2256.
Abstract 2270: Integrating 5hmC and gene expression data infers regulatory mechanisms linked to alternative mRNA splicing in breast cancer
Authors: Mitrea Cristina , Wijesinghe Priyanga , Dyson Greg , Girsch Emily , Bao Bin , Kruger Adele , Bollig-Fischer Aliccia
Published: August 2018

Epigenetic mechanisms, such as 5-methylcytosine (5mC), are known to play a major role in breast cancer. However, the role of 5-hydroxymethylcytosine (5hmC) DNA modification remains understudied. We hypothesize that 5hmC mediates redox regulation of gene expression in the triple negative breast cancer (TNBC) subtype. To address this, our objective was to highlight genes that may be the target of this process by identifying redox-regulated, antioxidant-sensitive, gene-localized 5hmC changes associated with mRNA changes in TNBC cells. We proceeded to develop an approach to integrate data sets generated by a methodology called Pvu-sequencing, which measures 5hmC in the genome, and RNA-sequencing. The result of our approach to merge genome-wide, high-throughput TNBC cell line data to identify significant, concordant 5hmC and mRNA changes in response to antioxidant treatment, that perturbs redox signaling, produced a gene set with relevance to alternative mRNA splicing and cancer stem cell function. Key genes identified included TAR DNA binding protein (TARDBP), vimentin (VIM), and splicing factor proline and glutamine rich (SFPQ). Moreover, we have established a method that will be useful for continued research of 5hmC in TNBC cells and tissue samples.

Citation Format: Cristina Mitrea, Priyanga Wijesinghe, Greg Dyson, Emily Girsch, Bin Bao, Adele Kruger, Aliccia Bollig-Fischer. Integrating 5hmC and gene expression data infers regulatory mechanisms linked to alternative mRNA splicing 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 2270.
Abstract 2282: VIP: A system biology platform for cell line centric integrative analysis of molecular and functional genomics data
Authors: Fernandez Julio , Ding Ying , Kan Zhengyan
Published: August 2018

Cancer is a heterogeneous disease that is classified by its tissue of origin or molecular characteristics such as genetic alterations that drive tumorigenesis. Large-scale efforts using loss-of-function genetic screens to systematically identify genes essential for the proliferation and survival of cancer cells provide a powerful approach for studying cancer biology and discovering drug targets. However, cancer cell lines from different lineages or molecular background vary in their dependencies on specific genes or pathways. Functional ablation of a gene may be only lethal in one segment of cancer cell lines harboring certain molecular deficiencies or activation of a specific oncogenic signaling pathway, a phenomenon called synthetic lethality. A key challenge here would be to identify the true synthetic lethal interactions from a combinatorially large number of possible interactions between molecular aberrations and gene-level sensitivity to functional perturbation. With recent advances in large-scale studies such as CCLE and Achilles, genome-wide functional genomics screens using CRISPR-Cas9 or shRNA technologies as well as comprehensive molecular profiles have become available for a large number of cancer cell lines. Here we present the Variant Interpretation Portal (VIP), a system biology tool designed to enable integrative analysis of molecular and functional genomics data in cell lines for identifying synthetic lethal interactions. VIP consists of a command-line pipeline and a web-based user interface. The VIP pipeline rigorously filters out germline events and classifies genomic variants into multiple functional tiers. The VIP web portal provides users with a graphic interface to perform exploratory visual analyses of associations between two variables or multiple variables, where a variable could be a genetic alteration or a gene-level sensitivity profile. VIP also enables systematic search for significant association between one variable, such as the sensitivity profile, vs. a database of variables such as histology or molecular attributes. VIP is optimized to perform real-time analytics and enables the incorporation and analysis of user-provided data. The code can be accessed from https://github.com/juferban/vip.

Citation Format: Julio Fernandez, Ying Ding, Zhengyan Kan. VIP: A system biology platform for cell line centric integrative analysis of molecular and functional genomics data [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 2282.
Abstract 2296: STAR-SEQR: Accurate fusion detection and support for fusion neoantigen applications
Authors: Jasper Jeff , Powers Jason G. , Weigman Victor J.
Published: August 2018

Genomic structural variation and associated RNA fusions are a common clinical feature known to be involved in the initiation and pathogenesis of cancer. This complex class of variants also has significant implications on therapeutic decisions and has emerging roles in evidence-based clinical applications. Consequently, fusion detection is an emerging aspect of precision medicine that enables clinical utility of fusions as a therapeutically-relevant target which includes small molecules, biologics, and neoantigen-directed approaches.Here we present STAR-SEQR, an algorithm that uses multiple levels of evidence to detect and quantify fusions from RNA-Seq data. STAR-SEQR is a fast and accurate tool that goes beyond fusion detection and also provides rich annotation and useful reporting features to aid in the adoption of fusions in clinical diagnostics. Notably the software produces fusion expression values, PCR primers, fusion RNA sequence, and predicted peptide sequence to facilitate downstream applications.To address the analytical performance of STAR-SEQR to existing tools, we utilized previously characterized synthetic datasets and real-world sample data with matching DNA sequencing. Of note, in a dataset of 50 synthetic fusions, STAR-SEQR had the highest accuracy of all tools tested and called 49/50 events with no false positives. STAR-SEQR has also been run on several large clinical datasets and the fusion events identified have displayed strong overlap with identified DNA structural variants. STAR-SEQR also performed well in the ongoing ICGC-TCGA DREAM SMC-RNA Challenge and achieved the highest F1 score in the simulated data round with an overall average of 0.96. Analytical lab testing has also been performed using the Seracare Fusion RNA Mix V2 sample containing 15 clinically significant fusions with known concentrations in the low range of detectability. STAR-SEQR accurately called 13/15 events with the other events having no identifiable read alignments. We have also benchmarked methods comparing FFPE material, range of read lengths, and library methods where STAR-SEQR demonstrated excellent tradeoff between sensitivity and precision and generally outperformed other tools.In summary, STAR-SEQR has excellent analytical performance that surpasses existing fusion detection tools. It is broadly applicable to RNA-Seq methods, computationally efficient, and robust across sample characteristics. Lastly, STAR-SEQR is explicitly designed to enable fusion-directed clinical diagnostics and support cancer immunotherapy approaches that utilize fusion neoantigens.

Citation Format: Jeff Jasper, Jason G. Powers, Victor J. Weigman. STAR-SEQR: Accurate fusion detection and support for fusion neoantigen applications [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 2296.