bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 16: 3,3'-diindolylmethane induces cytoglobin expression and synergizes with poly ADP ribose polymerase inhibitor PJ34 to inhibit triple negative breast cancer cell growth
Authors: Wooten Jonathan V. , Mavingire Nicole , Rowland Leah , Matthews Jason , Brantley Eileen
Published: August 2019

Triple negative breast cancer (TNBC), characterized by tumors that lack expression of the estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), carries a poor prognosis. While recently approved poly ADP ribose polymerase (PARP) inhibitor olaparib shows favorable activity in patients with TNBC harboring tumors deficient in DNA repair enzyme BRCA1, patients with TNBC possessing BRCA1-proficient tumors are largely unresponsive to olaparib. Emerging evidence suggests that small molecules that activate aryl hydrocarbon receptor (AhR) signaling have the capacity to confer anticancer actions. 3,3′-diindolylmethane (DIM), an AhR ligand, is the major metabolite of indole-3-carbinol (I3C) found in cruciferous vegetables such as broccoli. Patients often consume natural product-derived AhR ligands while undergoing chemotherapy. It is therefore crucial to enhance our understanding of nutraceutical-pharmaceutical interactions. We previously demonstrated the ability of synthetic AhR ligands to induce the expression of putative tumor suppressor cytoglobin (CYGB) and inhibit Akt signaling in breast cancer cells. Since PARP inhibitor PJ34 has been shown to synergize with Akt inhibitors we hypothesize that DIM induces CYGB expression and synergizes with PJ34 to inhibit TNBC cell growth. Using the Alamar Blue assay, we found that DIM substantially enhanced the sensitivity of TNBC BRCA1 proficient cells to PJ34, though knockdown of CYGB did not significantly influence the responsiveness of cells to DIM. Chromatin immunoprecipitation followed by next-generation sequencing data revealed that DIM promoted the binding of AhR to the CYGB promoter in breast cancer cells. Finally, DIM induced CYGB gene expression in TNBC cells as determined by quantitative PCR. Taken together, our data suggest that DIM upregulates CYGB in TNBC cells and synergizes with PJ34 to confer anticancer actions in TNBC. Our data provide a rationale for incorporating the use of natural product-derived AhR ligands as a strategy to enhance PARP inhibitor efficacy in patients with TNBC that have BRCA1-proficient tumors.

Citation Format: Jonathan V. Wooten, Nicole Mavingire, Leah Rowland, Jason Matthews, Eileen Brantley. 3,3'-diindolylmethane induces cytoglobin expression and synergizes with poly ADP ribose polymerase inhibitor PJ34 to inhibit triple negative breast cancer cell growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 16.
Abstract 1601: Genetic and epigenetic intratumor heterogeneity of lung adenocarcinoma
Authors: Zhao Wei , Hua Xing , Zhang Tongwu , Consonni Dario , Pesatori Angela Cecilia , Shi Jianxin , Landi Maria Teresa
Published: August 2019

Genomic studies have revealed remarkable intratumoral heterogeneity (ITH) in lung adenocarcinoma (LUAD) and increasing evidence suggests its impact in cancer treatment. However, to what extent epigenomic abnormalities and somatic copy number alterations (SCNAs) are involved in shaping genetic clones in lung tumors and are associated with clinical outcome is under-appreciated. Here we applied Infinium HumanMethylation450K BeadChips, Infinium Global Screening Arrays and ultra-deep (>500X) targeted sequencing of 35 LUAD driver genes to 369 samples (including 77 normal tissues) from 84 LUAD patients to investigate the genetic and epigenetic architecture of subclonal diversification. SCNAs were mostly clonal events. For patients with more than three tumor regions assayed, 66% SCNAs were located on the trunk of the evolutionary trees. Similar evolutionary trajectories were inferred from SCNAs and DNA methylation. The driver genes’ sequencing depth allowed to identify subclonality even in TP53, EGFR, and BRAF mutations, which were largely reported as clonal events in previous studies. Elevated copy number ITH was associated with higher risk of death, while no significant association was found between clinical outcome and DNA methylation ITH or heterogeneous CpG island methylator phenotype (CIMP), in contrast with the observed prognostic capability of DNA methylation ITH in hematological malignancies. These findings expand our understanding of the coevolution of genetic and epigenetic aberrations in tumorigenesis, the subclonal complexity for therapeutic targets and the implication of ITH in cancer prognosis.

Citation Format: Wei Zhao, Xing Hua, Tongwu Zhang, Dario Consonni, Angela Cecilia Pesatori, Jianxin Shi, Maria Teresa Landi. Genetic and epigenetic intratumor heterogeneity of lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1601.
Abstract 1602: Genomic profiling of lung cancer associated with idiopathic pulmonary fibrosis
Authors: Noro Rintaro , Miyanaga Akihiko , Fukuizumi Aya , Kunugi Shinobu , Sugano Teppei , Omori Miwako , Minegish Yuji , Usuda Jitsuo , Seike Masahiro , Kubota Kaoru , Hirao Mamiko , Matsuda Kuniko , Gemma Akihiko
Published: August 2019

Idiopathic pulmonary fibrosis (IPF) is reportedly associated with an increased risk of lung cancer. However, optimal diagnosis and treatment for lung cancer associated with IPF remains unclear. In this study, we aimed to clarify the mechanism of carcinogenesis and progression in lung cancer with IPF. We used tumor tissues and adjacent non-tumor lung tissues from 29 lung cancer patients who had undergone complete surgical resection at Nippon Medical School Hospital between 2013 and 2017. Whole-Exon Sequencing was performed on 29 paired samples, consisted of 19 lung cancers with IPF (IPF group) and 10 lung cancers with normal lung (non-IPF group). The candidate gene alterations discriminating between the IPF and non-IPF group, were identified using the random-forest method, RelifF method along with the data from Catalogue Of Somatic Mutations In Cancer (COSMIC). Twenty-five gene alterations were specifically found in IPF tissues and/or tumor tissues with IPF. Whenever 5 of 25 genes including MUC2 and TTF1, were altered in both IPF tissues and tumor tissues, 20 of 25 genes including CADM1, were altered in only tumor tissues. We are undergoing the validation study using other tissues in independent cohorts. Among the candidate genes, Cell adhesion molecule genes (CADM1) gene alterations were frequently found in 15 out of 19 in only tumor tissues with IPF. The CADM1 protein expression was decreased in tumors than in non-tumor fibrotic tissues by western blotting. The CADM1 induced the epithelial-mesenchymal transition (EMT) on the multifunctional cell process involved in the pathogenesis of fibrosis in vitro study. Whenever the down-regulation of CADM1 was frequently detected in various human cancers through its allelic loss as well as hypermethylation within promoter region in addition to inactivate gene mutation, the up-regulation of CADM1 was frequently detected in paired IPF tissues. The CADM1 may be a target candidate in lung cancer associated with IPF.

Citation Format: Rintaro Noro, Akihiko Miyanaga, Aya Fukuizumi, Shinobu Kunugi, Teppei Sugano, Miwako Omori, Yuji Minegish, Jitsuo Usuda, Masahiro Seike, Kaoru Kubota, Mamiko Hirao, Kuniko Matsuda, Akihiko Gemma. Genomic profiling of lung cancer associated with idiopathic pulmonary fibrosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1602.
Abstract 1603: Valproic acid and hydralazine reverse increased mammary cancer risk and upregulate Cdkn2a/p16 in mice exposed to a high fat diet in utero
Authors: Hilakivi-Clarke Leena A. , Andrade Fabia de Oliveira , Nguyen Nguyen , Bouker Kerrie
Published: August 2019

Maternal or paternal high fat (HF) diet that modifies the epigenome in germ cells and fetal somatic cells can program increased susceptibility to breast cancer among offspring. Resulting epigenetic changes include transgenerational upregulation of DNA methyltransferases (DNMTs). We studied here if this increased breast cancer risk can be reversed by treating HF offspring with a well-tolerated drug that inhibits DNA methyl transferase (DNMT; hydralazine), combined with a histone deacetylase (HDAC) inhibitor valproic acid (VPA). Adult C57BL/6NTac mouse offspring of dams fed either corn oil -based HF or control diet during pregnancy were treated with 5 g/kg/day VPA and 5 mg/kg/day hydralazine in drinking water, starting after mice received 7,12-dimethylbenz[a]anthracene (DMBA) to initiate mammary cancer. Treatment with VPA/hydralazine prevented the increase in mammary cancer risk associated with in utero HF diet exposure: it reduced mammary tumor multiplicity and lengthened tumor latency, compared with non-treated HF offspring. These drugs downregulated DNMT3a protein levels, and reversed down-regulation of Cdkn2a/p16 mRNA in the mammary tumors of HF offspring. p16 is a tumor suppressor that is often epigenetically silenced in human breast cancers. However, in control offspring not exposed to HF diet in utero, VPA/hydralazine increased mammary tumor incidence and burden. Further, this treatment upregulated genes involved in the unfolded protein response pathway in in utero control diet exposed animals that were already upregulated in non-VPA/hydralazine treated mammary tumors from in utero HF diet exposed animals, including HIF-1α, NFkB, PERK and SQSTM1 p62. Thus, VPA and hydralazine had opposing effects on breast cancer risk in HF and control offspring, suggesting the importance of individually tailoring breast cancer prevention strategies.

Citation Format: Leena A. Hilakivi-Clarke, Fabia de Oliveira Andrade, Nguyen Nguyen, Kerrie Bouker. Valproic acid and hydralazine reverse increased mammary cancer risk and upregulate Cdkn2a/p16 in mice exposed to a high fat diet in utero [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1603.
Abstract 1604: Modulating effects of genistein in a mouse model of conditional BRCA1 deletion and triple negative breast cancer cells
Authors: Donovan Micah G. , Selmin Ornella I. , Doetschman Thomas C. , Romagnolo Donato F.
Published: August 2019

Germline mutations in BRCA1 (BRCA1+/-) confer ~72% risk of breast cancer, the majority of which are triple negative breast cancer (TNBC). Hypermethylation of BRCA1 is observed at high frequency in sporadic TNBC and may play a role in tumor development in BRCA1 mutation carriers. The aryl hydrocarbon receptor (AhR) coordinates epigenetic silencing of BRCA1 and is overexpressed in some TNBC. The purpose of our study is to investigate the effect of dietary genistein on BRCA1 epigenetic regulation, the AhR pathway and mammary tumorigenesis in BRCA1+/- and BRCA1+/+ mice. We used Cre-lox recombination to derive a mouse model of conditional BRCA1+/-. We used BRCA1F22/24 (The Jackson Laboratory, stock no. 017835) mice, which harbor loxP sites flanking exons 22-24 of the BRCA1 gene. We crossed dams that were heterozygous for BRCA1F22/24 (BRCA1+/FL) and transgenic for Cre recombinase (TG) under control of the mouse mammary tumor virus (MMTV) promoter with wildtype NJ males to derive our colony. Breeding pairs were administered either control or genistein-enriched (4 ppm) diets upon set up, which were continued throughout the life of the offspring. Changes in mRNA expression and protein levels were determined, respectively, by RT-PCR and Western blot. Crewas not expressed in mammary glands of non-TG offspring and Cre expression had no effect on BRCA1 mRNA levels in BRCA1+/+ mice, which do not harbor BRCA1 loxP sites. BRCA1 expression was ~40% decreased in mammary glands of TG, BRCA1+/FL mice compared with TG, BRCA1+/+ mice. Hepatic BRCA1 expression was not changed, confirming conditional BRCA1 knockdown. Preliminary data indicate BRCA1 expression in mammary glands of genistein-fed TG, BRCA1+/+ mice was elevated (~1.3 fold) compared with control-fed mice. Moreover, the genistein diet induced a compensatory increase in BRCA1 expression in mammary glands of TG, BRCA1+/FL mice. We found genistein rescued BRCA1 levels in TNBC HCC38 cells that have constitutively active AhR and hypermethylated BRCA1. These data suggest dietary genistein may have protective effects against tumorigenesis in these mice. To that end, we are currently monitoring tumor development, BRCA1 methylation, and changes in the AhR pathway in BRCA1+/+ and BRCA1+/FL mice fed either the genistein-enriched or control diet.

Citation Format: Micah G. Donovan, Ornella I. Selmin, Thomas C. Doetschman, Donato F. Romagnolo. Modulating effects of genistein in a mouse model of conditional BRCA1 deletion and triple negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1604.
Abstract 1605: Time-dependent maternal soybean genistein exposure leads to later-life breast cancer chemoprevention in mice
Authors: Li Yuanyuan , Chen Min , Li Shizhao , Tollefsbol Trygve
Published: August 2019

Breast cancer is the most common type of cancer and the second leading cause of death among women in the United States. Studies have shown that both environmental and genetic factors contribute to breast cancer risk over women's lifespans. Early-life nutritional status has a significant impact on the uterine environment and subsequent fetal development, predisposing the developing fetus to certain diseases such as breast cancer in adult life. During these windows of susceptibility including maternal pre-pregnancy, pregnancy and lactation periods, certain dietary exposure during these critical time periods may change breast cancer risk in an individual’s later life. Alterations of the maternal diet have been shown to induce modifications in the fetal epigenome. Nevertheless, the vulnerability to maternal nutrition status during the critical developmental stage provides an excellent opportunity to re-program epigenetic profiles that may lead to a beneficial outcome such as cancer prevention in the offspring. The bioactive dietary component, genistein (GE) enriched in soybean products, is an important epigenetic modulator that can prevent various cancers including breast cancer. Our study focuses on how maternal dietary soybean GE exposure during the specific time periods may prevent breast cancer in later-life and the potential mechanisms. In this study, we included multiple exposure time points of maternal GE diet (250 mg/kg) including prior-pregnancy (PP-GE), long-term (LT-GE) and short-term (ST-GE) exposures to further determine the efficacy of these strategies on transplacental chemoprevention of breast cancer in the progenies of two spontaneous breast cancer transgenic mouse models. Our pilot study indicates a time-dependent effect of maternal GE exposure on early-life breast cancer development in spontaneous breast cancer mouse models. We also integrated transcriptome and methylome data from mouse breast tumors and identified several candidate genes such as Trp63 and Tprg in response to maternal GE treatment, and considered to play important roles in regulation of development and tumorigenesis. These results suggest that an appropriate exposure window to soybean dietary GE could be a key factor for prevention of human breast cancer and comprehensive mechanisms may be involved in dietary GE-induced in utero breast cancer intervention.

Citation Format: Yuanyuan Li, Min Chen, Shizhao Li, Trygve Tollefsbol. Time-dependent maternal soybean genistein exposure leads to later-life breast cancer chemoprevention in mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1605.
Abstract 1608: Time-restricted feeding attenuates pulmonary metastasis of Lewis lung carcinoma in mice fed a high-fat diet
Authors: Yan Lin , Sundaram Sneha
Published: August 2019

Circadian rhythms, which cycle approximately every 24 hours, control patterns of daily functions, e.g. feeding and fasting, rest and activity, and sleeping and waking. Altering the finely tuned circadian rhythms by an erratic lifestyle (e.g. disruption of the daily feeding and fasting pattern) leads to metabolic disorders, including obesity. Obesity is a risk factor for cancer. Obese cancer patients are at a greater risk of recurrence and metastasis than patients with normal body weight. We hypothesized that time-restricted feeding (TRF) attenuates high-fat diet-enhanced metastasis. In a metastasis model of Lewis lung carcinoma (LLC), male C57BL/6 mice were fed the standard AIN93G diet (16% of energy from soybean oil) or a high-fat diet (HFD) containing 45% of energy from soybean oil with or without dark phase restricted feeding (12 hours per day) for 10 weeks. Pulmonary metastases from a primary tumor, established by subcutaneous injection of LLC cells, were quantified. The percent fat body mass of the TRF group was lower than that of the HFD group and remained similar to that of the AIN93G group. There was no difference in energy intake between the TRF and HFD groups. The number and size of lung metastases were significantly higher in the HFD group than in the AIN93G group; however, there were no differences in these measurements between the TRF and the AIN93G groups. Time-restricted feeding prevented HFD-induced increases in plasma concentrations of glucose, insulin, proinflammatory cytokines (leptin, monocyte chemotactic protein-1, and plasminogen activator inhibitor-1), and angiogenic factors (angiopoietin-2, hepatic growth factor, and vascular endothelial growth factor). We conclude that TRF attenuates the HFD-enhanced pulmonary metastasis of LLC. This protection may be through the entrainment of metabolic regulators to the fixed feeding time that results in reductions in body adiposity and associated cancer-promoting inflammatory and angiogenic factors.

Citation Format: Lin Yan, Sneha Sundaram. Time-restricted feeding attenuates pulmonary metastasis of Lewis lung carcinoma in mice fed a high-fat diet [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1608.
Abstract 1614: Coconut kernel extract as a novel chemopreventive agent that target cancer stemness
Authors: Sorra Sandhya , Talukdar Joyeeta , Gogoi Gayatri , Li Hong , Baishya Debabrat , Das Bikul
Published: August 2019

Cancer stemness can be defined as integrated molecular programs that confer stem cell phenotype to cancer cells. Cancer stemness is associated with drug resistance, immune evasion and metastasis. Our ongoing work indicates that oncogene MYC may enhance cancer stemness. We are interested to identify novel dietary agents that can target MYC mediated cancer stemness pathway. Coconut (Cocos nucifera L.) kernel extract (CKE) is traditionally used in tradition Indian medicine as anti-inflammatory diet. Here, we have investigated the potential CKE mediated targeting of MYC mediated skin carcinogenesis.

Methods: To determine tumor-suppressing activity of isolated CKE in vivo, we used a DMBA/TPA-mediated skin cancer in Balb/c mice. C-MYC expression in skin tumor was studied by immuno-histochemistry. The bioactive component of CKE was studied by performing histopathology and immunohistochemistry.

Results: CKE treatment decreased DMBA/TPA induced tumorigenicity by 200-fold (p<0.001, n=10). Histological and Immuno histo-chemistry studies suggested that CKE treatment significantly inhibited over expression of c-Myc protein on skin tumorigenesis induced by DMBA/TPA. Additionally, CKE treatment also shows significant inhibitory effect on lipid peroxidase and stimulatory effect on glutathione, catalase and superoxide dismutase activities in tissues treated with DMBA/TPA. Additionally, in vitro study showed that CKE reduces DMBA/TPA induced stemness in skin keratinocytes. CKE contains lauric acid as per analysis performed by high performance liquid chromatography and Nuclear magnetic resonance. However, purified lauric acid alone did not exhibit potent anti-stemness activity in vitro as compared to CKE.

Conclusions: These findings demonstrate that CKE is a tumor suppressing agent for chemically induced skin cancer. CKE prevent DMBA/TPA induced oxidative stress and potentially act as an inhibitor of MYC-induced cancer stemness.

Citation Format: Sandhya Sorra, Joyeeta Talukdar, Gayatri Gogoi, Hong Li, Debabrat Baishya, Bikul Das. Coconut kernel extract as a novel chemopreventive agent that target cancer stemness [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1614.
Abstract 1618: Breast cancer screening in low and lower - middle income country : A program in Vietnam
Authors: Dang Voc Tai , Dao Tu Van , Tran Thuan Van , Tran Huong Thi
Published: August 2019

Background: From 1980 to 2010, new breast cancer cases increased by more than 50% worldwide. Disease burden increased even more rapidly in low- and middle-income countries (LMICs), where over half of breast cancer cases now occur. In Vietnam, approximately 15229 new cases of breast cancer were diagnosed with 6103 resulted deaths in 2018. Breast cancer can be detected early by screening; however, it is not covered by medical insurance. Mammogram is currently one of the most reliable screening tools for breast cancer. Regular mammograms can help detect breast cancer early, thus allowing for early treatment Purposes: To raise public awareness on breast cancer prevention and early detection, while promoting a habitual routine of breast self - examination and breast cancer screening participation; to call on companies to include breast cancer screening on the periodic health examination for female employees. Methods: We collected data on risk factors of breast cancer. Breast Imaging-Reporting and Data System (BI-RADS fifth edition) scores from the radiology reports were utilized. The information collected from women who completed the questionnaires included: age, BMI, family history of breast cancer, personal history of breast or ovarian cancer, number of pregnancies, number of babies born, number of abortion, number of miscarriage, stillbirth, hormonal medication use (hormone replacement therapy and daily oral contraceptive), age of menarche, menopause, smoking habit, and breast self-examination results. Results: There were 10,000 Vietnamese women who were over 40 years old (over 35 years old if their mother or their sister had breast cancer) participated in this program. Rate for regular breast self-examination was 19.1%. In the 40 to 55 years-old age group, the rate was 70%, 2.2% for women aged 35-39 years (with a family history of breast cancer). Eight women were diagnosed with breast cancer, the incidence rate was 80 per 100,000 population, respectively. Conclusions: The total fee for a breast cancer screening in Viet Nam is approximately $25 ($20 for a mammogram and $5 for consultation fee). This remains one of the best solutions to detect breast cancer early and reduce the overall burden of cancer treatment costs on the already strained Vietnamese health system.

Note: This abstract was not presented at the meeting.

Citation Format: Voc Tai Dang, Tu Van Dao, Thuan Van Tran, Huong Thi Tran. Breast cancer screening in low and lower - middle income country : A program in Vietnam [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1618.
Abstract 1621: Multiplex analysis of proteins for cancer diagnosis: A case study using ActivSignal technology
Authors: Alexandrov Ilya , Mackenzie Malcolm , Brandina Irina
Published: August 2019

Pancreatic cancer is one of the deadliest types of cancer, killing over 50,000 each year in the US, and with a five-year survival rate below 8%. However, currently there are no reliable diagnostic tests for pancreatic cancer, and the great majority of cases are detected at a late stage, with bleak mortality rates as a result. The ActivSignal IPAD platform monitors activity of 26 cancer signaling pathways in multiplex, by examining phosphorylation status or expression of 70 protein targets. The technology utilizes pairs of antibodies per each protein target to ensure high specificity. These antibody pairs are carefully tested and selected. Detection will only take place if both antibodies in a pair bind to their specific target molecule during the analysis phase - avoiding false hits. The ActivSignal IPAD platform can be used to profile cell culture samples, tissues and different blood fractions. The IPAD assay requires a very small amount of sample. All these characteristics make it potentially adaptable for diagnostics, simultaneously profiling multiple proteins targets. We have tested the assay in a preliminary analysis of human pancreatic cancer patients. Several control and pancreatic ductal adenocarcinoma (PDAC) blood samples were used for analysis. The assay can be performed on a very small volume of material, and 100 microliters of each sample was obtained from a collaborating academic medical center. The profiling was performed on 40 previously identified, relevant proteins. The comparison of Normal controls and PDAC patient samples gave a clear pattern that discriminated these two population groups with a great degree of certainty. Thus, giving a proof of concept that the assay can be used for diagnostic development for pancreatic cancer detection, an urgent unmet need.

Citation Format: Ilya Alexandrov, Malcolm Mackenzie, Irina Brandina. Multiplex analysis of proteins for cancer diagnosis: A case study using ActivSignal technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1621.
Abstract 1625: Challenges of screening applications for early detection of cancer using liquid biopsy
Authors: Kermani Bahram G. , Huecker Sarah , Kirsch Stefan , Polzer Bernhard
Published: August 2019

In the recent years, early detection of cancer using next-generation sequencing (NGS) has been en vogue, due to its potential to drastically improve the survival rate of cancer patients. Liquid biopsy is often viewed as the modus operandi for early detection, as taking biopsies from the actual organs is not practical for widespread screening tests. Among others, two main approaches attempted for early detection are based on cell-free tumor DNA (ctDNA) and circulating tumor cells (CTCs). The rarity of ctDNA and CTC is often debated as a major potential challenge for detection of cancer at early stages. In this work, we will discuss several other challenges that are necessary to address for developing a practical and high-quality screening application for early-stage detection of cancer. We will also provide a framework in which much of these challenges can be addressed. While a reasonable sensitivity is needed for such test to be of value, the most prominent matter regarding screening for cancer is specificity. Due to low prevalence of cancer, what may appear as a high specificity (e.g., 99%) could actually be insufficient, as it translates to a low positive predictive value (PPV) (e.g., in the 10% range). A low PPV would result in a large number of false positives in the test. These false positives would cause follow-up tests that are not only costly, but also could trigger unnecessary anxiety for the patients. A comprehensive validation process is another critical element in early detection. While it is tempting to perform validation based, solely, on groups of Healthy and Cancer patients, it can be shown that some signals caused by Benign conditions could highly resemble those of Cancer patients, and therefore result in false positives. We will show that distinguishing Benign from Cancer necessitates detection of more complex patterns, as opposed to simplistic measures such as genome-wide copy number variation (CNV). Yet another challenge in a liquid biopsy test is identification of the tissue-of-origin. Due to the mixed-signal problem inherent in ctDNA-based technologies, we argue that they face a higher challenge, as compared to CTC-based counterparts, for obtaining this goal. In conclusion, we will show how a system based on CTCs, whole genome sequencing (WGS), and artificial intelligence (AI) could provide an appropriate framework for addressing much of the challenges in early detection of cancer for a true screening application with the specificity in the 99.99% range.

Citation Format: Bahram G. Kermani, Sarah Huecker, Stefan Kirsch, Bernhard Polzer. Challenges of screening applications for early detection of cancer using liquid biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1625.
Abstract 1643: Discovery pipeline of cancer transcriptomic biomarkers using machine learning
Authors: Kim Eileen
Published: August 2019

Introduction: Cancer affects millions of people and causes nearly 1 in 6 deaths worldwide. Precision oncology holds potential in guiding cancer treatment on a molecular basis and elucidating targetable cancer pathways. This study aims to create a discovery pipeline that uses cancer patients’ transcriptomes and machine learning algorithms to predict cancer patient survival.

Methods: Transcriptomic and phenotypic data from cancer patients were downloaded from The Cancer Genome Atlas (TCGA). Initial genes were selected using univariate cox proportional hazard models to predict overall survival across all cancer types. Co-expressed selected genes were clustered, creating gene sets per cancer subtype. Then, an amalgam of LASSO and elastic-net regularized generalized linear models (GLMNET), gene bootstrapping, random forest without/with shadow features (Boruta), and recursive feature elimination were used. Monte Carlo iterations were performed for GLMNET to assess model stability and over-/underfitting.

Results: The highest hazard ratios (HRs) and lowest p-values resulted from the univariate cox proportional hazards model (e.g. for the RASGEF1A gene in a uterine serous carcinoma model, HR=2.8e8, p=0.005) and subsequent GLMNET models (e.g. 392 genes for uterine endometrioid carcinoma, HR=2.89e8, p=0.00873). Boruta before GLMNET yielded lower HRs and higher p-values (e.g. 11 genes for uterine serous carcinoma, HR=2, p=0.0517). Bootstrapping genes before GLMNET generally yielded much lower HRs and higher p-values.

Conclusions: We were able to model survival risk in cancer patients with a variety of methods. The best method so far is univariate gene selection and GLMNET, although random forest is promising. Next steps include exploring random forest models further, investigating the biology of prognostic models, using disease-specific survival, analyzing possible confounders, using Breslow-Wilcoxon or accelerated failure time models, replacing histological with molecular-signature-based cancer subtypes, and exploring alternative methods for prognosis prediction. Supported by the Medical Scholars Program, Medical College of Georgia, Augusta, GA.

Citation Format: Eileen Kim. Discovery pipeline of cancer transcriptomic biomarkers using machine learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1643.
Abstract 1644: Pancreatic cancer survival prediction using machine learning and comparing its performance with TNM staging system and prognostic nomograms
Authors: Osman Mohamed H.
Published: August 2019

Background:

Pancreatic cancer is one of the deadliest cancers with a 5-year survival rate of only 6%. Patients with cancer often want to know how long they have left to live and it’s the first question patients ask after diagnosis. Reliable predictions are very important for achieving more personalized care and better management. However, the accuracy of physicians' clinical predictions of survival is poor. Predicting pancreatic cancer survival is challenging due to different tumor characteristics, treatments and patient populations. In this study, we evaluate the performance of Machine Learning (ML) in survival prediction compared to TNM system and published nomograms.

Methods:

Pancreatic cancer patients were identified through the Surveillance, Epidemiology and End Results database (SEER). Clinical data of the patients were extracted including: age, sex, race, marital status, tumor site, tumor histology, grade, tumor size, extension, Lymph Node (L.N) involvement, metastasis, cancer sequence, TNM stage, surgery, radiotherapy, chemotherapy, examined (L.N), positive (L.N) and survival months. Patients’ records were randomly divided into a training set (80%) and a validation set (20%). ML algorithms were tested to predict survival at 6, 12 and 24 months as well as TNM staging system and two nomograms.

Results:

A total number of 22,700 patients were identified through SEER from 2004 – 2013 with median survival of 12 months. The most common primary sites were head of pancreas (62.8%), tail (13.2%), and body (10.7%). Random Forests algorithm achieved better results compared to other models. The trained model yielded Area under the Receiver Operating Characteristic Curve (AUCs) of 86.6% at 6 months, 83.4% at 12 months and 82.2% at 24 months. Compared to TNM staging system which achieved AUCs of 66.6% at 6 months, 65.5% at 12 months and 57% at 24 months. The nomograms achieved AUCs of 71.1% and 55.2% in predicting 1-year-survival.

Sensitivity of the trained model were 80%, 75% and 79% at 6, 12 and 24 months, respectively. The most important characteristics which influenced the model prediction performance were: age at diagnosis, surgery and tumor size.

Conclusion:

Machine learning achieved a much better performance compared to TNM staging system and prognostic nomograms. Improved survival prediction can help in in making better treatment decisions and planning social and care needs.

Citation Format: Mohamed H. Osman. Pancreatic cancer survival prediction using machine learning and comparing its performance with TNM staging system and prognostic nomograms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1644.
Abstract 1653: Application of high-density tiling CRISPR screen technology to identify chromatin remodeler complex targets for drug discovery
Authors: Soares Luis , Bocker Michael , Zhou Qianhe , Kadoch Cigall , Chan Ho Man
Published: August 2019

The mammalian SWI/SNF (mSWI/SNF or BAF) complexes are widely mutated in different human pathologies, presenting new therapeutic opportunities in a range of genetically well-defined cancers, including lung, endometrial, malignant rhabdoid tumor, synovial sarcoma, and others. In each of these settings, disruption of different SWI/SNF subunits have been shown to contribute to the tumorigenic potential via distinct mechanisms. This observation suggests the potential for a range of therapeutic targeting strategies to effectively inhibit cancer cell proliferation. Using high-density tiling sgRNA CRISPR/Cas9 screens, we have developed large-scale efforts to systematically identify critical protein functional domains within chromatin remodeling complex components to inform drug discovery strategies across several different cancer indications. Using this approach, we have successfully identified and validated critical functional domains in mSWI/SNF complex components with promising drug target potential in indications such as BRG1-mutated non-small cell lung adenocarcinoma and synovial sarcoma.

Citation Format: Luis Soares, Michael Bocker, Qianhe Zhou, Cigall Kadoch, Ho Man Chan. Application of high-density tiling CRISPR screen technology to identify chromatin remodeler complex targets for drug discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1653.
Abstract 1679: Neoepitope screening in colorectal cancer patients by custom exome panel profiling somatic mutations
Authors: Venkatramanan Raghavee , Deutsch Kerry , Golez Inah , Shroff Pallavi , Seale Spencer , Ralph Brendan , Dow Sally. , Anderson Evan , Tahir Saman , Malge Anjali , Braastad Corey , Anderson Steven
Published: August 2019

Colorectal cancer (CRC) is one of the major causes of global mortality. Recent clinical advances in T cell therapy using antibodies that block inhibitory T cell signals have been transforming cancer therapy. Studies show that somatic mutations in protein coding regions produce tumor-specific antigens, or neoantigens. CRC warrants deeper investigation into the non-synonymous exonic mutations that seem to be drivers in tumor development. Tumor mutation burden (TMB) and the abundance of neoantigens are highly correlated and it has been shown that TMB can be estimated using targeted sequencing panels. The aim of this study is to investigate 10 matched tumor/normal CRC samples using a panel targeting 422 genes covering about 1.7 Mb to screen for potential neoepitope candidates. Although sequencing and bioinformatics pipelines are developed to effectively filter neoantigens, it is still unclear which antigens elicit a T cell response. A review of the tools used in neoepitope prediction shows that it is not only a very complex task, but demands high sequencing depth. Comparing currently available tools will enable us to understand the strengths and shortcomings of each algorithm, and develop a custom pipeline framework.

Note: This abstract was not presented at the meeting.

Citation Format: Raghavee Venkatramanan, Kerry Deutsch, Inah Golez, Pallavi Shroff, Spencer Seale, Brendan Ralph, Sally. Dow, Evan Anderson, Saman Tahir, Anjali Malge, Corey Braastad, Steven Anderson. Neoepitope screening in colorectal cancer patients by custom exome panel profiling somatic mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1679.
Abstract 1687: Identification of bladder cancer subtypes with different sensitivities to immunotherapy
Authors: Chu In-Sun , Song Bic-Na , Leem Sun-Hee
Published: August 2019

Bladder urothelial carcinoma (BLCA) is pathologically categorized as non-muscle-invasive (NMIBC) and muscle-invasive (MIBC) bladder cancers. But its clinical heterogeneity has been suggested that biologically relevant subtypes may exist within and between NMIBC and MIBC. Here we identified that BLCA could be subgrouped into four major classes with distinct molecular characteristics regardless of previously known clinicopathological factors, using a series of unsupervised learning approaches. The predictor to discriminate distinct molecular subgroups of BLCA was constructed in a training cohort and validated in six independent cohorts with a total of 1,992 samples. The predictor showed a prognostic significance of the four subtype of BLCA, especially aggressive clinical behavior of the class 3 subtype. Interestingly, class 3 subtype has distinct biological features associated with potential responsiveness to immunotherapy, such as high somatic mutation rates and alterations of genes involved in DNA damage response and repair (DDR). Analyses of anti-PD-L1-treated BLCA patient tumor samples suggested that class 3 subtype was correlated with response to immune checkpoint inhibitors. Our findings have the potential to lead to the improvement of the current molecular classification system of BLCA and the achievement of better clinical outcomes for high-risk patients with BLCA treated with immunotherapy.

Note: This abstract was not presented at the meeting.

Citation Format: In-Sun Chu, Bic-Na Song, Sun-Hee Leem. Identification of bladder cancer subtypes with different sensitivities to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1687.
Abstract 1688: Integrative sequencing discovers a novel PGAP3-SRPK1 gene fusion in sinonasal undifferentiated carcinoma
Authors: McKean Erin L. , Birkeland Andrew C. , Neal Molly E. Heft , Kulkarni Aditi , Foltin Sue K. , Jewell Brittany M. , McHugh Jonathon B. , Marentette Lawence J. , Brenner John Chad
Published: August 2019

Sinonasal Undifferentiated Carcinoma (SNUC), a rare and aggressive tumor arising from the sinonasal cavity, remains a difficult-to-treat disease with poor overall survival. There are no agreed upon treatment algorithms and research efforts have focused on identifying new genetic mutations for novel targeted therapies. To date, targeted sequencing studies have identified IDH2 and SMARCAB1 as potential SNUC driver alterations, however the molecular alterations found in SMARCAB1 wild type tumors are unknown. Here, using whole exome sequencing, we characterize a series of 7 SNUC tumors and a SNUC cell line and discover recurrent aberrations to the SWI/SNF, MAGE and FAT gene families. We also validate a novel ALK mutation, recurrent ERBB2 copy number amplifications and a previously undescribed PGAP3-SRPK1 gene fusion in the SNUC cell line. Further investigation of the PGAP-SRPK1 fusion gene reveals a change in the active site with loss of three of nine active site residues. Functional studies are ongoing to determine the importance of the PGAP3-SRPK1 gene fusion for oncogenic phenotypes. This discovery extends the need for comprehensive characterization of gene family mutation status in SNUC and supports a need to understand the downstream molecular mechanisms in order to improve therapeutic strategies for this disease.

Citation Format: Erin L. McKean, Andrew C. Birkeland, Molly E. Heft Neal, Aditi Kulkarni, Sue K. Foltin, Brittany M. Jewell, Jonathon B. McHugh, Lawence J. Marentette, John Chad Brenner. Integrative sequencing discovers a novel PGAP3-SRPK1 gene fusion in sinonasal undifferentiated carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1688.
Abstract 1697: Molecular features of refractory metastatic breast cancer
Authors: Chen Zhanhong , Zhang Yuzi , Zhao Jing , Cai Shangli , Yin Yongmei
Published: August 2019

Background: Breast cancer is the most frequently diagnosed cancer in women worldwide and metastatic disease remains generally incurable, indicating a need for new drug discovery for metastatic breast cancer. In this study, we investigated the molecular features of refractory metastatic breast cancer.

Methods: 74 metastatic refractory breast cancer patients who received molecular screening using next generation sequencing (NGS) between 2015 and 2017 were included in this analysis. Clinical and pathologic characteristics of these patients were reviewed.

Results: Among the 74 patients, 27%, 51.4%, 10.8%, 10.8% had hormone receptor (HR)-negative HER2-negative, HR-positive HER2-negative, HR-positive HER2-positive, HR-negative HER2 positive. 54.1%, 48.6%, 9.5%, 47.3% had liver, lung, brain, bone metastasis. The most significantly mutated genes in refractory HR-positive breast tumors included TP53 (54.3%), PIK3CA (52.2%), CCND1 (19.6%) and ESR1 (15.2%). The most significantly mutated genes in refractory HR-negative breast tumors included TP53 (82.1%), PIK3CA (50%), MYC (14.3%), NF1 (14.3%) and KRAS (10.7%). Genes in PI3K/AKT/mTOR pathway were significantly mutated in 76.1% of HR-positive and 82.1% of HR-negative refractory breast tumors, respectively. Mutation of genes involved in DNA damage response pathway were observed in 23.9% of HR-positive tumors and 32.1% of HR-negative tumors. 21.7% of HR-positive tumors and only 3.6% of HR-negative tumors harbored at least one gene alteration in FGFR pathway (P = 0.04). 30.4% (17/74) of HR-positive tumors and 10.7% (3/28) of HR-negative tumors carried at least one gene alteration in CDK pathway (P = 0.50). 63.6% of tumors with alterations in FGFR pathway concurrently harbored alterations in CDK pathway. Alterations in FGFR or CDK pathway were significantly correlated with liver metastasis (P = 0.001). In addition, TP53 mutation was significantly correlated with brain metastasis (P = 0.022).

Conclusions: These results provide a better understanding of molecular targets in refractory metastatic breast cancer which may lead to an improvement in the development of novel therapeutic strategies.

Citation Format: Zhanhong Chen, Yuzi Zhang, Jing Zhao, Shangli Cai, Yongmei Yin. Molecular features of refractory metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1697.