bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4949: Longitudinal monitoring of cell-free DNA in patients with small cell lung cancer reveals dynamic insights into treatment efficacy and disease relapse
Authors: Lovly Christine M. , Almodovar Karinna , Iams Wade T. , Meador Catherine B. , York Sally , Horn Leora , Raymond Christopher K. , Hernandez Jennifer , Lim Lee P.
Published: July 2017

Introduction: Small cell lung cancer (SCLC) is a highly lethal neuroendocrine malignancy that accounts for approximately 10-15% of all lung cancers and is responsible for approximately 30,000 deaths annually in the United States and 200,000 deaths worldwide every year1. There is an urgent need to develop novel treatment strategies for patients with this disease. We sought to improve the quality of patient care by establishing a liquid biopsy assay for rapid, noninvasive monitoring of disease burden.

Design: The SCLC assay relies on targeted next-generation DNA sequencing of cell-free DNA (cfDNA) collected from patient plasma. The assay targets a panel of 14 genes that are frequently mutated in SCLC2. We examined a total of 141 plasma samples from a cohort of 27 patients. 11 patients had limited stage SCLC and 16 patients had extensive stage SCLC. The analyzed plasma samples were collected during the course of patient treatment and included time points before and after chemotherapy or immunotherapy.

Results: We detected somatic, disease-associated mutations in the cfDNA of 78% of patient samples (21/27). The allele frequency of cfDNA ranged from ≤0.5% to ≥85%. The most commonly mutated genes were TP53 and RB1, which were found in 17/27 and 10/27 samples, respectively. We also detected single nucleotide variants in PIK3CA (3/27) and PTEN (1/27) as well as copy number variants in MYC and MYCL1 (2/27). The observed mutant allele frequencies in longitudinal samples tracked closely with treatment responses. Strikingly, we found instances where the assay detected the reappearance of tumor-associated markers several weeks before clinical evidence of relapse was detected.

Conclusions: cfDNA sequencing allows for improved monitoring of disease burden, depth of responses to treatment, and timely warning of disease relapse in patients with SCLC.

References:

1. Society, A.C., Cancer Facts and Figures 2015. American Cancer Society, Atlanta, Ga, 2015.

2. George, J. et al., Comprehensive genomic profiles of small cell lung cancer, Nature 524:47

Citation Format: Christine M. Lovly, Karinna Almodovar, Wade T. Iams, Catherine B. Meador, Sally York, Leora Horn, Christopher K. Raymond, Jennifer Hernandez, Lee P. Lim. Longitudinal monitoring of cell-free DNA in patients with small cell lung cancer reveals dynamic insights into treatment efficacy and disease relapse [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4949. doi:10.1158/1538-7445.AM2017-4949
Abstract 5194: Focal radiation enhances paclitaxel therapy in a mouse model of triple negative breast cancer
Authors: Franklin Maryland , Dailey Thomas , Leopold Wilbur
Published: July 2017

Triple negative breast cancer (TNBC) accounts for 15-20% of all breast cancers in the US. In general, patients have poorer prognosis and therapeutic intervention is more challenging due to insensitivity to hormonal and anti-HER2 therapies. Therapeutic options include chemotherapy and/or radiation (RT) treatment. In this work we utilized HCC70, a human TNBC cell line, grown subcutaneously in NSG mice. We investigated whether the combination of focal RT and paclitaxel would improve anti-tumor activity over paclitaxel alone. RT therapy has typically been delivered in low doses over long periods of time. More recently higher fractions of RT are being given in shorter time intervals. Utilizing the Small Animal Radiation Research Platform (SARRP; Xstrahl, Suwanee, GA) we compared a low dose (2.5Gy) fractionated regimen to a higher dose but less frequent regimen (8Gy, QDx3) either as monotherapy or in combination with paclitaxel (15mg/kg weekly). The total cumulative dose of radiation was 24-25Gy in both radiation regimens. Paclitaxel alone produced moderate activity with a 10 day tumor growth delay and no tumor regressions. Treatment with low dose RT resulted in tumor stasis for ≥68 days, but there were no tumor regressions or tumor free survivors (TFS). Treatment with 8Gy, produced a 75% incidence of confirmed partial regressions (PR) and a 25% incidence of complete regressions (CR) with no TFS. In this group we observed slightly more body weight loss (BWL), more frequent clinical signs, and more frequent need for food and water supplementation than with the fractionated RT regimen. Mean BWL was ~10% with a nadir around 8-10 days post first RT dose. BWL was recovered over the next 1-2 week period. The combination of low dose focal RT with paclitaxel produced activity similar to that with high dose radiation (50% PR, 40% CR, and 1 TFS). Treatment with paclitaxel plus 8Gy RT was highly efficacious, producing an 80% incidence of CRs, all of which remained tumor free at study day 108. The remaining mouse experienced tumor stasis in excess of 63 days. Thus, a higher dose of focal RT given in shorter intervals in combination with systemic paclitaxel resulted in the most efficacious therapeutic strategy but at the cost of increased BWL and clinical signs.

Citation Format: Maryland Franklin, Thomas Dailey, Wilbur Leopold. Focal radiation enhances paclitaxel therapy in a mouse model of triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5194. doi:10.1158/1538-7445.AM2017-5194
Abstract 5264: Chemoprevention of rat oral carcinogenesis by black raspberry phytochemicals
Authors: Oghumu Steve , Knobloch Thomas , Ahn-Jarvis Jennifer , Weghorst Logan , Horvath Kyle , Geuy Paul , Weghorst Christopher
Published: July 2017

It is expected that in 2016, there will be an estimated 48,330 new cases and 9,570 deaths due to oral cancer in the US, which is about one person every hour every day. Due to the epithelial field defects associated with oral carcinogenesis, tumor recurrence and second primary tumor incidence are common. Recently conducted Phase I Clinical trials demonstrate the ability of black raspberries (BRBs) to modulate inflammatory biomarkers of molecular efficacy that supports a chemopreventive strategy against oral cancer. From these human trials we have established a molecular signature of BRB responsive biomarkers. However, it is essential that a preclinical animal model of BRB chemoprevention which recapitulates the fundamental features of human oral carcinogenesis be developed, so that we can evaluate potential mechanisms of action and validate molecular biomarkers of BRB efficacy. We therefore established the ability of BRB to inhibit oral lesion formation in a rat model of 4-nitroquinoline 1-oxide (4NQO) induced oral carcinogenesis and examined molecular efficacy using a clinically relevant transcriptional signature. Oral cancer was induced in F344 rats using 4NQO in drinking water for 10 weeks followed by regular drinking water for 16 weeks. Rats were administered a diet containing 5 or 10 percent lyophilized BRBs. Tongue tissues were examined for lesion multiplicity, incidence and histopathological features. Clinically derived pro-inflammatory and pro-survival molecular biomarkers were also determined by real-time PCR and ELISA. Dietary administration of 5 and 10 percent BRBs reduced combined lesion incidence and multiplicity by -39.3% and -28.6% respectively. Histopathological analyses of tongue sections further demonstrate the chemopreventive ability of dietary BRB administration in the rat model. Pro-survival and pro-inflammatory biomarkers were downregulated in BRB administered 4NQO induced rats compared to untreated 4NQO induced rats. Our study shows that dietary administration of BRB inhibits oral carcinogenesis in the rat 4NQO model. The rat 4NQO model is suitable for interrogating mechanisms of action of BRB-mediated oral cancer chemoprevention.

Citation Format: Steve Oghumu, Thomas Knobloch, Jennifer Ahn-Jarvis, Logan Weghorst, Kyle Horvath, Paul Geuy, Christopher Weghorst. Chemoprevention of rat oral carcinogenesis by black raspberry phytochemicals [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5264. doi:10.1158/1538-7445.AM2017-5264
Abstract 5269: Cryptotanshinone activate Nrf2 expression through microRNA regulations
Authors: Dongoran Rachmad A. , Wu Tien-Yuan
Published: July 2017

Cryptotanshinone is a diterpene quinone derived from the roots of Salvia miltiorrhiza Bunge. An increasing number of studies have demonstrated that cryptotanshinone has the pharmacological activities such as anti-oxidative stress, anti-bacteria, anti-inflammation, and anti-cancer. Cryptotanshinone has been found to increase the ARE expression level induced by the Nrf2 and decrease Keap1 expression. This study investigated Nrf2 and Keap1-related microRNA to understand the mechanisms of cryptotanshinone in antioxidant activities. HepG2 cells were treated with cryptotanshinone 2.5 μM in DMEM medium with 1% FBS for 5 days. Total RNA was obtained for small RNA sequencing and real-time PCR analyses. The analyses revealed that Cryptotanshinone had the potential to inhibit miR-27a-5p, miR-142-5p, miR-28 and miR-93-5p levels, which subsequently increased the Nrf2 mRNA level. On the other hand, the Keap1 mRNA level was suppressed through up-regulation of miR-23a and down-regulation of miR-7-5p. Moreover, Nrf2 and its related downstream anti-oxidant enzymes such as NQO1 and UGT were increased and the Keap1 protein level was decreased. These findings suggest that cryptotanshinone possesses the cancer chemoprevention activity in up-regulation of Nrf2 mRNA and protein levels through the suppression of inhibitory microRNA. Future investigations that extend the current study can focus on pharmacological mechanism of cryptotanshinone as a cancer chemoprevention agent, and the safety of long-term uptake of cryptotanshinone for cancer prevention.

Citation Format: Rachmad A. Dongoran, Tien-Yuan Wu. Cryptotanshinone activate Nrf2 expression through microRNA regulations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5269. doi:10.1158/1538-7445.AM2017-5269
Abstract 5360: DNA repair increases sequencing accuracy without altering actual mutation frequency in clinical samples
Authors: Liu Pingfang , Chen Lixin , Ettwiller Laurence , Dimalanta Eileen , Davis Theodore B. , Evans Thomas C.
Published: July 2017

Targeted cancer therapy based on genomic alterations can be remarkably effective. Currently, cancer genome profiling using next generation sequencing (NGS) is routinely applied in cancer care to guide personalized treatment. The accuracy of this profiling directly impacts therapeutic choices and the outcomes of patient care. We previously showed that false positive variants are abundant and can account for a major fraction of identified somatic variations in publicly available datasets (doi: http://dx.doi.org/10.1101/070334). These false positive variants show signs of mutagenic DNA damage. We further demonstrated that enzymatic DNA repair increases sequencing quality by lowering damage-induced background noise. Therefore, enzymatic DNA repair has the potential to improve sequencing accuracy, avoiding incorrect somatic variant calls and consequently reducing incorrect diagnostic conclusions. In this study, we investigated whether enzymatic DNA repair introduces any bias to NGS libraries using analysis by droplet digital PCR (ddPCR) and deep sequencing. DNA Reference Standards containing multiple common cancer mutations (Horizon Discovery, Inc.) were spiked into formalin-fixed paraffin-embedded (FFPE) DNA isolated from tumor samples from different tissue types at defined frequencies (0.5-10% quantified by ddPCR). Genotyping of the FFPE DNA ensured that they were free of any of the spiked-in mutations. After DNA repair and library preparation, mutation frequencies were quantified by ddPCR, and compared to the mutation levels in input DNA and control libraries without repair. Deep sequencing of 151 cancer genes including these spike-ins showed no difference in mutation frequency for the spiked-in mutations between the control and repair groups. However, the number of false positive variant calls was reduced in the repair group. Our data demonstrates that DNA repair significantly increases sequencing accuracy without altering the frequency of actual mutations in tumor samples.

Citation Format: Pingfang Liu, Lixin Chen, Laurence Ettwiller, Eileen Dimalanta, Theodore B. Davis, Thomas C. Evans. DNA repair increases sequencing accuracy without altering actual mutation frequency in clinical samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5360. doi:10.1158/1538-7445.AM2017-5360
Abstract 5383: Non-invasive diagnosis of early-stage lung cancer via targeted high-throughput DNA methylation sequencing of circulating tumor DNA (ctDNA)
Authors: Cai Xuyu , Gao Yangbin , Shen Hui , Laird Peter , Fan Jian-bing , Xu Weihong , Liang Wenhua , He Jianxing
Published: July 2017

Current state-of-the-art lung cancer early screening involves using low-dose CT scan to identify lung nodules smaller than 3cm in diameter. However, it’s still a clinical dilemma to differentiate between malignant and benign nodules.

We took the approach of methylation profiling by high-throughput bisulfite DNA sequencing in tissue samples to identify specific methylation signatures. We learned methylation patterns that differentiate malignant vs. benign lesions from tissue samples by in-depth data mining, and then used pattern matching to classify plasma samples. Given the usual low amount of ctDNA in plasma, we also developed an ultra-sensitive library preparation method to perform targeted bisulfite DNA sequencing from as low as 1ng of cfDNA or 1mL of plasma.

From a training set of 88 tissue samples, which includes 60 malignant specimens with different subtypes (invasive adenomas, IA; minimally invasive adenomas, MIA; atypical adenomatous hyperplasia, AAH; adenocarcinoma in situ, AIS; carcinoid; lymphoepithelioma-like carcinoma of the lung, LELC; squamous carcinoma, SC; as well as 28 benign specimens in different categories including hematomas, granuloma, tuberculosis, inflammatory pseudotumor (IPT), sclerosing hemangiomas (SHL) and infections, we were able to achieve a sensitivity of 95% for identification of malignant lesions, with a specificity of 78.6%. From an independent validation set of 45 plasma samples, we achieved a sensitivity of 94.7% and a specificity of 85.7% for differentiating patients with malignant tumor from patients with benign lesions. Specifically, our assay is demonstrated to be highly sensitive towards early-stage lung cancer detection, with a sensitivity of 93.3% in a total of 15 patients with stage IA/B lung cancer.

In summary, we have developed a highly sensitive blood-based non-invasive diagnostic assay for identification of early stage lung cancer, which can aid clinical decisions for patients with a CT scan positive for lung nodules. This approach can also be extended to non-invasive early screening for various cancer types.

Citation Format: Xuyu Cai, Yangbin Gao, Hui Shen, Peter Laird, Jian-bing Fan, Weihong Xu, Wenhua Liang, Jianxing He. Non-invasive diagnosis of early-stage lung cancer via targeted high-throughput DNA methylation sequencing of circulating tumor DNA (ctDNA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5383. doi:10.1158/1538-7445.AM2017-5383
Abstract 5443: Developing a novel miR-15a mimic as a potential therapeutic molecule to eliminate resistant colorectal cancer stem cells
Authors: Fesler Andrew T. , Liu Hua , Wu Ning , Ju Jingfang
Published: July 2017

In the last 15 years, it has become well established that microRNA play important roles in cancer biology. Due to their ability to regulate the expression of important target genes, aberrant expression of miRNAs has been linked to cancer development and progression. Based on these important functions, there is great interest in developing miRNA based therapeutics. In colorectal cancer, treatment using 5-flurouracil (5-FU) based chemotherapy has improved patient outcomes. However, there remain challenges associated with chemoresistance and recurrence for patients with advanced stage colorectal cancer. miRNA based therapeutics may represent an potential novel therapeutic option for colorectal cancer therapy either alone or in combination with 5-FU based chemotherapy. miR-15a was of the first miRNAs identified to be associated with cancer, and has been shown to have important roles in several tumor types. miR-15a is downregulated in colon cancer and associated with poor patient prognosis. We have identified several important cancer related targets of miR-15a in colon cancer, including YAP1, DCLK1, BMI1 and BCL2. Through the regulation of these targets, miR-15a expression can be used as a potent inhibitor to reduce colon cancer cell proliferation, invasion and improve sensitivity to 5-FU, as well as decreasing tumor growth in vivo mouse colon tumor models using colon cancer stem cells. In the interest of developing miR-15a based colon cancer therapeutics, we have made a modified miR-15a mimic that shows enhanced abilities to disrupt resistant colon cancer cell proliferation and induction of cell cycle arrest when compared to unmodified miR-15a. Following transfection with miR-15a mimic, cell number was reduced by 84% compared to control and 66% compared to miR-15a precursor. Cell cycle analysis showed that G1/S ratio was increased from 1.07 for control to 2.87 for precursor miR-15a and 7.07 for miR-15a mimic. This miR-15a mimic also maintains its ability to regulate these important target genes in colon cancer stem cells. In mouse models using colon cancer stem cells, miR-15a mimic has demonstrated therapeutic potential by reducing tumor growth. Based on these findings, there is potential that modified miR-15a could be adapted for treatment of patients to improve survival of advanced stage colorectal cancer patients.

Citation Format: Andrew T. Fesler, Hua Liu, Ning Wu, Jingfang Ju. Developing a novel miR-15a mimic as a potential therapeutic molecule to eliminate resistant colorectal cancer stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5443. doi:10.1158/1538-7445.AM2017-5443
Abstract 5465: Persistent oxidative stress in mouse intestinal and colonic epithelial cells after exposure to 12C-ion radiation
Authors: Suman Shubhankar , Kumar Santosh , Fornace Albert J. , Datta Kamal
Published: July 2017

Purpose: 12C-ion radiotherapy is demonstrating favorable results compared to photon radiotherapy for select cancers. While normal tissue exposure is lower with 12C-ions relative to γ-rays, it cannot be completely eliminated and therefore, late tissue toxicity, inflammation and secondary carcinogenesis cannot be ruled out. The goal of this study was to assess the extent of persistent oxidative stress (POS) after 12C radiation exposure and compare the results to that after γ radiation exposure.

Methods and Materials: Mice (C57BL/6J; 6 to 8 weeks; male) were irradiated with 0.5 or 1.3 Gy of γ or 12C-ion, and intestinal (IEC), colonic (CEC) epithelial cells and tissues were collected 2 months after radiation exposure. In epithelial cells, intracellular ROS, mitochondrial superoxide, mitochondrial membrane potential (MMP), and cardiolipin oxidation were studied by flow-cytometry. Superoxide dismutase (SOD), catalase, and NADPH oxidase activity along with lipid oxidation were also assessed in epithelial cells using biochemical assays.

Results: Our results clearly showed radiation quality and dose-dependent induction of POS. Both intestine and colon showed a higher elevation of intracellular ROS, mitochondrial superoxide, NADPH oxidase activity, and mitochondrial cardiolipin oxidation after 12C relative to γ radiation. Moreover, antioxidant enzyme activity in intestine and colon was also significantly reduced in 12C-irradiated mice. Compared to γ radiation, membrane lipid damage was remarkably higher in both intestine and colon of 12C-ion irradiated mice. At 0.5 Gy, persistent oxidative damage indicated by 4-hydroxynonenal was 3-fold in colon and 1.6 fold in intestine after 12C relative γ radiation.

Conclusions: Mitochondrial deregulation, increased NADPH oxidase activity and loss of SOD and catalase activities were the major contributory events in 12C-ion-induced POS in mouse GI-tissues. Compared to intestine, colon was more susceptible to POS induction that might be due to progressive cell turnover in intestine resulting in faster elimination of initial damage signal in a given time than colon. Taken together, our data suggest that normal tissue exposure to 12C radiation carries higher long-term risk relative to γ-rays at comparable doses and further detail evaluation is warranted.

Citation Format: Shubhankar Suman, Santosh Kumar, Albert J. Fornace, Kamal Datta. Persistent oxidative stress in mouse intestinal and colonic epithelial cells after exposure to 12C-ion radiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5465. doi:10.1158/1538-7445.AM2017-5465
Abstract 5487: Identification of super-enhancer-associated cancer genes provides novel therapeutic targets in adult T-cell leukemia/lymphoma
Authors: Sanda Takaomi , Wong Regina WJ , Cao Phuong TN , Leong Wei Zhong , Yam Alice WY , Zhang Tinghu , Iida Shinsuke , Okamoto Takashi , Ueda Ryuzo , Gray Nathanael S. , Ishida Takashi
Published: July 2017

Super-enhancers are often enriched at cancer genes in various malignancies. Identification of such enhancers would pinpoint critical factors that directly contribute to pathogenesis. Adult T-cell leukemia/lymphoma (ATL) is a highly aggressive lymphoproliferative disorder that arises from CD4+ mature T-lymphocytes. A recent genome-wide sequencing study revealed a large number of genetic and chromosomal abnormalities. However, there is still a lack of functional evidence for these genetic abnormalities in ATL pathogenesis due to the large mutational burden and the considerable genetic heterogeneity. Here, we performed super-enhancer profiling combined with gene expression analysis in primary ATL samples and cell lines. Super-enhancers are frequently enriched at genes involved in T-cell activation and T-cell receptor signaling pathway in both ATL and normal CD4+ T-cells, reflecting the origin of leukemia cells. Super-enhancers at the CCR4 gene, a known therapeutic target in ATL, were observed in all ATL cases. Additionally, we identified previously-uncharacterized genes that were highly activated in ATL cells and required for cell growth. A small-molecule inhibitor of CDK7 efficiently downregulated the expression of these genes and inhibited cell growth. Our study provides a novel strategy to identify critical cancer genes in cancer.

Note: This abstract was not presented at the meeting.

Citation Format: Takaomi Sanda, Regina WJ Wong, Phuong TN Cao, Wei Zhong Leong, Alice WY Yam, Tinghu Zhang, Shinsuke Iida, Takashi Okamoto, Ryuzo Ueda, Nathanael S. Gray, Takashi Ishida. Identification of super-enhancer-associated cancer genes provides novel therapeutic targets in adult T-cell leukemia/lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5487. doi:10.1158/1538-7445.AM2017-5487
Abstract 5488: APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL
Authors: Li Zhaodong , Abraham Brian , Berezovskaya Alla , Farah Nadine , Liu Yu , Leon Theresa , Fielding Adele , Tan Shi Hao , Sanda Takaomi , Weintraub Abraham , Li Benshang , Shen Shuhong , Zhang Jinghui , Mansour Marc , Young Richard , Look Thomas
Published: July 2017

Oncogenic driver mutations are those that provide a proliferative or survival advantage to neoplastic cells resulting in clonal selection. Although most cancer causing mutations have been detected in the protein-coding regions of the cancer genome, driver mutations have recently also been discovered within noncoding genomic sequences. Thus, a current challenge is to gain precise understanding of how these unique genomic elements function in cancer pathogenesis, while clarifying mechanisms of gene regulation and identifying new targets for therapeutic intervention. Here we report a C-to-T single nucleotide transition that occurs as a somatic mutation in noncoding sequences 4 kb upstream of the transcriptional start site of the LMO1 oncogene in primary samples from patients with T-cell acute lymphoblastic leukaemia. This single nucleotide alteration conforms to an APOBEC-like cytidine deaminase mutational signature, and generates a new binding site for the MYB transcription factor, leading to the formation of an aberrant transcriptional enhancer complex that drives high levels of expression of the LMO1 oncogene. Since APOBEC-signature mutations are common in a broad spectrum of human cancers, we suggest that noncoding nucleotide transitions such as the one described here may activate potent oncogenic enhancers not only in T-lymphoid cells but in other cell lineages as well.

Citation Format: Zhaodong Li, Brian Abraham, Alla Berezovskaya, Nadine Farah, Yu Liu, Theresa Leon, Adele Fielding, Shi Hao Tan, Takaomi Sanda, Abraham Weintraub, Benshang Li, Shuhong Shen, Jinghui Zhang, Marc Mansour, Richard Young, Thomas Look. APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5488. doi:10.1158/1538-7445.AM2017-5488
Abstract 5530: Evidence linking aquaporin-3 loss to increased invasiveness in bladder cancer
Authors: Roy Arpita , DeSilva Dinuka M. , Bottaro Donald P.
Published: July 2017

Bladder cancer (BCa) is the most common type of urothelial cancer (UC). According to American Cancer Society, in 2016, diagnoses of 76,960 new cases of bladder cancer (BCa) and 16,390 BCa associated deaths have been estimated. More than 90% of bladder cancer starts in the innermost transitional epithelium (urothelium) of the bladder. Aquaporin 3 (AQP3), one of 13 members of a transmembrane channel forming protein family (AQP0-12), has an N-terminal basolateral sorting signal and localizes to the basolateral membrane in epithelial tissues. Recent studies have shown that AQP3 expression is decreased in UC thus supporting a new hypothesis that alteration of the expression of AQP3 plays a role in the pathogenesis of UC. However, it remains to be determined whether AQP3 is involved in the invasion and metastasis of UC cells. In the present study, human bladder cancer cell lines of different grades, SW780 (G1) and TCCSUP (G4) were studied. Transcript and protein levels of AQP3 expression were significantly higher in low grade, SW780 cells when compared to the higher-grade TCCSUP cells. Inhibition of AQP3 by CuSO4 or siRNA specific knockdown of AQP3 resulted in increased migration in the wound-healing scratch assay. Over-expression of AQP3 plasmid resulted in reduced migration. It is known that epithelial cell polarity contributes to tumor suppression and that loss of E-cadherin is a crucial step in epithelial-to-mesenchymal transition (EMT). Our results indicate that AQP3 overexpression induced expression of E-cadherin, consistent with a role for AQP3 as a tumor suppressor by maintaining epithelial cell polarity and inhibiting EMT in BCa. Conversely, reduced AQP3 levels leading to reduced E-cadherin levels in high-grade BCa cells may result in loss of cell polarity, increased invasiveness and increased EMT.

Citation Format: Arpita Roy, Dinuka M. DeSilva, Donald P. Bottaro. Evidence linking aquaporin-3 loss to increased invasiveness in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5530. doi:10.1158/1538-7445.AM2017-5530
Abstract 554: Accurately identifying neoantigens utilizing both DNA and RNA somatic variants in an enhanced platform
Authors: Boyle Sean M. , Harris Jason , Bartha Gabor , Alla Ravi , Karbelashvili Mirian , Chervitz Steve , Montana Aldrin , Rowell Craig , Jonganeel Patrick , Kirk Scott , McClory Rena , West John , Chen Rich
Published: July 2017

The identification of neoantigens is a crucial step in the development of neoantigen-based personalized cancer vaccines and other immunotherapies. Accurately predicting which neoantigens are likely to be immunogenic remains a key challenge owing to the complex processes involved in determining neoantigen immunogenicity including the antigen presenting machinery, likelihood of MHC class I and II binding, similarity to self, and ability to interact with the TCR.

We have developed a neoantigen detection pipeline built upon our analytically validated Accuracy and Content Enhanced (ACE) Exome and Transcriptome sequencing platform and somatic variants calling pipeline through combined DNA and RNA analysis. The analytical performance of these pipelines is greater than >97% sensitivity for small variants (RNA and DNA) with a specificity of >98% (DNA) and a fusion sensitivity of >99% (RNA).

Within our neoantigen pipeline, variants that are detected by our DNA and RNA cancer analysis pipelines are processed for antigen identification, including SNVs, indels, and fusion events. Importantly, both in-frame and out-of-frame events are accurately considered by transcript, allowing for detection of a wealth of candidate neoantigens. Our pipeline includes assessment of important immunologic components including HLA prediction, MHC binding (class I and II), immunogenicity, similarity to self, and similarity to known antigens. Additionally, peptides are evaluated for variant allele frequency in both the RNA and DNA of the tumor sample and gene expression level is considered. Collectively, our ImmunoID product provides a comprehensive assessment of features that may be used for identifying and ranking potentially immunogenic neoantigens.

To assess the effectiveness of this pipeline in predicting immunogenic neoantigens, we assembled a gold-set of 23 known, previously experimentally-validated immunogenic neoantigens from the literature. We spiked in these neoepitopes into exome data and assessed the ability of our neoantigen pipeline to find and rank these immunogenic known neoantigens. Preliminary results show our neoantigen pipeline is able to accurately identify 22 out of 23 (~96%) of the spiked in neoantigens as being potentially immunogenic.

Citation Format: Sean M. Boyle, Jason Harris, Gabor Bartha, Ravi Alla, Mirian Karbelashvili, Steve Chervitz, Aldrin Montana, Craig Rowell, Patrick Jonganeel, Scott Kirk, Rena McClory, John West, Rich Chen. Accurately identifying neoantigens utilizing both DNA and RNA somatic variants in an enhanced platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 554. doi:10.1158/1538-7445.AM2017-554
Abstract 5540: Transcriptional control of signaling pathways in T-cell lymphoblastic leukemia by Ikaros tumor suppressor
Authors: Hu Tommy , Soliman Mario , Kapadia Malika , Dovat Elanora , Payne Jonathan , Song Chunhua , Dovat Sinisa
Published: July 2017

Cellular proliferation in T-cell acute lymphoblastic leukemia is regulated by multiple signaling pathways. The Phosphoinositide 3-kinase (PI3K)/AKT pathway is frequently dysregulated in T-ALL. Targeting the PI3K pathway has shown promise as a novel therapeutic approach for T-ALL. However, regulation of the PI3K pathway is still not well understood. Here, we report that PI3K activity in T-ALL can be controlled by transcriptional regulation of key members of this pathway, PIK3CD and PIKFYVE. DNA binding analysis of primary T-ALL using qChIP revealed that the tumor suppressor protein, Ikaros, binds the promoter regions of PIK3CD and PIKFYVE. Since Ikaros acts as a regulator of transcription, we tested whether Ikaros binding to PIK3CD and PIKFYVE affects their expression. Overexpression of Ikaros results in reduced transcription of PIK3CD and PIKFYVE in T-ALL. Targeting Ikaros with a specific shRNA, resulted in increased transcription of PIK3CD and PIKFYVE in T-ALL. Together, these results demonstrate that Ikaros functions as a transcriptional repressor of both PIK3CD and PIKFYVE, and suggest that Ikaros can regulate the PI3K pathway in T-ALL. It has been previously shown that Ikaros function in B-cell acute lymphoblastic leukemia is regulated by oncogenic Casein Kinase II (CK2). We tested whether Ikaros ability to repress transcription of PIK3CD and PIKFYVE is regulated by CK2. Inhibition of CK2 by a specific pharmacological inhibitor, CX-4945, resulted in increased Ikaros binding to the promoters of PIK3CD and PIKFYVE, as well as in transcriptional repression of both of these genes. These results suggest that Ikaros function as a repressor of PIK3CD and PIKFYVE transcription is impaired by CK2 in T-ALL. CK2 inhibition restores Ikaros-mediated transcriptional repression of PIK3CD and PIKFYVE, which results in downregulation of the PI3K pathway. In conclusion, the presented data demonstrate that the PI3K signaling pathway is regulated by transcriptional repression of PIK3CD and PIKFYVE by Ikaros in T-ALL. Results reveal interplay between two signaling pathways in T-ALL, CK2 and PI3K, where CK2 positively regulates the PI3K pathway by inhibiting Ikaros function. These data reveal novel mechanisms that regulate cellular proliferation in T-ALL.

Citation Format: Tommy Hu, Mario Soliman, Malika Kapadia, Elanora Dovat, Jonathan Payne, Chunhua Song, Sinisa Dovat. Transcriptional control of signaling pathways in T-cell lymphoblastic leukemia by Ikaros tumor suppressor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5540. doi:10.1158/1538-7445.AM2017-5540
Abstract 5547: A computational approach to predict tissue level cell cycle regulatory network for normal proliferating and cancer cells
Authors: Sheng Tao , Cao Sha , Zhang Chi , Xu Ying
Published: July 2017

Cell cycle control and regulation has been widely studied in terms of cyclin-dependent kinases (CDKs) activities, while only limited information are available on tissue contexts and signaling. In this study, we adopted a systems biology approach aiming to comprehensively capture how tissue level signaling events orchestrate cell cycle phases in a CDKs activities independent manner in both of normal and tumor tissues. We have applied our in house gene co-expression and bi-clustering analysis on a collection of 8 single cell transcriptomic sequencing datasets of normal proliferating human embryonic cells, 17 RNA-seq transcriptomic datasets of inflammatory tissues and 30 microarray data sets of chronic inflammatory diseases as normal proliferating reference and TCGA RNA-seq data for 20 cancer types aiming to identify cell cycle associated gene co-expression modules. Our results suggest that the tissue level signaling events are generally show distinct regulatory structures between tumor and normal tissues: 1) the Rho GTPase signaling pathways that control cell polarity, activate in G2/M transition phase in normal tissue, while mainly in G1 and S phases in tumor. 2) Focal adhesion kinases (FAK) drives G1/S transition in normal tissues, while activated in multiple phases in tumor. 3) Hippo signaling for cell size control activates at G2/M transition phase in normal tissue while in multiple phases in tumor. In addition, we have also generated tissue level regulatory networks for cell cycle controls by predicting possible collective effects of extra- and intra-cellular signaling for both normal proliferating and cancer cells.

Citation Format: Tao Sheng, Sha Cao, Chi Zhang, Ying Xu. A computational approach to predict tissue level cell cycle regulatory network for normal proliferating and cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5547. doi:10.1158/1538-7445.AM2017-5547
Abstract 5559: Using cancer dependency data to discover tumor suppressive and oncogenic functional modules
Authors: Pan Joshua , Meyers Robin M. , Michel Brittany C. , Sizemore Ann E. , Vazquez Francisca , Weir Barbara A. , Hahn William C. , Tsherniak Aviad , Kadoch Cigall
Published: July 2017

Efforts to define protein complexes and their functional networks are critical for systems-level understanding of the pathways involved in human cancer. Current methods to catalog human protein complexes via physical interaction are often unable to resolve functional differences between complex members or infer relationships governed by sub-stoichiometric interactions. While functional wiring maps in yeast have been generated by measuring epistatic interactions between pairs of genes, efforts to scale this concept in individual human cell lines have been met with challenges and have only been able to characterize limited numbers of genes at a time.

We have developed a scalable approach that can measure functional similarity without the constraints of pairwise genetic interaction experiments. Using data from genome-wide RNAi and CRISPR dropout screens performed in hundreds of cancer cell lines, we leveraged the heterogeneity of gene dependencies across cancer types to measure functional similarity between thousands of genes at once, which in turn allowed us to recreate known inter- and intra-complex functional relationships and to uncover tumor suppressive and oncogenic functional modules in cancer-relevant pathways such as proteolysis, metabolism and transcription.

Applying these approaches to the mammalian SWI/SNF (BAF) chromatin remodeling complex, which is mutated in over 20% of human cancer, revealed three functional modules that arose separately during metazoan evolution, one of which is entirely novel and uncharacterized. We then performed biochemical experiments that fully support three specialized complex configurations, each with distinct size, subunit composition, and function. These data reorganize the BAF complex into previously unrecognized modules that better explain mutational burden in human cancer. Notably, we observe that that all known BAF-driven, highly penetrant rare cancers and neurodevelopmental disorders involve disruption within a single functional module we defined, underscoring the value of evaluating disease genomics through the lens of functional modularity.

Citation Format: Joshua Pan, Robin M. Meyers, Brittany C. Michel, Ann E. Sizemore, Francisca Vazquez, Barbara A. Weir, William C. Hahn, Aviad Tsherniak, Cigall Kadoch. Using cancer dependency data to discover tumor suppressive and oncogenic functional modules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5559. doi:10.1158/1538-7445.AM2017-5559
Abstract 5567: A scalable and integrated computational and experimental workflow to identify new driver genes in cancer genome data
Authors: Horn Heiko , Lawrence Michael S. , Chouinard Candace R. , Shrestha Yashaswi , Hu Jessica Xin , Worstell Elizabeth , Shea Emily , Ilic Nina , Kim Eejung , Kamburov Atanas , Kashani Alireza , Hahn William C. , Campbell Joshua D. , Boehm Jesse S. , Getz Gad , Lage Kasper
Published: July 2017

High throughput sequencing has revolutionized the study of the cancer genome, enabling numerous discoveries in basic and clinical research. However, considerable sample sizes are required to find cancer driver genes with intermediate and low mutation frequencies, and for a large proportion of patients the molecular cause (e.g. driver gene(s)) of disease is unknown. Here, we describe an integrated computational and experimental workflow that combines cancer genome data, molecular network information, multiplexed in vivo tumorigenesis assays, and reanalysis of driver-gene-negative cancer patients to predict and validate new driver genes. We develop a statistic, network mutation burden, that combines molecular network information with data from 4,742 cancer genomes to accurately classify known driver genes across 21 tumor types and predict 62 driver gene candidates.Of these, 35 gene candidates were tested in multiplexed in vivo tumorigenesis cell assays using sensitized immortalized human embryonic kidney (HA1E-M) and immortalized human lung epithelial (SALE-Y) cell lines.Tumor formation in vivo was observed for 11 genes (2 in HA1E-M, 3 in SALE-Y, 6 in both). By reanalyzing 242 lung adenocarcinoma patients with an unknown molecular cause of disease we show that two of these candidates, TFDP2 and AKT2, are significantly amplified in multiple samples.Overall, we describe a scalable combined computational and experimental framework to predict and validate driver genes across many tumor types. Our proof-of-concept approach should become increasingly useful as the number of cancer genomes continues to grow.

Citation Format: Heiko Horn, Michael S. Lawrence, Candace R. Chouinard, Yashaswi Shrestha, Jessica Xin Hu, Elizabeth Worstell, Emily Shea, Nina Ilic, Eejung Kim, Atanas Kamburov, Alireza Kashani, William C. Hahn, Joshua D. Campbell, Jesse S. Boehm, Gad Getz, Kasper Lage. A scalable and integrated computational and experimental workflow to identify new driver genes in cancer genome data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5567. doi:10.1158/1538-7445.AM2017-5567
Abstract 5592: Metformin improves immune function of exhausted peripheral CD8+ T cells derived from cancer patients
Authors: Watanabe Mototsugu , Eikawa Shingo , Shien Kazuhiko , Yamamoto Hiromasa , Shien Tadahiko , Soh Junichi , Doihara Hiroyoshi , Toyooka Shinichi , Miyoshi Shinichiro , Udono Heiichiro
Published: July 2017

Background: Immunotherapy has been developed and shown a drastic effect on several malignancies. However, in the tumor microenvironment, CD8+ tumor infiltrating lymphocytes (CD8+ TILs) are repeatedly exposed to tumor antigens and lose their anti-tumor activities. We have recently shown that metformin can show anti-tumor effect thorough improving immune function in mouse models. Increased numbers of such multifunctional CD8+ TILs have well correlated with tumor retardation, suggesting an underlying mechanism of metformin in tumor immunity. The objectives of this study are to evaluate the efficacy of metformin on human immune function.

Methods: We obtained peripheral blood mononuclear cells (PBMC) from healthy volunteers (HV) and cancer patients (CP) before and after taking metformin orally for about 2 weeks. We cultured the PBMC in a presence of stimulation with phorbol 12-myristate 13-acetate (PMA) / ionomycin in vitro for 6 hours. Expressions of markers for immune-check points (PD-1 and Tim-3) were examined together with accumulated intracellular cytokines, IFN-γ, IL-2 and TNF-α by flow cytometry analysis.

Results: We obtained consents for take part in our clinical research from 20 HV and 15 CP (10 breast cancer, 4 metastatic lung cancer and 1 primary lung cancer). CD8+ T cells which expressed both of PD-1 and Tim-3 derived from CP were higher than those of HV (p = 0.041). Increased production of multiple cytokines, IFN-γ, IL-2 and TNF-α was observed in CD8+ T cells of almost all cancer patients by metformin treatment and its increasement was significant (p < 0.01), whereas marginal difference before and after metformin administration was detected in the samples from healthy volunteers so far (p = 0.051).

Conclusion: Metformin treatment might be useful in reversion of exhausted CD8+T cells in cancer bearing patients.

Citation Format: Mototsugu Watanabe, Shingo Eikawa, Kazuhiko Shien, Hiromasa Yamamoto, Tadahiko Shien, Junichi Soh, Hiroyoshi Doihara, Shinichi Toyooka, Shinichiro Miyoshi, Heiichiro Udono. Metformin improves immune function of exhausted peripheral CD8+ T cells derived from cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5592. doi:10.1158/1538-7445.AM2017-5592