bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4142: Conformational dynamics of the chimeric kinase DNAJB1-PRKACA, the driver for fibrolamellar hepatocellular carcinoma
Authors: Tomasini Michael D. , Wang Yingiie , Karamafrooz Adak , Hall James , Taylor Susan S. , Beuming Thijs , Veglia Gianluigi , Simon Sanford M.
Published: August 2018

In fibrolamellar hepatocellular carcinoma (FLC) there is a single common genetic alteration in all tumors: A deletion in one copy of chromosome 19 resulting in the fusion of the first exon of DNAJB1, encoding the J-domain of heat shock protein 40, with exons 2-10 of the catalytic subunit of protein kinase A, PRKACA [1]. This produces an enzymatically active chimeric protein. Expression of the chimera in mouse liver either by recreating the deletion by CRISPR/Cas9, or expression, in trans, by a transposon is sufficient to produce FLC [2]. We used molecular dynamics simulations, NMR, and SAXS to analyze the conformational dynamics of the native and chimeric kinase. The most significant differences were in the amino domain with the chimera in an ensemble of conformations. Some structures had the J-domain tucked under the large lobe of the kinase, similar to that reported in the crystal structure, and in others the J-domain was dislodged from the core of the kinase, swinging free in solution. These simulated dislodged states were captured experimentally both by NMR and small angle X-ray scattering. Modeling of the different conformations onto the RIIβ holoenzyme revealed no obvious steric interactions suggesting that the J-domain does not preclude formation of the holoenzyme. The flexible conformations appear to be independent of the nucleotide/substrate binding mode as they were observed in ATP, ADP, Apo, and ATP-PKI bound states.

[1] Honeyman, J. N. et al. Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma. Science 343, 1010-1014 (2014).

[2] Kastenhuber, E. R. et al. DNAJB1-PRKACA fusion kinase interacts with β-catenin and the liver regenerative response to drive fibrolamellar hepatocellular carcinoma. Proc. Natl. Acad. Sci. 201716483 (2017). doi:10.1073/pnas.1716483114

Citation Format: Michael D. Tomasini, Yingiie Wang, Adak Karamafrooz, James Hall, Susan S. Taylor, Thijs Beuming, Gianluigi Veglia, Sanford M. Simon. Conformational dynamics of the chimeric kinase DNAJB1-PRKACA, the driver for fibrolamellar hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4142.
Abstract 4149: Inhibition of ribonucleotide reductase (RNR) in Ewing sarcoma cells results in suppression of protein synthesis
Authors: Koppenhafer Stacia , Goss Kelli , Gordon David
Published: August 2018

Ewing sarcoma is a highly aggressive bone and soft tissue cancer that is caused by the EWS-FLI1 fusion protein. EWS-FLI1 is required for tumor growth and survival. However, directly targeting EWS-FLI1 with drugs has been challenging and an alternative therapeutic approach is to identify unique vulnerabilities incurred by the oncoprotein. In previous work, we identified that Ewing sarcoma cells are uniquely vulnerable to drugs that inhibit ribonucleotide reductase (RNR), which is the rate limiting enzyme in the synthesis of deoxyribonucleotides. Furthermore, we also showed that blocking the function of checkpoint kinase 1 (CHK1), a major regulator of the response to impaired DNA replication, using either a small molecule inhibitor or siRNA-mediated knockdown causes synergistic toxicity with gemcitabine, an irreversible inhibitor of the RRM1 subunit of RNR, in Ewing sarcoma cells. In the current work, we identifiy that inhibition of RNR in Ewing sarcoma cells in vitro and in vivo results in the suppression of protein synthesis. Moreover, we have found that the treatment of Ewing sarcoma cell lines with gemcitabine results in an increase in the active (unphosphorylated) form of 4E-BP1, which is a well-described inhibitor of protein translation. However, in contrast to the Ewing sarcoma cells, treatment of other cell types with gemcitabine did not alter 4E-BP1 phosphorylation or protein synthesis. Currently, ongoing work is focused on the in vivo testing of gemcitabine, alone and in combination with CHK1, ataxia telangiectasia and rad3-related protein (ATR), and protein synthesis inhibitors, as a novel therapeutic approach for the treatment of Ewing sarcoma.

Citation Format: Stacia Koppenhafer, Kelli Goss, David Gordon. Inhibition of ribonucleotide reductase (RNR) in Ewing sarcoma cells results in suppression of protein synthesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4149.
Abstract 415: A single molecule detection system for comprehensive analysis of cancer related cellular pathways
Authors: Furtado Manohar R. , Fang Rixun , Burns Norman , Burich Rebekah , Le Catherine , Ivaturi Soumya , Hartlage Rob , Zizminskas Ed , Jahncke Jim , Mack Philip C. , Staker Bryan P.
Published: August 2018

The purpose of this study was to evaluate the system capabilities of a new single-molecule detection platform capable of both genomic and proteomic analysis of cellular pathways using very small amounts of tumor material. The system has 4-color optics, single-fluorophore detection capability, localization of molecules to within a 20nm area, a flow cell with an area of 940 mm2 and the ability to detect > 109 molecules on the surface. NSCLC cell lines were cultured and untreated or treated with the EGFR tyrosine kinase inhibitor erlotinib. Cells were harvested and used to generate protein lysates, isolate mRNA and gDNA. Cellular molecules were covalently attached to an epoxysilane-coated surface on the flow cell and then repeatedly probed 10-15 times with labeled antibodies and oligonucleotides to detect, count and quantitate proteins, protein phosphorylation levels, mRNAs, fusion transcripts, and DNA mutations. We detected protein phosphorylation changes for EGFR, ERK, MET and MEK comparable to that observed by traditional western blots; however, the system required only 0.5 to 2 cell equivalents of protein lysate, containing sub pico-Molar levels of protein. We demonstrated robust and statistically significant detection of 2-fold changes in protein levels across 3 slides, in triplicate lanes and performed over 3 non-consecutive days by 3 operators (Tukey-Kramer tests). We also detected 8 mRNAs, with no PCR amplification required, in a multiplexed format with relative levels similar to that observed with TaqMan® qPCR tests. We demonstrated protein detection at ~ 100% recovery compared to an ELISA test and nucleic acid recovery at ~ 30% with no amplification. We also detected exon 19 deletions in EGFR, point mutations at L858R, T790M in EGFR and V600E in BRAF, at 0.5% minor allele levels, by using an oligonucleotide ligation assay off-chip and then attaching the ligated product to the surface. mRNA levels were detected using 10-20 cell equivalents of RNA. We believe the system will enable comprehensive analysis of cancer-related pathways, requiring only a few cells, to help decipher cellular pathway activity induced by driver mutations and consequently help with selection of efficacious drugs tailored for specific individuals based on comprehensive molecular analysis.

Citation Format: Manohar R. Furtado, Rixun Fang, Norman Burns, Rebekah Burich, Catherine Le, Soumya Ivaturi, Rob Hartlage, Ed Zizminskas, Jim Jahncke, Philip C. Mack, Bryan P. Staker. A single molecule detection system for comprehensive analysis of cancer related cellular pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 415.
Abstract 4153: Commissioning and radiobiological verification of the small animal radiotherapy research platform (SARRP)
Authors: Kane Jonathan L.
Published: August 2018

Preclinical radiation biology has become increasingly sophisticated due to the implementation of advanced small animal image guided radiation platforms into laboratory investigation. Small animal radiotherapy devices enable state-of-the-art image guided therapy (IGRT) research to be performed in small animal cancer models by combining high-resolution cone beam computed tomography (CBCT) imaging with an isocentric irradiation system. The technological evolution from simple, broad field irradiation configurations, to more sophisticated dose deliveries for preclinical radiobiology experiments has introduced new dosimetry challenges for preclinical small animal cancer research. Because of this, robust QA and dosimetry techniques are a key part of using novel treatment platforms using very small irradiation fields. In this study, we present a dosimetric study of the small animal radiotherapy research platform (SARRP, Xstrahl Inc.) focusing on the small field dosimetry. Physical dosimetry was assessed using ion chambers and radiochromic film, investigating the impact the beam focus size has on the dose rate output as well as beam characteristics (beam shape and penumbra variations). Two film reading modalities have been used to assess the dose output using the 0.5 mm diameter aperture. This study establishes that FilmQA Pro is a suitable tool for small field dosimetry, with a sufficiently small sampling area (0.1 mm) to ensure an accurate measurement. Furthermore, all small field dosimetry data generated in this study are equally comparable with our Monte Carlo simulations for both focal spot sizes. Overall, it was observed that the small focal spot, while having a lower dose-rate output was shown to produce a more stable and homogenous beam with minimum penumbra over time when compared to the larger focal spot. These findings suggest that when preclinical stereotactic irradiation fields are used, a practical compromise (time to deliver a desired dose and field homogeneity) needs to be considered when deciding the optimum treatment plan and beam configuration used.

Citation Format: Jonathan L. Kane. Commissioning and radiobiological verification of the small animal radiotherapy research platform (SARRP) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4153.
Abstract 4172: Radiation-induced blood-tumor barrier permeability in a preclinical model of lung cancer brain metastasis
Authors: Sprowls Samuel A. , Shah Neal , Mohammad Afroz S. , Pinti Marc , Tallman Rachel M. , John Devin U. , Lockman Paul R.
Published: August 2018

BACKGROUND: Lung cancer has the highest mortality rate among all cancers and accounts for over half of newly diagnosed brain metastases each year. Standard therapeutic advancements are prolonging lives of lung cancer patients with each new approved formulation, however patients with brain metastases have limited options and no curative measures currently exist. Current treatment modalities for brain metastases from primary lung cancer include differing methodologies of radiotherapy (whole brain radiotherapy and/or stereotactic radiosurgery), systemic chemotherapies, and neurosurgery. Radiation in many cases is not ablative, but palliative. Herein we demonstrate the ability of radiotherapy to influence blood-tumor barrier permeability in a novel preclinical model of lung cancer brain metastasis.

METHODS: Athymic female nude mice were intracardially injected with our novel PC-9-BR brain specific lung cancer cell line. Tumors were allowed to develop and monitored using bioluminescent imaging. Using the Xstrahl XenX small animal irradiator, we were able to deliver 26 Gy to the right hemisphere of the immobilized mouse. 4 hours post radiotherapy, mice were perfused with the passive permeability marker Oregon Green, followed by an indocyanine green (bound to albumin) washout to infer vascular space. Brains were then extracted, snap frozen in isopentane (-50°C), and sliced to 20μm. Florescence was quantified using a MVX microscope and cellsense software.

RESULTS: Analysis of irradiated brain regions demonstrated statistically significant more accumulation of the passive permeability marker, Oregon Green, compared to the contralateral hemisphere.

CONCLUSIONS: Radiation induced permeability was witness in mice after a single dose of 26 Gy when compared to non-irradiated tumor tissue 4 hours post treatment.

FURTURE DIRECTIVES: Experiments utilizing ionizing radiation to simulate treatment of CNS metastases could reveal better adjunctive chemotherapeutic regimens and or provide insight to the mechanism underlying this enhanced permeability.

Citation Format: Samuel A. Sprowls, Neal Shah, Afroz S. Mohammad, Marc Pinti, Rachel M. Tallman, Devin U. John, Paul R. Lockman. Radiation-induced blood-tumor barrier permeability in a preclinical model of lung cancer brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4172.
Abstract 4177: An IL13Rα2 peptide inhibits colorectal cancer metastatic progression
Authors: Casal Ignacio , Jaén Marta , Bartolomé Rubén A.
Published: August 2018

Interleukin 13 receptor α2 (IL13Rα2) is an excellent tumoral marker for metastatic colorectal cancer and glioblastoma. Our goal was to block IL-13 binding to IL13Rα2 by using IL13Rα2 synthetic peptides in order to delay or suppress metastatic spread and progression. Peptides were selected from the D1 binding region.

Synthetic peptides were synthesized using solid phase chemistry. Two metastatic colorectal cancer cell lines (KM12SM and SW620) plus two glioblastoma cell lines were used for testing proliferation, adhesion, migration and invasion. We used Biacore assays to demonstrate direct interaction between the peptides and IL-13. In vivo experiments with nude mice were performed to study mice survival to metastasis after peptide treatment.

Peptides containing the highly preserved WKTIITKN motif of the D1 binding domain of IL13Rα2 demonstrated a strong capacity to inhibit migration, invasion and proliferation in metastatic colorectal cancer and glioblastoma cells. Alanine scanning experiments indicated that, at least, residues 82K, 83T, 85I and 86T were essential for IL-13 binding to IL13Rα2. IL13Rα2 D1 peptide inhibited IL-13-mediated cell signaling through FAK, Src, AKT and ERK1/2 in colorectal cancer and glioblastoma cell lines. Moreover, the D1 peptide abolished ligand-mediated receptor internalization and degradation. To improve bioavailability and resistance to proteolytic digestion for in vivo administration, we prepared the D enantiomer version of the peptide. Mice inoculated with metastatic colorectal cancer cells and treated with the enantiomer version of the D1 peptide showed a remarkable increase in survival.

In conclusion, the D1 enantiomer peptide blocked the IL-13/IL13Rα2 binding, paving the way to develop novel and promising therapeutic strategies to inhibit metastatic progression in colorectal cancer and other solid tumors, including glioblastoma.

Citation Format: Ignacio Casal, Marta Jaén, Rubén A. Bartolomé. An IL13Rα2 peptide inhibits colorectal cancer metastatic progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4177.
Abstract 4180: Game-changing restraint of Ros-damaged phenylalanine, upon tumor metastasis
Authors: Anselmino Nicolás , Chiarella Paula , Ortiz Emiliano G. , Leonardi Daiana B. , Jaworski Felipe M. , Vikers Sofia Lage , Giudice Jimena , Woloszynska-Read Anna , Meiss Roberto P. , Rugiero Raul , Gueron Geraldine , Vazquez Elba S.
Published: August 2018

An abrupt increase in metastatic growth as a consequence of the removal of primary tumors suggests that the concomitant resistance (CR) phenomenon might occur in human cancer. CR occurs in murine tumors and ROS-damaged phenylalanine, meta-tyrosine (m-Tyr), was proposed as the serum anti-tumor factor primarily responsible for CR. Herein, we demonstrate for the first time that CR happens in different experimental human solid tumors (prostate, lung anaplastic, and nasopharyngeal carcinoma). Moreover, m-Tyr was detected in the serum of mice bearing prostate cancer (PCa) xenografts. Primary tumor growth was inhibited in animals injected with m-Tyr. Further, the CR phenomenon was reversed when secondary implants were injected into mice with phenylalanine (Phe), a protective amino acid highly present in primary tumors. PCa cells exposed to m-Tyr in vitro showed reduced cell viability, downregulated NFκB/STAT3/Notch axis, and induced autophagy; effects reversed by Phe. Strikingly, m-Tyr administration also impaired both, spontaneous metastasis derived from murine mammary carcinomas (4T1, C7HI, and LMM3) and PCa experimental metastases. Altogether, our findings propose m-Tyr delivery as a novel approach to boost the therapeutic efficacy of the current treatment for metastasis preventing the escape from tumor dormancy.

Citation Format: Nicolás Anselmino, Paula Chiarella, Emiliano G. Ortiz, Daiana B. Leonardi, Felipe M. Jaworski, Sofia Lage Vikers, Jimena Giudice, Anna Woloszynska-Read, Roberto P. Meiss, Raul Rugiero, Geraldine Gueron, Elba S. Vazquez. Game-changing restraint of Ros-damaged phenylalanine, upon tumor metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4180.
Abstract 4188: Preoperative supplementation of branched-chain amino acids suppresses Osteopontin expression in patients with hepatocellular carcinoma
Authors: Hiroshima Yukihiko , Yabushita Yasuhiro , Kikuchi Yutaro , Kawagushi Daisuke , Murakami Takashi , Ichikawa Yasushi , Endo Itaru , Tanaka Kuniya
Published: August 2018

Background: Recently, the new effect of branched-chain amino acid (BCAA) on Osteopontin (OPN), which correlates with cancer progression, has been reported. The aim of this study was that preoperative administration of BCAA could improve prognosis via degradation of OPN expression in hepatocellular carcinoma (HCC).

Methods: Human hepatocellular carcinoma cell lines were treated with BCAA (2nM), and investigated OPN expression, cell proliferation and invasion in vitro. Next, patients undergoing elective liver resections for HCC (n=72) were randomized to receive or not receive preoperative oral supplementation with BCAA. OPN protein levels in HCC patients were examined using immunohistochemistry and compared with the clinicopathologic features of the tumors.

Results: Experimentally, the expression levels of OPN were significantly decreased in HCC cells treated with BCAA. BCAA treatment significantly decreased cell invasion. In the clinical setting, OPN expression correlated with HBV or HCV infection (p = 0.03), venous invasion (p = 0.02) and liver fibrosis (p = 0.07). There was no difference in both DFS and OS between OPN-positive and OPN-negative group, and preoperative BCAA administration did not improve prognosis, either. For the patients without late recurrence, OPN-positive group showed significantly poor outcome in DFS (p = 0.047), and preoperative BCAA administration improved DFS (p = 0.062).

Conclusions: OPN expression was associated with cancer cell invasion and intrahepatic metastasis. BCAA treatment suppressed HCC cell invasion and preoperative BCAA administration prevented early intrahepatic recurrence by decreasing the expression level of OPN in HCC.

Citation Format: Yukihiko Hiroshima, Yasuhiro Yabushita, Yutaro Kikuchi, Daisuke Kawagushi, Takashi Murakami, Yasushi Ichikawa, Itaru Endo, Kuniya Tanaka. Preoperative supplementation of branched-chain amino acids suppresses Osteopontin expression in patients with hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4188.
Abstract 4192: C-terminal HSP90 inhibitor, L80, targets cancer stem cell (CSC)-like property and suppresses metastasis via JAK/STAT3 inactivation in triple-negative breast cancer
Authors: Cho Tae-Min , Oh Eunhye , Sung Daeil , Kim Yoon-Jae , Jang Seojin , Lee Jeewoo , Kim Ji Young , Seo Jae Hong
Published: August 2018

Purpose: Triple-negative breast cancer (TNBC) harbors high level of cancer stem cell (CSC)-like populations, which is associated with aggressive phenotype leading to tumor cell dissemination and poor clinical outcomes. Therefore, new drugs that effectively target both CSCs and tumor bulk cells are needed to improve clinical outcomes. The 90-kDa molecular chaperone heat-shock protein, HSP90 has been implicated in cancer progression and metastasis by modulating the stabilization and maturation of many oncogenic proteins. Our objective was to investigate the effects of L80 on cancer stem-like characteristics, cell proliferation and metastasis in TNBC in vitro and in vivo.

Experimental Design: The effect of L80 on TNBC cell lines in vitro was evaluated in terms of cell viability, apoptosis and mammosphere-forming ability and expression of JAK/STAT3 signaling-related factors. An orthotopic injection model with 4T1 mammospheres with self-renewability was used to examine the effect of L80 on tumor growth, angiogenesis and metastasis.

Results: L80 treatment caused a significant induction of apoptosis, accompanied by caspase-3/-7 activation and the dysregulation of JAK/STAT3 activation in TNBC cells. The latter phenomenon was associated with impairment of cancer stem-like trait, concomitant with a significant suppression of mammosphere formation. To confirm the physiological relevance of our in vitro findings, we examined the impact of L80 on allografted tumor growth, angiogenesis and metastasis in vivo. L80 administration impedes tumor growth and subsequently suppresses angiogenesis, as evidenced by a marked reduction in number of CD31-positive microvessels in the L80-treated groups compared to their counterparts. L80 administration leads to a significant reduction in lung and liver metastases, coinciding with decreased MMP-2 and MMP-9 levels in circulating blood. These responses were intimately associated with dysregulation of JAK/STAT3 activation.

Conclusion: C-terminal HSP90 inhibitor, L80 suppresses tumor growth and metastasis via suppression of JAK/STAT3 activity and CSC-like property. These findings suggest that HSP90 could be a promising target for treatment of metastatic TNBC.

Citation Format: Tae-Min Cho, Eunhye Oh, Daeil Sung, Yoon-Jae Kim, Seojin Jang, Jeewoo Lee, Ji Young Kim, Jae Hong Seo. C-terminal HSP90 inhibitor, L80, targets cancer stem cell (CSC)-like property and suppresses metastasis via JAK/STAT3 inactivation in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4192.
Abstract 4199: Resveratrol induced REG III and inhibited head and neck cancer progression
Authors: Ota Ichiro , Mikami Shinji , Masui Takashi , Kimura Takahiro , Uemura Hirokazu , Okamoto Hideyuki , Takasawa Shin , Kitahara Takashi , Shobatake Ryogo
Published: August 2018

Head and neck squamous cell carcinoma (HNSCC) is one of the 10 most common malignancies in the world and known for clinical progression and poor prognosis. Despite the recent progress of the treatment for improving locoregional control in HNSCC patients, that for recurrence and metastatic control remains insufficient, indicating that there is a continued need for improved treatment strategies. Therefore, the key molecules that enhance chemo- and radio-sensitivity in HNSCC and identification of reliable biomarkers for predicting the recurrence and metastasis would be desirable to improve the prognosis of HNSCC. The human regenerating gene (REG) expression has been reported to be associated with progression of various cancers. Recently, we have reported that REG III expression is associated with an improved survival rate for HNSCC patients as a reliable biomarker. Herein, we investigated the inducer for REG III expression in HNSCC cells and found that resveratrol significantly increased the REG III promoter activity and REG III mRNA. In addition, we demonstrated that the effects of resveratrol on cancer cell progression in HNSCC in vitro and in vivo. To reveal the effects of resveratrol on HNSCC cell proliferation, cell proliferation was measured by using WST-8 assay. Resveratrol significantly inhibited cell growth in FaDu and HSC-4 HNSCC cells. Secondly, to check the effects of resveratrol on chemo- and radio-sensitivity in HNSCC cells, HNSCC cells were expose to cisplatin and radiation, respectively. Resveratrol significantly increased the sensitivity of cisplatin and radiation in HNSCC cells. We also examined the effects of resveratrol on cancer invasion using 24-well Matrigel-coated Transwells. Resveratrol significantly attenuated the cancer invasion of HNSCC cells. Moreover, to assess resveratrol-induced chemo-sensitivity in vivo, we established a xenograft model of HNSCC in BALB/c nude mice. The tumor volumes in the mice receiving combined administration of resveratrol and cisplatin were significantly lower than those of resveratrol or cisplatin alone. These results strongly suggest that resveratrol can inhibit head and neck cancer progression through the REG III expression pathway and can be a potential sensitizer for anticancer therapy for patients with HNSCC.

Citation Format: Ichiro Ota, Shinji Mikami, Takashi Masui, Takahiro Kimura, Hirokazu Uemura, Hideyuki Okamoto, Shin Takasawa, Takashi Kitahara, Ryogo Shobatake. Resveratrol induced REG III and inhibited head and neck cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4199.
Abstract 4202: Resection of primary osteosarcoma tumors terminates self-seeding, increasing lung metastasis
Authors: Roberts Ryan D. , Saraf Amanda J. , Pommellet Helene Le , Evans Randall , Gross Amy C.
Published: August 2018

Like many solid tumors, osteosarcoma (OS) kills patients through metastatic spread. In the case of OS, metastasis occurs almost exclusively to lung. Metastases most often arise after both resection of a primary tumor and completion of chemotherapy. In seeking to understand this long-appreciated pattern of spread, we sought to explore whether the presence of a primary tumor protects mice from developing OS lung metastasis through the process of self-seeding, and whether resection then faciliates metastatic lung colonization. Our data show that resection of a primary orthotopic tumor triggers the spread of OS tumor cells into the lung. Mice bearing a primary tumor have fewer labeled tumor cells recovered in the lung after IV inoculation. Many labeled cells can be recovered in the primary tumor. Supernatants from OS cell cultures drive OS cell chemotaxis with greater potency than serum. Several specific soluble factors produced by OS cells also drive chemotaxis of those same cells. Disruption of these signals may prevent self-seeding. Manipulation of this system may be used to remove OS cells from circulation.

Citation Format: Ryan D. Roberts, Amanda J. Saraf, Helene Le Pommellet, Randall Evans, Amy C. Gross. Resection of primary osteosarcoma tumors terminates self-seeding, increasing lung metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4202.
Abstract 4214: Characteristics of carcinoembryonic antigen-producing colorectal cancers: A population based study
Authors: Groover Sarah , Thirunavukarasu Pragatheeshwar , Payton Mark E. , Karippot Asha , Kaul Rashmi
Published: August 2018

Serum Carcinoembryonic Antigen (CEA) is a tumor marker often found to be elevated in colorectal cancer patients. Elevated CEA has been strongly associated with poor prognosis. However, not all colon cancer tumors produce CEA, and little is known about the patient and tumor characteristics between CEA-producing and non-CEA-producing tumors. We performed a retrospective analysis of all patients (n=120,571) diagnosed with colorectal adenocarcinoma from 2010 to 2014 in the National Cancer Institute's Surveillance, Epidemiology and End Results (SEER) database. All patients were designated as either positive/elevated (C1) or negative/normal (C0) based on the pretreatment serum CEA level. We performed univariate and multivariate analyses to identify variables associated with CEA-producing tumors. Of the 68,856 (57.1%) with available CEA information, 33,426 (48.5%) were C1. Median age was 65 years and 36,479 (53.0%) were male. Compared to C0 cancers, C1 cancers were significantly more likely (P<0.001) to be female (49.3%% vs. 47.9%), black (58.4%), separated or never married (55.0% and 54.8%, respectively), higher grade (39.0%, 46.2%, 51.1% and 52.3% of well, moderately, poorly, and undifferentiated cancers, respectively), and of signet ring cell histology (61.1%). Multivariate analysis showed age, sex, race, marital status, and TNM stage to be independent prognostic factors associated with the diagnosis of CEA-producing tumors. This is the first report to describe differences in patient and tumor characteristics between CEA-producing and non-CEA-producing tumors in a large American population. About half of all colorectal adenocarcinomas are associated with elevated pre-treatment serum CEA levels. CEA-producing tumors are associated with female gender, non-Caucasian race, separated or never married marital status at diagnosis, and more extensive local, regional and metastatic disease.

Citation Format: Sarah Groover, Pragatheeshwar Thirunavukarasu, Mark E. Payton, Asha Karippot, Rashmi Kaul. Characteristics of carcinoembryonic antigen-producing colorectal cancers: A population based study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4214.
Abstract 4242: Ethnic disparities in the risk of cardiac death following cancer diagnosis: A population-based study
Authors: Gad Mohamed M. , Saad Anas M. , Al-Husseini Muneer J. , Abushouk Abdelrahman I. , Ahmed Haitham M.
Published: August 2018

Background: Cancer-related cardiac complications and mortality have been well studied. However, the disparities among racial and ethnic groups have not been addressed on a large scale. In this study, we aimed to investigate the racial and ethnic disparities associated with cardiac death in cancer patients.

Methods: Data were collected from The Surveillance, Epidemiology and End-Results program of the National Cancer Institute. We defined an "event" as death due to a cardiac cause within ten years after cancer diagnosis, and observed patients who experienced the event during that period. Then, we calculated the Observed/Expected (O/E) ratio and the excess risk per 10,000 person-years to estimate the change of risk following the diagnosis in different ethnicities, when compared to the general population.

Results: We reviewed 4,671,989 cancer patients, of whom 163,255 died due to a cardiac cause within the ten years following cancer diagnosis. The overall risk of cardiac death increased significantly in this period with an O/E ratio of 1.16 and an excess risk of 11.66 per 10,000. The sample was divided into 2 groups: Whites with a total O/E ratio of 1.11, and non-Whites with a total O/E ratio of 1.38. When examined for the risk in the first 5 years after diagnosis, Whites and non-Whites demonstrated significant increase in the risk with O/E of 1.12 and 1.39, respectively. However, when examined for the long-term risk more than 5 years after diagnosis, only non-Whites had a significant increase with an O/E of 1.21, while Whites with a cancer diagnosis had the same risk of cardiac death as Whites without cancer diagnosis with an O/E of 1.00. The sample was then further subdivided according to ethnicity into non-Hispanic Whites, Blacks, American Indians (or Alaska natives), Asians (or Pacific islanders), and Hispanics. All groups showed a significantly increased risk of cardiac death following a cancer diagnosis (O/E=1.13, 1.36, 2.33, 1.44, and 1.05, respectively).

Conclusion: Non-White patients with a prior cancer diagnosis had a significantly higher long-term risk of cardiac death compared to noncancer patients. Accordingly, careful attention should be paid to the cardiovascular status assessment of those patients to mitigate the added risk of cardiac mortality due to cancer-related morbidities. Further studies are warranted to determine why cardiac event risk increases at a discrepantly higher rate in minority patients with a cancer diagnosis.

Citation Format: Mohamed M. Gad, Anas M. Saad, Muneer J. Al-Husseini, Abdelrahman I. Abushouk, Haitham M. Ahmed. Ethnic disparities in the risk of cardiac death following cancer diagnosis: A population-based study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4242.
Abstract 4254: Associations of sleep, quality of life and energy level with breast cancer mortality and recurrence: The Shanghai Breast Cancer Survival Study
Authors: Zhu Jingjing , Bao Pingping , Cai Hui , Shi Liang , Zheng Ying , Zheng Wei , Shu Xiao-ou
Published: August 2018

Background: Sleep disorder is highly prevalent among breast cancer patients. Whether sleep disorder is associated with breast cancer prognosis has rarely been investigated. The objective of this study is to prospectively assess the association of self-reported sleep difficulty and sleep quality with total mortality and breast-cancer specific mortality/recurrence in the Shanghai Breast Cancer Survival Study.

Methods: This study included 4,219 women with stage I-III breast cancer diagnosed at an age between 20 to 75 years. Information on sleep attributes was collected at approximately 18 months and 36 months after breast cancer diagnosis. Information on disease recurrence and survival status was obtained via in-person follow-up and via record linkage with vital statistics registry data. Cox proportional hazard model was used to derive hazard ratios (HR) and confidence intervals (CIs) for all-cause mortality and breast cancer-specific mortality/recurrence. Stratified analyses according to self-reported overall quality of life, depression and energy level assessed at 18 months were also conducted.

Results: During a median follow-up of 9.8 years (range: 0.1-12.2 years), 757 deaths due to any causes and 672 breast cancer recurrences or related deaths were recorded after the 18-month post-diagnosis survey. Sleep difficulty and low sleep quality were not significantly associated with total or breast-cancer specific mortality/recurrence. The respective HRs were 0.98 (95% CI: 0.79, 1.22) and 1.01 (95% CI: 0.77, 1.31) for total mortality and 1.04 (95% CI: 0.82, 1.31) and 0.93 (95% CI: 0.69, 1.26) for breast cancer-specific mortality/recurrence. On the other hand, low quality of life, depression and low energy level were significantly associated with increased total mortality, with HRs of 3.19 (2.45, 4.15), 1.61 (1.21, 2.14) and 1.53 (1.23, 1.91), respectively. These three factors did not modify the association of sleep measurements with breast cancer outcomes (all P-interactions > 0.10).

Conclusions: In a large population-based cohort study, we did not observe any significant association of sleep difficulty and poor sleep quality with increased risk of death and recurrence in breast cancer patients. Instead, low quality of life and energy level were found to be associated with disease prognosis and thus they could be important indicators for targeting population with poor breast cancer prognosis.

Citation Format: Jingjing Zhu, Pingping Bao, Hui Cai, Liang Shi, Ying Zheng, Wei Zheng, Xiao-ou Shu. Associations of sleep, quality of life and energy level with breast cancer mortality and recurrence: The Shanghai Breast Cancer Survival Study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4254.
Abstract 4261: Pathways of metastatic bladder cancer from a longitudinal patient data set
Authors: Mason Jeremy M. , Hasnain Zaki , Miranda Gus , Gill Karanvir , Newton Paul K. , Gill Inderbir S. , Kuhn Peter
Published: August 2018

Bladder cancer (BCa), the 6th commonest cancer in the U.S., is highly lethal when metastatic. Sites and patterns of patient-specific metastatic spread are deemed random and unpredictable. Whether BCa metastatic patterns can be quantified and predicted more accurately is unknown. We used a prospective, longitudinal dataset of 3,505 BCa patients who underwent definitive treatment following diagnosis and were continuously enrolled (1971-2016; mean follow-up 6.13 years). Metastases developed in 30% (n=1,040) of patients, with 5-year survival rate of 18%, compared to 72% in those without metastases (n=2,465). The three commonest metastatic sites at time-of-first progression were pelvis (n=283; 27.2%), bone (n=274; 26.3%), and lung (n=247; 23.8%). We illustrate metastatic pathway progression as color-coded, circular, tree-ring diagrams (primary in the center; metastatic sites outwards). Markov chain modeling, denoting nodes as potential anatomic metastatic sites, indicated higher probability of spread from the bladder to pelvis (15.6%), bone (15.6%), and lung (13.9%), categorizing 4 of 10 anatomical sites as ‘spreaders' and 2 as ‘sponges'. We created a dynamical, data-visualization, web-platform that displays temporal, spatial and Markov modeling figures with predictive capability. For contrasting subgroups, this platform indicated differences in transition probabilities, rank-ordering of metastatic sites, and spreader/sponge node classification. Spatiotemporal patterns of BCa metastasis and sites of spread indicate underlying organotropic mechanisms in the prediction of response. This recognition opens the possibility of organ site-specific therapeutic targeting in the oligo-metastatic disease setting. In the precision medicine era, visualization of complex, time-resolved clinical data will enhance management of post-operative, metastatic BCa patients.

Citation Format: Jeremy M. Mason, Zaki Hasnain, Gus Miranda, Karanvir Gill, Paul K. Newton, Inderbir S. Gill, Peter Kuhn. Pathways of metastatic bladder cancer from a longitudinal patient data set [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4261.
Abstract 4265: Computational models of the role of base excision repair in sensitization of cancer cells to 5-fluorodeoxyuridine
Authors: Qian Mengdi , Almasan Alexandru , Gürkan-Çavusoglu Evren
Published: August 2018

The purpose of this study is to computationally analyze the effect of inhibition of base excision repair (BER) in the response of cancer cells to treatment with 5-fluorodeoxyuridine. 5-fluorouracil (5-FU) and its metabolite 5-fluorodeoxyuridine (5-FdU) are standard treatments for different solid tumors and especially for colon cancer. In the literature, it is shown that the depletion of uracil DNA glycosylase (UDG), one of the enzymes that initiate the BER pathway, enhanced the cytotoxicity of 5-FdU, making UDG a potential target to enhance efficacy of chemotherapeutic agents. It is also shown that the activity of UDG is significantly higher in colon cancer cells compared to normal tissue. We have developed a computational model of the BER pathway to capture the BER dynamics in colon cancer cell lines after treatment with 5-FdU. Our model is composed of a series of ordinary differential equations where the parameters are the kinetic rate constants and the enzyme concentrations. We have used the data from the literature to initially parameterize our models. We have then used least square estimation to find the parameters that will capture the BER time course for colon cancer cells after 5-FU treatment using the experimental data from the literature. We have performed sensitivity and identifiability analyses to determine the parameters that are reliably estimated. The experimental data from the literature showed that the depletion of UDG resulted in incorporation of uracil and 5-FU in the DNA. We have computationally replicated this effect by decreasing the protein concentration of UDG in the models and simulating the amount of remaining 5-FU in the DNA after BER with reduced activity has taken place. We have studied the depletion effect for different protein concentrations of UDG and the results have shown that the accumulation of 5-FU in these colon cancer cells correlate with the level of UDG. The suppression of UDG activity has the potential to enhance the outcome of treatment with 5FdU, and we will use the developed computational models to quantitatively optimize these effects in our future work.

Citation Format: Mengdi Qian, Alexandru Almasan, Evren Gürkan-Çavusoglu. Computational models of the role of base excision repair in sensitization of cancer cells to 5-fluorodeoxyuridine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4265.
Abstract 4266: Computational exploration of mechanistic determinants of ADC pharmacokinetics using QSP modeling strategies
Authors: Wilkins A. Katharina , Matteson Andrew , Gruenbaum Lore , Park Jennifer , Burke John M. , Apgar Joshua F.
Published: August 2018

The pharmacokinetics of antibody drug conjugate (ADC) therapeutics typically show a discrepancy between the PK of total antibody (conjugated and unconjugated antibody) and that of conjugated antibody, carrying one or more payload molecules. This discrepancy is often attributed strictly to deconjugation (Kamath, 2014), however recent evidence suggests that the underlying mechanisms may be more complex. This work employs a computational quantitative systems pharmacology (QSP) approach that generates a hypotheses to better understand the impact of drug antibody ratio (DAR) and the resulting changes in molecular properties on overall PK and relative payload disposition as observed in preclinical and clinical studies. Our work establishes the benefit of using computational models to design novel ADCs and to optimize the discovery and development of existing ADCs to better enable clinical trial design.

References: Kamath, A. V., and Iyer, S. (2014). Preclinical Pharmacokinetic Considerations for the Development of Antibody Drug Conjugates. Pharmaceutical Research, 32(11), 3470-3479.

Citation Format: A. Katharina Wilkins, Andrew Matteson, Lore Gruenbaum, Jennifer Park, John M. Burke, Joshua F. Apgar. Computational exploration of mechanistic determinants of ADC pharmacokinetics using QSP modeling strategies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4266.
Abstract 427: High-quality whole-genome sequencing of FFPE samples
Authors: Bailey Shannon T. , Lund Jim , Wang Hao , Cui Weiren , Hao Chen , Sun Hongye , Gulcher Jeffrey R.
Published: August 2018

Next-generation sequencing analysis of formalin-fixed, paraffin-embedded (FFPE) samples has the potential to lead to major advances in cancer treatment and prevention. However, whole-genome sequencing of these samples has remained challenging due to the difficult process of isolating high-quality DNA and distinguishing true variant calls from artifacts. Previous studies have attempted to overcome these challenges by using whole-exome sequencing or smaller exon panels at high coverage depths to analyze FFPE samples. While these approaches have produced useful results, they have had varying degrees of success, tend have coverage biases due to probe capture issues, and are limited to only a fraction of the genome. Thus, there has not been widespread adoption of using FFPE samples for next-generation sequencing.

In an attempt to improve on the process of next-generation sequencing of FFPE samples, we first developed an efficient DNA extraction method that produces high quantities of high-quality DNA. Whole-genome sequencing of DNA generated by this method demonstrated uniform high coverage that was comparable to DNA prepared from fresh frozen samples at the same sequencing depth. This result is in contrast with data generated from DNA isolated by a traditional FFPE extraction method, which had lesser sequencing coverage even with twice the sequencing depth. Further analysis of the data generated using our method demonstrated similar numbers of mutations called and mutational signatures without artifact contamination.

We extended this analysis to a large cancer cohort consisting of over 1,000 FFPE samples in tumor normal pairs that were up to 6 years old. Whole-genome sequencing of these samples demonstrate that there was an average of 98% of the genome covered at 20X or greater using our method with no drop off for the older samples. Mutational analyses of these samples demonstrate similar findings as that previously published using TCGA datasets.

In summary, our study of greater than 1,000 samples is the largest report of whole-genome sequencing of FFPE samples to date. Our results demonstrate the feasibility of using our method to assay tissues stored in archival tissue biobanks, analyze patient samples for clinical trial recruitment, or examining sections as part of normal clinical workflows, all of which hold the potential for greatly benefiting human health.

Citation Format: Shannon T. Bailey, Jim Lund, Hao Wang, Weiren Cui, Chen Hao, Hongye Sun, Jeffrey R. Gulcher. High-quality whole-genome sequencing of FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 427.
Abstract 4270: Success of T-cell immunotherapy predicted by a mathematical model of the adaptive immune system and evolving cancer cells
Authors: George Jason Thomas , Levine Herbert
Published: August 2018

It is now well-established that a patient's adaptive immune system plays an important role in identifying and eliminating cancer cells in much the same way that intracellular pathogens are cleared during infection. From a therapeutic standpoint, the adaptive immune system is unique in that it can co-evolve alongside a developing tumor. At present, the dynamics and survival probability of a mutating threat in the presence of an adaptive immune system has yet to be quantified. Here, we consider a foundational population model of a foreign invader faced with innate or adaptive immune pressure. We find that optimal growth strategies depend on whether or not the invading threat may mutate as well as the mode of immune detection. Our early model predicts that decreases in thymic output seen in advanced age may substantially affect the ability to recognize a growing population of cancer cells and recapitulates general features found in age-dependent AML incidence. This mathematical framework is able to predict the success of recent immunotherapeutic strategies, including personalized neoantigen vaccines. Our model serves as an attempt at modeling stochastic cancer evolution alongside an adaptive immune compartment.

Citation Format: Jason Thomas George, Herbert Levine. Success of T-cell immunotherapy predicted by a mathematical model of the adaptive immune system and evolving cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4270.