bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5545: Integrated system-level analyses of androgen receptor variant networks to identify novel prostate cancer-relevant genes
Authors: Magani Fiorella , Bray Eric R. , Zhao Ning , Peacock Stephanie , Burnstein Kerry L.
Published: July 2017

Unbiased high-throughput approaches provide a global view of the massive genetic and transcriptomic changes that occur in and potentially drive cancer. Such approaches permit the discovery of novel markers and therapeutic targets. Current treatments for advanced prostate cancer (PC) focus on inhibiting the androgen receptor (AR). However, PC inevitably progresses to a stage termed castration-resistant prostate cancer (CRPC), which is incurable. In CRPC, C-terminal truncated, constitutively active AR splice variants (such as AR-V7) play key transcription-regulatory roles resulting in treatment resistance and disease progression. However, designing high-affinity drugs to target the amino terminus of AR and AR variants is a major challenge due to the intrinsic disorganized structure of this region. Thus there is an imperative need to identify novel AR-V7 hub genes in PC that may serve as therapeutic targets. We performed an extensive and highly robust gene expression meta-analysis on PC patient samples. We defined gene modules correlated with disease progression using a powerful systems biology approach termed Weighted Gene-Co-expression Network Analysis (WGCNA). Further, we mapped the AR-V7 interactome for the first time using a novel high-throughput synthetic genetic array screening in yeast, known as Yeast Augmented Network Analysis (YANA). YANA was performed by crossing yeast expressing AR-V7 with a large collection of yeast strains lacking non-essential genes, and identifying those genes that caused a change in yeast growth (fitness). Human orthologs of the identified yeast genes were used to build an AR-V7 functional gene network. Finally, we combined the results from our independent system-level analyses with experimental data to identify hub genes that are upregulated in PC patients, regulated by AR-V7, and also functionally interact with AR-V7. The identified genes not only include select genes previously linked to PC, such as members of the cyclin and topoisomerase families, but also genes that have not been previously linked to AR-V7 activity or PC progression. Moreover, our gene expression signature predicts a higher risk of PC recurrence after primary treatment in patients. In sum, we show here an unbiased and novel gene discovery strategy using bioinformatics in concert with experimental approaches to identify new candidate genes in CRPC that may lead to prognostic markers and future targeted therapies.

Citation Format: Fiorella Magani, Eric R. Bray, Ning Zhao, Stephanie Peacock, Kerry L. Burnstein. Integrated system-level analyses of androgen receptor variant networks to identify novel prostate cancer-relevant genes [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 5545. doi:10.1158/1538-7445.AM2017-5545
Abstract 5554: Metabolic reprogramming in non-small cell lung cancer: a precision oncology approach
Authors: Tavassoly Iman , Iyengar Ravi
Published: July 2017

Lung cancers are among the most common invasive cancers worldwide and annually lead to high mortality and morbidity. Genomic alterations have been known to control the evolution of hallmarks of cancer in a dynamic way. These molecular alterations combined with epigenomic and post-genomic modifications contribute to formation of these neoplasms. Multiplicity of these changes has made development of personalized therapeutic regimens for these cancers a complex problem. Metabolic reprogramming is one of the main mechanisms in progression of cancers. There have been efforts to model the metabolic reprogramming in cancer using metabolic networks of cancer cells, but there has been no computational framework to model these metabolic transitions in cancer for precision and personalized medicine. We have combined computational, mathematical and experimental methodologies to develop a platform for precision oncology in non-small cell lung cancer (NSCLC) by in silico models of metabolic switches. Our integrative analysis of genomic data from NSCLC has led to discovery of genomic signatures controlling metabolic reprogramming in NSCLC with KRAS mutations. This discovery was proved in vivo and in vitro using drugs blocking different metabolic pathways. We have shown that NSCLC cells and tumors which carry KRAS mutations and have these genomic signatures are addicted to the pentose phosphate pathway (PPP). We have verified and proved the predictive value of these genomic signatures using Patient Derived Xenograft (PDX) tumor models of NSCLC. We are developing a mathematical and computational framework to model these metabolic switches. Our platform is capable of using genomic data from a cell line or tumor to determine the metabolic dependency of them quantitatively and predict the optimized personalized treatments for modulating metabolic pathways aiming to control cancer progression.

Citation Format: Iman Tavassoly, Ravi Iyengar. Metabolic reprogramming in non-small cell lung cancer: a precision oncology approach [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 5554. doi:10.1158/1538-7445.AM2017-5554
Abstract 5555: Integrative network variomics reveals complex genotype to phenotype relationships in cancer
Authors: Sahni Nidhi , Yi Song
Published: July 2017

Proteins interact with other macromolecules in complex cellular networks for signal transduction and biological functions. Recently a deluge of genomic information becomes available from patients stricken by a variety of cancer types. In cancer, genetic aberrations have been traditionally thought to abolish the entire gene function. It has been increasing appreciated that each genomic mutation of a gene could have a subtle but unique effect on protein function or network rewiring, contributing to diverse phenotypic consequences across cancer patient populations. In this study, we designed an integrative multi-omics platform using systems biology approaches to functionally assess the effects of cancer genetic variants. We compared a broad spectrum of mutation classes for a wide range of mechanistic effects on gene function in the context of signaling networks. Our results reveal a functional landscape of context-specific signaling network perturbations underlying cancer genetic heterogeneity at the base-pair resolution. Such information is critical for understanding the complex pleiotropic effect of cancer genes, and provides a possible link between genotype and phenotype in cancer. Furthermore, this study suggests new perspectives in targeted therapy and precision medicine.

Citation Format: Nidhi Sahni, Song Yi. Integrative network variomics reveals complex genotype to phenotype relationships in 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 5555. doi:10.1158/1538-7445.AM2017-5555
Abstract 5558: Deconstruction of a human tumor microenvironment
Authors: Balkwill Frances R. , Pearce Oliver M. , Delaine-Smith Robin , Maniati Eleni , Nichols Sam , Wang Jun , Bessant Conrad , Knight Martin
Published: July 2017

The purpose of this study was to understand the relationships between the molecular mechanisms of disease progression and higher-order features such as tissue stiffness, extent of disease and cellularity in the tumor microenvironment, TME. Using samples of human high-grade serous ovarian cancer metastases, ranging from normal to heavily diseased, we identified molecular components of the TME using transcriptomic and proteomic analysis. We integrated these data against higher-order features of the tissue, namely the biomechanics, cellularity, and disease score. We then used bioinformatics and multivariate statistics to identifying components of the TME that best model the higher-order features. For the first time, we revealed the complexity of extracellular matrix remodeling during metastases development, defining patterns of extracellular-matrix associated genes and proteins that predicted both extent of disease and tissue modulus. This allowed us to identify a core group of twenty-two matrix-associated molecules that modeled the dynamic process of tissue remodeling during tumor progression. We used these data to generate a ‘matrix index’, a quantitative measure of the gene expression of the twenty-two molecules. In cancer transcriptomic databases, this matrix index had prognostic significance in thirteen solid cancers including high-grade serous ovarian cancer, even after multivariate analysis. We conclude that there may be a common host matrix response to human solid cancers.

Citation Format: Frances R. Balkwill, Oliver M. Pearce, Robin Delaine-Smith, Eleni Maniati, Sam Nichols, Jun Wang, Conrad Bessant, Martin Knight. Deconstruction of a human tumor microenvironment [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 5558. doi:10.1158/1538-7445.AM2017-5558
Abstract 5562: Integrating evolutionary dynamics into treatment of metastatic castrate-resistant prostate cancer: a pilot multidisciplinary study
Authors: Zhang Jingsong , Cunningham Jessica J. , Brown Joel S. , Gatenby Robert A.
Published: July 2017

Background: Prior studies have investigated “intermittent therapy” to delay hormone resistance in prostate cancer but did not explicitly include quantitative analysis of the evolutionary dynamics. We hypothesize that evolution-informed strategies may prolong time to progression but require a multidisciplinary effort to simulate intratumoral Darwinian dynamics and design a clinically feasible treatment protocol.

Methods: We investigate intratumoral evolutionary dynamics during treatment of metastatic castrate resistant prostate cancer (mCRPC) with abiraterone, which blocks CYP17A1 autosynthesis of testosterone from endocrine precursors. We build a mathematical model assuming three competing phenotypes: (i) TP cells express CYP17A1 and produce testosterone; (ii) T+ cells require exogenous androgen; and (iii) T- cells are androgen-independent and resistant to abiraterone. Model predictions were tested in a pilot clinical trial.

Results: Mathematical Model: Computer simulations demonstrate continuous maximum dose abiraterone treatment produces competitive release of resistant T- cells. However, limited treatment designed to maintain residual TP and T+ populations and suppress proliferation of T- cells was predicted to prolong response while lowering the required drug dose. Clinical Trial: In a pilot clinical trial, 11 men with asymptomatic mCRPC were treated with abirateone according to an evolution-informed, patient-specific algorithm based on the modeling results. Pre-treatment biopsies (available for 3 patients) demonstrated the predicted tumor subpopulations. Cycles of response and regrowth similar to model simulations were observed with cycle lengths varying from 3 months to > 1 year. Over a median follow up period of 18 months, 10 subjects remain responsive to Abiraterone without PSA or radiographic progression. Median time to PSA progression significantly (P<0.001) exceeds the 11.1 months historical control. As predicted by the simulations, tumor control required significantly less abiraterone with average cumulative dose less than 40% of standard of care (P<0.001).

Conclusion: Integration of mathematical models and Darwinian first principles into trial design, may allow patient-specific modifications to prolong response while lowering drug doses in mCRPC.

Citation Format: Jingsong Zhang, Jessica J. Cunningham, Joel S. Brown, Robert A. Gatenby. Integrating evolutionary dynamics into treatment of metastatic castrate-resistant prostate cancer: a pilot multidisciplinary study [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 5562. doi:10.1158/1538-7445.AM2017-5562
Abstract 5564: The interplay between etiology-dependent genomic and epigenetic signatures: The paradigm of liver cancer
Authors: Haviv Izhak , Perez Shira , Lavi-Itzkovitz Anat , Kaspi Antony , Tover Ana , El-Osta Assam , Yaari Gur , Stemmer Salomon , Gal-Tanamy Meital
Published: July 2017

The evolutionary theory assumes that occurrence of mutations in cancer is random. However, recent studies suggest that passenger mutations are not randomly scattered in cancer genomes and that chromatin organization dictate mutations profiles. Hepatocellular carcinoma (HCC) serves as a model of diverse spectrum of cancers, since it is induced by a number of well-known etiological agents, mainly Hepatitis C virus (HCV) and Hepatitis B virus (HBV). This provides a unique opportunity to test whether different etiological agents dictate distinct mutational landscapes across the genome through a unique epigenetic signature. The HCC-specific genomic mutations were studied in 80 HCC biopsies from three etiology groups - HBV, HCV, or other. To explore the mutational signature we performed target high-resolution sequencing that enables the detection of low-frequency passenger mutations. By using this strategy we identified novel distinct etiology-dependent regional mutations signature in specific genes and pathways in HCC that was not detected previously by exome sequencing of liver tumors. These observations suggest that viral infection modulate somatic mutations causing HCC. To explore the link between genomic signature and genome wide chromatin organization we studied the epigenetic changes occur following HCV infection. Epigenetic analysis unraveled known and novel pathways that are controlled by the virus such as Hepatic lipid metabolism, cell motility, cell cycle and immunity. Invers correlation between high mutation rate and enrichment of chromatin modifications associated with active transcription provides a link between etiology and cancer genome. Our novel approach offers a perspective into the mechanisms that shape mutational signature development in cancer.

Note: This abstract was not presented at the meeting.

Citation Format: Izhak Haviv, Shira Perez, Anat Lavi-Itzkovitz, Antony Kaspi, Ana Tover, Assam El-Osta, Gur Yaari, Salomon Stemmer, Meital Gal-Tanamy. The interplay between etiology-dependent genomic and epigenetic signatures: The paradigm of liver 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 5564. doi:10.1158/1538-7445.AM2017-5564
Abstract 5568A: A network based analysis for the treatment of triple negative breast cancer
Authors: Fleisher Brett A. , Ait-Oudhia Sihem
Published: July 2017

Background: Triple-negative breast cancer (TNBC) is a complex heterogeneous disease characterized by the absence of three hallmark receptors: human epidermal growth factor receptor 2 (HER2), estrogen receptor (ER), and progesterone receptor (PR). Compared to other breast cancer subtypes, TNBC is more aggressive, has a higher prevalence in African Americans, and more frequently affects younger patients. Currently, TNBC lacks clinically-accepted targets for tailored therapy, warranting the need for candidate biomarkers.

Methods: BiomarkerBase, a biomarker knowledgebase developed by Amplion uses a comprehensive list of synonyms to identify biomarkers registered in the records of clinical trials via the government website clinicaltrials.gov. Under each of the registered breast cancer biomarkers (with the exceptions of HER2, ER, and PR), sub-searches were conducted for clinical trials that explicitly used TNBC (or the full name, triple negative breast cancer) in the title of the biomarkers’ studies. Of note, most trials in this review were completed phase II or III. The selected candidate biomarkers were classified into four FDA biomarker categories (surrogate, prognostic, predictive, or pharmacodynamic (PD)) as well as by location (blood/plasma, cell surface, cytoplasm, or nucleus). Current literature about the biomarkers was further examined using PubMed. There, we sought to find papers that studied how the biomarkers may interact. These markers were further organized into a “cellular protein network” that demonstrates potential connectivity.

Results: Blood biomarkers include VEGF/VEGFR and IL-8; cell surface biomarkers include EGFR, IGFBP, c-Kit, c-Met, and PD-L1; cytoplasm biomarkers include PIK3CA/AKT/mTOR-related metabolites (GPC, PCh, Lactate/ glucose), pPKM2, F1,6BP, SPHK1, STAT1/IRF2BP2, S6, p4E-BP1, SUV39H1, PTEN, and ALDH1; and nucleus biomarkers include BRCA1, the glucocorticoid receptor (GR), TP53, and Ki67. Table 1 provides an overview of the examined surrogate, prognostic, predictive, and PD biomarkers in TNBC in addition to current literature found in PubMed that provides support for their potential use.

Conclusion: To date, there are no clinically-validated biomarkers for TNBC, which has hindered the development of tailored therapy for both chemosensitive and refractory TNBC. Before validation and use of these biomarkers occurs, stringent-clinical criteria must be met first. The list and cellular protein network provided is an inventory and reference point for promising biomarkers for breakthrough, targeted therapies in TNBC.

Citation Format: Brett A. Fleisher, Sihem Ait-Oudhia. A network based analysis for the treatment 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 5568A. doi:10.1158/1538-7445.AM2017-5568A
Abstract 557: SPOP mutant subclass prediction and its impact on prostate cancer prognosis
Authors: Liu Deli
Published: July 2017

SPOP mutations define a distinct and key molecular class of prostate cancer, but there is no signature to identify SPOP mutant subclass based on transcriptional data, and its impact on prognosis and clinical outcomes of prostate cancer patients is unknown.

We developed the SPOP mutant transcriptional signature with high sensitivity and specificity based on transcriptional data. After we predicted SPOP mutant subclass from a large cohort project with transcriptional signature, we studied its association with clinicopathologic variables and prognosis in prostate cancer patients. On univariate analysis, SPOP mutant subclass was associated with lower preoperative serum prostate-specific antigen, extraprostatic extension and older patients (p<0.05). On multivariate analysis, SPOP mutant subclass was associated with metastasis (p<0.05). Combined SPOP mutant status and CAPRA-S models have slightly better prediction for metastasis. On Kaplan-Meier analysis, we found the significant association of SPOP mutant subclass with better patient outcomes of metastasis, and patients without radiation therapy with even better metastatic outcomes.

The SPOP mutant subclass could be predicted by using our SPOP mutant signature purely based on transcriptional data. Clinical and prognosis difference were found among SPOP mutant subclass.

Citation Format: Deli Liu. SPOP mutant subclass prediction and its impact on prostate cancer prognosis [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 557. doi:10.1158/1538-7445.AM2017-557
Abstract 5574: Retinoic acid as a therapeutic adjuvant in low-grade gliomas
Authors: Rao Aparna , Zhang Xiaoran , Kim Jason , Pomerantz Alexander , Kim Youngmi , Holland Eric , Amankulor Nduka
Published: July 2017

Introduction: Malignant gliomas are incurable brain tumors and the most common primary brain tumors in adults. Mutations in isocitrate dehydrogenase (IDH) are enriched in a subset of malignant low-grade gliomas (MLGGs) that arise as lower grade neoplasms and steadily progress to more aggressive and universally fatal glioblastomas (GBMs) usually within 5-10 years after initial diagnosis. Gliomas with IDH1/2 mutations are characterized by hypermethylation of multiple genes, including immune genes, thereby rendering them highly immune evasive. Retinol binding protein 1 (RBP1) gene, that encodes a protein involved in retinoic acid (RA) generation, is significantly hyper-methylated in IDH mutant cells. Since RA is instrumental in the induction of multiple immune genes including immune-activating ligands such as NKG2D ligands (NKG2D-L), we hypothesized that treatment of IDH mutant cells with RA will increase the expression of NKG2D-L on the tumor cells, leading to increased recognition and lysis by immune cells. In addition, we hypothesized that RBP1 methylation was crucial to development of the IDH mutant immune-evasive phenotype.

Methods: Primary glioma cells (IDH WT and mutant) were treated with 1μM RA for 48 hours. The cells were assessed for changes in expression of NKG2D-L and other type-1 immune response genes. Effect of RA treatment on NK killing and immune cell chemotaxis were evaluated. We also assessed the impact of RBP1 knock-down in IDH WT cells. Finally, we evaluated the efficacy of RA as a therapeutic modality for low-grade gliomas in a murine model.

Results: RA-treated IDH mutant gliomas had a higher expression of NKG2D-L and a higher sensitivity to killing by NK cells, when compared with untreated IDH mutant cells. RA treatment of IDH mutant cells also induced increased chemotaxis of NKs and CD8+ T cells in a CCL2-dependant manner. In addition, RA demonstrated superior anti-tumor efficacy in vivo, compared with controls. Finally, we demonstrated that RBP1 knock-down in IDH WT cells was sufficient to replicate the immune evasive phenotype observed in IDH mutant cells.

Conclusions: RA treatment reverses the immune evasion in IDH mutant cells primarily by inducing the upregulation of NKG2D-L and by mediating increased NK and CD8+ T cell chemotaxis via CCL2 induction. Additionally, we established that RBP1 gene silencing is crucial for the development of the immune evasive IDH mutant phenotype.

Note: This abstract was not presented at the meeting.

Citation Format: Aparna Rao, Xiaoran Zhang, Jason Kim, Alexander Pomerantz, Youngmi Kim, Eric Holland, Nduka Amankulor. Retinoic acid as a therapeutic adjuvant in low-grade gliomas [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 5574. doi:10.1158/1538-7445.AM2017-5574
Abstract 559: Estimation of immune cell content in bulk tumour tissue using reference profiles from single-cell RNA-seq data
Authors: Schelker Max , Du Jinyan , Feau Sonia , Klipp Edda , Schoeberl Birgit , MacBeath Gavin , Raue Andreas
Published: July 2017

Although therapeutics that modulate the immune system provide remarkable benefit for many cancer patients, predicting who will respond remains an unsolved problem. As interactions between the immune system and cancer are governed by a complex network of cell-cell interactions, knowing the specific immune cell composition of a solid tumour may be essential in predicting response to immunotherapy. Here, we describe how to derive the cellular composition of a solid tumour from bulk gene expression data by mathematical deconvolution, using consensus cell type-specific gene expression profiles from recently published tumour-derived single-cell RNA sequencing data. Notably, successful deconvolution depends on these new data, as previously-available profiles from peripheral blood are insufficient. The presented method makes the problem of obtaining a patient’s tumour immune cell composition from existing databases like The Cancer Genome Atlas as well as in the clinical setting computationally tractable.

Citation Format: Max Schelker, Jinyan Du, Sonia Feau, Edda Klipp, Birgit Schoeberl, Gavin MacBeath, Andreas Raue. Estimation of immune cell content in bulk tumour tissue using reference profiles from single-cell RNA-seq 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 559. doi:10.1158/1538-7445.AM2017-559
Abstract 5596: Intratumoral administration of a TLR9-adjuvanted nanoparticle cancer vaccine stimulates more effective immunity in both injected and un-injected tumor sites compared to subcutaneous administration
Authors: Naik Edwina , Ying Chi , Milley Robert , Calacsan Carlo , Chipman Stewart , Tüting Thomas , Coffman Robert , Guiducci Cristiana
Published: July 2017

Therapeutic success of a cancer vaccine requires substantial expansion of vaccine-primed CTL and efficient differentiation to polyfunctional T cells capable of migrating from the site of vaccination to metastatic sites. We have evaluated the tumor itself as a potential site of vaccination, compared to vaccination at subcutaneous sites distant from the tumor. For vaccination, we have developed a highly efficient nanoparticle platform comprised of multiple copies of a CpG-rich oligonucleotide (a TLR9 agonist) and long peptide tumor antigens, both covalently linked to the sucrose polymer Ficoll. Multiple peptide antigens where studied, including ovalbumin and a long peptide comprising epitopes from three melanocyte differentiation antigens. In all of these models, intratumoral vaccination was superior to subcutaneous vaccination for elimination of both injected tumors and, more importantly, distant site skin and lung metastases. Intratumoral vaccination substantially increased the magnitude of the systemic CTL response measured in the blood and in the spleen and enhanced capacity cell homing to distant site tumors. A greater fraction of tumor-antigen specific CD8+ T cells generated in the tumor were polyfunctional, expressing both IFN-γ and TNF-α. They were also less exhausted as measured by decreased overall PD-1 levels, increased T bet and the increased number of PD-1+ cells that retained cytotoxicity and proliferative capacity. Intratumoral vaccination also induced spread of the CD8+ T cell response to tumor antigens not included in the vaccine. These results demonstrate that direct intratumoral immunization with peptide antigens combined with a strong TLR9-activating adjuvant significantly increases the magnitude and quality of vaccine-primed CTL and enhances control of metastatic disease.

Note: This abstract was not presented at the meeting.

Citation Format: Edwina Naik, Chi Ying, Robert Milley, Carlo Calacsan, Stewart Chipman, Thomas Tüting, Robert Coffman, Cristiana Guiducci. Intratumoral administration of a TLR9-adjuvanted nanoparticle cancer vaccine stimulates more effective immunity in both injected and un-injected tumor sites compared to subcutaneous administration [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 5596. doi:10.1158/1538-7445.AM2017-5596
Abstract 5599: Soluble PD-L1 as a surrogate biomarker of metastatic progression and resistance to antiangiogenic therapy
Authors: Mastri Michalis , Tracz Amanda , Shi Yuhao , Bjarnason Georg , Nguyen Tran , Rini Brian , Ebos John M.L.
Published: July 2017

Immune-checkpoint inhibitors are now approved for the treatment of early- and late-stage cancers. These include agents that block the T-cell regulatory protein programmed cell death 1 (PD-1) from being activated by the PD-1 ligand 1 (PD-L1) expressed on cancer cells. There is an urgent need to identify biomarkers of PD-1 pathway inhibition that would predict patient populations responsive to treatment and/or serve as surrogates for drug activity and resistance. PD-L1 expression on tumors is currently a biomarker candidate, but reliable detection and quantification methodologies have proven challenging to standardize. Recently, a soluble PD-L1 (sPD-L1) fragment was identified that can derive from cell-bound PD-L1. Retrospective clinical examinations of sPD-L1 levels in cancer patients suggest a potential use as a surrogate for disease progression and response to treatment; but few preclinical studies have been performed to test this predictive value. We undertook experiments to evaluate plasma sPD-L1 in mouse tumor models during localized primary tumor growth (after orthotopic cell implantation) and spontaneous metastatic disease progression (after surgical removal of the primary). Mouse syngeneic and human xenograft implantation models included breast, kidney, colon, and melanoma cell systems. Our results show that circulating plasma sPD-L1 can correlate with primary and metastatic progression in a stage and model specific manner. Next, we evaluated sPD-L1 following treatment with neutralizing antibodies to PD-1 and PD-L1 in tumor-free mice and found significant dose-dependent sPD-L1 increases, suggesting systemic changes may have utility as a measurement of target saturation and dosing independent of tumor growth. Finally, with current approvals of PD-1 inhibitors in renal cell carcinoma (RCC) patients previously treated with antiangiogenic agents that block vascular endothelial growth factor (VEGF), we evaluated plasma in mouse models of sunitinib resistance - a VEGF receptor tyrosine kinase inhibitor (RTKI). Our results demonstrate that VEGF pathway resistance yields changes in sPD-L1 and may be useful in predicting response to PD-1 pathway inhibition in the refractory setting. Together, these investigations suggest that circulating sPD-L1 changes during disease progression (both local and disseminated) may serve as a potential predictive biomarker for immune-checkpoint and antiangiogenic therapy.

Citation Format: Michalis Mastri, Amanda Tracz, Yuhao Shi, Georg Bjarnason, Tran Nguyen, Brian Rini, John M.L. Ebos. Soluble PD-L1 as a surrogate biomarker of metastatic progression and resistance to antiangiogenic therapy [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 5599. doi:10.1158/1538-7445.AM2017-5599
Abstract 5614: Novel mRNA purification method with RNaseIII improves efficacy of RNA chimeric antigen receptor T cells
Authors: Foster Jessica , Choudhari Namrata , Resnick Adam , Barrett David
Published: July 2017

Chimeric Antigen Receptor (CAR) T-cells made with mRNA offer a transient and safe alternative to viral CARs, mitigating the concern for persistent unwanted side effects from constitutively active T-cells. Previous studies have shown that mRNA CARs are transiently effective, but lack CAR persistence and have struggled to show success across tumor types. We hypothesized the efficacy of mRNA CARs could be improved by utilizing recent advancements in RNA technology including the use of modified uracil and a novel purification method with RNaseIII to prevent double stranding that induces toxicity. Using the established CD19 CAR model in B-cell acute lymphoblastic leukemia, we created mRNA CARs using previously described methods and compared them to mRNA CARs created using modification of uracil and/or purification to remove any aberrant double stranded mRNA. Comparing the modified and purified mRNA CAR T cells to those created using prior methods of making mRNA, both modified and purified mRNA CAR T cells showed a two-fold increase in expression of the CAR on their surface initially, as well as a two-fold improvement in cytotoxic killing of leukemia cells in vitro that persisted for up to five days. Both the modified and purified mRNA CAR T cells also showed reduced expression of negative checkpoint regulators compared to original RNA CAR T cells. However, in vivo studies using a patient-derived xenograft model with a single dose of CAR T cells revealed purified RNA CAR T cells offered the most robust 2-log enhanced suppression of leukemic burden. RNaseIII is a novel purification technique that has not yet been reported in the literature for RNA manufacturing. Our results provide a time efficient purification method that can be easily incorporated into RNA production for use in clinical trials, and poise RNA CARs for increased efficacy as new CAR targets emerge and are being tested. Additional studies are ongoing investigating if the observed improved efficacy will translate to improved cytotoxicity in solid tumor models.

Citation Format: Jessica Foster, Namrata Choudhari, Adam Resnick, David Barrett. Novel mRNA purification method with RNaseIII improves efficacy of RNA chimeric antigen receptor T 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 5614. doi:10.1158/1538-7445.AM2017-5614
Abstract 5622: Acquired resistance to EGFR-TKI upregulates the expression of PD-L1 and promotes immune escape in lung cancer
Authors: Peng Shunli , Li Qi , Wang Wei
Published: July 2017

Background and purpose: Acquired resistance is a severe problem of EGFR inhibitors (EGFR-TKIs) therapy in lung cancer patients. Immune checkpoint therapy is a new revolution in cancer treatment with dramatic outcomes in a subset of patients. In this study, we explored the possibility of immune checkpoint therapy in lung cancers with three well-known resistant mechanisms to EGFR-TKIs, T790M, MET amplification and hepatocyte growth factor (HGF), and investigated internal regulation mechanisms.

Experimental Design: PD-L1 expression and immune escape ability were evaluated in EGFR-TKIs resistant lung cancer cells by MET amplification, HGF, and T790M, as well as T790M transfected-human renal derived cells (293FT). MAPK and PI3K pathways were investigated simultaneously. PD-L1 gene deleted resistant cells were used in NOD-SCID xenograft models to evaluate immune escape in vivo.

Results: All of three resistant mechanisms increased PD-L1 expression. Both MAPK and PI3K pathways are involved in MET amplification or HGF induced PD-L1 overexpression, whereas only MAPK pathway mediated it in T790M-transfected cells. The decreased cytotoxicity of lymphocytes can be restored by anti-PD-L1 antibodies. Moreover, xenograft tumors by EGFR-TKIs sensitive cells but not resistant cells responded to treatment of human lymphocytes. However, deletion of PD-L1 successfully restored cytotoxicity of lymphocytes in EGFR-TKIs resistant tumors.

Conclusion: Acquired Resistance to EGFR-TKIs augments the expression of PD-L1 and promotes immune escape in EGFR mutant lung cancer. Immune checkpoint therapy might be a promising alternative therapeutic strategy for NSCLC that acquired resistant to EGFR-TKIs.

Note: This abstract was not presented at the meeting.

Citation Format: Shunli Peng, Qi Li, Wei Wang. Acquired resistance to EGFR-TKI upregulates the expression of PD-L1 and promotes immune escape in lung 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 5622. doi:10.1158/1538-7445.AM2017-5622
Abstract 5632: Thyroid carcinoma in The Sudan
Authors: Ahmed Mohamed ElMakki
Published: July 2017

Introduction: Goiter is endemic in Sudan and thyroidectomy is a daily practice in most surgical lists across the country. The most common indications are cosmoses and pressure with respiratory choking. In 10% of cases a surprise histopathology on cancer is reported . This study aims to report on thyroid carcinoma on patients presenting to the surgical department in Khartoum Teaching Hospital.

Methods: This study is an overview on pattern, clinical presentation a management of thyroid carcinoma in Khartoum during the period 2007 - 2014. Thyroidectomy was the standard procedure when feasible and postoperative radio iodine given. External radiotherapy was given in aggressive anaplastic carcinoma.

Results: 166 patients with thyroid cancer were studied. The mean age was 51 +/-SD 17yrs and the age range between 15 - 85 years. Male to female ratio was 1.0:2.4. Clinical presentation was a goiter that was showing a recent rapidly growth with either respiratory choking, pain and dysphagia. Follicular carcinoma was 43%,papillary 27%, anaplastic 10% 2%medullary. Sarcoma and lymphoma 5% and missing data in 13%. Six per cent of patients presented with lung and bone metastasis. 20 patients had long standing goiter before development of cancer. Different types of total thyroidectomy done in 81%, no surgery in 7% and missing data in 12%. 18 patients needed postoperative tracheostomy, 7 developed permanent hypocalcaemia, 15 recurrent nerve palsy and a 30 days mortality was 10% and all were anaplastic carcinoma where recurrence occurred within weeks following thyroidectomy or dublking in most cases.

Conclusion: Patients with thyroid cancer presents late. The dominance of follicular type indicates the significance of underlying endemic goiter in its etiology. Anaplastic is very aggressive and lethal outcome.

Citation Format: Mohamed ElMakki Ahmed. Thyroid carcinoma in The Sudan [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 5632. doi:10.1158/1538-7445.AM2017-5632
Abstract 5636: Targeting of NOXA overexpression in anaplastic thyroid cancer (ATC)
Authors: Finnberg Niklas K. , Abdulghani Junaid , Ehya Hormoz , El-Deiry Wafik
Published: July 2017

Anaplastic thyroid cancer (ATC) is a rare, aggressive and fatal cancer with a median survival of 3-5 months after diagnosis. Our long-term goal is to develop better therapies based on the biology of ATC that contributes to improved tumor response and a reduced risk of potential side-effects. We recently showed that the anti-apoptotic BCL2 family member MCL1 is overexpressed in a subset of ATC and that targeting of MCL1 with quinacrine leads to increased sensitization to the BRAF inhibitor sorafenib. To further investigate the importance of BCL2 family proteins in ATC, we analyzed gene expression data from several published independent gene expression studies. We discovered that both papillary thyroid cancer (PTC) and ATC surprisingly overexpress the mRNA of the pro-apoptotic BCL2 family member NOXA. However, despite the observed overexpression of NOXA mRNA in several ATC cell lines, we find that NOXA protein expression, by contrast, is low. NOXA protein has previously been shown to be subject to ubiquitination and proteasomal degradation. Indeed, through bioinformatics, we find overexpression of several ubiquitin enzymes in ATC suggesting that the half-life of NOXA protein may be selectively reduced in this tumor type. We are further assessing differences in the turnover of NOXA protein in ATC cells and are investigating if restoring NOXA protein expression may synergize with the pharmacologic targeting of MCL1 and other anti-apoptotic BCL2 family members. Interestingly, through TCGA analysis, we discovered that BCL2 overexpression is associated with a poor prognosis in thyroid cancer (THCA) patients. Indeed, treatment with the BCL2/BCLXL inhibitor navitoclax showed encouraging efficacy and synergized with the neddylation inhibitor MLN4924 in the ATC cell line 8505C. This was based on the expectation that MLN4924 would rescue NOXA protein expression. We are pursuing mechanistic studies in a larger panel of thyroid cancer cell lines and in vivo efficacy and toxicity studies. We conclude that restoring NOXA protein expression can together with the rational targeting of anti-apoptotic BCL2 family members may allow for the expansion of the limited ATC-selective treatment strategies currently available.

Citation Format: Niklas K. Finnberg, Junaid Abdulghani, Hormoz Ehya, Wafik El-Deiry. Targeting of NOXA overexpression in anaplastic thyroid cancer (ATC) [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 5636. doi:10.1158/1538-7445.AM2017-5636
Abstract 5640: The prognostic role of estrogen receptor beta in a female cohort of colorectal cancer
Authors: Topi Geriolda , Ehrnström Roy , Palmquist Ingrid , Lydrup Marie-Louise , Sjölander Anita
Published: July 2017

Background: The estrogen receptor beta (ERβ) is the predominant estrogen receptor in the colon mucosa, and has been reported to have anti-proliferative and pro-apoptotic effects. However, the role of estrogen signaling in colorectal cancer (CRC) progression remains unclear.

Aim: To investigate the prognostic role of ERβ in a female cohort of CRC.

Methods: A tumor tissue microarray of primary CRCs from 333 female patients was stained with a mouse monoclonal anti-ERβ antibody. The intensity of staining was evaluated using immunohistochemistry technique. The expression of ERβ was scored using the semi-quantitative method [IRS (immune-reactive score) = SI (staining intensity) x PP (percentage of positive nuclei)]. Overall survival (OS) and disease-free survival (DFS) were the primary outcomes. Preliminary results are presented.

Results: From 321 patients eligible for survival analysis only 315 had successful measurement of ERβ (141 with low expression and 174 with high expression). The univariate analysis showed no effect of ERβ on OS, but high ERβ was associated with lower risk of cancer recurrence as indicated by DFS (HR, 0.61; CI, 0.38-1.02). Cox multivariate analysis indicated that, compared to low expression, high expression of ERβ was significantly associated with a decreased risk of cancer recurrence (HR, 0.39; CI, 0.20-0.77), after adjustment for age, tumor stage, tumor intravascular invasion and hormonal contraception use. Likewise, high ERβ expression was associated with better OS in patients with cancer stage I-III (HR, 0.52; CI, 0.29-0.94) that did not receive adjuvant treatment after operation. Premenopausal women had a higher mean of IRS for ERβ compared to postmenopausal women (p = 0.03).

Conclusion: High levels of ERβ significantly correlate with a decreased risk of cancer recurrence in CRC patients. We also noted longer overall survival in the subgroup of patients with cancer stage I-III that had not received adjuvant treatment after operation. The same results of OS were observed for colon cancer patients, but not for rectal cancer patients. A possible explanation could be that most of the rectal cancer patients have undergone radiotherapy before surgery, which might affect the status of ERβ.

Citation Format: Geriolda Topi, Roy Ehrnström, Ingrid Palmquist, Marie-Louise Lydrup, Anita Sjölander. The prognostic role of estrogen receptor beta in a female cohort of colorectal 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 5640. doi:10.1158/1538-7445.AM2017-5640
Abstract 5660: Tumor cell death caused by INT230-6 induces protective T cell immunity
Authors: Bloom Anja C. , Bender Lewis H. , Walters Ian B. , Clark Katharine T. , Terabe Masaki , Berzofsky Jay A.
Published: July 2017

Standard care for many types of cancer involves systemic administration of cytotoxic agents. This may result in low drug concentration at tumor sites, which limits cell killing. More recently it has been shown that cytotoxic formulations designed for intratumoral delivery improve drug efficacy presumably by increasing drug concentration at the tumor site. Furthermore, it has been discovered that the mechanisms of anticancer agents extend beyond direct tumor cell lysis. One major aspect is that cell death often induces an immune response. Different types of cell death such as necrosis, apoptosis and autophagic cell death induced by cytotoxic agents trigger immune responses with varying degrees of inflammation and involving different types of immune cells. The ideal immune responses that may give maximum benefit to patients would be strong and long lasting anti-tumor T cell responses. In this study, a novel, tissue and cell diffusive cytotoxic formulation, INT230-6, was administered intratumorally over 5 sequential days into subcutaneous 300mm3 murine Colon26 tumors. Treatment resulted in regression from baseline of 100% of the tumors and up to 80% complete response (CR). We then analyzed the T cell responses in the protection induced by INT230-6. No animals achieved a CR after CD8 or CD8/CD4 double depletion at treatment onset, indicating a critical T-cell role in tumor regression. Mice with CRs were protected from re-challenge by either subcutaneous or intravenous re-inoculation of the Colon26. The protection was abrogated by CD4/CD8 double depletion prior to the re-challenge, indicating that immunological T cell memory was induced and was necessary for protection. Hence, INT230-6 given locally to treat tumors induces tumor-specific protective T cell immunity. Colon26 tumors express the endogenous retroviral protein gp70 containing the AH-1 CTL epitope. AH-1-specific CD8 T cells were detected in tumors of mice without treatment. However, these highly expressed PD-1. This was consistent with the observation that the PD-1 blockade enhanced the efficacy of INT230-6. Conversely, INT230-6 enhances the efficacy of checkpoint inhibitors.

Citation Format: Anja C. Bloom, Lewis H. Bender, Ian B. Walters, Katharine T. Clark, Masaki Terabe, Jay A. Berzofsky. Tumor cell death caused by INT230-6 induces protective T cell immunity [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 5660. doi:10.1158/1538-7445.AM2017-5660