bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-067: Cargocytes: A novel cell therapy platform to drive anti-tumor immunity
Authors: Klemke Richard L. , Wang Huawei , Liu Bei , Alarcon Christina , Watson Felicia
Published: August 2019

Adoptive cell therapy has emerged as a powerful new tool to treat cancer and other diseases. However, the clinical utility of many cell-based therapies is limited by inadequate production of therapeutic factors, production of unwanted factors, unwanted engraftment into the tumor, and poor controllability resulting in poor pharmacokinetics. Genetic and bioengineering strategies can overcome many limitations, but modification of genomic DNA or the introduction of new genetic material into therapeutic cells raises substantial safety concerns, ultimately making FDA approval difficult. To address these limitations, we developed a novel platform for cell-based therapies in which any cell type, including immortalized cells, can be extensively engineered and loaded with therapeutic cargo, and then rendered safe for patient administration through removal of the nucleus. Enucleated cells (Cargocytes) retain many desired biologic functions (endogenous and engineered), such as viability up to 72 hours, retention of cell surface markers/proteins, secretion of bioactive molecules, robust in vitro and in vivo chemotaxis, and delivery of a wide range of cancer-fighting cargos. Using this technology, we demonstrate that Cargocytes derived from hTERT-immortalized mesenchymal stem cells (hTERT MSCs) and engineered to express therapeutic levels of IL-12 can potently activate an anti-tumor immune response in a preclinical mouse model of triple negative breast cancer. hTERT MSC-derived Cargocytes robustly delivered IL-12 to the tumor with definable pharmacokinetics, activated known IL-12 biomarkers, and induced infiltration of tumor-fighting immune cells that inhibited tumor growth and improved animal survival. In addition, co-administration of Cargocytes secreting IL-12 and anti-PD-L1 antibodies further improved animal survival without notable adverse events. Collectively, our findings indicate that Cargocytes provide a new means to deliver powerful immunomodulatory biologics to malignant tumors in a safe and controllable manner. The genetic tractability and excellent safety profile of the Cargoycte platform enables bioengineering of a wide range of designer therapeutics derived from genetically modified cells, immortalized stem cells, and even cancer cells, each with improved clinically relevant functions.

Citation Format: Richard L. Klemke, Huawei Wang, Bei Liu, Christina Alarcon, Felicia Watson. Cargocytes: A novel cell therapy platform to drive anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-067.
Abstract LB-068: Tomivosertib (eFT508), a potent and highly selective inhibitor of MNK1 and MNK2, enhances CAR T cell activity through modulating T cell differentiation
Authors: Goel Vikas K. , Sharma Rajesh K. , Staunton Jocelyn , Stumpf Craig R. , Young Nathan P. , Thompson Peggy A. , Chiang Gary G. , Webster Kevin R.
Published: August 2019

Chimeric antigen receptor (CAR) T cells have shown great promise in treating hematopoietic malignancies, such as leukemia and non-Hodgkin’s lymphoma. The efficacy and durability of CAR T cell therapy have been correlated with higher levels of T stem cell memory (TSCM) and T central memory (TCM) populations. Accordingly, various strategies to enrich these CAR T cell populations are of intense interest. It is well-established that the PI3K/mTOR pathway plays an important role in T cell activation and differentiation, and perturbations in this pathway can enhance T cell memory populations. Work from our group has demonstrated that MNK modifies mTOR signaling and T cell differentiation. Here, we demonstrate that the MNK1/2 inhibitor tomivosertib can substantially increase TCM and TSCM populations in both primary murine and human T cells. Tomivosertib treatment of murine OT-I T cells biases T cell differentiation towards a TCM (CD8+ CD44+ CD62L+) population upon SIINFEKL peptide stimulation in vitro without adverse effects on T cell proliferation, interferon-γ production or cytotoxic function. Similar effects are seen in vivo, where tomivosertib treatment also enriches the TCM cell pool in a SIINFEKL vaccine-induced OT-I adoptive T cell transfer model, which results in increased persistence as demonstrated by a higher memory-recall T cell response upon re-challenge. Furthermore, addition of tomivosertib during production of human CAR (anti-CD19 scFv-4-1BB-CD3ζ) T cells leads to a significantly increased population of TSCM (CD8+ CD45RO CD45RA+ CD27+ CD95+) cells. Based on these data, the combination of tomivosertib with CD19-directed CAR T cells was assessed in the CD19+ Pfeiffer DLBCL model in vivo. Daily oral administration of tomivosertib in combination with CD19-directed CAR T cells results in improved efficacy in comparison to either monotherapy alone, consistent with tomivosertib promoting and maintaining TSCM populations in vivo. Tomivosertib is currently in multiple Phase II clinical trials as a monotherapy or in combination with checkpoint inhibitors.

Citation Format: Vikas K. Goel, Rajesh K. Sharma, Jocelyn Staunton, Craig R. Stumpf, Nathan P. Young, Peggy A. Thompson, Gary G. Chiang, Kevin R. Webster. Tomivosertib (eFT508), a potent and highly selective inhibitor of MNK1 and MNK2, enhances CAR T cell activity through modulating T cell differentiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-068.
Abstract LB-099: Prostate cancer-secreted CCN3/NOV promotes osteoblast differentiation via Wnt signal pathway and miR-608 suppression
Authors: Chen Po-Chun , Chao Chia-Chia , Chang An-Chen , Tang Chih-Hsin
Published: August 2019

Objective: NOV/CCN3 is a secreted protein that interacts with the extracellular matrix and thereby regulates many cellular functions, including cell division, chemotaxis, apoptosis, adhesion, motility, and ion transport. Recently, CCN3 expression have been implicated in progression of various cancer, and our previous study indicates that CCN3 increases the migration and invasion of prostate cancer (PCa) cells by regulation of ICAM-1 expression. Our research group also review the pivotal role CCN3 in bone metastasis of PCa by modulating the tumor-bone microenvironment. Moreover, evidence has highlighted the pivotal role of osteoblasts in osteoblastic bone metastasis in PCa.

Material and Methods: MC3T3-E1 osteoblast cells were incubated with conditioned media collected from PCa cells. The cell proliferation and osteogenic differentiation were evaluated by MTT assay and Alizarin red S staining. The osteogenic markers were also examined by Western blot and QPCR. Furthermore, the Wnt activation was tested by Western blot and luciferase reporter assay. Pretreatment with chemical inhibitor of Wnt was used to determine the regulatory role of Wnt in osteogenic differentiation in response to PCa CM. Finally, expression of miR-608 was investigated by QPCR and mimic miR-608 was used to certify the role of miR-608 in osteogenic differentiation in response to PCa CM.

Results: Here, we show that PCa-secreted CCN3 increases expression of osteoblastic differentiation factors including BMPs, Runx2 and Osterix. Furthermore, this effect is regulated by Wnt signal pathway or miR-608 repression. The present study supposes that PCa-secreted CCN3 can promote osteoblastic bone metastasis in PCa by activating Wnt signal and inhibition of miR-608 expression. Our present study provides an opportunity to develop CCN3 as a therapeutic target that prevents bone metastasis in PCa.

Citation Format: Po-Chun Chen, Chia-Chia Chao, An-Chen Chang, Chih-Hsin Tang. Prostate cancer-secreted CCN3/NOV promotes osteoblast differentiation via Wnt signal pathway and miR-608 suppression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-099.
Abstract LB-133: Tumor-promoting activity of CCL8 in involution-associated breast cancer
Authors: Farmaki Eleni , Kaza Vimala , Chatzistamou Ioulia , Kiaris Hippokratis
Published: August 2019

Postpartum breast cancers that develop within 5 years after child birth have a poor prognosis because of increased risk of metastasis and remain a principal cause of mortality for young women. Therefore understanding the molecular physiology of postpartum breast cancers is imperative as it may provide novel therapeutic options. The increased risk for breast cancer immediately after pregnancy is linked to the extensive remodeling of the mammary gland that is designated as mammary involution. Immune cells such as macrophages and neutrophils, activated by a chemokine and cytokine cascade during involution, are actively involved in mammary gland remodeling and contribute to the disease development. Among the various chemokines activated in involution, the role of CCL8 in the development of postpartum breast cancer has not been addressed despite recent evidence demonstrating its role in metastatic disease. Our results show that CCL8 mRNA and protein levels increase in mammary gland during involution. Tumor growth studies involving CCL8-deficient animals that had been implanted with cancer cells prior to pregnancy or during involution indicated that CCL8 is tumor-promoting specifically following lactation, during involution. CCL8 is responsible for recruiting F4/80-positive macrophages to the mammary gland during the second phase of involution. Thus we asked if CCL8 promotes tumor development by recruiting macrophages in the involuting mammary gland. Our studies showed that CCL8 attracts primarily M2 type macrophages and that depletion of macrophages by liposomal clodronate abolished the tumor-promoting effect of CCL8 in the wt animals but did not affect CCL8KO animals, at which the M2 macrophages were already absent. These results illustrate the role of CCL8 in the development of postpartum breast cancer by recruiting M2 macrophages and suggest the potential value of targeting CCL8 for disease management.

Citation Format: Eleni Farmaki, Vimala Kaza, Ioulia Chatzistamou, Hippokratis Kiaris. Tumor-promoting activity of CCL8 in involution-associated breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-133.
Abstract LB-154: Differential predictive modeling to grasp disparities among sub-populations
Authors: Yoo Wonsuk
Published: August 2019

Background: Many of these practical applications typically produce huge data sets that contain several thousands of objects with hundreds (or even thousands) of features that describe each object. Automatic modeling, organizingand interpreting these large-scale data sets is increasingly part of various disciplines, such as health, medicine, and biology. The study aims to propose a new framework for constrained learning of predictive models where we enforce additional constraints for the models to be as similar as possible.

Methods: We develop a new task of differential predictive modeling to solve the problem of differences in the data distributions by developing a continuum of predictive models. To achieve this, we construct a new framework for constrained learning of predictive models where we enforce additional constraints for the models to be as similar as possible. The major distinction of our approach with the existing methods is that none of the existing methods explore the model distance based on building the similar tree concept. We compute the distance between two datasets from the structural information about the induced trees without referring back to the original data statistics or the model statistics. Our 29-state Medicaid dataset, which contains 100% of the claims for 90% of all African American and 90% of all Hispanic and Latino Medicaid enrollees in the entire U.S. geo-coded at the zip code and county levels.

Principal Findings: The goal of the disparities work is to capture the differences across different population groups and provide a better understanding that can explain these differences. Using this model, we could be able to measure the group difference in a particular minority group and compare these differences across the other subgroups. This is useful in ranking the groups where the disparity varies from the highest to the lowest. The novelty of our approach is that it captures the disparity of groups through a systematic comparison of multivariate models which cannot be done using any of the existing methods available in the machine learning methods.

Conclusions: This model has the potential to dictate more aggressive new therapeutic treatments for specific subsets of high-risk patients. This project proposes new research directions in exploratory tools needed by the domain experts analyzing their data. It will provide significant insights for data analysis that can be utilized in various domains of science. One of the ultimate goals of the proposed research is the development of a clinician-friendly software and web-based analysis tool to analyze the health disparity multivariate data using the prediction models.

Citation Format: Wonsuk Yoo. Differential predictive modeling to grasp disparities among sub-populations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-154.
Abstract LB-158: Tribal sovereignty and approval for research in Native American communities
Authors: Goldtooth Carol , Teufel-Shone Nicolette , Gachupin Francine C.
Published: August 2019

Background: Native Americans (NAs) experience worse outcomes and lower chances of cancer survival than other racial groups in the US. Despite improvements in cancer screening techniques and major developments in cancer treatment in past decades, NA communities do not benefit equally from these advances. Furthermore, relatively little of the advancements in cancer research addresses the specific vulnerabilities and strengths in these communities. Community-based research with NA populations including cancer research is influenced by the ways tribes approach and approve research. Tribe specific approval processes are assertions of sovereignty and of tribal right to govern and manage activities on tribal lands. Researchers often interpret required tribal approval for research, presentation and publication as punitive and a barrier to timely research and dissemination.

Objective: An overview of the evolution and range of tribal research approval processes can address the cultural discordance faced by researchers and NA communities and supports researchers’ effort to gain approval to conduct much needed community-based cancer research.

Methods: This presentation outlines the diversity of tribal research processes, including established Tribal Institutional Review Boards (IRBs), Tribal Advisory boards, Tribal Council approval, and Indian Health Service (IHS) IRB approval. Guidance will be provided to inform the development of research study designs that meet the needs of the community and have the potential to guide cancer treatment practice and cancer prevention education. In addition, this review will demonstrate that respecting the distinct characteristics of separate tribes relative to experience with research and leadership oversight of research activities is important to obviate homogenization of NA communities and enhance the relevance of research.

Conclusion: Research design, implementation and interpretation are strengthened by tribal research approval processes by requiring researchers to justify their research methods, hypotheses and expected benefits to the community and NA populations. Concurrently, adhering to procedures, protocols and requirements established by tribal councils supports tribal sovereignty in action.

Citation Format: Carol Goldtooth, Nicolette Teufel-Shone, Francine C. Gachupin. Tribal sovereignty and approval for research in Native American communities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-158.
Abstract LB-175: Genome-wide scan of the effect of cis-eSNPs on gastric cancer in Chinese population
Authors: Ni Jing , Han Jing , Zhu Meng , Jin Guangfu , Hu Zhibin
Published: August 2019

Background: Previous genome-wide association studies (GWASs) have identified multiple single-nucleotide polymorphisms (SNPs) for gastric cancer risk. However, only a tiny fraction of heritability can be explained.

Methods: We performed a comprehensive analysis to evaluate the associations between cis-expression quantitative trait SNPs (eSNPs) and susceptibility to gastric cancer in two GWAS datasets, including 2,631 gastric cancer cases and 4,373 controls. Gene-based and pathway analysis were conducted by the sequence kernel association test (SKAT-C) and the adaptive rank truncated product (ARTP) method, respectively.

Results: A total of 314,518 eSNPs were remained after quality control, which mapped to 5,155 genes and 1,077 pathways. We identified six novel eQTL SNPs in unknown loci which can explain approximately 3.56% of the phenotypic variances combined with known GWAS related variants. Function analysis revealed that rs3129206 might affect the susceptibility of gastric cancer via regulating the expression of HSD17B8, while rs6930376 regulating the expression of PSORS1C3. Pathway-based analysis showed a total of seven potential pathways might account for the risk of gastric cancer (Pfdr<0.1).

Conclusion: Our findings demonstrate an overview of the associations between eSNPs and gastric cancer risk in Chinese population, which provide insight into genes and pathways that may be biologically relevant for risk of gastric cancer.

Citation Format: Jing Ni, Jing Han, Meng Zhu, Guangfu Jin, Zhibin Hu. Genome-wide scan of the effect of cis-eSNPs on gastric cancer in Chinese population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-175.
Abstract LB-205: A lipoplex-based mRNA nanovaccine for cancer immunotherapy
Authors: Hongxia Zhang , Xinru You , Xiaojuan Wang , Zining Wang , Feifei Xu , Jun Wu , Xiaojun Xia
Published: August 2019

Intracellular delivery of messenger RNA (mRNA)-based cancer vaccines have shown great potential to activate antitumor immune response for cancer prevention and therapy. In vivo delivery efficiency of mRNA has been greatly improved by various nucleotide chemical modifications and nanovector formulations, but the efficacy of mRNA vaccine remains unsatisfied. Here, we report a lipoplex-based mRNA nanovaccine that can markedly improve mRNA delivery in antigen presenting cells, activate T cell response, and induce robust antitumor immunity. The nanovaccine formulation contains three components: cationic polymer/lipid(poly(amidoamine)/alkylene oxide), DSPE-PEG2000, and epitope-encoding mRNA. With appropriate ratio, the optimized nanovaccine show effective mRNA delivery in dendritic cells, and strongly active antigen-specific immune response in vitro and in vivo. The mRNA@lipoplex nanovaccine enhanced mRNA uptake by dendritic cells, and significantly increased T cell activation reflected by IL-2 and IFN-γsecretion in an in vitro antigen presentation assay. Besides enhancing cross-presentation, nanoparticle itself can promote the expression of inflammatory cytokines such as IL-12 via stimulating NF-κB signal pathway in dendritic cells. In a tumor prevention setting, mRNA@lipoplex nanovaccine produced strong CD8+ T cell activation and great efficacy in preventing tumor development. Furthermore, treatment of established B16 and B16-OVA melanoma and MC38-OVA colon tumors with nanovaccine containing mRNA encoding cancer-associated antigen resulted in great therapeutic efficacy and prolonged survival. Re-challenge of tumor-free mice with MC38-OVA cells led to complete tumor rejection, suggesting long-term antitumor memory. In conclusion, our work presents a new means to deliver mRNA cancer vaccine, which in principle may be applied for immunotherapy for a wide range of tumor types.

Citation Format: Zhang Hongxia, You Xinru, Wang Xiaojuan, Wang Zining, Xu Feifei, Wu Jun, Xia Xiaojun. A lipoplex-based mRNA nanovaccine for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-205.
Abstract LB-209: Novel pathway prediction for colorectal cancer to liver metastasis through bioinformatics
Authors: Makondi Precious Takondwa , Huang Chien-Yu , Chang Yu-Jia
Published: August 2019

Background: Liver metastases are the most common cause of colorectal cancer (CRC) related deaths, with no reliable clinical predictors. Therefore, identifying potential candidate predictors is crucial for clinical application and management.

Methodology: The Gene Expression Omnibus (GEO) datasets GSE49355, GSE41258 and GSE81558 for genes and GSE54088 and GSE56350 for miRNAs were used to identify common differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) between paired primary CRC tissues and the corresponding liver metastatic tissues. Then, DEMs targets were identified from DEGs. These were verified in GEO datasets comprising gene, miRNA and miRNA exosome profiles of CRC patients with no distant metastases (M0) and distant metastases (M1); the interaction networks and pathways were also mapped.

Results: There were 49 upregulated and 13 downregulated DEGs, and 16 downregulated and 14 upregulated DEMs; between DEGs and DEMs targets, there were five upregulated and four downregulated genes. MiR-20a was significantly high in M1, with the combination of MiR-20a, -495, -576-5p and -449a offering a superior prediction value (sensitivity of 83.3%, specificity of 63.8%, AUC of 0.725). In miRNA exosomes, MiR-576-5p was significantly low in M1, while MiR-20a and -449a were highly expressed, and combination of miR-20a, -495, -576-5p, -449a, -619 and -382 provided best predictive value (sensitivity=75.0%, specificity=88.2%, AUC=0.875). The miRNA target CDH2 was significantly highly expressed in M1 while KNG1 and MMP2 were lowly expressed. The miRNA to gene interaction model was demonstrated, and enriched pathways were; regulation of IGF transport and uptake by IGFBPs, extracellular matrix organization, signal transduction and immune system.

Conclusion: This model predicts novel pathway for predicting CRC to liver metastases. This may be clinically applicable.

Citation Format: Precious Takondwa Makondi, Chien-Yu Huang, Yu-Jia Chang. Novel pathway prediction for colorectal cancer to liver metastasis through bioinformatics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-209.
Abstract LB-212: FCRF: An efficient algorithm for detecting circular fusion transcript from RNA-Seq data
Authors: Yu Han , Zhang Xuanping , Guan Yanfang , Chen Yongsheng , Xiao Xiao , Wang Jiayin
Published: August 2019

Fusion circular RNAs (f-circRNAs) are circular RNAs derived from rearranged genome translocations. Their formation is caused by back-splicing happening to the genome regions of aberrant chromosomal translocation. Their cancer-promoting roles have been implicated in recent studies. One of them adopted both in vivo and in vitro models to demonstrate the oncogenic roles of f-circRNAs including promoting cellular transformation, cell viability and resistance to treatment. Therefore, it is suggested that accurate identification of f-circRNA will contribute to cancer diagnosis and therapy. But until now there is only one tool called Acfs (accurate circRNA finder suite) ever mentioned detecting f-circRNAs whose primary job is to detect normal circRNAs and only 10 f-circRNAs have been tested for verification without considering realistic sequencing problems. Here, we proposed the first algorithm, FCRF (Fusion CircRNA Finder), to identify f-circRNAs from RNA-Seq data. The SAM file aligned by BWA was used as input, and paired fusion junction site locations would be output. After pre-processing and correcting the original data in consideration of the sequencing fault tolerance, we divided the candidates into balance set and unbalance set according to the relative aligned length. For balance set, we extracted reads from non-homologous chromosomes owing to the fusion events and further detected the paired clipping signals specific to fusion junctions. On the other hand, for unbalance set, we could not use the paired signal because BWA only reported one alignment for them. So we handled them with local similar sequence considering that each junction read has similar sequences with the other read spanning the same junction. Finally we searched all the candidate fusion junctions in accord with the threshold window size and cyclization characteristics, and then recorded two special junction site locations for each fusion-circRNA. We conducted a series of simulation experiments to evaluate our algorithm. The proposed algorithm FCRF achieved 95% on precision and 85% on sensitivity where Acfs output nothing from our improved dataset.

Note: This abstract was not presented at the meeting.

Citation Format: Han Yu, Xuanping Zhang, Yanfang Guan, Yongsheng Chen, Xiao Xiao, Jiayin Wang. FCRF: An efficient algorithm for detecting circular fusion transcript from RNA-Seq data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-212.
Abstract LB-233: Analysis of personalised circulating tumour DNA to monitor recurrence and metastasis in multiple cancer types
Authors: Wang Guan , Wei Jinwang , Wu Angela , Dai Chun , Sun Wending , Cai Xin , Xu Qiang
Published: August 2019

Purpose: The evaluation of circulating tumour DNA (ctDNA) is a promising tool to monitor tumour progression and guide personalised treatments. We evaluated ctDNA in plasma samples from 521 Chinese patients with more than 12 tumour types and explored ctDNA’s ability to predict tumour status, especially recurrence and metastasis.

Methods: We established a personalised ctDNA panel sequencing, which targeted trunk clonal somatic mutations of each patient calculated by CSMT-tools (monitors tumour load tools based on paired whole exon and cell-free DNA next generation sequencing data, PCT/CN2016/106284) and drug-resistant mutations. The ctDNA content fraction of all somatic mutations was then evaluated. Furthermore, 209 patients were followed up for ctDNA detection and routine examination.

Results: Whole exome sequencing was performed on 1121 patients, and 97% of patients were successfully designed personalised ctDNA assays using CSMT-tools. Currently, 521 Chinese patients mainly with colorectal, liver, lung, gastric cancer, glioma or cholangiocarcinoma received at least one ctDNA detection. 66.79%, 50.86%, 42.99%, and 25.72% of these patients had detectable ctDNA with ctDNA content fractions above 0.25%, 0.5%, 1%, and 5%, respectively. At ctDNA content fraction above 0.25%, the detection rate of ctDNA in major cancer types, excluding liver, pancreatic cancer and glioma, was higher than 70%. In glioma, the rate of ctDNA detection in blood was much lower than in cerebrospinal fluid (24.29% vs 80%). Moreover, dynamic changes of ctDNA were significantly correlated with clinical outcomes for patients, with a consistency rate of 89.51%. The consistency rate of most major cancer types was above 90%, but that of glioma (71.43%) and pancreatic cancer (60%) were lower. ctDNA content fraction increased in all patients with recurrence and metastasis, from 2.72 to 59.8 fold. We also detected a drug-resistance process in a lung cancer patient with EGFR_p.E746_A750del. EGFR_p.T790M was first detected after the patient was administered gefitinib for more than a year, 3 months earlier than radiologic progression. Conclusions: Our personalised ctDNA analysis can effectively detect ctDNA. Hence, it can predict tumour progression and guide precise treatment.

Citation Format: Guan Wang, Jinwang Wei, Angela Wu, Chun Dai, Wending Sun, Xin Cai, Qiang Xu. Analysis of personalised circulating tumour DNA to monitor recurrence and metastasis in multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-233.
Abstract LB-248: A novel multiplex assay for detection and quantitation of fatty acid synthase (FASN) in serum or plasma samples
Authors: Venkateswaran Neeraja , Nelson William M.
Published: August 2019

Many cancers overexpress FASN which catalyzes the final synthetic step of de novo fatty acid synthesis pathway. FASN has been considered as a potential drug target for several decades now. Many publications provide evidence of the elevated FASN with aggressive tumors, but still, there are very few inhibitors of FASN that have successfully been utilized as therapeutics in the clinical arena. An accurate measurement of FASN in association with tumor-specific markers in solid tumors and serum may help to propel forward the therapeutic significance of FASN inhibitors. With this objective in mind, we are currently working on the development of a multiplex assay for detection and quantitation of FASN and Cripto-1 in serum samples. We have optimized a magnetic fluorescent bead based multiplex sandwich immunoassay for detection and quantitation of FASN and Cripto-1 (CR-1) in human serum and plasma samples. We selected Cripto-1 to pair with FASN because it is an EGF-like domain carrying growth factor associated with a number of different types of human carcinomas. We use two different monoclonal antibodies for FASN and one for CR-1 as capture antibodies covalently coupled to magnetic fluorescent beads and a mixture of two biotin-labeled detection antibodies in this assay. The streptavidin-phycoerythrin (SAPE) conjugate is used to report the positive capture of a target in this assay. We have also included various internal controls in this assay to monitor the assay performance and assure quality of the reagents used in each well. The dynamic range of this assay was determined to be 100pg/mL to 100 ng/mL using recombinant FASN and Cripto-1 from commercial sources. The R2 values were 0.98 and above for each of the analytes and recovery of each standard were between 90 % and 125%. We spiked recombinant FASN and Cripto-1 in normal human serum and plasma at different concentrations and spike recovery was between 70 % and 130 %. We further evaluated this assay with some commercially obtained clinical samples. This presentation includes detailed results of this study.

Citation Format: Neeraja Venkateswaran, William M. Nelson. A novel multiplex assay for detection and quantitation of fatty acid synthase (FASN) in serum or plasma samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-248.
Abstract LB-265: ARAF activates RAS by antagonizing its interaction with NF1
Authors: Su Wenjing , Yaeger Rona , Na Na , Hechtman Jaclyn , Paroder Viktoriya , Misale Sandra , Han Sae-Won , Abdel-Wahab Omar I. , McCormick Frank , Rosen Neal , Yao Zhan
Published: August 2019

ARAF, BRAF and CRAF protein kinases are RAS effectors required for activation of ERK signaling. ARAF has relatively modest kinase activity and its biological functions are largely unknown. Here, we show that ectopic expression of ARAF but not B- or CRAF, leads to induction of RAS activation in cells with WT RAS. This phenomenon requires the binding of ARAF to RAS but not its kinase activity. ARAF was found to reduce inactivation of RAS by antagonizing its binding to the major RAS-GAP NF1. By this mechanism, the abundance of ARAF in cells determines cellular RAS-GTP levels, the dynamics of RTK-induced RAS activation and the biological consequences of RAS signaling. We find that a certain expression level of ARAF is required for growth factors induced proliferating or neural differentiation in PC12 cells. In RTK-dependent tumor cells, knocking down of ARAF leads to a reduction of RAS-GTP, thus impairs RAS signaling and the tumor growth. Furthermore, by investigating the tumor samples from MSK patients who are diagnosed with progressing disease after EGFR inhibitor treatment, we find the up-regulation of ARAF (including the ARAF gene amplification) is associated with EGFR inhibitor resistance in the lung cancer patients. We confirmed in cell line and xenograft models that a 5-fold elevation of ARAF expression is sufficient to eliminate RAS inhibition by EGFR inhibition and to cause resistance. Resistance in these cells could be overcome by combining EGFR and SHP2 inhibitors. The latter prevents EGFR activation of RAS-GTP exchange and thus would be expected with weaking the effects of NF1 inhibition by ARAF. Taken together, our work shows that ARAF directly activates RAS by antagonizing its interaction with NF1 and thus affects the duration and cellular response of growth factor activation and sensitivity of tumors to pharmacological inhibition of RTK-RAS signaling.

Citation Format: Wenjing Su, Rona Yaeger, Na Na, Jaclyn Hechtman, Viktoriya Paroder, Sandra Misale, Sae-Won Han, Omar I. Abdel-Wahab, Frank McCormick, Neal Rosen, Zhan Yao. ARAF activates RAS by antagonizing its interaction with NF1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-265.
Abstract LB-273: Development of small molecule MYC inhibitors that impair tumor growth and enhance anti-PD1 immunotherapy
Authors: Han Huiying , Jain Atul , Sargar Vinay , Anker Jonathan , Mishra Rama , Schiltz Gary , Abdulkadir Sarki A.
Published: August 2019

Small molecules MYC inhibitors that are efficacious and tolerated in vivo will provide invaluable chemical probes and potential therapeutic agents. We have used in silico screening coupled to a rapid in vivo screen in mice to develop a series of novel small molecule MYC inhibitors (MYCi) which engage MYC inside cells, disrupt MYC/MAX heterodimerization and inhibit MYC-regulated gene expression. The compounds enhanced MYC phosphorylation on threonine-58, leading to increased proteasome-mediated degradation of MYC. The initial lead, MYCi361, showed excellent in vivo anti-tumor efficacy in mice, inhibiting proliferation and inducing immunogenic cell death of tumor cells. MYCi361 treatment increased tumor infiltrating lymphocytes and induced tumor PD-L1 expression. Accordingly, treatment with MYCi361 sensitized tumors to anti-PD1 immunotherapy. MYCi361 however showed a narrow therapeutic index. We therefore undertook additional medicinal chemistry optimization, which yielded the related molecule, MYCi975, which combined in vivo efficacy with remarkable tolerability. These findings support the potential of small molecule MYC inhibitors as chemical probes and possible therapeutic leads.

Citation Format: Huiying Han, Atul Jain, Vinay Sargar, Jonathan Anker, Rama Mishra, Gary Schiltz, Sarki A. Abdulkadir. Development of small molecule MYC inhibitors that impair tumor growth and enhance anti-PD1 immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-273.
Abstract LB-285: SAGA functions in development and disease
Authors: Dent Sharon Y. , Farria Aimee , Koutelou Evangelia
Published: August 2019

Our research is focused on defining the functions of histone modifying enzymes in normal cells, so that we can understand how alterations in these activities contribute to tumor development or progression. Our recent studies on the SAGA complex, which houses both histone acetyltransferase (HAT) and deubiquitylase (DUB) activities, revealed that the Gcn5 HAT, is an important co-activator for Myc in regulating self-renewal of mouse ES cells. Gcn5 is also important for Myc functions as a Yamanaka factor in stimulating conversion of differentiated cells towards an induced pluripotent state. These developmental functions predict that Gcn5 will also be important during Myc functions as an oncogene. In support of this idea, recent studies reveal that deletion of Gcn5 delays lymphoma onset and more than doubles survival of Eμ-Myc mice. The SAGA DUB module is also implicated in cancer, as the USP22 catalytic subunit is overexpressed in several highly aggressive human tumors. We have created USP22 knock out mice to probe the functions of this DUB. Our data indicate that USP22 drives TGF-beta and receptor tyrosine kinase signaling pathways that are critical both to normal developmental processes and to oncogenesis. Altogether, our studies indicate that both Gcn5 and USP22 may provide unique targets for development of new cancer therapies.

Note: This abstract was not presented at the meeting.

Citation Format: Sharon Y. Dent, Aimee Farria, Evangelia Koutelou. SAGA functions in development and disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-285.
Abstract LB-290: Telomere dysfunction is a driver of inflammatory bowel disease
Authors: Chakravarti Deepavali , Multani Asha , Dey Prasenjit , Hu Baoli , Zhao Di , Chang Kyle , Xizeng Mao , Wang Guocan , Terranova Christoper , Liao Wen-ting , Spring Denise , Hou Pingping , Zhang Jianhua , Okhuysen Pablo , Vilar Eduardo , Estes Mary K. , blutt Sarah , Wang Alan , DePinho Ronald
Published: August 2019

The molecular instigators and therapeutic strategies for inflammatory bowel disease (IBD) are limited. Here, telomere dysfunction is shown to activate pAtm/c-Abl-mediated phosphorylation and stabilization of Yap1 up-regulates pro-IL-18 expression, a major pro-inflammatory factor in IBD. This signaling axis cooperates with gut microbiome which stimulates cytosolic receptors causing activation of caspase-1, which in turn cleaves pro-IL-18 into its mature IL-18 form. Epithelial-derived IL-18 leads to recruitment of IFNγ-secreting T cells and other immunocytes to provoke classical IBD pathology. Consistent with a role for DNA damage signaling as a driver of IBD, newly diagnosed IBD patient samples exhibited elevated expression of pγH2AX, YAP1, Caspase-1 and IL-18 along with significantly reduced telomere lengths compared to healthy tissue controls. Alleviation of IBD pathology can be achieved in mice via telomerase reactivation in intestinal epithelium or pharmacological inhibition of Atm, Yap1, or caspase-1 as well as antibiotic treatment - each intervention dramatically reducing pro-IL-18 cleavage and inflammation. Thus, telomere dysfunction-induced activation of the Atm-Yap1-pro-IL-18 pathway identifies DNA damage signaling as a key instigator and promoter of IBD, illuminating several novel therapeutic strategies for disease interception and management.

Note: This abstract was not presented at the meeting.

Citation Format: Deepavali Chakravarti, Asha Multani, Prasenjit Dey, Baoli Hu, Di Zhao, Kyle Chang, Mao Xizeng, Guocan Wang, Christoper Terranova, Wen-ting Liao, Denise Spring, Pingping Hou, Jianhua Zhang, Pablo Okhuysen, Eduardo Vilar, Mary K. Estes, Sarah blutt, Alan Wang, Ronald DePinho. Telomere dysfunction is a driver of inflammatory bowel disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-290.
Abstract LB-316: Suppression of tumor angiogenesis and metastasis by targeting a novel p38-driven tumor-stromal crosstalk
Authors: Bakin Andrei V. , Zonneville Justin , Walden Rebecca , Grant Sydney , Colligan Sean , Miller Alexandra , Truskinovsky Alexander M. , Abrams Scott
Published: August 2019

Triple-negative breast cancers (TNBCs, ER/PR/HER2-negative) pose significant clinical challenges largely due to a lack of targeted therapy. Our prior work revealed a novel tumor-stromal crosstalk that increases p38 kinase signaling in the breast tumor microenvironment (TME). Here, we examined the effects of systemic blockade of p38 signaling in the relevant TNBC models. Blockade of p38 with a selective p38 inhibitor Ralimetinib reduced tumor growth and metastasis to the lungs and liver. Histology revealed that p38 blockade greatly reduced tumor angiogenesis. Within the TME, we found a massive infiltration of myeloid cells i.e. polymorphonuclear (PMN) myeloid-derived suppressor-like cells (MDSC-like) to the lungs and liver of tumor-bearing (TB) mice. Further, TB-mice showed a significant rise in the numbers of granulocytes and monocytes in the circulation, and the accumulation of CD163+ macrophages in the TME. Blockade of p38 greatly reduced these responses. In contrast, p38 blockade increased abundance of cytotoxic CD8+ T-cells in the TME. Addressing the mechanism, we found that inactivation of p38 in tumor cells was sufficient to reduce the influx of macrophages to the tumor, suggesting a tumor-driven mechanism of mobilization or expansion of myeloid cell populations. Further, depletion of PMN-MDSC-like cells and neutrophils using anti-Ly6G antibody reduced metastases to the lungs and liver. Assessing the prognostic value of our results, we found an inverse correlation of CD163 levels with metastasis-free survival in patients with breast cancer. Together, these results demonstrate that p38 kinase promotes breast cancer growth and colonization to distant organs by regulating mobilization of pro-tumor myeloid cells. This p38-driven mechanism highlights a novel target for treatment of patients with TNBC or advanced disease.

Citation Format: Andrei V. Bakin, Justin Zonneville, Rebecca Walden, Sydney Grant, Sean Colligan, Alexandra Miller, Alexander M. Truskinovsky, Scott Abrams. Suppression of tumor angiogenesis and metastasis by targeting a novel p38-driven tumor-stromal crosstalk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-316.
Abstract LB-323: Atrx deletion delays tumor formation and increases radiosensitivity of a primary mouse model of soft tissue sarcoma
Authors: Floyd Robert W. , Luo Lixia , Kirsch David
Published: August 2019

Soft tissue sarcomas are tumors of the connective tissue that account for an estimated 12,000 new cancer cases annually and carry a poor prognosis with a five year survival rate of 50% despite treatment. An important research objective in improving therapy for soft tissue sarcoma patients is to understand how genetic mutations affect soft tissue sarcoma development and radiation response. Intriguingly, next-generation sequencing data from The Cancer Genome Atlas and other massive cancer sequencing efforts have identified Alpha Thalassemia and Mental Retardation X-linked, or ATRX, as the second most frequently mutated gene in soft tissue sarcoma. The vast majority of these ATRX mutations are frameshift mutations. To dissect the role of ATRX in soft tissue sarcoma development and therapeutic response, we generated a primary mouse model of soft tissue sarcoma. This model utilizes Cre-LoxP technology to conditionally activate oncogenic KrasG12D, delete p53, and delete both alleles of Atrx (KPA) in mouse hindlimb Pax7+ muscle satellite cells. When compared to mice with activation of oncogenic KrasG12D, deletion of p53 and at least one wild-type Atrx allele (KP), KPA mice showed a significant delay in time to tumor formation (35 vs. 58 days median), but no significant difference in tumor growth rate as measured by time to tumor quintupling. Next, we generated primary soft tissue sarcoma cell lines from our KP mouse model, and performed CRISPR-Cas9 mediated knockout of Atrx to generate isogenic cell lines. Testing of these isogenic cell lines revealed that Atrx deletion in soft tissue sarcoma cells increased sensitivity to double strand break inducing chemotherapeutics and ionizing radiation, but not to single strand break inducing chemotherapeutics in vitro. In clonogenic assays, Atrx deletion increased radiosensitivity of soft tissue sarcoma cell lines more than fourfold across all radiation doses tested. We next used our KP and KPA models to test the effect of Atrx deletion on radiosensitivity in vivo. Results showed that, relative to the KP model, Atrx deletion improved the response of soft tissue sarcomas to radiation therapy in vivo, increasing the time to tumor quintupling after radiation by 20%. Further analysis demonstrated that Atrx deletion significantly increases mitotic segregation defects after ionizing radiation, suggesting a potential mechanism for the radiosensitivity observed in our studies. Our in vivo study provides the first insight into how ATRX alters the development and therapeutic response of soft tissue sarcoma.

Citation Format: Robert W. Floyd, Lixia Luo, David Kirsch. Atrx deletion delays tumor formation and increases radiosensitivity of a primary mouse model of soft tissue sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-323.
Abstract LB-325: Developmental hierarchy in Langerhans cell histiocytosis
Authors: Halbritter Florian , Farlik Matthias , Bock Christoph , Hutter Caroline
Published: August 2019

Langerhans Cell Histiocytosis (LCH) is a neoplastic disease characterized by the accumulation of CD1a+CD207+ cells of unknown origin. Constitutive activation of the ERK signaling pathway is a common feature of LCH, but the pathogenesis of this disease remains unclear. Here we present a comprehensive analysis of the composition of LCH lesions that provides new insight into the development and molecular mechanisms of this disease.

We used a multilayered approach employing immunohistochemistry, flow cytometry, single- cell RNA-sequencing, and ATAC- sequencing of LCH biopsies obtained from different patients. Based on the single- cell RNA expression data, we identified different LCH cell populations within LCH lesions that display distinct pathway signatures, including a stem-cell-like, proliferative state. Computational analysis discovered a hierarchy between these cells that suggest a directed developmental program in each tumor. Finally, functional chromatin mapping inferred distinct regulatory signatures discriminating the different cell states.

Taken together, our study shows at single-cell resolution that there is considerable intra-tumoral heterogeneity in LCH and provides detailed insight into the molecular framework underlying tumor development. Our transcriptomic and epigenomic analyses have generated a reference map of subpopulations of LCH cells with distinct functional and phenotypic properties. We propose that the lesions are comprised of different LCH cell subsets that arise in an intrinsic developmental process. This work can serve as a template for the analysis of tumorigenesis beyond LCH.

Citation Format: Florian Halbritter, Matthias Farlik, Christoph Bock, Caroline Hutter. Developmental hierarchy in Langerhans cell histiocytosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-325.