bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1502: Cell state mapping reveals a role for a stress program in melanoma
Authors: Baron Maayan , Tagore Mohita , Hunter Miranda , Kim Isabella S. , Moncada Reuben , Yan Yun , Campbell Nathaniel R. , White Richard M. , Yanai Itai 
Published: September 2020

Abstract
Transcriptional profiling has revealed a diverse range of cell states in cancer, but the function of these various states remains elusive. Using a combination of zebrafish melanoma modeling and human validation, we have identified a conserved stress-like state that confers intrinsic drug resistance and is associated with poor patient survival. Single cell sequencing of a series of transgenic zebrafish melanoma tumors revealed 3 distinct cell states that correspond to a neural crest, melanocyte or stress-like state. The existence of these 3 states was confirmed using spatial transcriptomics, a method that does not require tissue dissociation or cell sorting. The stress-like state expresses genes such as fos, hsp70 and ubb, proteins which are all required for adaptation to diverse cellular stresses. A transgenic reporter of the stress like state demonstrates that it has higher tumor seeding capabilities compared to non-stressed cells, and confers intrinsic resistance to MEK inhibitors, a commonly used melanoma therapeutic. The stress program can be induced by extrinsic processes such as heat shock, and confers resistance to MEK inhibitors in both zebrafish and human melanomas. Our study identifies a population of stress-like cells that are present from the time of tumor initiation, suggesting that the transcriptional seeds of therapeutic failure are established during the earliest steps of tumorigenesis.
Citation Format: Maayan Baron, Mohita Tagore, Miranda Hunter, Isabella S. Kim, Reuben Moncada, Yun Yan, Nathaniel R. Campbell, Richard M. White, Itai Yanai. Cell state mapping reveals a role for a stress program in melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1502.
Abstract 1510: Immune regulators identified in undifferentiated pleomorphic sarcoma (UPS) subpopulations
Authors: Haddox Candace Lynn , Bao Junjie , Barrientos Tomasa , Alman Benjamin A. 
Published: September 2020

Abstract
Introduction: UPS is a common subtype of soft tissue sarcoma with limited effective systemic therapies. We previously showed that a murine model of UPS has various subpopulations (SPs), characterized by distinct morphology, molecular changes, and oncogenic behaviors that likely contribute to the overall behavior of UPS. Here, we aimed to characterize interactions between UPS SPs to identify pathways important in UPS progression.
Methods: We used a murine model of UPS that recapitulates the human disease. Cre recombinase drives oncogenic KRAS-G12D, P53 deletion, and expression of confetti fluorescent protein to allow for in vivo lineage tracing. Individual SPs were isolated via FACS and cultured in the presence of conditioned media (CM) from other individual SPs. Growth rate was assayed using the IncuCyte system (Essen BioScience), and cell proliferation was measured using the Click-iT EdU flow cytometry assay kit. Invasion and migration were assayed using a cell culture insert with or without Matrigel, with CM or non-CM in the lower chamber. Cells migrating/invading into the lower chamber were counted. We performed proteomics analysis on the CM from the SP that potentiated growth and invasion to define the secretome of this SP. The CCL2/CCL7/CCL8 inhibitor, bindarit, was added to CM and cell confluency was assessed as above. RNAseq data from The Cancer Genome Atlas (TCGA) were used to generate immune infiltration scores in human UPS samples. These scores were correlated with expression of lead candidates from our secretome analysis.
Results: CM from one UPS SP (SP-1) increased the growth rate and invasion/migration of one other SP (SP-2). Proteomics analysis identified 233 secreted proteins in the CM from SP-1, including 37 with two-fold higher abundance compared to SP-2. Among these, several immunoregulatory proteins were identified, including serpine 1, CCL2, CCL7, CXCL1, and CX3CL1. Culture with bindarit abolished the effect of SP-1 CM on growth rate. Additionally, we found several semaphorins in the secretomes of SP-1 and SP-2, and emerging evidence suggests a key role for semaphorins in cancer progression and immune regulation. Semaphorin expression correlated with immune infiltration scores in human UPS samples.
Conclusions: We identified a UPS SP that positively regulates oncogenic behaviors of other SPs through secreted factors. Additionally, several of these secreted proteins play key roles in immune regulation. Given promising activity of immunotherapy in UPS, these proteins warrant further investigation.
Citation Format: Candace Lynn Haddox, Junjie Bao, Tomasa Barrientos, Benjamin A. Alman. Immune regulators identified in undifferentiated pleomorphic sarcoma (UPS) subpopulations [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1510.
Abstract 1535: Identification of novel epithelial-mesenchymal transition inducers and their clinical significance in colorectal cancer
Authors: Ishikawa Satoshi , Nishida Naohiro , Fujino Shiki , Ogino Takayuki , Takahashi Hidekazu , Miyoshi Norikatsu , Uemura Mamoru , Matsuda Chu , Mizusima Tsunekazu , Yamamoto Hirofumi , Mimori Koshi , Mori Masaki , Doki Yuichiro , Eguchi Hidedoshi 
Published: September 2020

Abstract
Purpose. Cancer tissues contain a substantial amount of stromal tissues, and transcriptome derived from bulk samples originates from a mixture of the cancer epithelium and stroma. Gene signature of epithelial-mesenchymal transition (EMT) cells is similar to that of stromal cells; therefore, gene signature that we considered to be related EMT might be only contamination of stroma. Here, we identify novel EMT inducers by analysis of independent gene expression profiles in the colorectal cancer epithelium and stroma.
Materials and Methods. Gene expression data of pure epithelial tissue was obtained using laser microdissection technique from 13 colorectal cancer tissues. Next, the ratio of each gene expression in the stroma to in the epithelium and correlation of each gene expression with a target gene derived from The Cancer Genome Atlas (TCGA) is plotted in two dimensions, and correlation coefficients are calculated. We regard genes with high correlation coefficients but highly expressed in the epithelium as candidates of EMT inducers. We manipulate the expression of some candidate genes in colorectal cancer cell lines to investigate the alterations of EMT markers and migration ability in vitro.
Results. We extract 91 new putative EMT-related genes in silico. They are highly expressed in similar cell lines to known EMT markers in a public database. Furthermore, some candidates have reported having a relation to EMT, and that indicates the validity of this procedure. The knockdown of three candidate genes upregulates epithelial gene expression and downregulates mesenchymal gene expression. The knockdown of one of the three genes reduces cell migration. In contrast, overexpression of the gene downregulates epithelial gene expression and leads to cell migration.
Conclusion. We identify novel EMT inducers successfully using purified gene expression data. They could be new prognostic markers and therapeutic targets of colorectal cancer.
Citation Format: Satoshi Ishikawa, Naohiro Nishida, Shiki Fujino, Takayuki Ogino, Hidekazu Takahashi, Norikatsu Miyoshi, Mamoru Uemura, Chu Matsuda, Tsunekazu Mizusima, Hirofumi Yamamoto, Koshi Mimori, Masaki Mori, Yuichiro Doki, Hidedoshi Eguchi. Identification of novel epithelial-mesenchymal transition inducers and their clinical significance in colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1535.
Abstract 1542: Roles of extracellular ATP in inducing EMT and CSC-like changes to promote early steps of metastasis in non-small lung cancer cell lines
Authors: Song Jingwen , Evers Maria , Chen Xiaozhuo 
Published: September 2020

Abstract
Cancer is a major death-causing disease worldwide, and metastasis, a hallmark of cancer, is associated with up to 90% of all cancer-related deaths. Metastasis requires ATP, and the tumor microenvironment (TME) has much higher concentrations of intratumoral and extracellular ATP (eATP) than healthy tissue, implying that eATP may have potential roles in tumor development and progression. Our previous ATP studies, cited by a Nature Review Cancer paper in 20181 showed that eATP is internalized by cancer cell through macropinocytosis, and it promotes cancer cell growth, survival, and drug resistance. However, how intratumoral eATP plays roles in metastasis remains largely unclear. Our 2019 published results show that eATP promotes cancer migration and invasion, initiates epithelial to mesenchymal transition (EMT), alters expression level of EMT related protein markers such as ZEB1, SNAIL, SLUG in human non-small lung cancer cell (NSCLC) lines2. It has been reported that the EMT and cancer stem cells (CSCs) share some molecular links, but the detailed mechanisms involved are still unknown. Recently, we have found the eATP significantly induces the gene expression level of CSC transcription factors (TFs): SOX2, NANOG and OCT4 in A549 cells in a time-dependent manner. We have also found that, after A549 cells were pretreated with 0.5mM for 6 hrs, the ATP-pretreated A549 cells were able to show significantly increased migration and invasion even in the absence of ATP addition. Based on all these results, we hypothesize that extracellular ATP functions as a messenger, a signal facilitator, an energy molecule, and a transcription cofactor to induce EMT and CSC-like features to promote metastasis in NSCLC. RNAseq and metabolomics studies are being used to determine the transcriptional and metabolic changes associated with the ATP induced EMT and CSC process in NSCLC. The completion of the project will not only unravel eATP's roles in EMT and CSC induction and early steps of tumor metastasis, but also potentially provide novel promising therapeutic targets for inhibiting tumor metastasis.
Citation Format: Jingwen Song, Maria Evers, Xiaozhuo Chen. Roles of extracellular ATP in inducing EMT and CSC-like changes to promote early steps of metastasis in non-small lung cancer cell lines [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1542.
Abstract 1543: Development of a novel ECAD-EmGFP reporter line for pancreatic cancer MET study and drug discovery
Authors: Douglas Diana , Kumari Sangeeta , Huuskonen Jarkko , Shu Weiguo 
Published: September 2020

Abstract
World-wide, metastasis continues to be the leading cause of death in cancer patients1. Although epithelial-to-mesenchymal transition (EMT) and mesenchymal-to-epithelial transition (MET) have been implicated in the progression of cancer metastasis and drug resistance, their mechanistic pathway and specific role in disease progression is not fully understood2. As such, the development of a reporter line that enables the real-time monitoring of the changing status of cells will not only aid in dissecting the EMT/MET pathway in the research field, but could also become a robust platform for new cancer drug development.
E-cadherin, an adhesion protein expressed in epithelial cells, is upregulated in pancreatic cancer cells during MET and is associated with an increase in tight junctions and apico-basal polarity, as well as a change in morphology3,4. Here, we developed a novel PANC-1 ECAD-EmGFP reporter line using CRISPR/Cas9 genome-editing technology. In this cell line, the emerald green fluorescent protein (EmGFP) reporter was incorporated into the last exon of the endogenous E-cadherin gene, enabling real-time monitoring of MET status in live cells. The ECAD-EmGFP knock-in allele was confirmed at genomic, transcriptional, and translational levels. Functional data revealed that miRNA-200 treatment induced the increased expression of ECAD-EmGFP, and decreased expression of Snail, a transcription factor associated with mesenchymal traits. These changes in marker gene expression, as well as the decrease in invasive capacity upon induction, suggest that cells have undergone MET. This cell line is a valuable tool for dissecting the molecular mechanisms underlying EMT and MET and for evaluating or screening compounds targeting EMT and MET in pancreatic cancer.
1. Dizon DS, et al. Clinical Cancer Advances 2016: Annual Report on Progress Against Cancer from the American Society of Clinical Oncology. J Clin Oncol 34: 987-1011, 2016. 2. Nieto MA, et al. EMT: 2016. Cell 166: 21-45, 2016. 3. Polireddy K, et al, Targeting Epithelial-Mesenchymal Transition for Identification of Inhibitors for Pancreatic Cancer Cell Invasion and Tumor Spheres Formation. PLOS ONE 11(10): e0164811, 2016 4. Wong S, et al. E-cadherin: Its dysregulation in carcinogenesis and clinical implications. Critical Reviews in Oncology / Hematology 121: 11- 22, 2018
Citation Format: Diana Douglas, Sangeeta Kumari, Jarkko Huuskonen, Weiguo Shu. Development of a novel ECAD-EmGFP reporter line for pancreatic cancer MET study and drug discovery [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1543.
Abstract 1598: Reprogramming of immunosuppressive tumor microenvironments by multifunctional nanoemulsion and enhance immune checkpoint blockade therapy
Authors: Jin Seung Mo , Lee Sang Nam , Lim Yong Taik 
Published: September 2020

Abstract
The low response rate of current cancer immunotherapy suggests the presence of few antigen-specific T cells and a high number of immunosuppressive factors in tumor microenvironment (TME). Toll-like receptor (TLR) 7/8 agonist-based adjuvants have been widely used to activate antigen-presenting cells (APCs) and induce antigen-specific therapeutic T cells. However, the incorporation of TLR 7/8 agonists also induces immunosuppressive factors, such as Indoleamine 2,3-dioxygenase (IDO) in APCs and tumor cells, which results in the formation of immunosuppressive TME. In this research, we report the assemblable immune-modulating suspension (AIMS) consisting of TLR 7/8 agonist and IDO inhibitor, which was designed to down-regulate the immune-suppressive factors (TGF-β, IL-10, myeloid-derived suppressor cells, regulatory T cells) and to increase the infiltration of cytotoxic T lymphocytes. The best combination of immune-modulating agents in AIMS, we called supra-adjuvant, was selected by screening possible combinations of commercialized TLR 7/8 agonists and IDO inhibitors based on the ratio of pro- and anti-inflammatory cytokines. Paclitaxel was also introduced into AIMS to induce immunogenic cell death (ICD) and in situ vaccination efficacy with TLR 7/8 agonist at the tumor bed. Local administration of AIMS increased infiltrated T cells in both local and distant tumors, and inhibited the metastasis of tumors to lung significantly. AIMS also reshaped the TME from ‘cold tumor' to ‘hot tumor' successfully, and increased the responsive rate of immune checkpoint blockade therapy (ICBT) significantly. Taken together, the AIMS composed of supra-adjuvant and ICD-inducer is expected to be used as a platform for the re-programming of immunosuppressive TME and the induction of synergistic cancer immunotherapy with ICBT.
Citation Format: Seung Mo Jin, Sang Nam Lee, Yong Taik Lim. Reprogramming of immunosuppressive tumor microenvironments by multifunctional nanoemulsion and enhance immune checkpoint blockade therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1598.
Abstract 1620: MDM2 P1 and P2 promoters have different roles in tumorigenesis
Authors: Phinichkusolchit Narisa , Jamieson Thomas , Ridgway Rachel , Athineos Dimitris , Crawford Kerryanne , Vlatkovic Nikolina , Boyd Mark , Sansom Owen , Blyth Karen 
Published: September 2020

Abstract
The murine double minute 2 (MDM2) protein is an E3 ubiquitin ligase most notable for priming tumour-suppressor p53 for degradation. MDM2 contains two promoters - the constitutive P1 and the inducible P2. The p53-independent P1 promoter is responsible for basal levels of MDM2, whilst the p53-dependent P2 promoter is activated upon stress responses. Although the oncogenic functions of MDM2 are well understood, less is known about the individual roles of the promoters and their contribution to tumorigenesis and stress responses. To tease apart the roles of the promoters, we have used genetically engineered mouse (GEM) models null for the P1-promoter and mutated for the P2-promoter in the context of intestinal cancer, lymphoma and hepatocellular carcinoma (HCC). Here, we have shown that mice with heterozygous or homozygous loss of the P1-promoter in the APCMin/+ intestinal model have extended survival and reduced intestinal tumour burden in comparison to the P1- wild type (WT), APCMin/+ mice. Surprisingly, none of the P1-null APCMin/+ mice succumbed to intestinal tumours, but rather to thymic lymphomas. In the P1-null APCMin/+ lymphoma samples, we investigated the p53 functionality by examining the expression levels of p21, a p53 downstream target. Immunohistochemistry analysis clearly revealed that p53 is non-functional as p21 was not expressed, despite variations in p53 expression levels itself. This uncommon occurrence in the APCMin/+ model led us to investigate the role of the P1 and P2 promoters in the Eµ-Myc lymphoma model. Interestingly, in this model, heterozygous loss of the P1 promoter improves survival, while heterozygous loss of the P2 promoter accelerates lymphomagenesis. Our findings thus far indicate a differential role for the P1 and P2 MDM2 promoters in tumorigenesis. In addition to using GEM models, we are investigating the role of the MDM2 promoters in stress-induced HCC. These studies will allow for a better understanding of MDM2 functions, but also perhaps provide an alternative therapeutic strategy for cancers with aberrations in the p53-MDM2 signalling axis.
Citation Format: Narisa Phinichkusolchit, Thomas Jamieson, Rachel Ridgway, Dimitris Athineos, Kerryanne Crawford, Nikolina Vlatkovic, Mark Boyd, Owen Sansom, Karen Blyth. MDM2 P1 and P2 promoters have different roles in tumorigenesis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1620.
Abstract 1658: Anti-CEACAM binding protein for fluorescence visualization of primary colon cancer in patient-derived orthotopic xenograph mouse models
Authors: Hollandsworth Hannah M. , Amirfakhri Siamak , Filemoni Filemoni , Schmitt Verena , Wennemuth Gunther , Schmidt Alexej , Hoffman Robert M. , Singer Bernhard B. , Bouvet Michael 
Published: September 2020

Abstract
Background The Helicobacter outer protein (HopQ) is a novel surface-located Helicobacter pylori adhesion protein that binds to various human carcinoembryonic antigen-related cell adhesion molecules (CEACAM1, 3, 5, 6). Our aim was to validate fluorescence targeting of colorectal tumors in patient derived orthotopic xenograft models with fluorescently labeled HopQ.
Materials/Methods CEACAM binding protein HopQ was conjugated to near-infrared dye IR800CW (LI-COR). Western blotting was performed with various colon cancer cell lysates to determine CEACAM expression. Nude mice (n=4) received orthotopic implantation of patient-derived primary colon tumors and patient-derived colon cancer metastases. Mice were administered either 25 ug or 50 ug of HopQ-IR800CW via tail vein injection and imaged 48 hours later. Intravital images were analyzed using the Image Studio Software Small Animal Imaging Analysis to determine tumor-to-background ratio (TBR).
Results Western blotting demonstrated varied expression of CEACAM binding in all 15 patient derived colon cancer lysates. Dose response intravital imaging demonstrated TBR of 1.41 when administered 25 ug of HopQ-IR800CW and TBR 3.78 when administered 50 ug of HopQ-IR800CW.
Conclusion CEACAM binding protein HopQ shows promising use for fluorescence imaging of patient derived orthotopic colon cancer. HopQ may be useful for tumor detection for pre-surgical diagnosis and fluorescence-guided surgery.
Citation Format: Hannah M. Hollandsworth, Siamak Amirfakhri, Filemoni Filemoni, Verena Schmitt, Gunther Wennemuth, Alexej Schmidt, Robert M. Hoffman, Bernhard B. Singer, Michael Bouvet. Anti-CEACAM binding protein for fluorescence visualization of primary colon cancer in patient-derived orthotopic xenograph mouse models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1658.
Abstract 166: Absolute quantification of DNA methylation markers using methylation-sensitive restriction enzymes and multiplex digital PCR
Authors: Nell Rogier J. , Van der Velden Pieter A. 
Published: September 2020

Abstract
Aberrant DNA methylation plays important roles in the initiation and progression of cancer. Therefore, DNA methylation markers have important diagnostic and prognostic potential. However, accurate quantification of these markers remains challenging in clinical samples of limited quality or quantity. We introduce a novel, digital approach for the absolute quantification of the amount, density and allele-specificity of DNA methylation.
We designed an experimental setup combining efficient methylation-sensitive restriction enzymes with quantitative digital PCR. This allowed to measure a targeted density of DNA methylation independent of bisulphite conversion. In-silico simulations were performed to demonstrate the mathematical validity of the setup. A practical validation was carried out by quantifying RASSF1A promotor methylation in a variety of healthy and malignant reference samples and in an innovative calibration curve.
Furthermore, we extended our setup to a multiplex digital PCR experiment. Hereby, methylation markers may be analyzed together with physically linked genetic markers to determine the allele-specificity of the methylation.
Overall, our results show an accurate quantification of DNA methylation markers with digital PCR, independent of bisulphite conversion. Effective measurements with high precision could be obtained, even in minute amounts of DNA. Moreover, as the context-density and allele-specificity of methylation can also be determined, mechanisms in cancer biology can now be quantitatively assessed in a digital experiment.
Citation Format: Rogier J. Nell, Pieter A. Van der Velden. Absolute quantification of DNA methylation markers using methylation-sensitive restriction enzymes and multiplex digital PCR [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 166.