bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2501: Delineating mutational lineages with single cell DNA sequencing using multi-patient specific panels
Authors: Leighton Jake , Hu Min , Davis Alexander , Sei Emi , Wang Yong , Navin Nicholas 
Published: September 2020

Abstract
Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with high rates of metastasis. Although copy number aberrations (CNAs) and genome doubling have been extensively studied in relation to TNBC initiation, little is known regarding the timing and impact of point mutations during tumor initiation, outside of TP53. A major challenge in sequencing mutations in single cells is the significant cost of unbiased whole-exome analysis of many cells. To address this challenge, we developed an approach called multi-patient-panel (MPP) sequencing which involves first performing bulk deep-exome sequencing of many patient's tumors, after which hundreds of mutations are identified and pooled across patients to design a targeted panel for high-throughput single cell DNA sequencing. We applied MPP sequencing to profile 330 mutations across 23,000 single cells from 5 TNBC patients using a microdroplet system (Mission Bio). From this data we identified 1-4 major clonal subpopulations in each tumor which shared a common evolutionary lineage. Copy number data was inferred from the targeted panel coverage depth, which showed that CNAs were correlated with different subpopulations in the tumor. By integrating both the mutation and copy number data, we inferred phylogenetic lineages and identified the timing of mutations during primary tumor growth, which detected early truncal mutations (in addition to TP53) that were involved in the initiation of TNBC tumors. The MPP approach provides a powerful method to scale-up single cell DNA sequencing to tens of thousands of cells to detect mutations and infer cancer lineages and clonal substructure.
Citation Format: Jake Leighton, Min Hu, Alexander Davis, Emi Sei, Yong Wang, Nicholas Navin. Delineating mutational lineages with single cell DNA sequencing using multi-patient specific panels [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 2501.
Abstract 2506: Simultaneous DNA, RNA and protein analysis from single cells using a high-throughput microfluidic workflow for resolution of genotype-to-phenotype modalities
Authors: Mendez Pedro , Dhingra Dalia , Ooi Aik , Wang Shu , Gulati Saurabh , Beard Nigel , Manivannan Manimozhi , Björkman Jens , Kubista Mikael , Landberg Göran , Ruff David , Ståhlberg Anders 
Published: September 2020

Abstract
The TCGA, ICGC and other research consortiums has shown that an integral, multi-omic analysis of tumors is necessary in order to understand a more complete picture of the signaling pathways involved in development, evolution, prognosis and treatment resistance of tumors. However, in such studies, because different data modalities (“omics”) are analyzed separately, the information on how the co-existence of in the same cell is lacking. We report a new approach to measure multiple modalities simultaneously from up to 10,000 individual cells using high-throughput droplet microfluidics on the Tapestri platform, paired with next generation sequencing. Our triomic methodology evaluates targeted protein levels, mRNA transcript levels and somatic gDNA sequence variations (SNV & CNV) from the same cell. We employ oligonucleotide-conjugated antibody panels to probe cellular surface markers and targeted RNA and DNA amplification to resolve gene expression levels and genomic variants. Cell suspensions are first stained with cocktails of oligonucleotide-antibodies. These cells are loaded onto the Mission Bio Tapestri® microfluidic cartridge for generation of the first droplet. This droplet biochemistry allows for concurrent cell lysis and release of gDNA from chromatin scaffolding. A second droplet formation event brings together a barcoded bead and multiplex PCR amplification reagents. After amplification, the combined libraries are sequenced and demultiplexed bioinformatically yielding a multi-omics readout from the single-cells. Six protein surface markers, 35 transcripts and 88 genomic regions in 68 genes were interrogated with a 50:50 cell mixture of MCF7 and GM12878 cells. These targets play key roles in cellular migration, stemness, differentiation and proliferation. We intend to further explore the relationship between genotype-to-phenotype in breast carcinoma cell lines cultured in patient-derived scaffolds mimicking tumor microenvironments under different drug regimen conditions. We report the dynamic multimodal resolution and demonstrate utility of triomics in further illuminating cellular states and biological responses.
Citation Format: Pedro Mendez, Dalia Dhingra, Aik Ooi, Shu Wang, Saurabh Gulati, Nigel Beard, Manimozhi Manivannan, Jens Björkman, Mikael Kubista, Göran Landberg, David Ruff, Anders Ståhlberg. Simultaneous DNA, RNA and protein analysis from single cells using a high-throughput microfluidic workflow for resolution of genotype-to-phenotype modalities [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 2506.
Abstract 2517: Ectopic expression of miR-142-3p suppresses growth, migration, colony formation and induces apoptosis by down-regulating HMGA1, HMGA2, HMGB1 and HMGB3 in human cervical cancer cells
Authors: Sharma Priyanshu , Yadav Poonam , Karunagaran Devarajan 
Published: September 2020

Abstract
High Mobility Group (HMG) proteins are non-histone chromosomal proteins having molecular weight less than 30 kDa. Canonical HMG family of proteins include HMGA (A1 and A2), HMGB (B1, B2, B3, and B4) and HMGN (N1, N2, N3, N4 and N5). Overexpression of HMG proteins contributing to their oncogenic properties has been reported and thus inhibition of their expression is potentially a promising therapeutic strategy in different cancers. Earlier, our laboratory demonstrated that miR-214 downregulates HMGA1 and miR-34a downregulates HMGB1 leading to the suppression of growth, proliferative and invasive properties of human cervical and colorectal cancer cells. Prompted by these results, we tried to find a single miRNA which can target multiple HMG genes. To this end, TargetScan, miRWalk, and miRDB were used to find out miRNAs targeting more than one HMG gene. We found that miR-142-3p has its seed region binding sites in the 3'UTRs of HMGA1, HMGA2, HMGB1, and HMGB3. Survival analysis with OncoLnc server revealed that low miR-142-3p expression found in cervical cancer patients correlates with their poor survival. Strengthened by this classical miRNA-target inverse relationship, we hypothesized that miRNA-142-3p may act as a tumor suppressor by targeting multiple HMG genes in cervical cancer.
Doxycycline-responsive miR-142-3p expression constructs were used to generate stable cell lines and functional assays were performed. Through dual-luciferase reporter assays, we demonstrate that all the four HMG genes are direct targets of miR-142-3p in four cervical cancer cell lines (HeLa, SiHa, C33A, and CaSki). We observed the downregulation of the HMG genes (through qRT-PCR) upon miR-142-3p overexpression in the stable cell lines. Also, a significant reduction in cell viability after 72 and 96 hours concurrent with the highest expression levels of miR-142-3p. In colony formation assay, colony-forming potential of the cell lines was found to be severely compromised upon miR-142-3p overexpression. The scratch assay was also performed and a slower rate of migration was observed in miR-142-3p overexpressing cells. Annexin V staining indicated that miR-142-3p induces cell death via apoptosis. These results suggest that miR-142-3p may act as a tumor suppressor in cervical cancer highlighting it as a potential candidate for miRNA replacement therapy.
Citation Format: Priyanshu Sharma, Poonam Yadav, Devarajan Karunagaran. Ectopic expression of miR-142-3p suppresses growth, migration, colony formation and induces apoptosis by down-regulating HMGA1, HMGA2, HMGB1 and HMGB3 in human cervical cancer cells [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 2517.
Abstract 2557: 15-lipoxygenase-1 suppresses linoleic acid promotion of colorectal tumorigenesis through oxidative metabolism of PI3P_linoleic acid to inhibit membranous LRP5 recycling and WNT/β-catenin signaling activation
Authors: Liu Fuyao , Zuo Xiangsheng , Liu Yi , Deguchi Yasunori , Moussalli Micheline J. , Chen Weidong , Yang Peiying , Wei Bo , Tan Lin , Lorenzi Philip L. , Gao Shen , Jaoude Jonathan C. , Mehdizadeh Amir , Valentin Lovie A. , Wei Daoyan , Shureiqi Imad 
Published: September 2020

Abstract
Western-type diets have been increasingly enriched with linoleic acid (LA). The impact of excess dietary LA on cancer risk remains poorly understood although some studies suggest that high LA diets promote chemically-induced colorectal carcinogenesis (CRC) in rodent models. 15-lipoxygenase-1 (15-LOX-1), the main metabolizing enzyme of LA, is transcriptionally silenced during the early stages of CRC. Whether 15-LOX-1 impacts the effects of excess LA on CRC is unknown. Herein, we report that high dietary LA promoted CRC in intestinally targeted APC mutation (ApcΔ580) and azoxymethane-induced CRC mouse models by upregulating expression of LRP5, a Wnt receptor, and aberrant β-catenin activation. These effects were negatively regulated by 15-LOX-1 when this enzyme was transgenically expressed in intestinal epithelial cells. Complementary genetic deletion studies of 15-LOX-1 in mice further supported 15-LOX-1's suppressive effects on these events. Mechanistic studies showed that 15-LOX-1 peroxidation of LA in phosphatidylinositol-3-phosphates (PI3P_LA) into PI3P_13-HODE decreased PI3P binding to SNX17 and LRP5, which inhibited LRP5 recycling from endosomes to the plasma membrane, thereby leading to an increase of LRP5 lysosomal degradation. Our findings demonstrate for the first time the importance of linoleic acid metabolism by 15-LOX-1 within complex lipids such as PI3P in regulating LRP5 membranous abundance and subsequently Wnt/β-catenin aberrant signaling activation and CRC risk. These results strongly support the need to carefully consider the potential of increasing CRC risk by enriching the diets with LA especially for individuals with low 15-LOX-1 expression.
Citation Format: Fuyao Liu, Xiangsheng Zuo, Yi Liu, Yasunori Deguchi, Micheline J. Moussalli, Weidong Chen, Peiying Yang, Bo Wei, Lin Tan, Philip L. Lorenzi, Shen Gao, Jonathan C. Jaoude, Amir Mehdizadeh, Lovie A. Valentin, Daoyan Wei, Imad Shureiqi. 15-lipoxygenase-1 suppresses linoleic acid promotion of colorectal tumorigenesis through oxidative metabolism of PI3P_linoleic acid to inhibit membranous LRP5 recycling and WNT/β-catenin signaling activation [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 2557.
Abstract 2565: NANOG sustains ovarian cancer cell survival and disrupts ER stress signaling through BiP/PERK under glutamine depletion
Authors: Suen Astrid Man-Yee , Wong Ivy Tsz-Lo , Tse Cindy Yin-Si , Chan Ka-Kui , Wong Oscar Gee-Wan , Cheung Annie Nga-Yin 
Published: September 2020

Abstract
Metabolic reprogramming is a common hallmark of multiple cancers which functions to meet their high proliferation needs. High demand for the amino acid glutamine is frequently observed in many cancers. Catalyzed by glutaminase, glutamine is readily converted to glutamate which then further fuels the tricarboxylic acid cycle. In ovarian cancer, depletion of glutamine significantly inhibited cell growth suggesting that targeting glutamine metabolism might be an effective therapeutic strategy for ovarian cancer. However, the molecular mechanisms involved were not completely understood. In this study, we aim to identify molecular targets and the signaling involved in ovarian cancer cells under glutamine depletion. We observed that glutamine depletion stimulated the expression of the stem cell transcriptional factor NANOG in the serous ovarian cancer cell line OVCAR3. Stable knockdown of NANOG in OVCAR3 (shNANOG-OVCAR3) enhanced the level of reactive oxygen species under glutamine depletion. It was also found that under glutamine depletion, growth rate was not altered in shNANOG-OVCAR3 when compared to control shCtrl-OVCAR3 cells. However, shNANOG-OVCAR3 were more sensitive to glutamine depletion compared to shCtrl-OVCAR3 suggesting that NANOG is in part required to sustain growth of ovarian cancer cells under glutamine depletion. To further decipher the signaling involved in NANOG under glutamine depletion, expressions of markers of ER stress were detected by western blot. We found that shNANOG-OVCAR3 cells expressed lower levels of BiP, a master regulator of ER stress. Under glutamine depletion, knockdown of NANOG further enhanced the expression of phosphorylated PERK but did not alter the levels of cleaved ATF6 or phosphorylated IRE-1a, suggesting NANOG regulates ER stress pathway through BiP/PERK signaling in glutamine-depleted environment. Immunohistochemical studies were performed to determine the expressions of NANOG and BiP in our ovarian cancer patient cohort. NANOG expression was positively correlated with the expression of nuclear BiP. Total BiP expression was significantly higher in cancerous tissue than in benign and borderline ovarian tumor tissue. Altogether, these findings suggested a hitherto unreported role of the stem cell transcription factor NANOG in regulating ER stress through BiP/PERK signaling under glutamine depleted environment.
Citation Format: Astrid Man-Yee Suen, Ivy Tsz-Lo Wong, Cindy Yin-Si Tse, Ka-Kui Chan, Oscar Gee-Wan Wong, Annie Nga-Yin Cheung. NANOG sustains ovarian cancer cell survival and disrupts ER stress signaling through BiP/PERK under glutamine depletion [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 2565.
Abstract 2572: Compound C inhibits metabolic programming of ovarian cancer
Authors: Ghoneum Alia Dawlat , Gonzalez Daniela , Said Neveen 
Published: September 2020

Abstract
High grade serous ovarian carcinoma (HGSC) exhibits elevated energy demands to sustain rapid proliferation, survival and invasiveness. We have shown that Compound C, also known as Dorsomorphin, inhibits ovarian cancer growth, invasiveness and survival as well as interactions with mesothelial cells and macrophages. However, the effect of Compound C on metabolic programming has not been reported. The purpose of this study is to determine whether Compound C inhibits the malignant phenotypes of ovarian cancer through suppression of energy production. Therefore, we performed comprehensive metabolic profiling of ovarian cancer cells treated with Compound C. Our findings indicate that Compound C significantly inhibits ATP production in the ovarian cancer cell lines: OVCAR3, SKOV3 and IGROV1. Compound C inhibited basal and maximal mitochondrial respiration as well as the non-mitochondrial oxygen consumption in these three cell lines. Compound C had no effect on basal, induced or compensatory glycolysis. However, it significantly decreased the ratio of mitochondrial oxygen consumption rate to glycolytic proton efflux rate (mitoOCR/glycoPER), indicating a direct inhibitory effect of Compound C on mitochondrial electron transport chain and a bioenergetic shift from oxidative phosphorylation towards glycolysis. These results demonstrate for the first time, the direct inhibitory effect of Compound C on mitochondrial function as a novel mechanism of inhibition of the malignant phenotype of ovarian cancer cells.
Citation Format: Alia Dawlat Ghoneum, Daniela Gonzalez, Neveen Said. Compound C inhibits metabolic programming of ovarian 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 2572.
Abstract 2697: Single cell RNA sequencing and tumor cell heterogeneity in metastatic triple-negative breast cancer
Authors: Yang Dongbo , Dann Christopher , Pott Sebastian , Rosner Marsha 
Published: September 2020

Abstract
Tumor cell heterogeneity has been strongly implicated in metastatic progression of solid tumors such as breast cancer, leading to resistance and recurrence. We hypothesize that inhibiting metastasis will reduce tumor cell heterogeneity and thereby increase therapeutic sensitivity. To test this hypothesis, we expressed the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP or PEBP1) in triple-negative breast cancer (TNBC) cells as a means of comparing the variation in gene expression between individual cells in metastatic versus non-metastatic tumors. Xenograft tumors with or without exogenous RKIP expression were dissociated into single cell suspensions. We removed mouse as well as dead cells, and the remaining cells were loaded onto a microfluidic device (Fluidigm C1) for separation and library preparation. For each condition we performed three independent experiments yielding a total of 1569 cells. Initially, we performed controls to ensure that differences were not due to batch effects, cell cycle stage or sample quality. Clustering of single cells across all samples indicated that gene expression profiles are similar, confirming reproducibility. Gene ontology analysis of differentially expressed genes between cells with and without RKIP overexpression reveals gene sets that are important in tumor cell transitions from metastatic to non-metastatic states. These data will allow us to specifically test whether metastatic tumors are more heterogeneous than non-metastatic tumors in TNBC.
Citation Format: Dongbo Yang, Christopher Dann, Sebastian Pott, Marsha Rosner. Single cell RNA sequencing and tumor cell heterogeneity in metastatic triple-negative breast 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 2697.
Abstract 2720: The GPC3 metastasis suppressor induces the activation of p38 MAPK signaling pathway promoting dormancy at the secondary organ
Authors: Pastore Magali Delgado , Guereño Macarena , Lugones Ana C. , Peters Maria G. 
Published: September 2020

Abstract
GPC3 is a proteoglycan involved in the control of proliferation and survival, which has been linked to cancer. In this respect, we previously demonstrated that normal breast tissues exhibit high levels of GPC3, while its expression is diminished in tumors. However, the role of the GPC3 downregulation in breast tumor progression and its molecular and cellular operational mechanisms are not fully understood. In this study we showed that GPC3 reverts the epithelial-to-mesenchymal transition (EMT) underwent by mammary tumor cells, blocks metastatic dissemination and induces dormancy at secondary site. Using genetically modified murine breast cancer cell sublines, we demonstrated that the phospho-Erk/phospho-p38 ratio is lower in GPC3 reexpressing cells, while p21, p27 and SOX2 levels are higher, suggesting a dormant phenotype. In vivo metastasis assays confirmed that GPC3 reexpressing cells reduce their metastatic ability. Interestingly, the presence of dormant cells was evidenced in the lungs of inoculated mice. Dormant cells could reactivate their proliferative capacity, remain viable as well as tumorigenic, but they reentered in dormancy upon reaching secondary site. We also proved that GPC3 inhibits metastasis through the p38 MAPK signaling pathway activation. The in vivo treatment with a pharmacological inhibitor of p38 induced an increase in cell invasion of orthotopic tumors reexpressing GPC3, as well as in spontaneous and experimental metastatic dissemination. In conclusion, our study shows that GPC3 returns mesenchymal-like breast cancer cells to an epithelial phenotype, impairing in vivo metastasis and inducing tumor dormancy through p38 MAPK signaling activation. These results help to identify the genetic determinants of dormancy and suggest the translational potential of research focusing in GPC3.
Citation Format: Magali Delgado Pastore, Macarena Guereño, Ana C. Lugones, Maria G. Peters. The GPC3 metastasis suppressor induces the activation of p38 MAPK signaling pathway promoting dormancy at the secondary organ [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 2720.
Abstract 2723: XIAOPI formula inhibits breast cancer pre-metastatic niche formation via blocking TAMs/CXCL1 pathway
Authors: Wang Zhiyu , Zheng Yifeng , Wang Neng , Wang Shengqi , Yang Bowen , Lin Yi 
Published: September 2020

Abstract
Recent findings suggested that premetastatic niche (PMN) is a prerequisite in mediating cancer metastasis. Previously we demonstrated that XIAOPI formula could inhibit breast cancer lung metastasis via inhibiting tumor associated macrophages (TAMs)-secreted CXCL1. Herein, we aimed to explore the effects of XIAOPI formula on preventing breast cancer PMN formation and its underlying molecular mechanisms. It was found that XIAOPI formula could inhibit the proliferation of M2 phenotype macrophages and reduce CXCL1 expression in a dose-dependent manner. TAMs/CXCL1 signaling was subsequently found to stimulate the recruitment of c-Kit+/Sca-1+ HSPCs and their differentiation into CD11b+/Gr-1+ MDSCs, which were symbolic events accounting for PMN formation. Moreover, XIAOPI formula was effective in inhibiting HSPCs activation and blocking the proliferation and metastasis of breast cancer cells 4T1 induced by HSPCs and TAMs co-culture system, implying that XIAOPI was effective in preventing PMN formation in vitro. Breast cancer xenograft experiments further demonstrated that XIAOPI formula could inhibit breast cancer growth and metastasis in vivo. More importantly, XIAOPI formula significantly delayed the time of cancer cell seeding in the lung tissues. Meanwhile, the populations of HSPCs in the bone marrow and MDSCs size in both tumor and lung tissues were all remarkably declined by XIAOPI formula treatment. However, the inhibitory effects of XIAOPI formula could be relieved by CXCL1 overexpression in the TAMs. Taken together, our study provided preclinical evidence supporting the application of XIAOPI formula in preventing breast cancer PMN formation, and highlighted TAMs/CXCL1 as a potential therapeutic strategy for PMN targeting therapy.
Citation Format: Zhiyu Wang, Yifeng Zheng, Neng Wang, Shengqi Wang, Bowen Yang, Yi Lin. XIAOPI formula inhibits breast cancer pre-metastatic niche formation via blocking TAMs/CXCL1 pathway [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 2723.