bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4687: Gastric cancer stem cell-related marker LINGO2 is associated with cancer phenotype and poor patient survival
Authors: Park Soo Been , Jo Jung Hyun , Kim Chanyang , Lee Hee Seung , Jung Dawoon E. , Song Si Young 
Published: August 2019

Abstract
The expression of leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 2 (LINGO2), has been reported in Parkinson’s disease; however, its role in other diseases is unknown. Gastric cancer is the second leading cause of cancer death. Cancer stem cells (CSC) are a subpopulation of cancer cells that contribute to the initiation and invasion of cancer. We identified LINGO2 as a CSC-associated protein in gastric cancers both in vitro and in patient-derived tissues. We studied the effect of LINGO2 on cell motility, stemness, and tumorigenicity using cells sorted based on LINGO2 expression and LINGO2-silenced cells. Tissue microarray analysis showed that LINGO2 expression was significantly elevated in advanced gastric cancers. The overall survival of patients expressing high LINGO2 was significantly shorter than that of patients with low LINGO2. Cells expressing high LINGO2 showed elevated cell motility and tumorigenicity while LINGO2 silencing reversed these properties. Silencing LINGO2 reduced AKT/MEK/ERK phosphorylation and decreased EMT-associated markers - N-cadherin and Vimentin and stemness-associated markers - OCT4 and IHH. These indicate the involvement of LINGO2 in gastric cancer initiation and progression by altering cell motility, stemness, and tumorigenicity, suggesting LINGO2 as a putative target for gastric cancer treatment.
Citation Format: Soo Been Park, Jung Hyun Jo, Chanyang Kim, Hee Seung Lee, Dawoon E. Jung, Si Young Song. Gastric cancer stem cell-related marker LINGO2 is associated with cancer phenotype and poor patient survival [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 4687.
Abstract 4689: Subclone-specific evolution of tumor phenotypes – A framework to study subclone-specific gene expression from a combination of bulk DNA and single cell RNA sequencing data
Authors: Qiao Yi , Huang Xiaomeng , Brady Samuel , Bild Andrea , Bowtell David , Johnson William , Marth Gabor 
Published: August 2019

Abstract
Several approaches are now available for subclonal reconstruction of heterogeneous tumor biopsies from somatic variant allele frequencies measured in bulk DNA sequencing datasets, including our own SubcloneSeeker program. However, to understand how chemoresistance, relapse, or metastasis evolves at a subclonal level, we also need to study the molecular phenotype corresponding to each subclone. Single-cell RNAseq technologies now allow one to study the transcriptomic characteristics and phenotypic behaviors of individual cells, but new algorithms are needed to link these cells to the genomically defined tumor subclones they represent.
Here we present a computational approach to make such cell assignments, using a combination of bulk DNA sequencing data (WGS or WES), and single cell RNA sequencing (scRNAseq) collected from the same tissues. Subclones constructed from bulk DNA sequencing data are defined by specific combinations of somatic mutations (SNVs and CNVs). Our algorithm uses the scRNA-seq reads to assess which of these subclone-defining mutations are present in each individual cell, then utilizes a Bayesian probabilistic framework for making the cell-to-subclone assignment. This framework overcomes the challenges of sparse scRNA-seq read coverage, and maximizes the accuracy and efficiency of cell assignment.
We have successfully applied this method to multiple longitudinal and metastatic cancer patient datasets, representing both WES and WGS bulk DNA sequencing, as well as datasets collected using the 10X Chromium and Fluidigm C1 technologies. Our algorithm uses both somatically acquired CNV and SNV events in the tumor for cell assignment. Using our approach, as many of 80% of tumor cells could be assigned to specific subclones, enabling comparative gene expression and pathway analysis across subclones.
Citation Format: Yi Qiao, Xiaomeng Huang, Samuel Brady, Andrea Bild, David Bowtell, William Johnson, Gabor Marth. Subclone-specific evolution of tumor phenotypes – A framework to study subclone-specific gene expression from a combination of bulk DNA and single cell RNA sequencing 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 4689.
Abstract 4698: Development of a CRISPR-Cas9D10A targetable, high-complexity, single-cell barcoding approach for capture of treatment resistant subclones from heterogeneous cancers
Authors: Zhang Ze-yan , Ezhilarasan Ravesanker , Ding Yingwen , Wang Qianghu , Yang Jie , Long Lihong , Verhaak Roel G. , Sulman Erik P. 
Published: August 2019

Abstract
Cancers are composed of heterogeneous cell populations and the clonal evolution of these cells is one of the key reasons for treatment resistance and tumor recurrence. A fundamental challenge in studying clonal evolution in these tumors is the difficulty in capturing the phenotype-associated (e.g. treatment resistant) sub-populations from the heterogeneous population. We developed an approach to individually barcode and isolate specific cell subpopulations by constructing a Cas9D10A and paired-gRNA targetable unique reporter (CAPTURE) barcoding library with up to 36 million unique barcodes. This approach enabled us to uniquely barcode &gt; 1 million cells, track barcode distribution following treatment and then isolate the resistant subpopulation using the subpopulation-specific barcode. Proof of principle studies showed that specific barcoding cells, even at as low as 0.1%, could be efficiently isolated using barcode targeting and cell sorting. Applied our barcoding approach, we found that A375 cell acquired BRAF inhibitor resistance both from pre-exiting and late-emerging mechanisms. Colony formation experiments showed that the isolated subpopulations were indeed resistant clones. Whole exome, transcriptome and methylome analysis were applied to study the captured subpopulations. Our CAPTURE barcoding approach will enable the identification of the both pre-exiting and late-emerging genetic or epigenetic changes driving treatment resistance.
Citation Format: Ze-yan Zhang, Ravesanker Ezhilarasan, Yingwen Ding, Qianghu Wang, Jie Yang, Lihong Long, Roel G. Verhaak, Erik P. Sulman. Development of a CRISPR-Cas9D10A targetable, high-complexity, single-cell barcoding approach for capture of treatment resistant subclones from heterogeneous cancers [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 4698.
Abstract 4703: Single Cell CNV End to End workflow to uncover tumor heterogeneity in a murine breast cancer model
Authors: Gibbs Lee D. , Qian Jing , Webb Michelle , Chang Sharon , Manojlovic Zarko , Velazquez Enrique I. , McEachron Troy , Craig David W. , Carpten John D. 
Published: August 2019

Abstract
Background: Tumor heterogeneity is a hallmark of cancer and can have significant impact on identifying drivers, including those that may be therapeutically relevant. Although, the traditional sequencing of bulk tumor specimens provides invaluable information, sequencing of individual cells provides a true representation of the cellular heterogeneity that exists within a cancer. Novel technologies such as single cell copy number variation (scCNV) enable copy number profiling at a single cell resolution. Single Cell CNV generates genome wide sequencing libraries from single cells to reveal tumor heterogeneity and evolution of subclonal populations.
Methods: In this study, we utilized a scCNV assay to assess heterogeneity within the 4T1 murine breast tumor model. To accomplish this we have developed an end-to-end workflow including tissue dissociation, single cell library preparation, sequencing and data analysis. We injected 4T1 cells into the mammary fat pad of 4-6 week old BALB/c mice. Mice were sacrificed at 21 days and tumors were removed from the injection site and dissociated using Milteny’s Biotec Octo Dissociator. We utilized the 10X Genomics Chromium system to partition single cells and prepare sequencing libraries in parallel such that all DNA fragments produced within a partition are barcoded. Following library construction, the Illumina Novaseq 6000 system was used to sequence single cell libraries. Additionally, single cell libraries from a fraction of the 4T1 cells that were injected into the mammary fat and non-metastatic isogeneic cell line variants, 67NR and 168FARN, were also sequenced.
Results: We observed a pair of amplifications (&gt;8 copies) on chromosome 9 and three segments of amplification on chromosome 15 that were conserved throughout the injection site tumor cells. Interestingly, the amplifications on chromosome 15 encompass one of the most commonly observed breast cancer oncogenes, Myc, and the cell migration regulator, Skp2. Further, we observed three unique cluster of tumors cells which suggests the possibility of detecting major and minor clonal populations using this technology.
Conclusion: Our findings suggest scCNV will help us to improve characterizations of the entirety of a patient’s disease to uncover potential clones that are primed to induce metastasis, drug resistance, and relapse.
Citation Format: Lee D. Gibbs, Jing Qian, Michelle Webb, Sharon Chang, Zarko Manojlovic, Enrique I. Velazquez, Troy McEachron, David W. Craig, John D. Carpten. Single Cell CNV End to End workflow to uncover tumor heterogeneity in a murine breast cancer model [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 4703.
Abstract 4715: Combination of Tacedinaline and EHMT2 inhibition increases breast cancer cell death involving BIRC5 repression and GADD45A induction
Authors: Chu Pei-Yi , Lai Ji-Ching , Hou Ming-Feng , Lin Chang-Shen 
Published: August 2019

Abstract
The genomes of cancer cells are different from those of normal cells. These differences include genetic and epigenetic alterations, such as variations of DNA methylation and histone modifications, which cause differential gene expression, increased cell growth/migration capacity, and may induce resistance to anticancer therapy. Thus, epigenetic modulation may have a chance to correct abovementioned cancer cell’s aberrations in gene expression and cell behaviors, resulting in eradication of primary and/or suppression of refractory cancers.
Tacedinaline (CI-994) and UNC0638 are specific inhibitors of class I histone deacetylase (HDAC) and histone methyltransferase EHMT2 (G9a), which cause an increase of histone acetylation and a decrease of histone H3 dimethylation at lysine 9, respectively. Here we examined the therapeutic effect of CI-994 and UNC0638 combination on the triple-negative (MDA-MB-231) and estrogen receptor-positive (MCF-7) breast cancer cell lines.
The results showed that the combination of CI-994 and UNC0638 was able to induce more severe cell death than either agent alone. Although the sub-G1 fraction and Annexin V-positive cells were increased, CI-994 and UNC0638 did not significantly induce the activities of caspases 3, 8 and 9, suggesting the involvement of non-canonical and caspase-independent cell death mechanism. Instead, CI-994 suppressed the expression of BIRC5 (Survivin, a member of the inhibitor of apoptosis protein) and, in combination with UNC0638, induced the expression of GADD45A (involved in stress-induced apoptosis).
Mechanistically, combination of CI-994 and UNC0638 resulted in the changes of epigenetic marks, such as acetylation and methylation of histone H3, at the loci of BIRC5 and GADD45A, which were correlated with their altered gene expressions. Genetic knockdown of BIRC5 expression in MCF-7 decreased cell viability, supporting the pro-survival role of BIRC5 in breast cancer cells.
Importantly, the targets of CI-994 (HDAC1, HDAC2) and UNC0638 (EHMT2), as well as BIRC5 were overexpressed in breast cancer specimens, especially those of triple-negative breast cancer (TNBC), based on the analyses of The Cancer Genome Atlas dataset. Meanwhile, the expression of GADD45A was downregulated. BIRC5 upregulation and GADD45A downregulation in breast cancer were associated with patient’s overall survival.
These results suggest that Tacedinaline and UNC0638, or targeting the class I HDAC and EHMT2, may be a potential strategy to treat breast cancer including TNBC.
Citation Format: Pei-Yi Chu, Ji-Ching Lai, Ming-Feng Hou, Chang-Shen Lin. Combination of Tacedinaline and EHMT2 inhibition increases breast cancer cell death involving BIRC5 repression and GADD45A induction [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 4715.
Abstract 4734: Response of bladder and colon cancer cells to combined treatment with bromodomain and histone deacetylase inhibitors
Authors: Lea Michael A. , Patel Niyati , desBordes Charles 
Published: August 2019

Abstract
Since bromodomains of proteins bind acetylated histone lysine side chains while histone deacetylase inhibitors increase the level of histone acetylation, it seemed possible that bromodomain inhibitors might counteract some cellular responses to the action of histone deacetylase inhibitors. We have examined this possibility in bladder and colon cancer cells treated with combinations of bromodomain and histone deacetyalase inhibitors. Actions on growth and on the induction of alkaline phosphatase activity by histone deacetylase inhibitors were investigated. Compounds studied were the bromodomain inhibitors JQ1, I-BET763, olinone and RVX208 and the histone deacetylase inhibitors butyrate, RGFP966 and valproate. The cells studied were ones in which alkaline phosphatase activity is induced by histone deacetylase inhibitors. They were bladder cancer lines 5637, HT1197 and HT1376 and colon cancer lines Caco-2 and HT29. The combination that most clearly showed decreased induction of alkaline phosphatase activity by a bromodomain inhibitor was butyrate plus JQ1. If this action represents blocking combination of bromodomain-containing transcription factors with acetylated histones one might anticipate that inhibitory effects of histone deacetylase inhibitors on growth might be mitigated by combination with bromodomain inhibitors. However, the tendency was for additive effects on growth inhibition in accord with some data in the literature. Of the bromodomain inhibitors that were studied, JQ1 was the most effective as a growth inhibitor and olinone was the least effective. The mechanism for additive effects of bromodomain and histone deacetylase inhibitors on growth remains to be defined but antagonistic effects on cell differentiation appear possible.
Citation Format: Michael A. Lea, Niyati Patel, Charles desBordes. Response of bladder and colon cancer cells to combined treatment with bromodomain and histone deacetylase inhibitors [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 4734.
Abstract 4752: Exon-16-skipping HER2 contributes to osimertinib-resistance through Src-independent manner in EGFRL858R/T790M-positive non-small-cell lung cancer
Authors: Hsu Chia-Chi , Liao Bin-Chi , Liao Wei-Yu , Markovets Aleksandra , Stetson Daniel , Thress Kenneth , Yang Chih-Hsin 
Published: August 2019

Abstract
Osimertinib is current recommended treatment for EGFR T790M-positive NSCLC following progression on prior EGFR tyrosine kinase inhibitor therapy. However, acquired resistance to osimertinib therapy inevitably developed after a period of effective treatment. We had a patient of EGFR L858R/T790M-positive NSCLC who initially responded to osimertinib therapy but eventually developed resistance. Plasma cell-free DNA analysis disclosed exon-16-skipping HER2 (HER2Δ16) in one osimertinib treated patient. HER2Δ16 was regarded as an oncogenic driver in breast cancer and has never been reported in lung cancer before. Therefore, it’s intriguing to investigate the role of HER2Δ16 in osimertinib resistance in NSCLC. The purpose of this study is to explore the mechanism of HER2Δ16-mediated resistance to osimertinib and to explore strategies to overcome the resistance.
We constructed and established H1975 cells stably expressing either vehicle, WT-HER2 or HER2Δ16. We observed that without osimertinib treatment, there was no difference in cell growth and the response to EGF-stimulation. However, when treated with osimertinib, H1975-HER2Δ16 cells were more resistant under normal and EGF-stimulating conditions compared to vehicle or WT-HER2 expressing cells. Moreover, osimertinib treatment in H1975-HER2Δ16 cells had less inhibitory effect on phosphor-ERK and phosphor-AKT compared to vehicle or H1975-WT-HER2 cells. Interestingly, co-treatment of osimertinib with Src-kinase inhibitor, dasatinib, failed to reverse the resistance, indicating that HER2Δ16-driven
osimertinib-resistance was independent of Src-kinase. Finally, we revealed that combination of osimertinib with the HER2 small molecular inhibitor, afatinib, can suppress cell growth in H1975-WT-HER2 and H1975-HER2Δ16 cells.
In summary, we have shown that HER2Δ16, may be a resistance mechanism to osimertinib in EGFR mutated NSCLC and that HER2Δ16-driven resistance was Src-kinase independent. Moreover, we found the HER2Δ16-driven resistance could be rescued by combination of osimertinib with afatinib.
Citation Format: Chia-Chi Hsu, Bin-Chi Liao, Wei-Yu Liao, Aleksandra Markovets, Daniel Stetson, Kenneth Thress, Chih-Hsin Yang. Exon-16-skipping HER2 contributes to osimertinib-resistance through Src-independent manner in EGFRL858R/T790M-positive non-small-cell lung 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 4752.
Abstract 4795: Oxidative stress by proguanil suppresses breast tumor growth
Authors: Gupta Nehal , Srivastava Sanjay 
Published: August 2019

Abstract
Breast cancer is one of the most common malignancies and the second leading cause of cancer related mortality among women in U.S., thus developing new strategies to control breast cancer is an important mission. Repurposing of old drugs as new anti-cancer drugs is important as it can save time and cost of drug development. Proguanil is used in combination with atovaquone for the treatment of malaria. In this study, we determined the anticancer effects of proguanil in breast cancer cells. Proguanil significantly reduced the viability of MDA-MB-231, HCC1806 and MCF-7 breast cancer cells with IC50 of 42μM, 44μM and 40μM respectively after 72 h of treatment and induced apoptosis as exhibited by FITC/Annexin assay and cleavage of caspase 3 as well as PARP. Proguanil also reduced the survival of several patient-derived cells with IC50 in the range of 30-40μM. The anti-cancer effects of proguanil were associated with the generation of ROS and persistent disruption of mitochondrial membrane potential. ROS generation by proguanil was about 2-3 fold more as compared to control in MDA-MB-231 and HCC1806 cells. The generation of ROS was inhibited when the cells were pretreated with a general antioxidant N-acetyl cysteine (NAC). Moreover, exposure of MDA-MB-231 and HCC1806 cells to proguanil was also associated with increased expression of Bax, p-H2AX, c-caspase9 and down-regulation of bcl-2 and survivin. We further evaluated the oxygen consumption rate with proguanil treatment in breast cancer cells using flux analyzer. Our results showed significant decrease in the mitochondrial respiration rate and ATP production rate after proguanil treatment. Furthermore, 20mg/kg proguanil when given orally suppressed the growth of 4T1 breast tumors in female Balb/c mice by 55%. Tumors from proguanil treated mice demonstrated increased apoptosis, which was related to the increased expression of p-H2AX and Bax. Taken together, these results show that proguanil is an effective inhibitor of in vitro and in-vivo growth of breast cancer cells. These findings provide the rationale for further clinical investigation of proguanil against breast cancer.
Citation Format: Nehal Gupta, Sanjay Srivastava. Oxidative stress by proguanil suppresses breast tumor growth [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 4795.
Abstract 4797: A novel Diiminoquinone targets colorectal cancer stem cells
Authors: Monzer Alissar , Jabotian Nayri , Zhu Jie S. , Kurth Mark J. , Kheir Wassim Abou , Haddadin Makhlouf , Gali-Muhtasib Hala 
Published: August 2019

Abstract
5-Fluorouracil (5-Fu) remains the standard chemotherapy for metastatic colorectal cancer, but drug resistance and unpredictable cardiotoxicity limit its effectiveness. The high recurrence rates and common resistance are thought to be due to a population of self-renewing cancer stem cells (CSCs). In this study, we synthesized four novel heterocyclic compounds that are similar in structure with quinones and tested their anticancer activity against HCT116 human colon cancer cells in 2D monolayer and 3D sphere cultures. In 2D, all compounds caused significant inhibition of colon cancer cell viability at concentrations non-cytotoxic to normal human FHs74Int intestinal cell lines. In 3D cultures, these heterocycles eradicated the self-renewal ability of the highly resistant cancer stem cells and inhibited colon sphere formation in first generation (G1), as well as subsequent generations. This study represents the first documentation of the activity of these novel heterocyclic compounds, particularly compound 6a, abbreviated as DIQ-3, which we propose to be an effective treatment strategy to prevent colon cancer recurrence by targeting colorectal CSCs. Our findings provide the basis for suggesting these non-toxic and stable compounds for additional testing against cancer.
Citation Format: Alissar Monzer, Nayri Jabotian, Jie S. Zhu, Mark J. Kurth, Wassim Abou Kheir, Makhlouf Haddadin, Hala Gali-Muhtasib. A novel Diiminoquinone targets colorectal cancer stem cells [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 4797.