bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1357: Functional characterization of FANCD2 in esophageal squamous cell carcinoma
Authors: Lei Lisa Chan , Yu Valen Zhuoyou , Ning Lvwen , Ko Josephine Mun-Yee , Wang Li Dong , Lung Maria Li 
Published: August 2018

Abstract
Introduction:
Esophageal squamous cell carcinoma (ESCC) has an especially high incidence in Northern China, where there is evidence for a significant familial association. We performed targeted next-generation sequencing (NGS) analysis on familial ESCC germline samples compared to non-cancer controls from the same high-risk region and compiled a list of candidate cancer predisposition genes. Interestingly, genes related to the Fanconi Anemia (FA) - BRCA pathway are enriched in the list. Among these FA-BRCA genes, Fanconi anemia complementation group D2 (FANCD2) was one of the top candidates, as it also had a high frequency of somatic mutations in ESCC tumor specimens. Therefore, we aim to characterize the role of FANCD2 in tumor development and explore its translational value.
Methods:
We knocked out the FANCD2 gene in ESCC cell lines using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technique to evaluate its potential oncogenic function in ESCC. Cell proliferation was measured by a MTT 2D clonogenic assay in vitro. Subcutaneous injection of the FANCD2 knockout ESCC cells into BALB/c-nude mice in vivo was performed to assess its functional impact on tumorigenesis. The single cell gel electrophoresis/comet assay was used to investigate the genome stability.
Results:
The FANCD2 knockout efficiency was confirmed by western blotting. Surprisingly, in vitro functional analyses showed that ESCC cells with FANCD2 knockout survive, with a greatly reduced growth rate and colony-forming ability. Consistent with the in vitro data, ESCC cells with FANCD2 knockout form significantly smaller subcutaneous tumors in nude mice. By applying the comet assay to examine the genome integrity, ESCC cells with FANCD2 knockout show significantly greater damage to the genome.
Conclusion:
These results suggest that FANCD2 plays an important role in supporting ESCC tumor growth. We attribute this to its core function in DNA repair ability and genome integrity maintenance.
Acknowledgement:
We acknowledge the grant support from the Hong Kong Research Grants Council Collaborative
Research Fund (C7031.15G to M.L.L.).
Citation Format: Lisa Chan Lei, Valen Zhuoyou Yu, Lvwen Ning, Josephine Mun-Yee Ko, Li Dong Wang, Maria Li Lung. Functional characterization of FANCD2 in esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1357.
Abstract 1383: A CRISPR-Cas9 tiling screen to identify functional domains within DNMT1 and/or DNMT3B that can be targeted for therapeutic intervention in AML
Authors: Bhogal Balpreet , Weir Barbara , Crescenzo Ramona , Kwon Min Chul , Philippar Ulrike , Attar Ricardo , Cowley Glenn , Pocalyko David 
Published: August 2018

Abstract
DNA methylation is an epigenetic mechanism that regulates gene expression during many stages of development, including genomic imprinting, stem cell regulation, and X-chromosome inactivation. Moreover, aberrant DNA methylation patterns, characterized by genome-wide hypomethylation and promoter-specific hypermethylation, are a prominent feature of cancer. Methylation of DNA at the 5-position of cytosines is mediated by the DNA methyltransferase (DNMT) protein family, which regulates both maintenance methylation (DNMT1) and de novo methylation (DNMT3A and DNMT3B). Loss-of-function mutations of DNMT3A have been identified in hematological malignancies including acute myeloid leukemia (AML), where DNMT3A is mutated in approximately 25% of known cases.
Published reports suggest the existence of a synthetic lethal interaction between DNMT3A and DNMT1/3B. To further study this potential genetic interaction, we are performing a CRISPR-Cas9 tiling screen to identify functional domains within DNMT1 and/or DNMT3B that are synthetic lethal with DNMT3A. We generated a lentiviral library containing 777 and 421 single guide RNAs (sgRNAs) that tile the coding region of DNMT1 and DNMT3B, respectively and performed viability screens in AML cell lines that are either wild-type or mutant for DNMT3A. This screen was designed to identify in-frame alterations within functional domains that lead to effects on cell viability. Next generation sequencing of sgRNAs identified three functional domains of DNMT1 which, when mutated, leads to decreases in cell viability. Current efforts are focused on verifying the essentiality of these functional domains using CRISPR-Cas9-based approaches as well as mutagenesis by integrated tiles (MITE)-seq analyses.
Citation Format: Balpreet Bhogal, Barbara Weir, Ramona Crescenzo, Min Chul Kwon, Ulrike Philippar, Ricardo Attar, Glenn Cowley, David Pocalyko. A CRISPR-Cas9 tiling screen to identify functional domains within DNMT1 and/or DNMT3B that can be targeted for therapeutic intervention in AML [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1383.
Abstract 1385: Galangin is an epigenetic modulator or BRCA1 and induces estrogen receptor alpha in triple negative breast cancer cells
Authors: Donovan Micah G. , Selmin Ornella I. , Romagnolo Donato F. 
Published: August 2018

Abstract
The aryl hydrocarbon receptor (AhR) is a driver of breast cancer progression and its overexpression is often observed in triple negative breast cancer (TNBC). Activation of AhR results in epigenetic silencing of the breast cancer 1 gene (BRCA1), a necessary factor in the transcriptional activation of estrogen receptor-alpha (ERα). The purpose of this study was to examine the capacity for galangin (GAL; 3,5,7-trihydroxy-2-phenylchromen-4-one), a natural AhR antagonist, to mimic the effects of synthetic AhR antagonists alpha-naphthoflavone (αNF, 2-phenylbenzo[h]chromen-4-one) and 3'-methoxy-4'-nitroflavone (MNF; 2-(3-methoxy-4-nitrophenyl)chromen-4-one) in regards to counteracting epigenetic silencing of BRCA1 and restoring ERα protein expression. We utilized TNBC cells with hypermethylated BRCA1 and constitutively active AhR (HCC38 cells) for these experiments. After 72h in phenol-red free media, cells were treated for up to 72h against a range of GAL, αNF, and MNF concentrations in the presence or absence of estradiol (E2). Transcript levels of AhR and its downstream target genes CYP1A1 and CYP1B1 were determined by real-time polymerase chain reaction (RT-PCR). Protein levels of BRCA1, ERα, and AhR were determined by Western blot. Treatment with GAL results in stabilization of BRCA1 and ERα protein levels, similarly to αNF and MNF. To determine potential mechanisms of these observations, we are currently conducting experiments to analyze changes in BRCA1 promoter methylation using methylation-specific RT-PCR (MSP) and DNA methyltransferase 1 (DNMT1) protein levels by Western blot. These data suggest the naturally occurring flavanoid GAL may be an effective compound for modulating epigenetic repression of BRCA1 and restoring ERα levels, which may provide options for anti-hormonal therapy in ERα-negative breast cancers.
Citation Format: Micah G. Donovan, Ornella I. Selmin, Donato F. Romagnolo. Galangin is an epigenetic modulator or BRCA1 and induces estrogen receptor alpha in triple negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1385.
Abstract 1405: PAX2 induces tubular structure in ovarian cancer cells
Authors: Alwosaibai Kholoud 
Published: August 2018

Abstract
In adult tissues, PAX2 protein is expressed in normal oviductal epithelial cells (OVE) but not in normal ovarian surface epithelial cells (OSE). Recent studies reported that PAX2 is expressed in serous ovarian carcinoma cases but the role of PAX2 in enhancing ovarian cancer is unrevealed yet. The aim of this study is to understand the biological consequences after Pax2 overexpression in mouse ovarian surface epithelial (MOSE) cells. We found that Pax2 overexpression in MOSE cells induced the formation of vascular channels both in vitro and in vivo, which indicate a possible contribution of PAX2 to ovarian cancer progression by increasing the vascular channels to supply nutrients to the tumor cells.
Citation Format: Kholoud Alwosaibai. PAX2 induces tubular structure in ovarian cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1405.
Abstract 1411: Proteogenomic analysis of the syngeneic mouse gastric stem cell-like cancer cell line
Authors: Yang Hanna , Kim Hark Kyun 
Published: August 2018

Abstract
Gastric cancer is the third main cause of cancer deaths worldwide. To understand molecular mechanism of gastric cancer incidence and metastasis, we generated NCC-S1M lacking Smad4, Trp53 and Cdh1, which is the unique syngeneic gastric cancer cell line transplant model in the scientific society. NCC-S1M showed cancer stem cell-like features and strong tumor-initiating potential. Using proteogenomic analysis of NCC-S1M, we elucidated the specific signaling pathways that control gastric cancer stem cell-like properties and immune checkpoint. Cd274, Ccne1 and Il1rl1 were overexpressed and their protein levels were higher than normal gastric tissues. Cd274 encodes PD-L1, which is one of the important immune checkpoint proteins. The growth rate of NCC-S1M allograft was reduced after treatment with anti-PD-1. When Smad4 was ectopically expressed in NCC-S1M, Cd274 expression was decreased. In addition, TGF-β treatment induced reduction in Cd274 expression of Smad4 overexpressed NCC-S1M cells even more comparing with normal Smad4 overexpressed NCC-S1M. The knockdown of Il1rl1 in NCC-S1M reduced tumorigenicity and in vivo chemoresistance. We demonstrated that NCC-S1M focally amplified Ccne1 gene through array comparative genomic hybridization. Ccne1 knocked down NCC-S1M showed reduced metastatic potential. The proteogenomic characterization of NCC-S1M explains that Smad4 is important for PD-L1 immune evasion and that Il1rl1 has a significant role in cancer stem cell-like properties. Furthermore, it could imply that Ccne1 regulates metastasis.
Citation Format: Hanna Yang, Hark Kyun Kim. Proteogenomic analysis of the syngeneic mouse gastric stem cell-like cancer cell line [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1411.
Abstract 1419: Dissection of single-cell transcriptional and translational regulation by digital mRNA and protein quantification
Authors: Lam Gretchen , Shum Eleen , Chang Christina , Shah Hemi , Jensen Devon , Ghadiali James , Martin Jody , Rosenfeld David , Fan Christina H. 
Published: August 2018

Abstract
The immune system consists of complex gene regulatory networks that allow a rapid transition of different cellular states during an immune response. Cell-surface marker analysis using flow cytometry or single cell RNA-seq has allowed characterization of immune subpopulations and a greater understanding of the complexity of immune cells. However, restrictions on protein-only or RNA-only analysis can greatly limit the understanding of how genes are regulated in cells. For example, many cell surface markers - such as CD4 in T cells - has thousands of protein copies per cell using antigen density calculations, yet is fueled by a small number of mRNA transcripts per CD4+ T cell. Moreover, conventional whole-transcriptome analysis of mRNA can further mute the expression detection of CD4 mRNA in T cells due to the abundance of housekeeping ribosomal genes. To bridge the understanding of protein and mRNA expression differences, we used Ab-Seq on BD RhapsodyTM platform to provide digital quantification of both protein and mRNA expression level in single cells. An oligo-conjugated antibody panel against immune-relevant cell-surface markers was created and used for this multi-omic gene expression profiling effort. This approach is coupled with mRNA analysis using the BD Rhapsody Immune Response Panel, a targeted method of RNA-seq that allows a higher sensitivity of immune markers than conventional whole transcriptome assays. We studied the dynamics of early T cell activation in vitro to understand this response on transcriptional, post-transcriptional, and translational levels. Different time points following anti-CD3 and anti-CD28 treatment were collected and multiplexed on to BD Rhapsody cartridge for single cell capture and analysis. Using Ab-Seq on BD Rhapsody, we were able to detect the difference in mRNA and protein levels of crucial markers, allowing us to dissect the intricate gene regulatory pathways during an immune response in a single cell level.
Citation Format: Gretchen Lam, Eleen Shum, Christina Chang, Hemi Shah, Devon Jensen, James Ghadiali, Jody Martin, David Rosenfeld, Christina H. Fan. Dissection of single-cell transcriptional and translational regulation by digital mRNA and protein quantification [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1419.
Abstract 1468: ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator
Authors: Jahn Arne , Rane Grishma , Paszkowski-Rogacz Maciej , Sayols Sergi , Bluhm Alina , Han Chung-Ting , Draškovič Irena , Londoño Arturo , Kumar Alan Prem , Buchholz Frank , Butter Falk , Kappei Dennis 
Published: August 2018

Abstract
Telomeres consist of repetitive TTAGGG repeats and together with the shelterin complex protect the ends of linear chromosomes from DNA repair mechanisms. Due to telomere shortening with every cell division proliferating cells need to ensure telomere maintenance by telomerase or in about 15% of cancer cells via the recombination based alternative lengthening of telomeres. Recently ZBTB48 was identified as a novel telomere-associated factor throughout the vertebrate lineage. Here we show that ZBTB48 binds directly to telomeres in vitro and in vivo, independently of the telomere maintenance mechanism. Loss of the protein leads to longer telomeres indicating a role as negative regulator of telomere length. Furthermore RNAseq, ChIPseq and quantitative expression proteomics demonstrate a function as transcriptional activator for a small set of target genes, including mitochondrial fission process 1 (MTFP1). This regulatory role links its telomeric function to mitochondrial metabolism and might play a role in cancer development. In summary ZBTB48 is a novel telomere binding protein which regulates telomere length and transcriptional activity.
Citation Format: Arne Jahn, Grishma Rane, Maciej Paszkowski-Rogacz, Sergi Sayols, Alina Bluhm, Chung-Ting Han, Irena Draškovič, Arturo Londoño, Alan Prem Kumar, Frank Buchholz, Falk Butter, Dennis Kappei. ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1468.
Abstract 1482: SON represses RUNX1 expression and impairs megakaryocytic differentiation in Down syndrome acute megakaryoblastic leukemia (DS-AMKL)
Authors: Vukadin Lana , Park Eun young , Kim Jung Hyun , Ahn Erin Eun Young 
Published: August 2018

Abstract
Individuals with Down syndrome (DS) are highly predisposed to develop hematopoietic malignancies, especially acute megakaryoblastic leukemia (DS-AMKL). Generally, genes located on chromosome 21 tend to be increased in Down syndrome patients, but how these individual genes contribute to development of DS-AMKL is still unclear. SON, a gene located on chromosome 21, is upregulated in Down syndrome patients, and it has been reported that DS-AMKL cells have higher level of SON expression. The SON protein functions as a splicing factor and a transcription regulator in leukemia but the role of SON upregulation in DS-AMKL pathogenesis is still not fully elucidated. In addition, runt-related transcription factor 1 (RUNX1) is also located on chromosome 21, but its expression level is downregulated in DS-AMKL patients despite the increased gene dosage. We show that SON represses RUNX1 expression and blocks terminal megakaryocytic differentiation in DS-AMKL. Knockdown of SON in DS-AMKL cell lines leads to morphologic changes and increased cell adhesion. Moreover, cell surface marker analyses demonstrate that the depletion of SON induces increased CD41+ CD61+ populations as well as polyploidy cells, indicating megakaryocytic differentiation. Consistent with these results, SON deletion causes upregulation of RUNX1, which is a critical factor in the megakaryocytic differentiation. Furthermore, our data show that knockdown of SON increases several megakaryocytic transcription factors and decreases erythropoietic transcription factors, facilitating terminal megakaryocytic differentiation of leukemic blasts. Mechanistically, SON binds to the proximal promoter region as well as two intronic enhancer regions upstream of the proximal promoter at the RUNX1 gene locus, and suppresses transcription of RUNX1 by lowering the level of H3K4me3. Taken together, we propose that the increased genomic dosage of SON in Down syndrome impairs terminal differentiation of megakaryo-erythroblasts into mature megakaryocytes through binding to the RUNX1 promoter/enhancer to repress its transcription, which contributes to the higher incidence of AMKL in Down syndrome patients. Our results reveal a novel connection of SON to DS-AMKL pathogenesis and provide clinical importance of SON upregulation in DS. These findings suggest that SON could be a promising therapeutic target for DS-AMKL patients.
Citation Format: Lana Vukadin, Eun young Park, Jung Hyun Kim, Erin Eun Young Ahn. SON represses RUNX1 expression and impairs megakaryocytic differentiation in Down syndrome acute megakaryoblastic leukemia (DS-AMKL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1482.
Abstract 1483: Targeting oncogenic enhancer activity with a small-molecule CBP/P300 bromodomain inhibitor
Authors: Raisner Ryan , Bainer Russell , Chan Emily , Garcia Jesse , Merchant Mark , Gascoigne Karen 
Published: August 2018

Abstract
Transcriptional networks are often dramatically altered in cancer, this dysregulation occurring at both the genetic and epigenetic level. Recently much attention has been given to the role of enhancer-driven gene expression in cancer, with the observation that numerous key oncogenes are driven by super-enhancers. This opens up the possibility for therapeutic intervention with small molecules that modulate enhancer activity, leading to control of expression of otherwise un-drugable oncogenes. CBP/P300 are histone acetyl transferases (HATS) that are critical mediators of enhancer activity. Here we use a novel small molecule inhibitor of the CBP/P300 bromodomain to specifically probe the role of these HATS at enhancers, and more broadly evaluate the consequences of enhancer disruption on cancer cell growth in vitro and in vivo.
Citation Format: Ryan Raisner, Russell Bainer, Emily Chan, Jesse Garcia, Mark Merchant, Karen Gascoigne. Targeting oncogenic enhancer activity with a small-molecule CBP/P300 bromodomain inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1483.
Abstract 1491: Expression of osteopontin splicing isoforms in childhood B-cell precursor acute lymphoblastic leukemia
Authors: Bastos Ana Clara Santos da Fonseca , Blunck Caroline Barbieri Blunck , Ferreira Luciana Bueno , Pombo-de-Oliveira Maria do Socorro , Emerenciano Mariana , Gimba Etel R. 
Published: August 2018

Abstract
Osteopontin (OPN) suffers alternative splicing generating three OPN splicing isoforms (OPN-SI), named OPNa, OPNb and OPNc. However, OPN-SI roles in hematological malignancies (HMs) are still under investigation. Detection of specific gene rearrangements allows the identification of relevant prognostic subgroups of childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Patients harbouring the ETV6-RUNX1 rearrangement are classified as a good prognostic subgroup, while those with the KMT2A-AFF1 fusion are included into poor prognostic subgroup. This work aimed to analyze the expression levels of OPN-SI in BCP-ALL cell lines and patient samples. We tested 4 BCP-ALL cell lines: 207, ALL-PO, RS4;11 and REH. Patient samples included 28 samples from patients harbouring the ETV6-RUNX1 fusion and 26 samples presenting the KMT2A-AFF1 rearrangement. We found that these three OPN-SIs are expressed in all BCP-ALL cell lines and in 70% of both patient prognostic subgroups tested. Both 207 and REH cell lines displayed higher OPNc and OPNb levels than OPNa. We found that OPNc is expressed in higher levels than OPNb and OPNa in unfavorable prognostic subgroup and is also overexpressed in relation to OPNc levels in relation to the ETV6-RUNX1 fusion the comparative subgroup. Interestingly, we found that higher OPNc transcriptional levels are associated with poor prognostic features, such as central nervous system (CNS), initial white blood cell counting and high risk of relapse. In conclusion, we found that the three tested OPN-SI are expressed in most tested BCP-ALL cell lines and BCP-ALL human samples. Since higher OPNc levels are associated to prognostic features, our data provide early evidence that these OPN-SIs could specifically contribute to step BCP-ALL progression. Further work should investigate their putative applications as additional risk-stratification and prognostic markers for BCP-ALL, as well as, their roles on modulating HM progression.
Citation Format: Ana Clara Santos da Fonseca Bastos, Caroline Barbieri Blunck Blunck, Luciana Bueno Ferreira, Maria do Socorro Pombo-de-Oliveira, Mariana Emerenciano, Etel R. Gimba. Expression of osteopontin splicing isoforms in childhood B-cell precursor acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1491.