bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 142: cdk5 inhibition promotes neurogenesis while reducing self-renewal of brain tumor stem cells
Authors: Mukherjee Subhas , Olson Cheryl , Brat Daniel 
Published: August 2018

Abstract
Cancer stem cells are biologically potent and support tumor growth, in part by deregulating asymmetric stem cell division. Asymmetric cell division of stem cells is a type of mitotic division where a stem cell generates one stem and one differentiated cell. Cancer stem cells, however, tend to generate more stem-like dividing cells to promote neoplasm. To uncover mechanisms and potential therapeutic targets relevant to self-renewal in human glioma stem cells (GSCs), we performed a genetic screen for kinases that reverse the tumor phenotype of our novel adult Drosophila brain tumor model and found that knockdown of the brain-specific dCdk5 was highly effective in suppressing the self-renewing stem cell components. A highly specific CDK5 inhibitor is promoting neurogenesis among these fly brain cancer stem cells. These cancer stem cells, although they express glial markers in tumors, do not differentiate into glia upon CDK5 suppression. Additionally, while the tumor generation in adult flies completely disrupts the mushroom body, the main cognitive center in adult fly brain, the CDK5 inhibition partially rescues the mushroom body and extends life span of these flies. dCdk5 and its human ortholog CDK5 (79% identity) are aberrantly activated in some forms of cancer. We demonstrate that GBMs highly express CDK5 mRNA and protein, likely related to copy number gains of chromosome 7, with strong positive correlation with stem cell markers and marked effect on tumor-propagating properties. Using human GSCs isolated from tumor spheres and mouse xenografts, we found that CDK5 directly phosphorylates CREB1 independent of cAMP and stops stem cell renewal. These data together show that CDK5 inhibition not only can attenuate self-renewal properties of brain tumor stem cells, but also can promote neurogenesis, which could potentially become a better treatment strategy for patients and improve their cognitive function as well.
Citation Format: Subhas Mukherjee, Cheryl Olson, Daniel Brat. cdk5 inhibition promotes neurogenesis while reducing self-renewal of brain tumor stem 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 142.
Abstract 1424: Elucidating the microRNA-203 specific biological processes in glioblastoma cells from high-throughput RNA-sequencing
Authors: Ahir Bhavesh K. , Engelhard Herbert H. , Lakka Sajani S. 
Published: August 2018

Abstract
Glioblastoma (GBM) is the most common primary malignant intracranial adult brain tumor. Allelic deletion on chromosome 14q play an essential role in GBM pathogenesis, and this chromosome 14q site was thought to harbor multiple tumor suppressor gene associated with GBM, a region that also encodes microRNA-203 (miR-203). This study was conducted to identify gene expression profile changes associated with mir-203 expression by high-throughput RNA sequencing. Enrichment analyses for gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that mir-203 expression had a strong, negative effect on a number of fundamental and interconnected biological processes involved in cell growth and proliferation. The biological processes mostly influenced were p53 signaling pathway, FoxO signaling pathway, DNA replication, cell cycle, MAPK signaling pathway and Apoptosis. In total, 847 upregulated and 345 downregulated differentially expressed genes (DEGs) were identified in control versus miR203 expressing glioma cells. After GO enrichment, the downregulated DEGs and miR-203 predicted target genes such as BCL-2, SPARC, PDGFA, CREB were found to be mainly enriched in cell cycle regulation and apoptosis processes, whereas the upregulated DEGs, such as CCND1, E2F1 were involved in the DNA replication and cell cycle regulation of gene expression. We also demonstrate that mir-203 expression suppressed BCL-2 protein and mRNA by western blotting and qRT-PCR analysis. Moreover, co-transfection experiments using a luciferase-based reporter assay demonstrated that mir-203 directly regulated BCL-2 expression and BCL-2 overexpression suppressed mir-203 mediated cell death. Knowledge gained through this profiling study can facilitate targeted therapeutic interventions.
Citation Format: Bhavesh K. Ahir, Herbert H. Engelhard, Sajani S. Lakka. Elucidating the microRNA-203 specific biological processes in glioblastoma cells from high-throughput RNA-sequencing [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 1424.
Abstract 1430: Improved sample indexing for high fidelity demultiplexing to increase confidence in low frequency variant calling
Authors: Irish Jonathan C. , RoseFigura Jordan , Sandhu Sukhinder K. , Carrion Bita , Kurihara Laurie , Makarov Vladimir 
Published: August 2018

Abstract
Due to recent scientific advances, there is a growing demand for new indices with high fidelity to eliminate errors associated with certain index combinations and sequencing chemistries. These errors are due to insufficient edit distances (the minimum number of changes required to transform one index sequence to the other) between index sequences or index hopping. Recent publications have highlighted how sequencing reads are misassigned due to "index hopping" on Illumina patterned flow cells, such as the recently launched Illumina Novaseq which can generate billions of reads (&gt;100 exomes) in a single run. This misassignment canlead to false positives in ultra-sensitive assays where low frequency variants or nucleic acid species are monitored. We have observed misassignment due to insufficient edit distance among Illumina TruSeq HT i7 indices at a frequency up to 1.5%. Therefore, we developed 968nt i7 indices that can be paired with the existing TruSeq HT i5 indices to achieve 768 high throughput dual combinations, which were validated using a novel method on both Illumina's 2- and 4-channel technologies as both single and dual indices. This method involved thepreparation of 96 libraries with unique, non-overlapping inserts to facilitate tracking of index misassignment. This allowed us to assess not only which index has misassigned library molecules, but also pinpoint the origin and rate of misassignment within a single run. With our 96 i7 indices, misassignment was observed at rates &lt;0.1%. For even higher fidelity de-multiplexing, we have paired our 96 indices in a non-tandem manner for single use in both the i5 and i7 positions, known as Unique Dual Indices (UDIs). The use of UDIs further eliminates index read errors that misassign reads, enabling increased confidence in calling low frequency variants. UDIs can also eliminate PCR-induced chimerisms, which can significantly improve data from a variety of assays. We are validating 96 new indices as UDIs for avoidance of index hopping and for eliminating PCR-induced chimerism during multiplexed library amplification.
Citation Format: Jonathan C. Irish, Jordan RoseFigura, Sukhinder K. Sandhu, Bita Carrion, Laurie Kurihara, Vladimir Makarov. Improved sample indexing for high fidelity demultiplexing to increase confidence in low frequency variant calling [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 1430.
Abstract 1432: Deranged tyrosine metabolism drives tumorigenesis in liver cancer
Authors: Tong Man , Wong Tin Lok , Luk Steve Tin-Chi , Che Noelia , Guan Xin Yuan , Yuan Yun Fei , Lee Terence Kin-Wah , Ma Stephanie 
Published: August 2018

Abstract
Tyrosine, like other amino acids, is the building block for proteins as well as an alternative energy source for cellular functions. Liver is the major organ where tyrosine degradation takes place to produce intermediates or precursors for gluconeogenesis and ketogenesis. In normal liver, tyrosine can be converted to fumarate and acetoacetate through multiple steps of enzymatic reactions. In patients with liver cancer, an upregulation of serum tyrosine levels has been previously reported, suggesting a deregulated tyrosine catabolism in liver cancer. In this study, we observed a significant down-regulation of the five enzymes involved in tyrosine catabolism (TAT, HPD, HGD, GSTZ1 and FAH) in tumor samples compared with normal liver samples from TCGA database. Further, downregulation of the first three enzymes significantly correlates with overall and disease-free survival in liver cancer patients. Downregulation of these enzymes is also confirmed in a separate liver cancer patient transcriptome cohort of Asian ethnicity, as well as at the proteomic level by both Western blot and immunohistochemistry assays. Our group has previously reported that downregulation of the first tyrosine catabolizing enzyme TAT (tyrosine aminotransferase) could promote liver tumorigenesis. Here, we further investigate if reprogrammed tyrosine metabolism could promote cancer development by modulating gene expression and activity of the second enzyme HPD (4-hydroxyphenylpyruvate dioxygenase) in the tyrosine catabolism pathway. We found blocking HPD gene expression or its enzymatic activity could promote cell proliferation and tumor formation in liver cancer. This could be partially attributed to enhanced mitochondrial respiratory capacity accompanied with reduction in ROS level, NADP/NADPH ratio and DNA damage. Conversely, overexpression of HPD led to an opposing effect. Taken together, this study reveals an unreported alteration of tyrosine metabolism which drives cancer development in liver cancer.
Citation Format: Man Tong, Tin Lok Wong, Steve Tin-Chi Luk, Noelia Che, Xin Yuan Guan, Yun Fei Yuan, Terence Kin-Wah Lee, Stephanie Ma. Deranged tyrosine metabolism drives tumorigenesis in liver cancer [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 1432.
Abstract 1456: Integrin beta4-induced mitophagy promotes the lactate production of cancer-associated fibroblasts in breast cancer
Authors: Sung Jin Sol , Kang Suki , Lee Joo Hyun , Mun Seong Gyeong , Kim Baek Gil , Cho Nam Hoon 
Published: August 2018

Abstract
Integrin beta4 neoexpression is induced in cancer-associated fibroblasts (CAFs) by some triple negative breast cancer cells (MDA-MB-231 and BT-20) through a contact-dependent manner. Integrin beta4 expression is well known to contribute to the migration and survival of cancer cells. However, there is very little known about the role of integrin beta4 expression in CAFs, especially in the aspect of tumor progression. In our study, we found that the exogenous expression of integrin beta4 increased the lactate production of CAFs. The observation made us to hypothesize that integrin beta4 neoexpression is associated with the mitophagy, a cause for aerobic glycolysis, in CAFs. To confirm the assumption, the expression alteration of mitophagy-related genes was first screened in the CAF transfected with integrin beta4 overexpression plasmid. BCL2 interacting protein 3 like (BNIP3L) and microtubule associated protein 1 light chain 3 alpha-II (LC3-II) were significantly upregulated in the integrin beta4 overexpressing CAFs, which was reversed both in the knockdown of integrin beta4 expression and the treatment with an integrin beta4 inhibitor. Autophagosome maturation and lysosomal fusion were also increased in the integrin beta4 overexpressing CAFs compared to the control. Phosphorylation level of c-Jun was upregulated by integrin beta4 overexpression in CAFs and was able to bind to the putative promoter regions of BNIP3L and LC3-II. Taken together, these results demonstrate that integrin beta4 neoexpression induces upregulation of BNIP3L and LC3-II ultimately leading to mitophagy in CAFs, contributing to cancer metabolism via mitophagy-induced lactate production, namely reverse Warburg effect.
Citation Format: Jin Sol Sung, Suki Kang, Joo Hyun Lee, Seong Gyeong Mun, Baek Gil Kim, Nam Hoon Cho. Integrin beta4-induced mitophagy promotes the lactate production of cancer-associated fibroblasts in breast cancer [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 1456.
Abstract 1466: DAXX localizes ATRX to suppress alternative lengthening of telomeres in osteosarcoma
Authors: Soper Sarah Faith Clatterbuck , Yost Kathryn E. , Walker Robert L. , Pineda Marbin A. , Zhu Yuelin J. , Waterfall Joshua J. , Meltzer Paul S. 
Published: August 2018

Abstract
To maintain genome stability, proliferating cells must add telomere sequence to counteract the chromosome end replication problem. In normal cells, telomeres are lengthened through the action of the enzyme telomerase. In about 10-15% of tumors, however, telomeres are lengthened through a telomerase-independent mechanism known as Alternative Lengthening of Telomeres or ALT. Many tumors that use ALT have poor prognoses, so ALT represents an appealing therapeutic target. It has been previously observed that ALT tumors frequently carry mutations in ATRX, which partners with the protein DAXX in a chromatin remodeling complex that deposits histone variant H3.3. How these mutations facilitate the ALT pathway is not well understood. Previous work in our lab identified an ALT-positive osteosarcoma cell line, G292, in which ATRX is wild-type but DAXX has undergone a fusion event with the non-canonical kinesin KIFC3. The DAXX-KIFC3 fusion leads to a loss of DAXX function, and inducible restoration of wild-type DAXX reversibly abrogates ALT in this cell line. We observe that expression of wild-type DAXX results in localization of ATRX to PML bodies, increased occupancy of ATRX at telomeric chromatin, and higher levels of histone H3.3 at telomeres. We conclude that full-length DAXX is required for the functional localization of ATRX to telomeres. Leveraging this our inducible system, we continue to probe the role of the ATRX/DAXX complex in suppressing ALT.
Citation Format: Sarah Faith Clatterbuck Soper, Kathryn E. Yost, Robert L. Walker, Marbin A. Pineda, Yuelin J. Zhu, Joshua J. Waterfall, Paul S. Meltzer. DAXX localizes ATRX to suppress alternative lengthening of telomeres in osteosarcoma [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 1466.
Abstract 147: Targeting USP22 suppresses tumorigenicity and enhances sensitivity to cisplatin in cancer-initiating cells from lung adenocarcinoma through downregulating ALDH1A3
Authors: Zhang Keqiang , Yun Xinwei , Wang Jinhui , Bonner Melisa , Yang Lu , Wu Jun , Raz Dan J. 
Published: August 2018

Abstract
We previously found that loss of monoubiquitination of histone H2B (H2Bub1) was associated with poor differentiation and enhanced malignancy of lung adenocarcinoma. Herein, we investigated the expression and roles of USP22, an H2Bub1 deubiquitinase, in cancer-initiating cells (CICs) with stem cell-like characteristics from primary lung adenocarcinoma. CICs from patient-derived cancer tissues were isolated and characterized, and the association of USP22 with CICs was investigated using flow cytometry, aldehyde dehydrogenase (ALDH) activity, Western blot, and fluorescence microscope assays. The impact of USP22 on stem cell-like characteristics and cisplatin resistance in CICs was examined by in vitro tumorsphere formation, in vivo transplantation, and apoptosis assays. We identified that USP22 is predominantly expressed in CICs, a subpopulation of cells with high expression of CD133 stem cell biomarker. The expression of USP22 in CICs is dramatically reduced upon serum-induced differentiation. Moreover, knockdown of USP22 significantly suppressed in vitro tumorsphere formation and in vivo xenograft growth in NOD-SCID mice. Notably, USP22 is dramatically elevated in tumorsphere cells that survived cisplatin treatment, while knockdown of USP22 significantly sensitizes tumorsphere cells to cisplatin. Interestingly, ALDH1A3, a dominant isoform of ALDH implicated in enhancing cisplatin resistance in lung adenocarcinoma, is significantly downregulated upon knockdown of USP22 in tumorsphere cells. Furthermore, knockdown of ALDH1A3 significantly sensitizes tumorsphere cells to cisplatin. Therefore, our data indicate that USP22 plays critical roles in tumorigenicity and cisplatin resistance in lung adenocarcinoma, and targeting USP22 may represent a potential therapeutic approach to eliminate CICs in lung adenocarcinoma through downregulation of ALDH1A3 expression.
Citation Format: Keqiang Zhang, Xinwei Yun, Jinhui Wang, Melisa Bonner, Lu Yang, Jun Wu, Dan J. Raz. Targeting USP22 suppresses tumorigenicity and enhances sensitivity to cisplatin in cancer-initiating cells from lung adenocarcinoma through downregulating ALDH1A3 [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 147.
Abstract 1490: Molecular function of the read-through transcript PRR5-ARHGAP8
Authors: Sethi Jasmeen K. , Wong Oscar G. , Wong Esther S. , Cheung Annie N. 
Published: August 2018

Abstract
Background: Ovarian carcinoma is one of the most fatal malignancies in females. From the analysis of RNA-seq we have previously conducted to study the transcriptome of ovarian carcinoma upon knockdown of transcription factor hepatic nuclear factor 1β (HNF-1β), PRR5-ARHGAP8 was identified as the only read-through transcript not targeted for the nonsense-mediated decay pathway. Read-through transcription refers to the splicing of the intergenic region from two adjacent genes resulting in a chimeric transcript comprising of one or more exons from both genes. Although several of such transcripts are found in the transcriptome, their significance remains an enigma. Our aim was to ascertain the differential expression of the read-through transcript PRR5-ARHGAP8 in ovarian cancers and to determine its molecular functions.
Materials & Methods: The deregulation of PRR5-ARHGAP8 was validated by RT-qPCR in several ovarian carcinoma cell lines. The expression of this fusion transcript and the individual genes were studied in immortalised human ovarian surface epithelial (HOSE) cell lines, ovarian carcinoma cell lines, and matched tumour and non-tumour pairs from frozen patient samples. Overexpression of this transcript was achieved by transient transfection in HEK293T cells to study its effect on proliferation using MTT assays. RNA and protein lysates were also obtained at several time points to evaluate the pathways affected by RT-qPCR and western blot, respectively.
Results: There was an approximate 3- to 9-fold upregulation of PRR5-ARHGAP8 transcript with a decrease in the expression of PRR5 and ARHGAP8 transcripts in OVMANA, OVISE and KK ovarian carcinoma cell lines upon the knockdown of HNF-1β. Moreover, higher transcript levels of PRR5, ARHGAP8 and PRR5-ARHGAP8 were observed in ovarian carcinoma cell lines compared to HOSE cell lines and in ovarian cancer samples compared to the non-tumour counterparts. Overexpression of PRR5-ARHGAP8 in HEK293T cells resulted in the decrease of phosphorylated Akt protein expression and a reduction of cell viability. RT-qPCR analysis showed a decrease in E-cadherin and an increase in vimentin expression upon PRR5-ARHGAP8 overexpression.
Discussion: The present data suggests PRR5-ARHGAP8 is highly abundant in ovarian carcinomas and may mediate its effects on proliferation via the MAPK pathway and on migration by regulating the epithelial to mesenchymal transition. Overall, this study provides novel insights into the biological relevance of read-through transcription in carcinogenesis.
Citation Format: Jasmeen K. Sethi, Oscar G. Wong, Esther S. Wong, Annie N. Cheung. Molecular function of the read-through transcript PRR5-ARHGAP8 [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 1490.
Abstract 1492: High-efficiency, strand-specific, low-bias library preparation method for transcriptome profiling of low-input RNA
Authors: Nowosielska-Vecchietti Anetta 
Published: August 2018

Abstract
RNA Sequencing (RNA-seq) is a powerful technique for transcriptome analysis. It is widely used for gene expression analysis, detection of mutations, fusion transcripts, alternative splicing, and the study of post transcriptional modifications. RNA-seq is emerging as a powerful tool for molecular diagnostics as well, providing insights into the biological pathways and molecular mechanisms associated with disease progression including cancer. Recent improvements in next generation sequencing technologies (NGS) and sample barcoding strategies have resulted in significant cost reduction. As RNA-seq is increasingly adopted for molecular diagnostics, the quality and reproducibility of library preparation methods become more important. In addition, demand for library preparation methods that produce successful NGS libraries from very low input RNA or precious clinical samples is increasing.
To achieve these goals, we have developed an RNA-seq library preparation method which can be used across a wide range of input RNA (5-1000 ng total RNA). GC content analysis, gene body coverage and gene expression correlation show that these important parameters remain consistent across varying inputs, even though input amounts vary by two orders of magnitude. As a result, our method has increased sensitivity and specificity for low-abundance transcripts, and reduced PCR duplicates and sequence bias, delivering high quality strand-specific data. Our method is compatible with poly A-tail enriched and ribosomal RNA depleted samples as well as RNA extracted from FFPE (formaldehyde fixed paraffin embedded) tissue samples.
Citation Format: Anetta Nowosielska-Vecchietti. High-efficiency, strand-specific, low-bias library preparation method for transcriptome profiling of low-input RNA [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 1492.