bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 814: Involvement of unique endosomes in the Mieap-induced vacuoles formation during Mieap-mediated cancer cell death
Authors: Ikari Naoki , Nakamura Yasuyuki , Arakawa Hirofumi 
Published: August 2019

Abstract
Background: Mitochondria-eating protein (Mieap), a p53-inducible protein is known to have tumor suppressive functions by repairing or degrading unhealthy mitochondria. When Mieap degrades mitochondria, Mieap-induced vacuoles (MIVs) are formed to eat mitochondria, which subsequently induce iron-dependent cell death. Previously, we elucidated that the MIVs contain lysosomal proteins and degraded mitochondria, suggesting the MIVs represent non-canonical mitophagy. However, the process of MIV formation is still unclear.
Methods: The process of MIV formation was visualized by high spatial and temporal resolution confocal live cell imaging with the EGFP-tagged Mieap protein (EGFP-Mieap) that was ectopically expressed in A549 cells. To interpret the imaging data, we performed the Mieap-interactome analysis, and consulted the list of proteins immunoprecipitated by anti-Mieap antibody. Further, we investigated the mechanism for MIV formation using various deletion-mutant forms of EGFP-Mieap.
Results: The enforced expression of EGFP-Mieap generated characteristic endosomes whose membrane contained Mieap. The unique endosomes showed directed movement toward clusters of mitochondria, where MIVs were generated, and enlarged by eating mitochondria and fusing to each other. When we reviewed the list of Mieap-interacting proteins considering the directed movement, alpha tubulins were found to be included. The endosomes consisting of C-terminus deficient Mieap showed nondirected movement and accumulated at the edge of the cells.
Conclusions: Besides lysosomes and mitochondria, MIVs are derived from the Mieap-related endosomes via the endocytosis/pinocytosis. Possibly, the interaction between the C-terminus region of Mieap and alpha tubulins is critical for the endosome delivery to the mitochondria in MIV formation.
Citation Format: Naoki Ikari, Yasuyuki Nakamura, Hirofumi Arakawa. Involvement of unique endosomes in the Mieap-induced vacuoles formation during Mieap-mediated cancer cell death [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 814.
Abstract 819: DNA methylation genome-wide analysis in remnant gastric cancer
Authors: Ito Tomoaki , Sugimoto Kiichi , Orita Hajime , Maeda Masahiro , Moro Hiroshi , Ushijima Toshikazu , Katai Hitoshi , Wada Ryo , Sakamoto Kazuhiro , Sato Koichi , Brock Malcolm V. 
Published: August 2019

Abstract
Purpose: Although primary gastric cancers (PGC) and remnant gastric cancers (RGC) both originate from the same gastrointestinal organ, they have very distinct clinicopathological behaviors. Due to the importance of chronic inflammation in the carcinogenesis of gastric malignancies, we hypothesized that DNA promoter hypermethylation would play a critical role in the carcinogenesis of RGC as well as PGC.
Methods: We investigated the genome-wide DNA methylation patterns of PGC and RGC tissues from 48 patients from an academic medical center in Japan using the Infinium HumanMethylation450 BeadChip assay. The results were validated by quantitative methylation-specific PCR (qMSP) in separate, independent cohorts.
Results: We found that in our training cohort of 48 patients, genes from the gastric cancer tissues identified by the Infinium HumanMethylation 450 Beadchip clustered into high and low methylation groups on multivariate analysis (p=0.004, OR=12.33). PGCs contributed significantly to the high methylation group suggesting that the DNA promoter methylation status in PGC is higher than that in RGC. Supporting this conclusion was the finding that in a separate qMSP analysis in a test cohort, the gene A had significantly higher DNA promoter methylation in cancer tissues in the validation PGC tissues than in RGC.
Conclusion: This study demonstrated that DNA promoter methylation status in PGC is higher than in RGC. This result may reflect the effects of Helicobacter pylori on the induction of DNA methylation in the remnant stomach.
Citation Format: Tomoaki Ito, Kiichi Sugimoto, Hajime Orita, Masahiro Maeda, Hiroshi Moro, Toshikazu Ushijima, Hitoshi Katai, Ryo Wada, Kazuhiro Sakamoto, Koichi Sato, Malcolm V. Brock. DNA methylation genome-wide analysis in remnant gastric 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 819.
Abstract 82: Transforming of human osteoblasts with the combination of hTERT (T), SV40Tag (S) and c-Myc: Changes in phenotype and tumorigenesis capability
Authors: Zhang Zhongting , Wang Yifei , Zhang Wendong , Roth Michael , Gill Jonathan Benjamin , Xu Zhaohui , Tian Xiangjun , Wang Jing , Gorlick Richard 
Published: August 2019

Abstract
The etiology of osteosarcoma (OS), the most common primary malignant bone cancer in pediatric patients, still remains unknown. It is not clear where tat which point he osteosarcoma is originated from the osteogenic lineagein the osteogenic osteosarcoma arises., some consider Potential candidates in the literature include the human mesenchymal cells (hMSC) as the cell of origin in OS, whereas others believe theand osteoblast (OB) to be the most likely cell of origin. To understand the origin and molecular pathogenesis of osteosarcoma, we have transformed hMSCs and OBs differentiated from the same MSC with oncogenes hTERT (T), SV40Tag (S) and H-RAS (R) in series to check evaluate for spindle cell tumor formation in mice. Transformed MSC did not form osteoid, whereas OB-TSR tumor showed only scant production of osteoid, suggesting MSC may not be the origin of OS and the hTERT, SV40Tag and h-Ras may not be sufficient for osteoblast to form OS.
C-Myc is one of the genes that play a major role in oncogenic transformation of normal cells. It has been shown that c-Myc is overexpressed in OS cells and more than 10% OS patients carry c-Myc amplification mutations. We further decide to look intoThis served as the basis to examine the role of c-Myc in OS formation in the background of cells transformed by hTERT and SV40. OB transformed with hTERT and SV40Tag cells were further transfected with a retrovirus containing human c-Myc to obtain stable cell lines. Quantitative PCR and western blots assays detected both gene and protein expression patterns of c-Myc, respectively, in the transformed cell lines. Transformed cell lines were analyzed for proliferation, invasion, migration, and spheroid formation to determine the tumorigenic capacity capability. TThe tumorigenesis capability is found to be correlated with the level of c-Myc expression level based onby RT-PCR data. Furthermore, we used RNA-seq to analyze gene expression profiles of the transformed cell lines, compared with those forin comparison to primary OS cell lines and patient derived xenografts (PDXs). In -vivo tumorigenic assays, histological examination for osteoid production and chromosome analysis are still under way. Our study using an osteosarcoma model with transformed human cells may provide new insights on the cell origin of OS.
Citation Format: Zhongting Zhang, Yifei Wang, Wendong Zhang, Michael Roth, Jonathan Benjamin Gill, Zhaohui Xu, Xiangjun Tian, Jing Wang, Richard Gorlick. Transforming of human osteoblasts with the combination of hTERT (T), SV40Tag (S) and c-Myc: Changes in phenotype and tumorigenesis capability [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 82.
Abstract 825: TAPS: A bisulfite-free, base-resolution and quantitative sequencing method for cytosine modifications
Authors: Liu Yibin , Siejka Paulina , Velikova Gergana , Bi Ying , Tomkova Marketa , Schuster-Boeckler Benjamin , Song Chun-Xiao 
Published: August 2019

Abstract
Aberrant DNA methylation changes are powerful prognostic and predictive biomarkers in cancer diagnosis and treatment. For decades bisulfite sequencing has been the gold standard for DNA methylation analysis. However, this method relies on harsh deamination reaction of unmodified cytosine to uracil which degrades the majority of DNA and generates sequencing libraries with low complexity. Those drawbacks limit the applications on low-input samples and lead to poor sequencing quality, low mapping rates, uneven genome coverage and increased sequencing cost. Here, we present a novel bisulfite-free and base-resolution sequencing method, TET Assisted Pyridine borane Sequencing (TAPS), for direct detection of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) without affecting unmodified cytosine. We utilised TET enzymes to readily oxidize 5mC and 5hmC to 5-carboxylcytosine (5caC), which was then converted to dihydrouracil by pyridine borane via a previously unknown reductive decarboxylation/deamination reaction. This non-destructive method enables high-throughput sequencing with nanoscale input materials (genomic DNA and cell-free DNA) and preserve DNA up to 10 kbs long which could allow long read sequencing. We demonstrated that TAPS could directly replace bisulfite sequencing with higher mapping rates, more even coverage and lower sequencing costs, and enable more comprehensive, cheaper and faster methylome analyses. This would be a revolutionary tool for epigenetic study and facilitate both academic research and clinical diagnostics.
Citation Format: Yibin Liu, Paulina Siejka, Gergana Velikova, Ying Bi, Marketa Tomkova, Benjamin Schuster-Boeckler, Chun-Xiao Song. TAPS: A bisulfite-free, base-resolution and quantitative sequencing method for cytosine modifications [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 825.
Abstract 829: SOX2-mediated 5hmC dysregulation in GBM stem cells
Authors: Sudhir Sweta , Lopez-Bertoni Hernando , Lugo-Fagundo Maria , Lal Bachchu , Laterra John 
Published: August 2019

Abstract
Primary brain tumors are among the most devastating forms of cancer and glioblastoma (GBM) represents the most aggressive and lethal form of the disease. We now know that GBM contains small subsets of cells that display tumor-propagating stem-like phenotypes (i.e. glioma stem cells or GSCs) that act as critical determinants of resistance to current treatments and tumor recurrence for which there is no proven therapy. Altered patterns of DNA methylation are widely reported in human GBM. However, substantial knowledge gaps remain in our understanding of the molecular mechanisms responsible for this epigenetic dysregulation, its downstream consequences and its role in the GBM tumor-propagating phenotype. Understanding and ultimately targeting the epigenetic mechanisms that induce and maintain these tumor-propagating cell subsets is critical to improving GBM therapy and patient outcomes.
DNA methylation generally occurs in cytosine-guanine (CpG) sequences and is established by DNMTs, which catalyze the conversion of cytosine to 5-methylcytosine (5mC). DNA methylation is dynamically regulated and reversible by the ten-eleven translocation (TET) family of deoxygenases that catalyze the conversion of 5mC to 5-hydroxymethylcytosine (5hmC). Levels of 5hmC closely align with the differentiation state of cells; terminally differentiated cells contain high levels of 5hmC and less differentiated cells have very low levels. Multiple studies found negative correlations between 5hmC levels and glioma grade and loss of 5hmC correlates with poor prognosis of GBM patients. This strongly suggests that tumor suppressing epigenetic mechanisms are driven by TET-dependent 5hmC generation.
We now show that SOX2, a reprogramming transcription factor that induces GSCs, represses the TET2 and decreases 5hmC in multiple GSC isolates. TET2 repression using two independent shRNA hairpins efficiently decreased 5hmc levels and significantly enhanced self-renewal capacity and tumor growth capacity of low-passage GSCs. We also show that low concentrations of vitamin C, a TET enzyme cofactor, significantly increases 5hmC in low-passage GSCs. This epigenetic change induced by vitamin C associated with increased GSC death induced by temozolomide (TMZ), the main chemotherapeutic used to treat GBM. These findings support a mechanism by which SOX2 induces loss of 5hmC in GSCs by repressing TET2 and show that vitamin C can reverse this epigenetic tumor promoting pathway and potentially enhance GBM chemotherapeutics.
Citation Format: Sweta Sudhir, Hernando Lopez-Bertoni, Maria Lugo-Fagundo, Bachchu Lal, John Laterra. SOX2-mediated 5hmC dysregulation in GBM 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 829.
Abstract 836: From tobacco smoking to mutation signature: The role of epigenetic changes in human cancers
Authors: Chen Zhishan , Wen Wanqing , Cai Qiuyin , Long Jirong , Shu Xiao-ou , Zheng Wei , Guo Xingyi 
Published: August 2019

Abstract
Tobacco smoking is associated with a unique mutation signature in the human cancer genome. It is unclear whether tobacco smoking alters DNA methylations and gene expressions affect smoking-related mutation signature. In this study, we evaluated the smoking-related DNA methylation sites reported from five previous studies using peripheral blood cells to identify possible target genes. Using the mediation analysis approach, we evaluated whether the association of tobacco smoking with mutation signature was mediated through altered DNA methylation and expression of these target genes. Based on data obtained from 21,108 blood samples, we identified 374 smoking-related DNA methylation sites, annotated to 248 target genes. Using data from DNA methylations, gene expressions and smoking-related mutation signature generated from ~7,700 tumor tissue samples across 26 cancer types from The Cancer Genome Atlas (TCGA), we found 11 of the 248 target genes whose expressions were associated with smoking-related mutation signature at a Bonferroni-correction P &lt; 0.001. This included four for head and neck cancer, and seven for lung adenocarcinoma. In lung adenocarcinoma, our results further showed that smoking increased the expression of three genes, AHRR, GPR15, and HDGF, and decreased the expression of two genes, CAPN8, and RPS6KA1, which were consequently associated with increased smoking-related mutation signature. Additional evidence showed that the elevated expression of AHRR (cg14817490) and GPR15 (cg19859270), were associated with smoking-altered hypomethylations. Our findings provide novel insight into the contributions of tobacco smoking to carcinogenesis through complex molecular mechanisms of the evaluated mutation signature by altered DNA methylation and gene expression.
Citation Format: Zhishan Chen, Wanqing Wen, Qiuyin Cai, Jirong Long, Xiao-ou Shu, Wei Zheng, Xingyi Guo. From tobacco smoking to mutation signature: The role of epigenetic changes in human 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 836.
Abstract 84: Inhibition of Hedgehog signalling in ligand dependent tumours
Authors: Vaghjiani Vijesh G. , Cochrane Catherine , Watkins Neil , Mudge Stuart , Cain Jason E. 
Published: August 2019

Abstract
Hedgehog (Hh) signalling is evolutionarily conserved pathway that is critical during development and maintenance of stem cells in adults. Activation of the Hedgehog pathway can occur through either ligand-dependent or ligand-independent mechanisms. While mutations in key Hh signalling components (PTCH1, SUFU, SMO, GLI1) result in ligand-dependent signalling and constitutive activation in some cancers, the vast majority of cancers in which Hh signalling is implicated do not have pathway mutations and are therefore driven upstream at the level of Hh ligand. Despite this, there are no biomarkers that can predict which tumours are dependent on Hh ligand and are likely to be responsive to Hh pathway inhibition.
Using a panel of osteosarcoma cell lines derived from either radiation-induced or conditional Trp53 and Rb1 genetic inactivation murine models of osteosarcoma, we observed a dramatic increase in Gli1 mRNA, a downstream target of the Hh pathway, in response to Hh ligand stimulation in Trp53 and Rb1 deficient cells. This was accompanied by a significant increase in primary cilia frequency, a critical organelle for Hh pathway activation. Importantly, Hh response to ligand was abolished using the SMO inhibitor LDE225. Using osteosarcoma allograft models, we showed that LDE225-mediated inhibition of the Hh pathway resulted in reduced tumour growth and increased survival in ciliated Trp53 and Rb1-deficient allografts but no response in a non-ciliated Trp53 and Rb1 wildtype-allograft.
The sustained clinical use of SMO inhibitors ultimately leads to development of resistance. We next evaluated the efficacy of Itraconazole, a SMO inhibitor previously demonstrated to be effective in Hh-therapy resistant ligand-independent tumour models, in our ligand-dependent osteosarcoma models. We show that Itraconazole inhibits Hh pathway activation in response to ligand leading to reduced Gli1 mRNA in vitro, and reduced tumour growth and increased survival in vivo.
Collectively, this data implicates Trp53, Rb1 and primary cilia as a potential biomarker of Hh ligand responsiveness in osteosarcoma and response to Hh pathway inhibition by SMO inhibitors LDE225 and Itraconazole.
Citation Format: Vijesh G. Vaghjiani, Catherine Cochrane, Neil Watkins, Stuart Mudge, Jason E. Cain. Inhibition of Hedgehog signalling in ligand dependent tumours [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 84.
Abstract 840: Identification of novel colorectal tumor suppressor genes through genome-wide promoter hypermethylation analysis
Authors: Bazzocco Sarah , Dopeso Jose Higinio , Martínez-Barriocanal Águeda , Anguita Estefanía , Nieto Rocio , Sanchez Alex , Mariadason John M. , Arango Diego 
Published: August 2019

Abstract
Cancer initiation and progression are driven by both genetic and epigenetic changes. Although recent genome/exome sequencing efforts have significantly contributed to the thorough characterization of the genetic changes associated with the oncogenic process, further investigation is required to systematically identify the driver genes regulated by promoter hypermethylation. Using genome-wide analysis of the levels of promoter methylation (HumanMethylation27, Illumina) and the levels of mRNA expression (microarray analysis) in a panel of 30 colorectal cancer cell lines and 223 primary colorectal tumors (TCGA), we found a subset of 553 (5.6%) genes whose levels of promoter methylation showed a significant negative association with their expression. Higher overall methylation levels were associated with microsatellite instability (MSI), a CpG methylator phenotype (CIMP), faster proliferation and absence of APC mutations. Next, because genes that are epigenetically silenced could represent important drivers of the oncogenic process we investigated the role of the zinc finger transcriptional regulator ZNF238/ZBTB18, a gene silenced by promoter methylation, on the growth of colon cancer cells. Reintroduction of ZNF238 in HCT116 and HT29 colon cancer cells with low endogenous levels and promoter methylation of ZNF238, resulted in a significant reduction of cell proliferation both in vitro and in a subcutaneous xenograft NOD/SCID mouse model. Moreover, using immunohistochemical analysis with a validated antibody we found that ZNF238 is lost or reduced in the majority of the 133 primary colorectal tumors included in a tissue microarray, and that lower ZNF238 expression is associated with lymph node metastasis and shorter survival of patients with locally advanced colorectal cancer. In summary, we identified a set of 553 genes putatively silenced by promoter methylation in colorectal tumors that could significantly contribute to the oncogenic process. Moreover, as a proof of concept, we demonstrate that the epigenetically silenced gene ZNF238 has tumor suppressor activity and is associated with the survival of colorectal cancer patients.
Citation Format: Sarah Bazzocco, Jose Higinio Dopeso, Águeda Martínez-Barriocanal, Estefanía Anguita, Rocio Nieto, Alex Sanchez, John M. Mariadason, Diego Arango. Identification of novel colorectal tumor suppressor genes through genome-wide promoter hypermethylation analysis [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 840.
Abstract 847: Overexpression of long noncoding RNA FAM promotes cancer invasion and drug resistance in human liver cancer
Authors: Huang Po-Shuan , Lin Kwang-Huei 
Published: August 2019

Abstract
Hepatocellular carcinoma (HCC) is one of the most common and aggressive human malignancies worldwide. Most patients with HCC have an established background of chronic liver disease and cirrhosis, with major etiological and risk factors including chronic infection with hepatitis B virus (HBV) and hepatitis C virus (HCV). Long non-coding (lnc)RNAs are a class of non-protein coding transcripts longer than 200 nucleotides that regulate complex cellular functions, such as cell growth, differentiation, metabolism and metastasis. Increasing evidence has shown that lncRNAs regulate gene expression by targeting the production, splicing, decay, or translation of target mRNAs. Although deregulation of lncRNAs expression have been detected in HCC or many tumor types, there are still many novel lncRNAs have not been studied and the mechanisms underlying functional impairment and specific involvement of lncRNAs during hepato-carcinogenesis remain to be established. Here, we aimed to investigate the involvement of specific dys-regulated lncRNA-FAM and its molecular mechanism. FAM is overexpressing in HCC and correlates with tumor size, vascular invasion, and pathology stage. Overexpression FAM accelerates cell proliferation, invasion in HCC cells. Further, FAM is induced in the Doxorubicin (DOX) resistance HCC cells show in the Gene Expression Omnibus (GEO) Datasets analysis. Overexpression FAM did increase DOX-resistant in two HCC cell lines. After overexpression FAM, lysosome-associated membrane protein 2 (LAMP2) expression was enhanced which also correlated with DOX-resistant. From the co-immunoprecipitation analysis, FAM directly interacted with LAMP2 to protect its ubiquitination. Thus, FAM may play an oncogenic role during hepato-carcinogenesis.
Citation Format: Po-Shuan Huang, Kwang-Huei Lin. Overexpression of long noncoding RNA FAM promotes cancer invasion and drug resistance in human liver 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 847.