bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2760: Does a short open reading frame (sORF)-encoded protein participate in DNA repair
Authors: Hanakahi Les , Summerlin Matthew , Tang Yi-Chia , Heo Jinho 
Published: July 2016

Abstract
Non-homologous end joining (NHEJ) is one of the major mechanisms for rejoining of DNA double-strand breaks. Knowledge of the molecular mechanism of NHEJ will help us to understand how this process preserves genome integrity, and how NHEJ errors cause chromosomal rearrangements that lead to cancer. Several critical participants in the NHEJ pathway have been identified and some mechanistic steps have been characterized. At present, a significant gap in our understanding of NHEJ is how NHEJ factors assemble at DSBs. It is plausible that additional, as yet unidentified, factors contribute to NHEJ assembly. We have biochemical and biological data implicating a short open reading frame (sORF)-encoded protein in NHEJ. sORFs are found in all genomes. Ribosome profiling, mass spectroscopy and RNA sequencing have predicted the existence of numerous sORF-encoded proteins of &lt;100 amino acids in size. While the functional significance of the majority of these small proteins is not clear, we recently discovered that a 69 amino acid protein encoded by chromosome 7 open-reading frame 49 (C7orf49) interacts with critical NHEJ factors in human cells, and stimulates NHEJ in cell-free extracts. Treatment of cells with the DSB-inducing agent etoposide increased C7orf49 expression and nuclear localization, and knockdown of C7orf49 sensitized cells to etoposide. C7orf49-deficient cells exhibited a mild proliferation defect and increased sensitivity to etoposide. Our data suggest that this small protein may play an important role in double-strand beak repair by NHEJ and highlights the potential biological relevance of sORF-encoded proteins in the DNA damage response and in DNA repair.
Citation Format: Les Hanakahi, Matthew Summerlin, Yi-Chia Tang, Jinho Heo. Does a short open reading frame (sORF)-encoded protein participate in DNA repair. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2760.
Abstract 2765: Asbestos exposure-related DNA methylation markers: a validation study in non-small cell lung tumors
Authors: Kettunen Eeva , Stuopelytė Kristina , Hernandez-Vargas Hector , Wolff Henrik , Anttila Sisko L. , Herceg Zdenko , Jarmalaite Sonata , Husgafvel-Pursiainen Kirsti 
Published: July 2016

Abstract
Introduction. We have earlier explored the epigenome-wide DNA methylation in lung tumors. The study subjects, mostly smokers, consisted of lung cancer patients highly exposed to asbestos and those without exposure. We found methylation markers that associated either with sample type or exposure (asbestos or tobacco smoke) (Kettunen et al submitted). In this validation study, we focused on estimating the prevalence of the distinct methylation markers in a larger material of lung tumor patients with detailed exposure data available.
Study design, subjects, and methods. We investigated the DNA methylation of selected markers in a validation set of 69 non-small cell lung cancer cases, tumor (T) and normal lung (N) from each. The patients, given a written informed consent, had been interviewed for detailed data on work and smoking history (as tobacco smoking pack-years, PY), and the pulmonary asbestos fiber counts quantified. Smoking-related methylation was studied in lung cancer groups of heavy-smokers (PYs higher than 36) vs lighter-smokers (PYs 36 or less) whereas methylation in asbestos-exposed lung tumor patients were compared with that in non-exposed lung tumor patients. DNA methylation was studied in tumor (T) and matched peripheral normal (N) lung tissue using pyrosequencing.
Results. Numerous CpG positions in T vs N and eleven sites in asbestos-exposed tumors had indicated significant methylation variation (MVPs). Twenty-six differentially methylated positions (DMPs) having mean delta beta of at least 10% had been revealed in T vs N. Tobacco smoking- and asbestos exposure-related methylation sites were distinct, involving different CpG sites. We chose to validate five MVPs and four DMPs, both hypo- and hypermethylated CpG sites that were investigated using two instrumentation PSQ96MA and Pyromark Q24. The validation study set indicated good performance in pyrosequencing and we could demonstrate methylation of selected sites in relation to malignancy and exposure in this larger material.
Conclusions. The central observations of the methylation showing distinct changes in relation to sample types and patients’ exposure status could be validated in a larger material. Significant methylation variation was observed in lung tumors.
Citation Format: Eeva Kettunen, Kristina Stuopelytė, Hector Hernandez-Vargas, Henrik Wolff, Sisko L. Anttila, Zdenko Herceg, Sonata Jarmalaite, Kirsti Husgafvel-Pursiainen. Asbestos exposure-related DNA methylation markers: a validation study in non-small cell lung tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2765.
Abstract 2774: High levels of 5-hydroxymethylcytosine (5hmC) predict biochemical recurrence after prostatectomy in ERG negative prostate cancer
Authors: Strand Siri H. , Hoyer Soren , Lynnerup Anne-Sofie , Haldrup Christa , Storebjerg Tine M. , Borre Michael , Orntoft Torben F. , Sorensen Karina D. 
Published: July 2016

Abstract
Background: Prostate cancer (PC) can be stratified into distinct molecular subtypes based on TMPRSS2-ERG gene fusion status, but its potential prognostic value remains controversial. Likewise, routine clinicopathological features cannot clearly distinguish aggressive from indolent tumors at the time of diagnosis, thus new prognostic biomarkers are urgently needed. The DNA methylation variant 5-hydroxymethylcytosine (5hmC, an oxidized derivative of 5-methylcytosine) has recently emerged as a new diagnostic and/or prognostic biomarker candidate for several human malignancies. However, this remains to be systematically investigated for PC. In this study, we determined 5hmC levels in 311 PC (stratified by ERG status) and 228 adjacent non-malignant (NM) prostate tissue specimens by immunohistochemical analysis of a tissue microarray, representing a large radical prostatectomy (RP) cohort with long clinical follow-up. We investigated possible correlations between 5hmC and routine clinicopathological variables and assessed the prognostic potential of 5hmC by Kaplan-Meier, uni- and multivariate Cox regression analyses in ERG+ (n = 178) vs. ERG- (n = 133) PCs using biochemical recurrence (BCR) as endpoint.
Results: We observed a borderline significant (p = 0.06) reduction in 5hmC levels in PC compared to NM tissue samples, which was explained by a highly significant (p&lt;0.001) loss of 5hmC in ERG- PCs. ERG status was not predictive of BCR in this cohort (p = 0.73) and no significant association was found between BCR and 5hmC levels in ERG+ PCs (p = 0.98). In contrast, high 5hmC immunoreactivity was a significant adverse predictor of BCR after RP in ERG- PCs, independent of Gleason score, pathological tumor stage, surgical margin status, and pre-operative PSA level (HR (95% CI): 1.62 (1.15-2.28), p = 0.006).
Conclusions: This is the first study to demonstrate a prognostic potential for 5hmC in PC. Our findings highlight the importance of ERG stratification in PC biomarker studies, and suggest that epigenetic mechanisms involving 5hmC are important for the development and/or progression of ERG- PC.
Citation Format: Siri H. Strand, Soren Hoyer, Anne-Sofie Lynnerup, Christa Haldrup, Tine M. Storebjerg, Michael Borre, Torben F. Orntoft, Karina D. Sorensen. High levels of 5-hydroxymethylcytosine (5hmC) predict biochemical recurrence after prostatectomy in ERG negative prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2774.
Abstract 2783: Integrated genomics and epigenomics analysis reveals genome-wide effect of the DNA methyltransferase inhibitor 5-azacitidine (Aza) on regulation of transcription
Authors: Bai Yuchen , Palescandolo Emanuele , Whitaker John , Krishna Vinod , Bhargava Vipul , Saxena Satya , Yao Xiang , Pocalyko David , Bachman Kurtis 
Published: July 2016

Abstract
DNA methyltransferase inhibitors (DNMTi) such as 5-azacytidine(Aza) are clinically used in treating hematologic malignancies. Promising effects were also observed in solid tumors, although the exact mechanism underlining the efficacy was unclear. There has been accumulating evidence suggesting an enhanced immune response to the tumor cells following such epigenetic therapies. Cancer immunotherapies targeting checkpoint inhibition in combination with epigenetic agents such as a DNMTi could hold promise for those patients that do not respond to immunotherapies alone. Aza was also found to stimulate an interferon response in tumor cells via inducing expression of endogenous retroviruses. In this study, we were interested to further explore the mechanisms of AZA on transcription regulation across the whole regulome.
HCT-116 is a colon cancer cell line genetically defined by microsatellite instability (MSI) and mutations in KRAS(G13D) and PIK3CA(H1047R). In this study, HCT-116 cells were treated with DMSO (control) or 1μM Aza for 42 and 96 hours. RNA-seq, Mass spectrometry proteomics, RRBS, Chip-Seq, ATAC-Seq and Hi-C data was collected. Data was analyzed by integrative computational methods. Treatment with Aza resulted in global demethylation at CpG islands(CGI), which was moderately correlated with increased expression of the corresponding genes. DNA methylation, DNA accessibility, H3K4me3 (active promoter histone mark), H3K27me3 (repressive histone mark) and RNA expression revealed and cross-verified different states of genomic regions. Pathway and gene set enrichment analysis found activation of anti-viral defense and interferon pathways, as well as increased expression of cancer-testis antigens. IRF7 expression was increased by Aza, and IRF binding motifs were the most enriched TF motifs at the immediate promoter regions of the up-regulated genes. The data also suggested that Aza may remove gene repression by disrupting the scaffolding function of DNMTs. The effects of Aza on promoter-enhancer interactions were also examined by Hi-C. In conclusion, we found that DNMTi such as Aza regulates gene transcription through multiple modes of actions.
Citation Format: Yuchen Bai, Emanuele Palescandolo, John Whitaker, Vinod Krishna, Vipul Bhargava, Satya Saxena, Xiang Yao, David Pocalyko, Kurtis Bachman. Integrated genomics and epigenomics analysis reveals genome-wide effect of the DNA methyltransferase inhibitor 5-azacitidine (Aza) on regulation of transcription. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2783.
Abstract 2787: Expression of Olfactomedin 4 is regulated by methylation in the benign prostate epithelial cell-RWPE1 and PC-3 prostate cancer cells
Authors: Li Hongzhen 
Published: July 2016

Abstract
Expression of Olfactomedin 4 gene (OLFM4) plays a critical tumor suppressor role in human and murine prostate cancer. We have previously reported that loss or reduced OLFM4 expression is associated with the progression of human prostate cancer. We and others have further determined that deletions within the OLFM4 gene are present in about 10 to 25% of human prostate cancer samples. However, we have observed that loss of expression of OLFM4 were found in more than 58% of the samples obtained from advanced prostate cancer patients. Therefore, we sought to study the role of epigenetic factors in the regulation of OLFM4 gene expression in normal and prostate cancer cell lines. Methylation of CpG sites in the promoter region of key genes is an important epigenetic mechanism in cancer development. We examined the methylation status of CpG sites in the OLFM4 promoter region in the benign immortalized prostate epithelial cell line (RWPE1), androgen-responsive cancer cells (LNCaP, VCaP), and androgen-independent cancer cells (PC-3 and DU145).
There are eight CpG sites (-681, -666, -562, -486, -91, +4, +34) in the promoter regions of OLFM4 gene. The pattern of methylation status was detected and compared between RWPE1 cell and cancer cell lines LNCaP, VCaP, PC-3 and Du145. To test whether hypermethylation of CpG sites of OLFM4 gene can block the expression of OLFM4 gene, RWPE1 cells were treated with 5-azadeoxycytidine (5-Aza.) (5 μM) from 24h to 96h and PC-3 cells were treated with 5-azadeoxycytidine (5-Aza.) (5 μM) for 3 days and 7 days. The methylation status of CpG sites was compared in the presence or absence of 5-Aza. at different time points. The addition of 5-Aza. consistently reduced the percent methylation of the CpG sites. Correspondingly, the expression of the OLFM4 gene was induced after treatment with 5-Aza. in both RWPE1 and PC-3 cells. These results suggest that expression of OLFM4 is regulated by the methylation status of OLFM4 gene in the RWPE1 and PC-3 prostatic cell lines.
Citation Format: Hongzhen Li. Expression of Olfactomedin 4 is regulated by methylation in the benign prostate epithelial cell-RWPE1 and PC-3 prostate cancer cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2787.
Abstract 2794: Six-transmembrane epithelial antigen of prostate 4 (STEAP4): an important link between hypoxia, inflammation, nutrition and tumorigenesis in the intestine
Authors: Xue Xiang , Shah Yatrik 
Published: July 2016

Abstract
Hypoxia occurred in the inflammatory foci can further increase the pro-inflammatory response. Moreover, inflammatory hypoxia is critical for altering tissue metabolism and nutritional response, which can further sustain the inflammation and drive tumorigenesis. However, the mechanisms that link hypoxia, nutrition, inflammation and tumorigenesis are not clear. Through genome-wide expression analysis we identified six-transmembrane epithelial antigen of prostate 4 (STEAP4) as a gene highly induced by hypoxia. STEAP4 is an oxidoreductase that regulates inflammatory stress, fatty acid, glucose and iron metabolism. Here we demonstrate that the increase in STEAP4 is dependent on epithelial HIF-2α in mouse models of colitis. Luciferase reporter assay and ChIP assay confirmed that STEAP4 is a HIF-2α target gene. Compared to normal healthy controls, the gene expression of STEAP4 was highly induced in tissues from colitis patients. Transgenic mice overexpressing GFP-tagged STEAP4 specifically in intestinal epithelial cells demonstrated that STEAP4 was expressed primarily on the plasma and mitochondrial membrane. Interestingly, these mice had no change in serum and tissue minerals except for a slight increase in intestinal iron, specifically mitochondrial iron, but no change in systemic iron levels. STEAP4 transgenic mice were highly susceptible to acute experimental colitis model. Moreover, STEAP4 was increased in human colorectal cancer (CRC) and predicts poor prognosis. Consistently, tumor numbers in the STEAP4 transgenic overexpression mice were increased compared to wild-type littermates in a colitis-associated CRC tumor model. Mechanistically, overexpression of STEAP4 increased oxidative stress and DNA damage in the intestine. In conclusion, we have identified a novel gene induced in colitis and CRC that could link hypoxia-induced metabolic changes, inflammation and cancer.
Citation Format: Xiang Xue, Yatrik Shah. Six-transmembrane epithelial antigen of prostate 4 (STEAP4): an important link between hypoxia, inflammation, nutrition and tumorigenesis in the intestine. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2794.
Abstract 2796: Regulation of HIF-1α by hnRNP A18 contributes to tumor promotion under hypoxic conditions
Authors: Chang Elizabeth T. , Parekh Palak , Yang Qingyuan , Carrier France 
Published: July 2016

Abstract
The RNA-binding protein heterogenous ribonucleoprotein A18 (hnRNP A18) is a new protein translation regulator found to be elevated in many cancers. Previous work from our lab has shown that hnRNP A18 is able to bind and regulate the translation of a group of mRNAs under stress conditions, including hypoxia. Hypoxia has largely been recognized as an innate characteristic of solid tumors and plays numerous cellular and physiologic roles such as cell proliferation, invasion, migration, metastasis, and angiogenesis. Given its extensive function in solid tumors, combined with computational results showing a possible hnRNP A18 signature motif in the 3’UTR of HIF-1α, we sought to determine if hnRNP A18 binds HIF-1α mRNA and how this affects tumor promotion and growth. Results: Our data indicates that hnRNP A18 protein is able to bind HIF-1α mRNA. Under hypoxic conditions, down-regulation of hnRNP A18 significantly decreases HIF-1α mRNA stability, leading to reduced amounts of HIF-1α protein levels in melanoma cells. Treatment with CoCl2 increases hnRNP A18 protein levels in melanoma cells, but not in normal melanocytes. Additionally, colony survival assay demonstrates that down-regulation of hnRNP A18 decreases cells’ survival rates under a hypoxic environment. The functional significance of this effect was observed in a mouse xenograft model where down-regulation of hnRNP A18 significantly reduced melanoma and breast tumor growth. Immunohistochemistry staining of xenograft specimens showed overlapping localization of hnRNP A18 to the tumor hypoxic regions. Lastly, proteome profiling of the xenograft tumors showed a significant decrease of key angiogenic-related factors (e.g., angiogenin, endoglin, VEGF) when hnRNP A18 is reduced. Conclusion: Heterogenous ribonucleoprotein A18 is able to regulate HIF-1α mRNA and modulate its protein levels under hypoxic conditions. The oxygen-deprived regions generated in the central core of a solid tumor leads to up-regulation of hnRNP A18 and consequently HIF-1α, resulting in tumor growth and promotion. New therapeutics targeting hnRNP A18 would therefore be a logical next-step in developing a novel mechanism-based therapy for cancer treatment.
Citation Format: Elizabeth T. Chang, Palak Parekh, Qingyuan Yang, France Carrier. Regulation of HIF-1α by hnRNP A18 contributes to tumor promotion under hypoxic conditions. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2796.
Abstract 2797: Role of the ST6Gal-I glycosyltransferase in protecting tumor cells against hypoxia
Authors: Jones Robert B. 
Published: July 2016

Abstract
A change in surface glycosylation was one of the first identified hallmarks of a cancer cell, however an understanding of how altered glycosylation affects cancer cell biology remains unclear. Our group has shown that ST6Gal-I, a glycosyltransferase that adds negatively charged sialic acids to surface receptors in a α2-6-linked manner, is upregulated in many cancer types. Through modulating the activity of various receptors, ST6Gal-I can act as a pro-survival factor in a variety of settings, including resistance to some chemotherapeutics. Tumor microenvironment plays a crucial role in cancer progression. One key component of the tumor microenvironment is the availability of oxygen, and in solid tumors there can be areas of hypoxia. Hypoxia leads to the induction of hypoxia inducible factors (HIFs), which are transcriptional regulators of the cellular response to low oxygen tension. HIFs such as HIF-1a, regulate the transcription of many proteins necessary for cells to survive when challenged by hypoxia. In this study we demonstrated that forced overexpression of ST6Gal-I in both ovarian and pancreatic cancer cell lines increased the stabilization of HIF-1a after treatment with the hypoxia mimetics desferrioxamine and DMOG, and when grown in a hypoxic environment. Correspondingly, knockdown of ST6Gal-I inhibited the stabilization of HIF-1a in these same conditions. Additionally, ST6Gal-I activity stimulates pro-survival signaling through phosphorylated NFκB and AMPK in these same models. These signaling pathways have been shown to be important for cellular survival in hypoxic environments. Markers of HIF-1a-induced transcription were investigated through qRT-PCR, and it was revealed that the ST6Gal-I-mediated stabilization of HIF-1a increased the levels of PDHK1and GLUT1 mRNA. Both GLUT1 and PDHK1 promote the shift in glucose metabolism when cells are in a low oxygen environment. Taken together, these data indicate that ST6Gal-I acts as a pro-survival factor by eliciting a more robust response by HIF-1a. The finding that a glycosyltransferase regulates the cellular response to hypoxia represents a novel paradigm in hypoxia signaling.
Citation Format: Robert B. Jones. Role of the ST6Gal-I glycosyltransferase in protecting tumor cells against hypoxia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2797.