bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2891: High throughput single cell gene expression profiling by multiplex qPCR
Authors: Okino Steven T. , Kong Michelle , Ma Jason , Fenrich Joshua , Boveri Luca , Jouvenot Yann , Wang Yan 
Published: July 2016

Abstract
Single cell gene expression analysis is a powerful technique that provides a unique and insightful perspective on biological pathways and processes. Here we present a robust workflow that enables fast and accurate analysis of up to 100 genes in isolated single cells. Our workflow is highly sensitive, by assessing RNA reference standards we find that a single RNA transcript is detected with about 80% efficiency. We used this workflow to study differentiation in cultured NTera2 cells (NT2), a human embryonic stem cell model system. We analyzed untreated NT2 cells, and NT2 cells treated with low and high doses of retinoic acid (RA) for 10 days to initiate differentiation to a neuronal lineage. The expression levels of 16 genes were quantified in 164 single cells by multiplex real-time qPCR with two technical replicates. The entire experiment, from cultured cells to results, can be completed in 2-3 days and requires four 384-well qPCR plates for gene expression quantification. We find that control cells and cells treated with a high dose of RA (10 uM) are relatively homogeneous in the expression levels of the targeted genes. However cells treated with a low dose of RA (0.25 uM) exhibit significant heterogeneity with respect to gene expression; about half of the cells are similar to the high-dose RA cells, the other cells exhibit a wide range of partial differentiation. Interestingly, we find that LEFTY2 expression is almost exclusive to the low dose RA cells and strongly correlates with partial differentiation. A time-course study analyzing cell populations reveals that LEFTY2 is only transiently expressed in differentiating NT2 cells with peak expression at 3 days of high dose RA treatment. These findings imply that, in NT2 cells, LEFTY2 is a potential biomarker of early differentiation. In summary, we present an accurate, sensitive and robust single cell analysis procedure that uses standard reagents and platforms. We envision that this workflow will enable researchers to investigate cell heterogeneity in biological pathways in a cost-effective way.
Citation Format: Steven T. Okino, Michelle Kong, Jason Ma, Joshua Fenrich, Luca Boveri, Yann Jouvenot, Yan Wang. High throughput single cell gene expression profiling by multiplex qPCR. [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 2891.
Abstract 2903: Nuclear localization of a secretion protein NAG-1/GDF15
Authors: Min Kyung-Won , Silva Gabriel , Baek Seung J. 
Published: July 2016

Abstract
Nonsteroidal anti-inflammatory drug (NSAID)-activated gene (NAG-1, also known as GDF15) is a divergent member of the transforming growth factor-beta (TGF-β) superfamily, which exert their biological activity by binding to membrane receptors as a secretion protein. Abnormal regulation of TGF-β signaling can contribute to various diseases such as cancer. Although there is sequence similarity between NAG-1 and other TGF-β superfamily members, NAG-1 does not bind to the TGF-β receptors; therefore the biological consequence of NAG-1 remains to be elucidated. Here, we report that NAG-1 has two putative non-canonical nuclear localization signals (NLSs) that mediate NAG-1 nuclear localization. Nuclear import assay shows that NAG-1 enters the nucleus through nuclear pore complex (NPC) in the presence of ATP, indicating nuclear entry of NAG-1 is active transport. Furthermore, we found the nuclear export signal (NES) recognized by CRM1 at near N-terminal region of NAG-1, that is conserved across various mammalian species. Impeding NES via chemical or genetic approaches promotes nuclear accumulation of NAG-1. We also found that nuclear NAG-1 dampens TGF-β-mediated cell migration and invasion via the inhibition of DNA binding of Smads complex. Overall, our data suggest that nuclear NAG-1 affects TGF-β-induced metastasis activity in cancer cells.
Grant support: This work was supported by grant from the University of Tennessee Center of Excellence in Livestock Diseases and Human Health.
K Min, Current address: Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
Citation Format: Kyung-Won Min, Gabriel Silva, Seung J. Baek. Nuclear localization of a secretion protein NAG-1/GDF15. [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 2903.
Abstract 2908: The clinical significance of Nrf2 overexpression in esophageal cancer
Authors: Kitano Yuki , Baba Yoshifumi , Yamamura Kensuke , Shigaki Hironobu , Mima Kousuke , Kurashige Junji , Iwatsuki Masaaki , Sakamoto Yasuo , Miyamoto Yuji , Yoshida Naoya , Baba Hideo 
Published: July 2016

Abstract
Background: NF-E2-related factor 2 (Nrf2) is a key transcription regulator for antioxidant and detoxification enzyme and is overexpressed in various cancer cells. In this study, prognostic significance of Nrf2 expression in esophageal cancer was investigated. In addition, we examined the relationship between the expression of Nrf2 and cell proliferation using in vitro assay.
Methods: We immunohistochemically evaluated the protein expression of Nrf2 in the surgically resected specimens in 83 esophageal cancer patients. And ten esophageal cancer cell lines were utilized in vitro assay.
Results: We examined the protein expression of Nrf2 in 10 esophageal cancer cell lines. TE-11 cell had the highest expression of Nrf2, while KYSE30 had the lowest expression of Nrf2. Importantly, there was no correlation between the protein level and mRNA level of Nrf2 in these cell lines. The cell proliferation was inhibited in TE-11 cells, and not inhibited in KYSE30 cells by treatment with Nrf2-siRNA. Moreover, Flow Cytometry Assay revealed that knockdown of Nrf2 by siRNA arrested the cell cycle at G1 phase in TE-11 cells. In immunohistological study, Nrf2 was predominantly identified in the nucleus of esophageal cancer cells and the expression level of Nrf2 was higher in the tumor than normal esophageal epithelium (P&lt;0.001). There was no relationship between Nrf2 protein expression and clinicopathological characteristics. The overall survival of the high-Nrf2 expression group was significantly poorer than that of low-Nrf2 expression group (P = 0.004).
Conclusions: The expression of Nrf2 is up-regulated in esophageal cancer cell lines and resected tumor specimen. Our in vitro assay revealed that Nrf2 appeared to support cancer cell proliferation. Therefore, strategies to pharmacologically manipulate the level and / or activity of Nrf2 may have potential to reduce tumor growth and improve the prognosis of esophageal cancer patients.
Citation Format: Yuki Kitano, Yoshifumi Baba, Kensuke Yamamura, Hironobu Shigaki, Kousuke Mima, Junji Kurashige, Masaaki Iwatsuki, Yasuo Sakamoto, Yuji Miyamoto, Naoya Yoshida, Hideo Baba. The clinical significance of Nrf2 overexpression in esophageal 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 2908.
Abstract 2909: Correlation between the expression of Sox2, Oct4 and deltaNp63 in clinical samples of resected esophageal cancers
Authors: Inokawa Yoshikuni , Inaoka Kenichi , Sonohara Fuminori , Oya Hisaharu , Hayashi Masamichi , Niwa Yukiko , Iwata Naoki , Kobayashi Daisuke , Koike Masahiko , Kodera Yasuhiro , Nomoto Shuji 
Published: July 2016

Abstract
Background. DeltaNp63 is the oncogenic isoform in several squamous cell carcinomas including esophageal cancer (EC), however, the mechanisms of regulation of the expression are still unclear. Sox2 and Oct4 are well known transcription factors which function in cancer stemness. We supposed that these two molecules work as transcription factors on deltaNp63, and verified the expression of these genes in cases of resected squamous cell EC.
Methods. In 78 surgical specimens of squamous cell EC with no prior neoadjuvant therapy, messenger RNA (mRNA) expression of deltaNp63, Sox2 and Oct4 in EC tissues and corresponding normal tissues was analyzed by quantitative real-time reverse transcription-polymerase chain reaction assay. The mRNA expression was standardized to that of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA. The expressions were compared in terms of clinicopathological factors and prognosis of postoperative survivals.
Results. Peason correlation analysis showed significant correlations between expression of deltaNp63 and Sox2 in tumor tissues (r = 0.67, P&lt;0.001), and between deltaNp63 and Oct4 (r = 0.71, P&lt;0.001). The deltaNp63 expressions in tumor tissues were significantly higher than that in corresponding normal tissues (P&lt;0.001), whereas Sox2 and Oct4 did not show significant differences between cancer and non-cancerous tissues. Univariate analysis identified poor differentiation, lymphatic involvement and higher ratio (Tumor/Normal) of expression of Oct4 as significant prognostic factors for poor overall survival, however, lymphatic involvement was the only independent prognostic factor in multivariate analysis (hazard ratio: 5.34; P&lt;0.001).
Conclusions. Expression of deltaNp63 in EC tumor tissues showed positive correlation with expression of Sox2 and Oct4. Therefore, these two transcription factors may regulate the expression of deltaNp63. The deltaNp63 is not a strong prognostic factor, however, Oct4 might be a significant predictor for poor prognosis for overall survival in squamous cell EC.
Citation Format: Yoshikuni Inokawa, Kenichi Inaoka, Fuminori Sonohara, Hisaharu Oya, Masamichi Hayashi, Yukiko Niwa, Naoki Iwata, Daisuke Kobayashi, Masahiko Koike, Yasuhiro Kodera, Shuji Nomoto. Correlation between the expression of Sox2, Oct4 and deltaNp63 in clinical samples of resected esophageal cancers. [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 2909.
Abstract 291: Single cell analyses reveal resistance heterogeneity in EGFR mutant NSCLC
Authors: Niederst Matt J. , Zhang Huidan , Hu Haichuan , Cui Naiwen , Cai Yamei , Mulvey Hillary , Piotrowska Zofia , Sequist Lecia , Weitz David A. , Engelman Jeffrey A. 
Published: July 2016

Abstract
In EGFR mutant lung adenocarcinomas, the activating mutation to EGFR is the founder alteration, present in every cancer cell. Most patients with this genetic alteration respond to EGFR tyrosine kinase inhibitors, although the average duration of the response is only one year before the cancer develops acquired resistance. Efforts to identify the mechanisms underlying the resistance in patients have led to the identification of a resistance mechanism in the majority of cases. However, preliminary data is emerging indicating that multiple resistance mechanisms can be present within an individual patient's disease, and thus, classifying resistant disease with a single mechanism is an oversimplification. Here, utilizing single cell approaches on patient samples, we demonstrate heterogeneity within individual biopsies with respect to resistance mechanisms, epigenetic state, and sensitivity to TKI. Additionally, we observe that the fraction of T790M-positive cells is predictive of response to 3rd generation EGFR inhibitor treatment, suggesting that the degree of heterogeneity has important clinical implications. As therapies designed to target singular resistance mechanisms become more widely implemented, assessing heterogeneity will become increasingly critical in order to choose the most effective therapy for the patient.
Citation Format: Matt J. Niederst, Huidan Zhang, Haichuan Hu, Naiwen Cui, Yamei Cai, Hillary Mulvey, Zofia Piotrowska, Lecia Sequist, David A. Weitz, Jeffrey A. Engelman. Single cell analyses reveal resistance heterogeneity in EGFR mutant NSCLC. [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 291.
Abstract 2921: The retinoblastoma protein regulates hypoxia-inducible factor-1α-mediated transcriptional programs, tumor cell invasiveness, tumor growth and metastasis in human breast cancer cells
Authors: Takhar Mandeep K. , Labrecque Mark P. , Tam Kevin J. , Haegert Anne , Bell Robert H. , Altamirano-Dimas Manuel , Collins Colin C. , Prefontaine Gratien G. , Cox Michael E. , Bennewith Kevin L. , Beischlag Timothy V. 
Published: July 2016

Abstract
The retinoblastoma protein (Rb) is capable of attenuating the hypoxic response in tumor cells. This process is mediated by the hypoxia inducible factor 1α/2α (HIF1α/2α) and its dimerization partner the aryl hydrocarbon receptor nuclear translocator (ARNT/ HIF1β). Rb modulates HIF activity by virtue of its association with the thyroid hormone receptor/retinoblastoma interacting protein 230 (TRIP230), an essential cofactor of the HIF1α/ARNT transcriptional complex. We used short hairpin RNA (shRNA) technology and microarray analysis to interrogate the Rb-negative and wild-type MCF7 cell transcriptomes and generated lists of genes that were either up- or downregulated in response to both loss of Rb and hypoxia. We found that loss of Rb enhances the expression of hypoxia-regulated genes involved in invasion and epithelial-to-mesenchymal transition and significantly decreases the expression of genes involved in cell anchoring and differentiation in MCF7 and MDA-MB-231 breast cancer cells. Genes were validated using both qRT-PCR and immuno-blot analysis. Additionally, gene ontology analysis revealed that AKT and ERK1/2 are downstream effectors of hypoxic gene programs that are sensitive to loss of Rb. Furthermore, these factors regulate the acquisition of a more invasive phenotype in breast cancer cells. Finally, we found that Rb knockdown in combination with pre-treatment of cells with hypoxia increased growth of tumor foci in the lungs after i.v. injection and increased the development of spontaneous metastases from orthotopically implanted breast tumor cells in female NOD-SCID mice. Primary tumors lacking Rb demonstrated enriched protein levels of genes identified in our arrays when compared to negative control tumors. These results show that Rb is a negative modulator of hypoxia-regulated genetic programs by virtue of its direct effects on the HIF-complex. Understanding the HIF complex and the molecular mechanisms controlling the progression from benign tumors to metastasized and lethal forms will allow us to develop more specific breast cancer therapies.
Citation Format: Mandeep K. Takhar, Mark P. Labrecque, Kevin J. Tam, Anne Haegert, Robert H. Bell, Manuel Altamirano-Dimas, Colin C. Collins, Gratien G. Prefontaine, Michael E. Cox, Kevin L. Bennewith, Timothy V. Beischlag. The retinoblastoma protein regulates hypoxia-inducible factor-1α-mediated transcriptional programs, tumor cell invasiveness, tumor growth and metastasis in human breast 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 2921.
Abstract 2927: miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cell
Authors: Rasmussen Mads H. , Lyskjær Iben , Jersie-Christensen Rosa R. , Tarpgaard Line S. , Primdal-Bengtson Bjarke , Nielsen Morten M. , Pedersen Jakob S. , Hansen Tine P. , Hansen Flemming , Olsen Jesper V. , Pfeiffer Per , Ørntoft Torben F. , Andersen Claus L. 
Published: July 2016

Abstract
Oxaliplatin (oxPt) resistance in colorectal cancers (CRC) is a major medical problem, and predictive markers are urgently needed. Recently, miR-625-3p was reported as a promising predictive marker. Here, we have used in vitro models to show that miR-625-3p functionally induces oxPt resistance in CRC cells, and have identified signalling networks affected by mir-625-3p. The p38 MAPK activator MAP2K6 was shown to be a direct target of miR-625-3p, and, accordingly, was downregulated in patients not responding to oxPt therapy. miR-625-3p resistance could be reversed in CRC cells by anti-miR-625-3p treatment and by ectopic expression of a miR-625-3p insensitive MAP2K6 variant. In addition, by reducing p38 MAPK signalling using either siRNA technology, chemical inhibitors to p38 or by ectopic expression of dominant negative MAP2K6 protein we induced resistance to oxPt. Transcriptome, proteome and phosphoproteome profiles revealed inactivation of MAP2K6-p38 signalling as a possible driving force behind oxPt resistance.
Our study shows that miR-625-3p induces oxPt resistance by abrogating MAP2K6-p38 regulated apoptosis and cell cycle control networks, and corroborates the predictive power of miR-625-3p.
Citation Format: Mads H. Rasmussen, Iben Lyskjær, Rosa R. Jersie-Christensen, Line S. Tarpgaard, Bjarke Primdal-Bengtson, Morten M. Nielsen, Jakob S. Pedersen, Tine P. Hansen, Flemming Hansen, Jesper V. Olsen, Per Pfeiffer, Torben F. Ørntoft, Claus L. Andersen. miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cell. [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 2927.
Abstract 2938: Role of CD73 in promoting metastasis and resistance to 5-fluorouracil of colorectal cancer
Authors: Liu Xuan-hui , Wu Xian-rui , Chen Yu-feng , Wang Feng-wei , Zheng Xiao-bin , Xie Dan , Shen Bo , Wang Jian-ping , Wu Xiao-jian , Lan Ping 
Published: July 2016

Abstract
Background and aim: Our previous study showed that high expression of CD73 (ecto-5’-nucleotidase) was a poor prognostic biomarker in patients with colorectal cancer (CRC). However, the underlying mechanism is unclear. Metastasis and chemo-resistance are among the main causes for the poor outcomes of CRC. The aim of this study is to evaluate the role of CD73 in the metastasis and chemo-resistance in CRC.
Methods: The expression levels of CD73 were detected using quantitative RT-PCR and Western blot in 9 CRC cell lines and 3 5-FU-resistant cell lines (HCT8-FR, HCT116-FR, and RKO-FR). CD73 was overexpressed via lentiviral vector system and silenced using specific small interference RNA (si-CD73) in HCT8 and RKO. We then performed migration, invasion and MTS assays and wound healing assessment to evaluate the function of CD73 in cell progression and chemo-resistance. We conducted Cignal Finder Reporter Array to assess the main downstream signaling pathways of CD73.
Results: Increased expression of CD73 was found in all 3 5-FU-resistant cell lines. Inhibition of CD73 expression in HCT8 and RKO by si-CD73 attenuated the capacity of cell migration and invasion but increased the sensitivity to 5-FU. On the other hand, overexpression of CD73 in HCT8 and RKO increased the capacity for cell migration but decreased the sensitivity to 5-FU. CD73-induced migration and chemo-resistance was found to be associated with the activation of MAPK/ERK pathway.
Conclusions: High expression of CD73 was found to be associated with the metastasis and resistance to 5-FU via the activation of MAPK/ERK signaling pathway. This finding provides a molecular basis for the role of CD73 in the progression of CRC, suggesting a novel target for the treatment of CRC.
Citation Format: Xuan-hui Liu, Xian-rui Wu, Yu-feng Chen, Feng-wei Wang, Xiao-bin Zheng, Dan Xie, Bo Shen, Jian-ping Wang, Xiao-jian Wu, Ping Lan. Role of CD73 in promoting metastasis and resistance to 5-fluorouracil of colorectal 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 2938.
Abstract 2939: Heregulin-induced resistance against HER2-targeted therapies in HER2 positive breast and gastric cancer in vitro and in vivo
Authors: Nonagase Yoshikane , Yonesaka Kimio , Watanabe Satomi , Haratani Koji , Takahama Takayuki , Takegawa Naoki , Ueda Hiroto , Kawakami Hisato , Hayashi Hidetoshi , Takeda Masayuki , Sakamoto Haruka , Tamura Takao , Nakagawa Kazuhiko , Tsurutani Junji 
Published: July 2016

Abstract
Background
HER2-targeted therapies have been shown clinical benefits in patients with HER2 positive breast and gastric cancers. However, resistance against such targeted therapies eventually develops in most cases. Overexpression of heregulin, a ligand for HER3, has been reported as one of the resistant mechanism against HER2-targeted therapies. Upregulation of heregulin activates HER3-PI3K-AKT signaling, leading to the resistance against HER2-targeted therapies. We investigated the effects of heregulin in cell lines and evaluate its clinical impacts in HER2 positive breast and gastric cancers.
Materials and methods
We utilized transfected or recombinant heregulin to investigate the effect of heregulin on proliferation and apoptosis of SK-BR-3 and NCI-N87 cell lines treated with lapatinib, trastuzumab, trastuzumab-emtansine and paclitaxel. Clinical data and specimens were obtained from patients with HER2 positive breast and gastric cancers, evaluating their heregulin value from both serum and tissues using ELISA and RT-PCR, respectively.
Results
Heregulin transfection and recombinant heregulin conferred resistance against treatment with lapatinib, trastuzumab, and weak resistance against trastuzumab-emtansine, but no resistance against paclitaxel in HER2 positive cell lines. Clinical data of heregulin among patients treated with HER2-targeted therapies revealed that patients with relatively high heregulin value tended to have worse prognosis.
Conclusions
Together these data, overexpression of heregulin may at least in part play a role in resistance against HER2-targeted therapies in HER2 positive cancer patients. Further investigation is warranted to elucidate the relevance of treatments targeting heregulin-HER3-PI3K signaling.
Citation Format: Yoshikane Nonagase, Kimio Yonesaka, Satomi Watanabe, Koji Haratani, Takayuki Takahama, Naoki Takegawa, Hiroto Ueda, Hisato Kawakami, Hidetoshi Hayashi, Masayuki Takeda, Haruka Sakamoto, Takao Tamura, Kazuhiko Nakagawa, Junji Tsurutani. Heregulin-induced resistance against HER2-targeted therapies in HER2 positive breast and gastric cancer in vitro and in vivo. [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 2939.