bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract IA07: Metabolic heterogeneity in cancer cells and tumors
Authors: DeBerardinis Ralph J.
Published: May 2016

Most diseases are accompanied by altered metabolism at the cellular level. In cancer, metabolic reprogramming that is, the regulated alteration of metabolism as a consequence of tumorigenic mutations and other factors is viewed as an essential component of malignant transformation. It is unknown to what extent cell-autonomous vs. non-cell autonomous factors influence metabolic pathway choice. We performed metabolic profiling in a large panel of molecularly annotated non-small cell lung cancer (NSCLC) cell lines grown in standard monolayer culture in order to define the scope of cell-autonomous metabolic variability in this disease and to understand the mechanisms by which metabolic phenotypes are established. We then identified a new pathway that allows cells to tolerate a cell-extrinsic stress: the loss of anchorage dependence. Regardless of the intrinsic metabolic preferences in monolayer culture, NSCLC cells activated an unconventional pathway allowing reducing equivalents to shuttle from the cytosol to the mitochondria to counteract oxidative stress during anchorage loss. Finally, we performed clinical studies involving a combination of pre-surgical imaging and intra-operative 13C infusions to assess metabolic heterogeneity between individual NSCLC tumors in human patients, and to characterize the extent of metabolic heterogeneity within individual tumors. These studies revealed enhanced glycolysis and glucose oxidation in tumors compared to adjacent lung, regardless of driver mutation. Surprisingly, we also found that regional metabolic heterogeneity could be mapped prior to surgery by examining tissue perfusion using contrast MRI, and that glucose’s contribution to central carbon metabolism is inversely proportional to tumor perfusion. Together, these efforts identify a complex but finite set of metabolic phenotypes that support cell growth and may predict therapeutic vulnerabilities. They also underscore the potential for both existing and novel imaging approaches to inform about metabolic phenotypes in vivo, including phenotypes specified by both cell-intrinsic and cell-extrinsic factors.

Citation Format: Ralph J. DeBerardinis. Metabolic heterogeneity in cancer cells and tumors. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA07.
Abstract IA08: Hypoxia, metabolism, and tumor progression
Authors: Simon M Celeste
Published: May 2016

Solid tumors typically develop hostile microenvironments characterized by irregular vascularization and poor oxygen (O2) and nutrient supply. Whereas normal cells modulate anabolic and catabolic pathways in response to changes in nutrient availability, cancer cells exhibit unregulated growth even under nutrient scarcity. Recent studies have demonstrated that constitutive activation of growth-promoting pathways results in dependence on unsaturated fatty acids for survival under O2 deprivation. In cancer cells, this dependence represents a critical metabolic vulnerability that could be exploited therapeutically. I will review how this dependence on unsaturated lipids is affected by the microenvironmental conditions faced by cancer cells.

Citation Format: M Celeste Simon. Hypoxia, metabolism, and tumor progression. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA08.
Abstract IA13: Clonal dynamics of normal and malignant human mammary cell growth in xenografts
Authors: Eaves Connie J. , Nguyen Long , Pellacani Davide , Kannan Nagarajan , Lefort Sylvan , Balani Sneha , Cox Claire , Osako Tomo , Aparicio Samuel , Hirst Martin
Published: May 2016

Most human breast cancers have diversified genomically and biologically by the time they become clinically evident and little is known about their origin from normal human mammary cells, or the cellular and molecular mechanisms that lead to their genesis and evolution. We have developed methods to quantify, purify and characterize different subsets of normal human mammary cells and have used these to identify properties that may influence their propensity for transformation. We have also developed methods for inducing the rapid transformation in vivo of these purified subsets following their transplantation into immunodeficient mice. The results demonstrate the ability of a single oncogene (KRASG12D) to induce the formation of serially transplantable, polyclonal, invasive ductal carcinomas within 8 weeks of being introduced either subrenally or subcutaneously into immunodeficient mice. Both primary and secondary tumors are phenotypically heterogeneous and transcriptome analyses of primary tumors assign them to a “normal-like” category. DNA barcoding of the cells at the time of their initial transduction with KRASG12D has revealed a dramatic change in the numbers and sizes of clones they generate after 2 weeks in vivo. DNA barcoding also showed the unexpected appearance of many “new” clones in tumors generated upon passage into secondary recipients, thus recapitulating some features of in vivo passaged human breast cancer cell lines and patients’ tumor xenografts. This system challenges previous concepts about the process of human mammary oncogenesis and provides a new system for analyzing factors that can influence its speed, efficiency and heterogeneity of outcomes.

Citation Format: Connie J. Eaves, Long Nguyen, Davide Pellacani, Nagarajan Kannan, Sylvan Lefort, Sneha Balani, Claire Cox, Tomo Osako, Samuel Aparicio, Martin Hirst. Clonal dynamics of normal and malignant human mammary cell growth in xenografts. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA13.
Abstract IA16: Clonal evolution in breast cancer patients and patient derived xenografts
Authors: Aparicio Samuel
Published: May 2016

The notion that most cancers are ecosystems of evolving clones has implications for biological understanding and clinical application. The evolution of clonal composition has particular significance when evidence of positive or negative selection can be associated with the clonal genotype or epigenotype. Over the last 4 years next generation sequencing of tumors and methods for single cell analysis have opened up this approach for solid epithelial malignancies. I will discuss the implications of clonal evolution for cancer medicine and biological studies of cancer with reference to breast cancers. We have developed informatics approaches to population level clonal analysis and extended these to single cell measurements of genotypes. I shall discuss our more recent data from single cell sequencing and clonal analysis applied to clonal evolution of patient derived tumor xenografts, to illustrate the impact of clonal evolution on biological studies of cancer in model systems.

Citation Format: Samuel Aparicio. Clonal evolution in breast cancer patients and patient derived xenografts. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA16.
Abstract IA19: Cancer epigenomics: From knowledge to applications
Authors: Esteller Manel
Published: May 2016

For the last twenty-five years an increasing amount of evidence has shown the relevance of epigenetics in cell biology and tissue physiology, being DNA methylation aberrations in cancer the flag-ship for the recognition of its disturbance in human diseases. From the candidate gene approaches, new powerful technologies such as comprehensive DNA methylation microarrays and whole genome bisulfite sequencing has recently emerged that have reinforced the notion of epigenetic disruption in the crossroad of many sickness. From the poster-boy cases of MGMT and GSTP1 hypermethylation in the prediction of alkylating drug response and prostate cancer detection, respectively, to the personalized treatment of leukemia with small molecules targeted to fusion proteins involving histone modifiers such as DOT1L and MLL, the field has walked a long path. The current talk will focus in the epigenetic profiling, basically at the level of DNA methylation and histone modifications, that is starting to provide clinical value in the diagnosis, prognosis and prediction of response to drug therapies, with an emphasis in neoplasia, but without forgetting the novel advances in other human disorders. For cancer, we have already a wide view of the undergoing DNA methylation events that expand beyond classical promoter CpG islands of tumor suppressor genes and we have a growing list of mutated chromatin remodeler genes that contributes to the tumorigenesis process. It is time to apply this knowledge in practical clinical situations like the diagnosis of cancers of unknown primary, the screening of malignancies in high-risk populations or a biomarker selection of the patients that should receive treatment with epigenetic drugs.

Citation Format: Manel Esteller, Sr. Cancer epigenomics: From knowledge to applications. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA19.
Abstract IA21: Ras oncogene in cancer pathogenesis and therapy
Authors: Bar-Sagi Dafna
Published: May 2016

Mutations in ras genes are highly prevalent in human cancers and are universally predictive of resistance to virtually all anti-cancer therapeutic modalities. Mutant Ras proteins are endowed with a diverse set of biological capabilities that impinge on homeostatic mechanisms that control cell growth and survival. We have been interested in defining the molecular basis of these capabilities and delineating their contribution to the execution of the oncogenic program. Specifically, our recent efforts have focused on the impact of Ras-dependent oncogenic output on key elements of tumor evolution - metabolic reprogramming, immune evasion and genomic stability. The presentation will provide updates pertaining to these efforts highlighting newly identified Ras-dependent vulnerabilities that could potentially be exploited in the design of therapeutic interventions.

Citation Format: Dafna Bar-Sagi. Ras oncogene in cancer pathogenesis and therapy. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA21.
Abstract IA28: Preclinical strategies to target resistance in colorectal cancer: Opportunities and challenges
Authors: Trusolino Livio , Sassi Francesco
Published: May 2016

More than ten years after completion of the Human Genome Project, genetic alterations with causative roles in cancer have been identified. Inhibitors that target druggable mutant gene products have been developed. Finally, a number of these drugs have entered the clinic and are now used in patients.

Some fundamental issues need to be addressed before the informative potential of genome-wide molecular surveys is translated into clinical benefit. First, given the heavy mutational load accrued during neoplastic progression, driver alterations are difficult to distinguish from passenger events. Second, next-generation approaches are likely to identify previously neglected small subsets of very rare variants, which requires population-scale studies for statistically solid genotype/response correlations. Third, not always does the presence of an oncogenic driver predict response. Therefore, treatment paradigm may not be decided on the sole basis of the mutational status of a single gene with potential cancer-causing function, but rather on the basis of the heterogeneous context in which that mutation is found (precision medicine).

All these challenges also apply to metastatic colorectal cancer (mCRC). Less than 20% of mCRC patients respond to anti-EGFR antibodies, the gold standard targeted therapy, which calls for the identification of novel predictive biomarkers and suggests that uncharacterized drivers other than EGFR can sustain the growth of different CRC subsets. The categorization of tumor subpopulations featuring specific driver lesions, the validation of such lesions as targets, and the need for discrimination between “actionable” opportunities and those with weak clinical transferability require reliable preclinical models. The scope of our research is to refine genetic, mechanistic and therapeutic annotation of mCRC subsets using predictive in vivo models as a means to systematically increase the success rate of rationally based clinical trials that emanate from preclinical findings.

Citation Format: Livio Trusolino, Francesco Sassi. Preclinical strategies to target resistance in colorectal cancer: Opportunities and challenges. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA28.
Abstract IA31: Mechanisms of resistance to EGFR inhibitors in lung cancer
Authors: Jänne Pasi
Published: May 2016

Epidermal Growth Factor Receptor (EGFR) tyrosine kinase inhibitors (TKIs), including geftinib, erlotinib and afatinib are the standard of care for patients with advanced EGFR mutant non-small cell lung cancer. Treatment with an EGFR TKI leads to a response rate of ~60% and a median progression free survival ranging from 9 to 11 months. Acquired drug resistance inevitably develops in most of not all EGFR mutant lung cancer patients treated with EGFR inhibitors. The most common mechanism of acquired resistance is the development of a secondary EGFR T790M mutation. Other mechanism of resistance include activation of bypass signaling pathways (such as MET or HER2) and histological transformation. Over the last few years a series of new structurally distinct EGFR inhibitors have been identified and entered the clinic that are capable of inhibiting EGFR T790M. This class of mutant selective EGFR TKIs are effective both against the activating EGFR mutation and the drug resistant T790M but spare inhibition of wild type (WT) EGFR. This has enormous potential therapeutic implications as the side effects of all approved EGFR inhibitors is derived from inhibition of WT EGFR. Several of these agents, including AZD9291 and rociletinib (CO-1686) are in advanced stage clinical development. Both agents have been granted FDA’s breakthrough designation. In EGFR inhibitor resistant patients who have developed resistance to current clinical EGFR inhibitors through T790M, the response rates to either AZD9291 or rociletinib is over 60% with median progression free survivals of ~ 10 months. Current research efforts and clinical studies are focusing on a.) understanding mechanisms of drug resistance to this new class of EGFR inhibitors, b.) the development of rationale combination therapies and c.) use of these agents as initial treatment (instead of currently approved EGFR inhibitors) for patients with advanced EGFR mutant NSCLC.

Citation Format: Pasi Jänne. Mechanisms of resistance to EGFR inhibitors in lung cancer. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr IA31.
Abstract PR01: Oncogenic Kras-induced mitochondrial oxidative stress in pancreatic acini modulates the formation of precancerous lesions through autocrine EGFR signaling
Authors: Liou Geou-Yarh , Doeppler Heike , DelGirono Kathleen E. , Crawford Howard C. , Murphy Michael P. , Storz Peter
Published: May 2016

The development of pancreatic cancer requires both obtain of oncogenic Kras mutations and up-regulation of growth factor signaling. However, how oncogenic Kras regulates growth factor signaling in pancreatic cancer development is still unclear. Using a transgenic mouse model harboring an oncogenic Kras mutation and a 3D organoid explant culture of primary pancreatic acini, we here show that expression of mutant Kras in pancreatic acinar cells alters their mitochondrial metabolism, resulting in increased generation of mitochondrial reactive oxygen species (mROS). We further demonstrate that mROS induced by oncogenic Kras is required for transdifferentiating acinar cells to a duct-like phenotype and eventually progression to pancreatic intraepithelial neoplasia (PanIN), the most common precursor lesions of pancreatic ductal adenocarcinoma (PDAC). This transdiffentiation process is mediated by increased levels of epidermal growth factor receptor (EGFR) as well as its ligands, EGF and TGFα, through activation of the ROS-receptive transcription factors, NF-κB1 and NF-κB2. In Kas transgenic mice, the interception of KrasG12D-mediated generation of mROS significantly reduced the formation of pre-neoplastic lesions. Hence, our data provide mechanistic insight of how oncogenic Kras mutant crosstalks with growth factor signaling to cause the formation of pancreatic cancer.

Citation Format: Geou-Yarh Liou, Heike Doeppler, Kathleen E. DelGirono, Howard C. Crawford, Michael P. Murphy, Peter Storz. Oncogenic Kras-induced mitochondrial oxidative stress in pancreatic acini modulates the formation of precancerous lesions through autocrine EGFR signaling. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr PR01.
Abstract PR08: Macrophage-mediated trogocytosis leads to death of antibody-opsonized tumor cells
Authors: Velmurugan Ramraj , Challa Dilip K. , Ram Sripad , Ober Raimund J. , Ward E. Sally
Published: May 2016

The interplay between innate immune cells and antibodies to control cancerous growth is of central importance for mediating direct anti-tumor effects and the induction of long-lived anti-tumor immunity. Phagocytosis of antibody-opsonized cells by macrophages through Fcgamma receptor interactions is well characterized and leads to cell death through target cell engulfment into phagosomes. By contrast, the contribution of the related process called trogocytosis, involving the ingestion of limited amounts of the target cell by phagocytic cells, to cell attrition is less certain. In the current study we have developed a high throughput, quantitative assay to distinguish whole cell phagocytosis (WCP) and trogocytosis for different macrophage:breast cancer cell combinations. These analyses, combined with long term microscopic imaging, demonstrate that trogocytosis leads to target cell death. The implementation of multifocal plane microscopy to investigate trogocytic events at high spatiotemporal resolution reveals that these processes involve tubular extensions of opsonized tumor cells that are subsequently pinched off by the recipient macrophage. Of relevance to the design of second generation antibodies with improved efficacy, antibody engineering to enhance Fcgamma receptor interactions results in increased trogocytic activity. Collectively, these studies have significance to the rapidly expanding use of antibodies to treat cancer.

Citation Format: Ramraj Velmurugan, Dilip K. Challa, Sripad Ram, Raimund J. Ober, E. Sally Ward. Macrophage-mediated trogocytosis leads to death of antibody-opsonized tumor cells. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr PR08.
Abstract A04: LINC00467 regulates the autophagy signaling pathway STK11/AMPK
Authors: Guo Sujuan , Pridham Kevin , Sheng Zhi
Published: May 2016

Mounting evidence has established a fundamental role of autophagy (a self-digestion process) in tumor initiation and progression. Hence, targeting autophagy is a promising strategy for developing effective therapies to treat cancer. In our previous genome-wide RNA interference screen, we identified a set of genes that regulate autophagy in human chronic myeloid leukemia K562 cells. One of the candidates is LINC00467 (long intergenic noncoding RNA 00467), a long non-coding RNA (LncRNA) known for apoptosis regulation in neuroblastoma. LncRNA is a new RNA species with important role in gene expression regulation. Although the role of LncRNAs in apoptosis has been extensively studied. Whether or how LncRNA regulate autophagy has not yet been explored. Our previous work has established that LINC00467 regulates autophagy in different types of cancers. However, how LINC00467 regulates autophagy is largely unknown. To address this question, we first determined the stage of autophagy LINC00467 targets using a combination treatment of LINC00467 depletion and chloroquine and measuring the protein level of p62. We then monitored the activity of STK11/AMPK and MTOR, two autophagy signaling pathways, in K562 cells upon inhibition of LINC00467. We found that shRNA knockdown of LINC00467 in conjunction with chloroquine treatment significantly induced the formation of autophagic compartments manifested by the increase of Cyto-ID fluorescence. Moreover, LINC00467 knockdown substantially decreased the protein level of P62. These results indicate that Linc00467 suppresses the initiation of autophagy. To further probe the mechanism, we measured the activity of autophagy-promoting kinases STK11/AMPK, and autophagy-inhibiting kinase MTOR. Our results showed that Linc00467 knockdown substantially enhanced the activity/expression of STK11/AMPK while inhibiting that of MTOR, consistent with the inhibition of BCR-ABL using imatinib. Furthermore, We showed that LINC00467 inhibition led to a delayed degradation of STK11 mRNA. Taken together, our data demonstrates that LINC00467 suppresses autophagy through blocking STK11/AMPK. These results not only reveal a new LINC00467/STK11/AMPK pathway in autophagy regulation but also provide a basis for future therapeutic development.

Citation Format: Sujuan Guo, Kevin Pridham, Zhi Sheng. LINC00467 regulates the autophagy signaling pathway STK11/AMPK. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A04.
Abstract A07: Long noncoding RNA PANCRNA1 is a novel regulator of cell growth and motility in pancreatic ductal adenocarcinoma
Authors: Karaboga Husna , Jonsson Philip , Liu Yu , Lin Chin-Yo
Published: May 2016

Recent advances in sequencing technology have been increasing our understanding of non-protein coding regions in the mammalian genome. There is growing recognition that the majority of mammalian genome produces long non-coding RNA (lncRNA). Generally, their expression is lower than protein-coding genes and they are strikingly tissue-specific. Several studies have shown that they function in various aspects of cell biology. Abnormal expression and dysregulation of lncRNAs are associated with various types of cancer including pancreatic ductal adenocarcinoma (PDAC), which has the worst prognosis of the major cancers, with a 5-year survival rate of 5%, due to difficulties in early detection and limited therapeutic options. Although lncRNAs play important roles in cancer, they have not been extensively studied in PDAC. The goal of this study is to identify PDAC-related lncRNAs and characterize their functions in pancreatic cancer cells. Recently, we identified a potentially important lncRNA, PANCRNA1 (pancreatic cancer RNA 1), in PDAC progression through re-annotation of whole genome transcript RNA sequencing data of PDAC tissue samples from sequence read archive (SRA). Overexpressed candidates were determined in both early stage and metastatic PDAC tissue samples. PANCRNA1 shows a statistically significant higher expression profile in PDAC tissue samples. Its expression in different pancreatic cancer cell lines was confirmed (BxPC-3, MiaPaca-2 and Panc-1) by RT-qPCR. In order to investigate the effect of PANCRNA1 on pancreatic cancer cells, its expression was transiently knocked down using targeting siRNA. Statistically significant changes were reported on cell phenotype by measuring the rate of cell proliferation and motility. PANCRNA1 knock down reduced proliferation and cell motility in wound healing assays as compared to scrambled siRNA controls. To determine potential mechanisms underlying the observed effects of PANCRNA1 on pancreatic cancer cells, changes in epidermal growth factor receptor (EGFR) signaling, which contributes to pancreatic tumor cell proliferation, evasion of apoptosis, angiogenesis and metastasis were investigated. Knock down of PANCRNA1, decreased both EGFR transcript and protein levels. These results provide the first evidence for the expression and the function of PANCRNA1 in pancreatic cancer and the motivation for future studies to further elucidate its mechanisms of action and determine its possible application as a marker and target.

Citation Format: Husna Karaboga, Philip Jonsson, Yu Liu, Chin-Yo Lin. Long noncoding RNA PANCRNA1 is a novel regulator of cell growth and motility in pancreatic ductal adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A07.
Abstract A08: A novel lncRNA RGMB-AS inhibit NSCLC metastasis via upregulating the expression of target gene RGMB
Authors: Li Jin , Xiaoshun Shi , Jianxing He
Published: May 2016

Background: The relationships between long noncoding RNA (lncRNAs) and tumors have currently become one of the focuses on cancer studies. Our previous studies found repulsive guidance molecule b (RGMB) was downregulated in lung cancer which is associated with poor prognosis and cancer metastasis.The present study investigated the regulation of RGMB expression by lncRNA RGMB-AS and its role in lung cancer progression.

Methods: The expression of lncRNA RGMB-AS and RGMB were detected in 56 paired NSCLC tissues and adjacent normal tissues by qRT-PCR assay. The relations of lncRNA RGMB-AS and RGMB expression with clinicopathological factors of NSCLC patients were explored. The lncRNA RGMB-AS was downregulated and overexpressed in A549 and H1299 cells, and its role in lung cancer was further investigated in vitro and in vivo.

Results: The results of qRT-PCR showed that lncRNA RGMB-AS expression was significantly downregulated in NSCLC tissues than in adjacent normal tissues (P < 0.05). Correlation analysis indicated that the expression of lncRNA RGMB-AS and RGMB mRNA were positively correlated (P < 0.05). The downregulation of lncRNA RGMB-AS in NSCLC tissues were associated with poor overall survival status(P < 0.05). Downregulation of lncRNA RGMB-AS in A549 and H1299 cells subsequently results in reduced RGMB mRNA and protein expression. The downregulation/overexpression of lncRNA RGMB-AS significantly promoted/inhibited NSCLC cells metastasis in vitro and in vivo.

Conclusion: We identified lncRNA RGMB-AS which was downregulated in NSCLC patients and thereby to reduce RGMB expression. lncRNA RGMB-AS might inhibit lung cancer metastasis via the regulation on RGMB and other tumor suppressors.

Citation Format: Jin Li, Shi Xiaoshun, He Jianxing. A novel lncRNA RGMB-AS inhibit NSCLC metastasis via upregulating the expression of target gene RGMB. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A08.
Abstract A10: LncRNA MIR222HG transcribed from the miR-221/222 promoter are associated with the development of castration resistant prostate cancer
Authors: Qu Fangfang , Sun Tong , Wang Xiaodong , Lee Gwo-Shu Mary , Kantoff Philip W.
Published: May 2016

We previously found that microRNA-221 and 222 play a crucial role in regulating the AR function during the castration resistant prostate cancer (CRPC) development. We further investigated mechanisms involved in the differential expression of miR-221/222 in prostate cancer cell lines. Based on transcriptome and histone modification data, we recognized a putative promoter region located at 23.3 kb upstream of the miR-221/222. By further characterizing transcriptional events occurred in this promoter region, we identified a two- exonic, polyadenylated long non-coding RNA (lncRNA), MIR222HG. Forced over-expression MIR222HG significantly increased androgen-independent cell growth and repressed DHT induced PSA expression in LNCaP cells, a hallmark of CRPC phenotype. Expression level of MIR222HG is significantly associated with human prostate cancer progression from localized hormone sensitive prostate cancer (HSPC) to CRPC. Taken together, lncRNA MIR222HG, which is co-transcribed from miR-221/222 promoter region, mediated AR transcriptional regulation and may involved in transformation process from HSPC to CRPC. Further study on MIR222HG may help understand the CRPC development processes.

Citation Format: Fangfang Qu, Tong Sun, Xiaodong Wang, Gwo-Shu Mary Lee, Philip W. Kantoff. LncRNA MIR222HG transcribed from the miR-221/222 promoter are associated with the development of castration resistant prostate cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A10.
Abstract A26: Importance of long noncoding RNAs in human papillomavirus-related cancers
Authors: Barr Jamie A. , Hayes Karen E. , Martinez Ivan
Published: May 2016

The objective of this study is to identify the importance of long non-coding RNAs (lncRNAs) in the induction of carcinogenesis by high-risk human papillomavirus (HPV)-16 oncoprotein E6 in HPV-related cancers. Dysregulation of long non-coding RNAs (lncRNAs) occurs in most human cancers, however, there are only a few studies showing dysregulation of specific lncRNAs in human papillomavirus (HPV)-related cancers. High-risk HPV infection (e.g. HPV-16 and HPV-18) is one the most common causes of cervical cancer, as well as a subset of head and neck squamous cell carcinoma (HNSCC). It is well known that one of the main factors contributing to HPV-related carcinogenesis is the expression of high-risk HPV E6 viral oncoprotein and its interaction with several human proteins, such as the tumor suppressor p53 and the anti-apoptotic protein Bak. It is hypothesized that HPV-16 E6 changes the expression of host lncRNAs to regulate downstream processes important in the induction of carcinogenesis. To test this hypothesis, we stably express high-risk HPV-16 E6 in primary human keratinocytes and conducted high-throughput RNA sequencing analysis to identify HPV-16 E6-mediated changes in lncRNAs expression. Our preliminary data shows over 500 lncRNAs up- or down- regulated by greater than 2-fold with the expression of HPV-16 E6 compared to control. We validated the expression changes of many individual lncRNAs after the expression of HPV-16E6, via q-RT-PCR and Northern blots. In addition we observe similar expression patterns when comparing normal cells to HPV+ cervical cancer cell lines. Currently, we are characterizing specific lncRNAs of interest that are altered with expression of HPV-16 E6 by using 5' and 3' rapid amplification of cDNA ends (RACE) experiments as well as determining certain lncRNA's mechanism of action contributing to cancer by conducting knockdown and rescue experiments followed by behavior assays (e.g. invasion, angiogenesis, and proliferation). To aid in the determination of the function of the lncRNAs, we plan to use Fluorescence in situ Hybridization (FISH) assays to identify their localization. We believe this project will be significant in that it will identify and show the importance of lncRNAs in HPV-related cancers as well as give us new information about a novel mechanism by which high-risk HPV infection contributes to cervical and HNSCC carcinogenesis.

Citation Format: Jamie A. Barr, Karen E. Hayes, Ivan Martinez. Importance of long noncoding RNAs in human papillomavirus-related cancers. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A26.
Abstract A41: A single let-7 microRNA bypasses LIN28-mediated repression
Authors: Triboulet Robinson , Pirouz Mehdi , Gregory Richard I.
Published: May 2016

The let-7 miRNA family members are small non-coding RNAs that function as tumor suppressors and are frequently down-regulated in many different types of cancers upon reactivation of LIN28 oncogenes. Mammalian genomes contain twelve let-7 isoforms that suppress expression of a common set of target mRNAs comprising key oncogenes and mitotic regulators. LIN28 proteins selectively block let-7 biogenesis postranscriptionally. The current model for coordinate let-7 repression involves the LIN28 cold shock domain (CSD) binding the terminal loop and the two CCHC-type zinc fingers recognizing a GGAG sequence motif in precursor let-7 (pre-let-7) RNAs. Here we perform a systematic analysis of all let-7 miRNAs and find that a single let-7 family member, human let-7a-3 (and its murine ortholog let-7c-2), escapes LIN28-mediated regulation. Mechanistically, we find that the pre-let-7c-2 loop precludes LIN28A binding and regulation. These findings refine the current model of let-7 regulation by LIN28 proteins and have important implications for understanding the LIN28/let-7 axis in cancer.

Citation Format: Robinson Triboulet, Mehdi Pirouz, Richard I. Gregory. A single let-7 microRNA bypasses LIN28-mediated repression. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A41.
Abstract A44: Randomized adapter pools for microRNA sequencing of colorectal cancer cell lines and primary tumors
Authors: Eide Peter W. , Cekaite Lina , Xu Ping , Meza-Zepeda Leonardo A. , Dalmay Tamas , Lothe Ragnhild A.
Published: May 2016

Single-nucleotide resolution, high throughput and excellent precision make small RNA sequencing ideally suited for addressing a wide array of microRNA (miRNA) research questions. It is however known that adapter ligation introduces bias distorting the relation between sample expression levels and sequencing read counts. To investigate how this issue may affect studies aiming to identify miRNA biomarkers, we utilized the recently published High Definition library preparation protocol to generate miRNA profiles of 35 colorectal cancer cell lines, 55 primary cancer biopsies and 5 adjacent normal mucosa samples. The protocol minimizes ligation bias by means of randomized adapter pools. Comparing the resulting data against publicly available colorectal cancer miRNA datasets, we demonstrate that the High Definition protocol moderates read count distributions, increases accuracy and improves sensitivity while maintaining high reproducibility. Moreover, by taking advantage of the more quantitative read counts, the cancer cell line panel and the normal mucosa samples, we identify a set of miRNAs that are highly expressed in epithelial cancerous cells, deregulated in colorectal cancer as compared to normal mucosa and differentially expressed between established molecular subgroups. As such, these miRNAs present strong candidates for functional validation and biomarker testing. In conclusion, we here present High Definition miRNA sequencing data for a large panel of clinically relevant colorectal cancer samples highlighting the potential of improved small RNA library preparation methods.

Citation Format: Peter W. Eide, Lina Cekaite, Ping Xu, Leonardo A. Meza-Zepeda, Tamas Dalmay, Ragnhild A. Lothe. Randomized adapter pools for microRNA sequencing of colorectal cancer cell lines and primary tumors. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A44.
Abstract A45: GAS5-encoded intronic snoRNAs produce specific sdRNAs overexpressed in aggressive prostate cancer
Authors: Martens-Uzunova Elena S. , Kalsbeek Anton , Hoogstrate Youri , Baker Adam , Nielsen Soren Jensby , Visakorpi Tapio , Bangma Chris , Jenster Guido
Published: May 2016

Small non-coding RNAs, such as miRNAs, are implicated in carcinogenesis. To investigate changes in the entire small RNA transcriptome in prostate cancer (PCa) we analyzed 11 clinical sample pools representing different stages of PCa by deep sequencing. We found that most C/D-box small nucleolar RNAs (snoRNAs) are specifically processed to smaller snoRNA-derived RNAs (sdRNAs) highly expressed in PCa. In particular, SNORD78 produces sdRNAs strongly up-regulated in PCa. Together with 9 other snoRNAs, SNORD78 is encoded in the introns of the Growth Arrest Specific 5 gene (GAS5).

Examination of SNORD78 and the positioned in a neighboring intron SNORD44 showed that both snoRNAs produce predominantly one sdRNA fragment each, specifically originating from the 3'-arm (SNORD78) or the 5'-arm (SNORD44) of the precursor sequence. Inspection of the secondary structures of SNORD44 and SNORD78 revealed that they have a degenerated C'/D' box and can fold in a tight hairpin similarly to miRNAs. In contrast, SNORD74 and SNORD81 that also encoded in introns of GAS5, contain canonical C'/D' boxes and each produce three equally expressed sdRNAs.

Quantitative real time PCR analysis in an independent patient cohort of 106 fresh-frozen clinical samples confirmed the significant up-regulation of all four snoRNAs and their derivative sdRNAs in PCa samples compared to normal tissue. Interestingly, the increased expression of snoRNAs and sdRNAs was not associated with elevated levels of GAS5 transcript.

Based on these results, we conclude that (i) separate regulatory mechanisms control the posttranscriptional processing of the spliced GAS5 transcript and the encoded in its introns snoRNAs; (ii) SNORD44, SNORD78, SNORD74 and SNORD81 function as precursors of different sdRNAs; (iii) SNORD44, SNORD78, SNORD74 and SNORD81 and their derivative sdRNAs are significantly up-regulated in PCa and carry biomarker potential for this disease.

Citation Format: Elena S. Martens-Uzunova, Anton Kalsbeek, Youri Hoogstrate, Adam Baker, Soren Jensby Nielsen, Tapio Visakorpi, Chris Bangma, Guido Jenster. GAS5-encoded intronic snoRNAs produce specific sdRNAs overexpressed in aggressive prostate cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A45.
Abstract B05: MicroRNA-206 drives rhabdomyosarcoma differentiation through downregulation of PAX7
Authors: Hanna Jason A. , Garcia Matthew R. , Go Jonathan C. , Finkelstein David , Kodali Kiran , Pagala Vishwajeeth , Olson Eric N. , Peng Junmin , Hatley Mark E.
Published: May 2016

The goal of this work is to understand the mechanism of microRNA-206 (miR-206) induced differentiation in rhabdomyosarcoma (RMS). RMS is the most common soft tissue sarcoma of childhood with both histology and gene expression suggestive that RMS tumor cells resemble a developmental arrest of skeletal muscle. miR-206 is a skeletal muscle specific miRNA expression increases through normal muscle development and has decreased levels in RMS compared to normal skeletal muscle. Exogneous miR-206 replacement drives differentiation and cell cycle exit of RMS. However, the target genes responsible for the relief of the development arrest are largely unknown. Using a combinatorial approach with mRNA microarrays and tandem mass tag (TMT) proteome profiling we identified 165 mRNAs and 272 proteins downregulated in miR-206 mimic transfected RMS cells. Potential targets were validated with 3'UTR reporter assays as well as real-time PCR and immunoblot from miR-206 mimic transfected cells. Further analysis with genetic rescue identified the key targets responsible for the RMS differentiation block as PAX7, PAX3, CCND2, and NOTCH3. However, siRNA knockdown of these targets alone and in a pooled combination failed to induce differentiation to the same extent as miR-206 despite knockdown levels comparable to miR-206. Thus, target identification collectively is key to understanding the mechanism of miR-206 function in RMS, suggesting the one miRNA-one target model to be insufficient for the complex phenotype of miR-206 induced differentiation. Genetic deletion of miR-206 in a mouse model of RMS accelerated and exacerbated tumor development indicating that both in vitro and in vivo miR-206 possesses tumor suppressive properties. In addition, Notch3 and Pax7 levels were increased in knockout tumors compared to wild type, providing further evidence for these genes as key targets of miR-206 in RMS. These results illustrate that miR-206 relieves the differentiation arrest in RMS and suggests that miR-206 replacement therapy could be a potential therapeutic strategy.

Citation Format: Jason A. Hanna, Matthew R. Garcia, Jonathan C. Go, David Finkelstein, Kiran Kodali, Vishwajeeth Pagala, Eric N. Olson, Junmin Peng, Mark E. Hatley. MicroRNA-206 drives rhabdomyosarcoma differentiation through downregulation of PAX7. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B05.
Abstract B10: Overexpression of the lncRNA PVT1 contributes to the cervical cancer phenotype, possibly via association with nucleolin
Authors: Iden Marissa , Fye Samantha , Li Keguo , Chowdhury Tamjid , Ramchandran Ramani , Rader Janet S.
Published: May 2016

The plasmacytoma variant translocation 1 gene (PVT1) is an lncRNA that has been designated as an oncogene due to its contribution to the phenotype of multiple cancers. Although the mechanism by which PVT1 influences disease processes has been studied in multiple cancer types, its role in cervical tumorigenesis remains unknown. Thus, the present study was designed to investigate the role of PVT1 in cervical cancer in vitro and in vivo. PVT1 expression was measured by quantitative PCR (qPCR) in 121 invasive cervical carcinoma (ICC) samples, 19 normal cervix samples, and a cervical cell line (SiHa). Further, we used targeted knockdown in conjunction with functional assays to examine PVT1's effects on cervical cancer cell proliferation, migration and invasion, apoptosis, and cisplatin resistance. Our results demonstrate that PVT1 expression is significantly increased in ICC tissue versus normal cervix. PVT1 knockdown in cervical cancer cell lines resulted in significantly decreased cell proliferation, migration and invasion. Further, apoptosis and cisplatin cytotoxicity were significantly increased in PVT1 siRNA-transfected cells. Finally, we show that PVT1 associates with Nucleolin protein and may aid in its stabilization of GADD45A mRNA providing a possible mechanism by which PVT1 overexpression drives cervical carcinogenesis.

Citation Format: Marissa Iden, Samantha Fye, Keguo Li, Tamjid Chowdhury, Ramani Ramchandran, Janet S. Rader. Overexpression of the lncRNA PVT1 contributes to the cervical cancer phenotype, possibly via association with nucleolin. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B10.
Abstract B14: Tanshinones suppress AURKA through up-regulation of miR-32 expression in non-small cell lung cancer
Authors: ma zhongliang , zhang bingjie , li yanli
Published: May 2016

Tanshinones which includes tanshinone I (T1), tanshinone IIA (T2A), and cryptotanshinone (CT), are the liposoluble constituent of Salia miltiorrhiza, AURKA, an oncogene, encodes a serine-threonine kinase which regulates mitotic processes in mammalian cells. Here, we reported that tanshinones mediate AURKA suppression partly through up-regulating the expression of miR-32, one of miR-25 family. We found that tanshinones could inhibit cell proliferation, promote apoptosis, and impede cell-cycle progression, thus performing an antineoplastic function in non-small cell lung cancer (NSCLC). Additionally, we demonstrated that tanshinones attained these effects in part by down-regulating AURKA, corroborating previous reports. Our results showed that in NSCLC, similar effects were obtained with knock-down of the AURKA gene by siRNA. We also verified that AURKA was the direct target of miR-32. we also found that miR-32 can promote the expression of Let-7 family, however, let-7 family down-regulates the level of miR-32. Collectively, our results demonstrated that tanshinones could inhibit NSCLC by suppressing AURKA via up-regulating the expressions of miR-25 family, let-7 family and other related miRNAs.

Note: This abstract was not presented at the conference.

Citation Format: zhongliang ma, bingjie zhang, yanli li. Tanshinones suppress AURKA through up-regulation of miR-32 expression in non-small cell lung cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B14.
Abstract B20: miR-211 Functions as a metabolic switch in human melanoma cells
Authors: Mazar Joseph , Qi Feng , Lee Bongyong , Marchica John , Govindarajan Subramaniam , Shelley John , Li Jian-Liang , Ray Animesh , Perera Ranjan J.
Published: May 2016

The microRNA (miRNA) miR-211 negatively regulates genes that drive invasion of metastatic melanoma. Compared to normal human melanocytes, miR-211 expression is significantly reduced or absent in non-pigmented melanoma cells and lost during human melanoma progression. To investigate mechanisms of its tumor suppressor function, miR-211 was ectopically expressed in non-pigmented melanoma cells. Ectopic miR-211 expression destabilized hypoxia-inducible factor 1α (HIF-1α) and caused increased cell death during hypoxia. HIF-1α destabilization was correlated with down-regulation of a novel miR-211 target gene, pyruvate dehydrogenase kinase 4 (PDK4). We present evidence that resumption of miR-211 mediated down-regulation of PDK4 in melanoma cells caused hypoxia-induced cell death via HIF-1α destabilization. Thus the tumor suppressor miR-211 acts as a metabolic switch, and its loss is expected to promote cancer hallmarks in human melanomas.

Citation Format: Joseph Mazar, Feng Qi, Bongyong Lee, John Marchica, Subramaniam Govindarajan, John Shelley, Jian-Liang Li, Animesh Ray, Ranjan J. Perera. miR-211 Functions as a metabolic switch in human melanoma cells. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B20.