bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract IA14: Noncoding RNAs of viral and cellular origin: Links to oncogenesis
Authors: Steitz Joan A. , Lee Nara , Moss Walter N. , Yario Therese A. , Vilborg Anna , Passarelli Maria C. , Tycowski Kazimierz T. 
Published: May 2016

Abstract
EBER2 is a highly abundant nuclear noncoding RNA expressed by Epstein-Barr virus (EBV). Probing its possible chromatin localization by Capture Hybridization Analysis of RNA Targets (CHART) revealed EBER2's presence at the terminal repeats (TRs) of the latent EBV genome, overlapping previously identified binding sites for the important B-cell transcription factor PAX5. EBER2 interacts with and is required for PAX5 localization to the TRs. Knockdown of EBER2 or PAX5 decreases EBV lytic replication, underscoring the essential role of the TRs in viral replication, which is known to be linked to the onset of EBV-associated tumors. Recruitment of the EBER2-PAX5 complex is mediated by base pairing between EBER2 and nascent transcripts from the TR locus. The interaction is evolutionarily conserved in the related primate herpesvirus CeHV15 despite great sequence divergence in both EBER2 and the TRs. Using base pairing with nascent transcripts to guide an interacting transcription factor to its DNA target site in chromatin is a previously undescribed function for a trans-acting noncoding RNA.
We have uncovered a novel transcript type derived from human protein-coding genes that is represented by thousands of examples genome-wide. These RNAs, which we call DoGs for downstream of gene containing transcripts, are inducible by osmotic stress through an IP3 receptor signaling-dependent pathway, indicating active regulation. DoGs possess long non-coding regions (often &gt;45 kb) and remain chromatin bound. Their levels are increased by decreased termination of the upstream transcript, a previously undescribed mechanism for rapid transcript induction. Relative depletion of polyA signals in DoG regions correlates with increased levels of DoGs after osmotic stress. DoGs may play a role in reinforcing the nuclear scaffold after stress.
1. Lee, N., Moss, W., Yario, T., Steitz, J.A. (2015). An EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA. Cell 160, 607-618.
2. Vilborg, A., Passarelli, M.C., Yario, T.A., Tycowski, K.T. and Steitz, J.A. (2014). Widespread inducible transcription downstream of human genes. Mol. Cell. 59, 449-461.
Citation Format: Joan A. Steitz, Nara Lee, Walter N. Moss, Therese A. Yario, Anna Vilborg, Maria C. Passarelli, Kazimierz T. Tycowski. Noncoding RNAs of viral and cellular origin: Links to oncogenesis. [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 IA14.
Abstract IA23: Targeting nuclear noncoding RNAs
Authors: Corey David 
Published: May 2016

Abstract
RNA interference (RNAi) is well known as a mechanism for controlling mammalian mRNA translation in the cytoplasm, but what would be the consequences if it also functioned in cell nuclei? Although RNAi has also been found in nuclei of plants, yeast, and other organisms, there has been relatively little progress towards understanding the potential involvement of mammalian RNAi factors in nuclear processes including transcription and splicing. When RNAi factors bind small RNAs, they form ribonucleoprotein complexes that can be selective for target sequences within different classes of nuclear RNA substrates. The versatility of nuclear RNAi may supply a previously underappreciated layer of regulation to transcription, splicing, and other nuclear processes. This talk focuses on recent work targeting noncoding RNA at the frataxin and C9orf72 loci as examples for how nuclear RNAi can be used to control gene expression.
Citation Format: David Corey. Targeting nuclear noncoding RNAs. [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 IA23.
Abstract IA25: Regulatory control of lincRNA function through formation of complex RNA structural motifs
Authors: Chillon Isabel , Somarowthu Srinivas , Liu Fei , Pyle Anna Marie 
Published: May 2016

Abstract
While the regulatory role of lincRNAs is becoming increasingly appreciated, the functional role of RNA structures within these molecules is not well understood. We have embarked on a study to understand the folding of lincRNA molecules, and to identify functional structural modules within large RNA transcripts. Using approaches to promote the native folding of large RNA molecules, we have been purifying lincRNAs, mapping their structures with chemical probes, and then using this information to construct structural maps of lincRNA architecture. This work is complemented by phylogenetic and genetic approaches for exploring the functional relevance of RNA structures identified in our study. In this way, we have mapped the structure of lincRNAs such as HOTAIR and lincRNA p21, identifying novel structural motifs, enabling evolutionary comparisons and facilitating targeted mutational studies of lincRNA function.
Citation Format: Isabel Chillon, Srinivas Somarowthu, Fei Liu, Anna Marie Pyle. Regulatory control of lincRNA function through formation of complex RNA structural motifs. [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 IA25.
Abstract PR01: Strand-specific in vivo screen of cancer-associated miRNAs unveils key drivers and oncogenic targets
Authors: Ge Yejing , Zhang Liang , Nikolova Maria , Reva Boris , Fuchs Elaine 
Published: May 2016

Abstract
MiRNAs are evolutionarily conserved small non-coding RNAs that orchestrate a wide spectrum of physiological and pathological processes in stem cells (SCs) and human cancers. Intimately wired into oncogenic and tumor suppressive networks, miRs are valuable as not only diagnostic biomarkers but also therapeutic targets. Squamous cell carcinomas (SCCs) are among the most life-threatening human cancers world-wide. Using skin as paradigm, we describe the first panoramic view of miRs during the development, homeostasis and malignant transformation of skin epithelium, whose SCs are the target of most common SCCs. Focusing on abundant and enriched miRs in SCC-SCs versus normal skin SCs, we devised lentiviral miR expression platform and conducted pooled in vivo functional screens for oncomiRs in mice. Deep sequencing of genomic DNA from basal progenitors of tumors or unaffected skin epithelium revealed preferential enrichment of 29/169 miRs within the tumors. We followed up with the top hits and showed candidate miRs are indeed aberrantly induced in both mouse and human SCCs. After functionally documenting their tumor-promoting roles in mouse SCCs in vivo and human xenografts, we applied CRISPR technology to ablate the miR loci in cells derived from these SCCs, and then used lentiviral delivery methods to carry out specific miR rescues of the tumorigenic phenotype. To look for candidate targets of newly identified oncomiRs, we analyzed TCGA database that are inversely correlated with our candidate miR as well as genes that are de-repressed upon miR deletion. We discovered potent tumor suppressors whose knockdown rescued the deficit in tumor formation from oncomiR-deficient cells and whose overexpression reversed miR-driven tumorigenesis. Furthermore, we demonstrated CRISPR-mediated deletion of the endogenous miRNA binding site renders the target cells no longer sensitive to miRNA regulation. Finally, we pinpointed the cellular mechanism of how miR-target regulates SCC progression. Empowered by mouse genetics and high throughput approaches, our study has unveiled a rich set of putative miRs that drive skin SCC malignancy, and discovered their oncogenic targets. These findings shed new light on increasingly important oncomiR loci and its action on a devastating cancer.
This abstract is also presented as Poster A02.
Citation Format: Yejing Ge, Liang Zhang, Maria Nikolova, Boris Reva, Elaine Fuchs. Strand-specific in vivo screen of cancer-associated miRNAs unveils key drivers and oncogenic targets. [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 PR01.
Abstract PR02: The diverse roles of long noncoding RNAs in the p53 tumor suppressor pathway
Authors: Bendor Jordan , Zamudio Jesse , Jacks Tyler , Dimitrova Nadva 
Published: May 2016

Abstract
The p53 tumor suppressor is a transcription factor, which plays a central role in the cellular response to DNA damage and oncogenic stress. Using genetic approaches in the mouse as well as antisense technology, we have previously shown that the p53-regulated lncRNA, lincRNA-p21 activates the expression of its neighboring gene, the critical G1/S checkpoint mediator, p21. Mechanistically, we found that lincRNA-p21 localizes at its site of transcription, where it acts in cis to stabilize the binding of p53 and its transcriptional co-activator hnRNP-K at the promoter of p21. Importantly, using CRISPR-based approaches to modify the endogenous lincRNA-p21 locus in primary human fibroblasts, we show that the role of lincRNA-p21 in promoting p21 levels is conserved between mouse and human.
To expand our understanding of the contribution of lncRNAs to the p53 tumor suppressor pathway, we have performed p53 ChIPseq and RNAseq under conditions of oncogenic stress and identified multiple previously uncharacterized lncRNAs that are regulated in a p53-dependent manner. One of them, lincRNA-Dhx15 is a novel lncRNA expressed from a bidirectional promoter shared with the RNA helicase Dhx15. LincRNA-Dhx15 is a direct target of p53 by virtue of multiple p53 response elements located in its first intron and appears to be preferentially expressed under conditions of senescence. We have generated a conditional knockout of lincRNA-Dhx15 in the mouse and found that absence of lincRNA-Dhx15 leads to impaired induction of senescence following prolonged exposure to DNA damage. Moreover, by gene expression profiling, we observed a downregulation of a subset of p53 target genes, suggesting that lincRNA-Dhx15 plays a global role in the p53 pathway. Surprisingly, we found that lincRNA-Dhx15 is exported to the cytoplasm and appears to promote the translational of p53 itself. The mechanistic basis for lincRNA-Dhx15 function is under active investigation. Altogether, these studies reveal that p53-regulated lncRNAs act through diverse mechanisms to add important layers of regulation to the p53 transcriptional network.
Citation Format: Jordan Bendor, Jesse Zamudio, Tyler Jacks, Nadva Dimitrova. The diverse roles of long noncoding RNAs in the p53 tumor suppressor pathway. [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 PR02.
Abstract PR05: Dicer1 deletion: Sufficient for angiosarcoma development and a haploinsufficient tumor suppressor in rhabdomyosarcoma
Authors: Hanna Jason A. , Garcia Matthew R. , Rehg Jerold , Hatley Mark E. 
Published: May 2016

Abstract
In this study, the role of Dicer and microRNAs (miRNAs) is investigated in pediatric and adult soft tissue sarcomas with the hypothesis that understanding miRNAs and their biogenesis may provide biological insights into the pathogenesis of these diseases and identify novel therapeutic targets. In several mouse models of cancer, Dicer1 is thought to function as a haploinsufficient tumor suppressor where loss of a single allele promotes tumorigenesis yet loss of both alleles is detrimental to tumor formation. Heterozygous germline mutations in DICER1 in humans is associated with rare malignant and benign neoplasias including embryonal rhabdomyosarcoma (ERMS).
With DICER1 syndrome mutations found in ERMS, a pediatric soft tissue sarcoma resembling skeletal muscle precursors that fail to differentiate, we sought to further understand the role of Dicer and miRNAs utilizing a transgenic mouse model of ERMS combined with conditional Dicer1Flox/Flox null mice. The ERMS mouse model results from activation of a constitutively active SmoM2 allele with Cre recombinase expressed from the adipose protein 2 (aP2) promoter resulting in unrestrained hedgehog signaling in the aP2 lineage. Heterozygous Dicer1 loss led to increased penetrance of and a decrease in latency to onset of tumors. In agreement with the haploinsufficient tumor suppressor model, homozygous Dicer1Flox/Flox mice rarely developed tumors in stark contrast to wild type and heterozygous littermates. Furthermore, tumors that did develop in Dicer1Flox/Flox mice escaped Cre recombination and retained a flox allele indicating functional Dicer1 activity.
Serendipitously, aP2-Cre; SmoM2; Dicer1Flox/Flox mice that did not develop ERMS all developed multifocal angiosarcomas. This finding prompted the analysis of Dicer loss alone in the aP2 lineage and remarkably Dicer1Flox/Flox mice similarly developed angiosarcoma whereas Dicer1Flox/+ do not, providing evidence for Dicer loss independent of a cooperating oncogene driving tumorigenesis in a mouse model.
This study provides evidence for the role of Dicer and miRNAs in rhabdomyosarcoma and angiosarcomas. Further understanding the molecular mechanisms and genetic drivers of soft tissue sarcomas is critical for the development of novel targeted therapeutics. This is true especially for soft tissue sarcomas where treatment strategies and survival outcomes have not changed in decades despite numerous clinical trials.
This abstract is also presented as Poster B06.
Citation Format: Jason A. Hanna, Matthew R. Garcia, Jerold Rehg, Mark E. Hatley. Dicer1 deletion: Sufficient for angiosarcoma development and a haploinsufficient tumor suppressor in rhabdomyosarcoma. [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 PR05.
Abstract PR10: HiClinc-1, a highly conserved Cancer-Testis lncRNA, regulates cell proliferation and tumor onset
Authors: Hosono Yasuyuki , Prensner John , Iyer Matthew , Niknafs Yashar , Malik Rohit , Poliakov Anton , Cao Xuhong , Shavit Jordan , Mehra Rohit , Zhou Weibin , Chinnaiyan Arul M. 
Published: May 2016

Abstract
Long non-coding RNA (lncRNAs) have been shown to play an important role is a variety of cellular processes including cancer initiation and progression. Recently, we described a landscape of lncRNA using RNA-Seq data from more than 5000 cancer samples from 18 tissue types. Using novel bioinformatics based approach we were able to discover almost 50,000 novel transcripts. This list includes a subset of lncRNAs that contain ultra-conserved elements (UCE) termed “Highly Conserved Long Intergenic Non-Coding RNAs (HICLINCs)”. This provides a new opportunity for exploring the functions of highly conserved lncRNAs using genomic approaches.
Among them, we focus on an lncRNA which we have termed HiClinc-1 (Highly Conserved Intergenic long-noncoding RNA-1), that is specifically expressed only in testis in benign tissue, and re-expressed in a broad range of cancer types. We described that HiClinc-1 exists in the messenger Ribonucleoprotein (mRNP) complex and binds to Insulin-Like Growth Factor 2 mRNA Binding Protein 1 (IGF2BP1), one of the component of mRNP complex in both human and zebrafish. HiClinc-1 regulates cell proliferation both in vivo and in vitro through the regulation of IGF2BP1's downstream target Insulin-Like Growth Factor 2 (IGF2). HiClinc-1 also enhanced tumor growth in mouse xenograft model. Notably, Human-HiClinc-1 injection in zebrafish embryos accelerated the onset and growth of NRAS K61-induced melanoma. Similarly, HiClinc-1 knockout background showed delayed onset of NRAS K61-induced melanoma. Taken together, we identified a novel Cancer-Testis lncRNA, which is highly conserved through human to zebrafish that can be a potential therapeutic target for cancer treatment.
Citation Format: Yasuyuki Hosono, John Prensner, Matthew Iyer, Yashar Niknafs, Rohit Malik, Anton Poliakov, Xuhong Cao, Jordan Shavit, Rohit Mehra, Weibin Zhou, Arul M. Chinnaiyan. HiClinc-1, a highly conserved Cancer-Testis lncRNA, regulates cell proliferation and tumor onset. [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 PR10.
Abstract PR14: Potent knock down of lncRNAs in vitro and in vivo with antisense LNA™ GapmeRs
Authors: Lai Johnathan , Ozen Asli , Mouritzen Peter , Tolstrup Niels , Frandsen Niels Montano 
Published: May 2016

Abstract
Exiqon develops strategies for the optimal design of single stranded LNA™-enhanced antisense oligonucleotides (ASOs, also known as LNA™ GapmeRs) that catalyze RNaseH dependent degradation of target mRNAs and long non-coding RNAs (lncRNA). We have developed an empirically derived design algorithm to provide ASOs that achieve potent target knockdown with a high hit-rate. We describe the latest improvements to the design algorithm, including the incorporation of alignments to both spliced and unspliced transcriptomes in the Ensembl database, to provide maximal target specificity.
Many lncRNAs are nuclear retained or have long residence time in the nucleus. This makes them hard to target by RNAi based methods. However since RNaseH is almost exclusively present in the nucleus nuclear RNAs are expected to be particularly sensitive LNA™ GapmeR targets. We have tested LNA™ GapmeRs to knockdown multiple different RNA targets in vitro – including mRNA and lncRNA targets residing in either cytoplasmic or nuclear compartments. Our results demonstrate that all of these targets were equally efficiently silenced irrespective of the type of RNA target and its subcellular localization. We also report highly efficient and long lasting knockdown of a nuclear retained lncRNA in a broad range of tissues in mice subjected to systemic adminstration of a LNA™ GapmeR. LNA GapmeRs are therefore excellent tools for lncRNA loss of function analysis in vitro and in vivo and provide an excellent platform for therapeutic targeting of lncRNA.
Risk of hybridization based off-target activity with gapmers has traditionally been considered to be low. However in a recent publication1 it was shown that unless properly designed antisense off-target activity with gapmers can be quite significant. Surprisingly, particularly sensitive off-targets were frequently localized in introns of primary transcripts causing significant reduction of the amount of mature spliced mRNAs. Since RNaseH is confined to the nucleus we therefore speculated that the true target of gapmers might be unspliced primary transcripts in the nucleus rather than the spliced mature transcripts that are exported to the cytoplasm. We present data showing that intron targeting LNA GapmeRs often provide highly potent knockdown of the mature spliced RNA. These results have profound implications on therapeutic gapmer design.
1. Kamola PJ, Nucl. Acids Res. 2015, pii: gkv857
This abstract is also presented as Poster B45.
Citation Format: Johnathan Lai, Asli Ozen, Peter Mouritzen, Niels Tolstrup, Niels Montano Frandsen. Potent knock down of lncRNAs in vitro and in vivo with antisense LNA™ GapmeRs. [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 PR14.
Abstract A02: Neuroblastoma patient-derived orthotopic xenografts: Clinically relevant models for drug testing
Authors: Braekeveldt Noémie , Wigerup Caroline , Gisselsson David , Mohlin Sofie , Merselius My , Beckman Siv , Tadeo Irene , Berbegall Anna P. , Öra Ingrid , Navarro Samuel , Noguera Rosa , Påhlman Sven , Bexell Daniel 
Published: May 2016

Abstract
Widespread metastasis is a major problem for the treatment of high-risk neuroblastoma. Relevant neuroblastoma animal models are hence needed to study and target high-risk metastatic neuroblastoma.
We developed neuroblastoma patient-derived orthotopic xenografts (PDXs) using viably cryopreserved or fresh patient neuroblastoma fragments which were implanted orthotopically into immunodeficient NSG mice. Immunohistochemistry showed that PDXs retain neuroblastoma markers and a highly infiltrative growth pattern. Importantly, we found distant metastasis to lungs, liver and bone marrow. Single nucleotide polymorphism array analysis confirmed that PDXs maintain patient-specific chromosomal aberrations 1p del, MYCN amp and 17q gain. In vitro cultures established from the PDXs express neuroblastoma markers and retain their tumorigenic and metastatic ability in vivo after orthotopic injection. PDXs were highly vascularized with mouse endothelial cells and one PDX model formed tumor vasculature through co-engrafted human tumor endothelial cells. Tumors also contained pericytes, cancer-associated fibroblasts, macrophages and extracellular components resembling the patient disease. PDXs established in athymic nude mice additionally developed intratumoral lymphatic vessels and contained mouse-derived CD45+ lymphoid cells. Thus, PDXs maintain important tumor microenvironment hallmarks for high stage neuroblastoma. Furthermore, we demonstrate the feasibility of using short-term in vitro cultured PDX-derived cells as a drug-testing model, and show that the HIF2A oncogene is transcriptionally regulated at hypoxia via the PI3K/mTORC2 pathway in these cells. The results establish the PI3K and mTORC2 pathways as potential therapeutic targets of aggressive neuroblastoma.
In conclusion, neuroblastoma orthotopic PDXs resemble many clinical aspects of the patient disease, e.g., distant metastases, and PDXs are valuable models for preclinical drug testing.
Citation Format: Noémie Braekeveldt, Caroline Wigerup, David Gisselsson, Sofie Mohlin, My Merselius, Siv Beckman, Irene Tadeo, Anna P. Berbegall, Ingrid Öra, Samuel Navarro, Rosa Noguera, Sven Påhlman, Daniel Bexell. Neuroblastoma patient-derived orthotopic xenografts: Clinically relevant models for drug testing. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A02.