bluuebunny/crossref_metadata_2025 huggingface dataset:
Prespecified Candidate Biomarkers Identify Follicular Lymphoma Patients Who Achieved Longer Progression-Free Survival with Bortezomib–Rituximab Versus Rituximab
Authors: Coiffier Bertrand , Li Weimin , Henitz Erin D. , Karkera Jayaprakash D. , Favis Reyna , Gaffney Dana , Shapiro Alice , Theocharous Panteli , Elsayed Yusri A. , van de Velde Helgi , Schaffer Michael E. , Osmanov Evgenii A. , Hong Xiaonan , Scheliga Adriana , Mayer Jiri , Offner Fritz , Rule Simon , Teixeira Adriana , Romejko-Jarosinska Joanna , de Vos Sven , Crump Michael , Shpilberg Ofer , Zinzani Pier Luigi , Cakana Andrew , Esseltine Dixie-Lee , Mulligan George , Ricci Deborah
Published: April 2013

Purpose: Identify subgroups of patients with relapsed/refractory follicular lymphoma deriving substantial progression-free survival (PFS) benefit with bortezomib–rituximab versus rituximab in the phase III LYM-3001 study.

Experimental Design: A total of 676 patients were randomized to five 5-week cycles of bortezomib–rituximab or rituximab. The primary end point was PFS; this prespecified analysis of candidate protein biomarkers and genes was an exploratory objective. Archived tumor tissue and whole blood samples were collected at baseline. Immunohistochemistry and genetic analyses were completed for 4 proteins and 8 genes.

Results: In initial pairwise analyses, using individual single-nucleotide polymorphism genotypes, one biomarker pair (PSMB1 P11A C/G heterozygote, low CD68 expression) was associated with a significant PFS benefit with bortezomib–rituximab versus rituximab, controlling for multiple comparison corrections. The pair was analyzed under dominant, recessive, and additive genetic models, with significant association with PFS seen under the dominant model (G/G+C/G). In patients carrying this biomarker pair [PSMB1 P11A G allele, low CD68 expression (≤50 CD68-positive cells), population frequency: 43.6%], median PFS was 14.2 months with bortezomib–rituximab versus 9.1 months with rituximab (HR 0.47, P < 0.0001), and there was a significant overall survival benefit (HR 0.49, P = 0.0461). Response rates were higher and time to next antilymphoma therapy was longer in the bortezomib–rituximab group. In biomarker-negative patients, no significant efficacy differences were seen between treatment groups. Similar proportions of patients had high-risk features in the biomarker-positive and biomarker-negative subsets.

Conclusions: Patients with PSMB1 P11A (G allele) and low CD68 expression seemed to have significantly longer PFS and greater clinical benefit with bortezomib–rituximab versus rituximab. Clin Cancer Res; 19(9); 2551–61. ©2013 AACR.
Oncolytic Virotherapy Needs Trials, Not Access Programs
Authors: Harrington Kevin J.
Published: April 2013

Oncolytic virotherapy is a novel treatment for cancer that exerts direct lytic and indirect immune-mediated antitumor effects. A Finnish research team has reported on an advanced therapy access program for oncolytic adenovirus. The strengths and weaknesses of this approach are highlighted with a view to informing future study conduct. Clin Cancer Res; 19(10); 2595–7. ©2013 AACR.
Synergistic Anticancer Activity of Arsenic Trioxide with Erlotinib Is Based on Inhibition of EGFR-Mediated DNA Double-Strand Break Repair
Authors: Kryeziu Kushtrim , Jungwirth Ute , Hoda Mir Alireza , Ferk Franziska , Knasmüller Siegfried , Karnthaler-Benbakka Claudia , Kowol Christian R. , Berger Walter , Heffeter Petra
Published: April 2013

Arsenic trioxide (ATO), one of the oldest remedies used in traditional medicine, was recently rediscovered as an anticancer drug and approved for treatment of relapsed acute promyelocytic leukemia. However, its activity against nonhematologic cancers is rather limited so far. Here, we show that inhibition of ATO-mediated EGF receptor (EGFR) activation can be used to potently sensitize diverse solid cancer types against ATO. Thus, combination of ATO and the EGFR inhibitor erlotinib exerted synergistic activity against multiple cancer cell lines. Subsequent analyses revealed that this effect was based on the blockade of ATO-induced EGFR phosphorylation leading to more pronounced G2–M arrest as well as enhanced and more rapid induction of apoptosis. Comparable ATO-sensitizing effects were also found with PI3K/AKT and mitogen-activated protein/extracellular signal–regulated kinase (MEK) inhibitors, suggesting an essential role of the EGFR-mediated downstream signaling pathway in cancer cell protection against ATO. H2AX staining and comet assay revealed that erlotinib significantly increases ATO-induced DNA double-strand breaks (DSB) well in accordance with a role of the EGFR signaling axis in DNA damage repair. Indeed, EGFR inhibition led to downregulation of several DNA DSB repair proteins such as Rad51 and Rad50 as well as reduced phosphorylation of BRCA1. Finally, the combination treatment of ATO and erlotinib was also distinctly superior to both monotreatments against the notoriously therapy-resistant human A549 lung cancer and the orthotopic p31 mesothelioma xenograft model in vivo. In conclusion, this study suggests that combination of ATO and EGFR inhibitors is a promising therapeutic strategy against various solid tumors harboring wild-type EGFR. Mol Cancer Ther; 12(6); 1073–84. ©2013 AACR.
Abstract A12: Identification of microRNA-based therapeutic candidates using a unique lentiviral microRNA overexpression library
Authors: van Noort Paula I. , Babae Negar , Verhaegh Gerald W. , Gommans Willemijn M. , Cerisoli Francesco , Verheul Mark , Schiffelers Raymond M. , Griffioen Arjan W. , Schalken Jack A. , Berezikov Eugene , Cuppen Edwin , Schaapveld Roel Q. J. , Poell Jos B. , Prevost Gregoire P. , Bourajjaj Meriem , Vidic Suzanna , van Beijnum Judy R. , van Haastert Rick J. , Schultz Iman , de Gunt Thijs , van Hooij Onno
Published: April 2013

microRNA (miRNA) genes transcribed by RNA polymerase II generate small noncoding miRNAs of 18 to 24 nucleotides after maturation process. The mature miRNAs and their associated isomirs specifically bind to different mRNA transcripts, resulting in down regulation of multiple genes within the cell in a highly multiplexed way. miRNA expression profiles differ between human cell types suggesting cell-specific impacts of each miRNA on the regulation of different biological processes. Comparison of miRNA profiles of tumor samples and adjacent normal tissues showed that some miRNAs are up- or down- regulated and suggested their implication during tumor progression. However, such a miRNA profiling approach is not sufficient to identify the respective role of each miRNA gene during the tumorigenesis.

Here, to assess the individual role of each miRNA gene and its different isomirs in a specific cell environment, we have constructed a lentiviral miRNA expression library containing more than 1100 human known and novel miRNA precursors. The arrayed layout of our library allowed high-throughput screens with a large spectrum of functional read-outs using either normal or tumor cells. To exemplify this approach, the results of three different screens will be presented; i.e. identification of miRNAs that inhibit the BRAF pathway, miRNAs that inhibit tumor angiogenesis and miRNAs that stimulate the mesenchymal to epithelial transition. In addition, beyond this hit identification step, we will present detailed characterization of the role of the identified miRNAs in tumor progression by means of molecular and cellular functional assays.

Combining our unique miRNA expression library with a functional screening platform has allowed the identification and the further characterization of several miRNAs able to significantly impact on tumor behavior supporting the therapeutic interest of some candidates.

Citation Format: Paula I. van Noort, Negar Babae, Gerald W. Verhaegh, Willemijn M. Gommans, Francesco Cerisoli, Mark Verheul, Raymond M. Schiffelers, Arjan W. Griffioen, Jack A. Schalken, Eugene Berezikov, Edwin Cuppen, Roel Q. J. Schaapveld, Jos B. Poell, Gregoire P. Prevost, Meriem Bourajjaj, Suzanna Vidic, Judy R. van Beijnum, Rick J. van Haastert, Iman Schultz, Thijs de Gunt, Onno van Hooij. Identification of microRNA-based therapeutic candidates using a unique lentiviral microRNA overexpression library [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A12.
Abstract A13: The microRNA-200 family overcomes cisplatin resistance by targeting ceramide glycosylation
Authors: Cai Chunxiao , Ashktorab Hassan , Pang Xiaowu , Zhao Yuan , Sha Wei , Liu Yulan , Gu Xinbin
Published: April 2013

Background: Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a newly identified tumor suppressor that is frequently downregulated in a variety of human cancers. Our previous work revealed that the low expression of CHD5 in colorectal cancer is correlated with CHD5 promoter CpG island hypermethylation. In this study, we investigated the effect of microRNA-211 (miR-211)-regulated CHD5 expression on colorectal tumorigenesis. Methodology/Principal Findings: miR-211 was predicted to target CHD5 by TargetScan software analysis. A stably expressing exogenous miR-211 colorectal cancer cell line (HCT-116miR-211) was generated using lentiviral transduction and used as a model for in vitro and in vivo studies. The expression level of miR-211 in HCT-116miR-211 cells was upregulated by 16-fold compared to vector control cells (HCT-116vector). Exogenous miR-211 directly binds to the 3′ untranslated region (3′ UTR) of CHD5 mRNA, resulting in a 50% decrease in CHD5 protein level in HCT-116miR-211 cells. The levels of cell proliferation, tumor growth, and cell migration of HCT-116miR-211 cells were significantly higher than HCT-116vector cells under both in vitro and in vivo conditions, as determined using the methods of MTT, colony formation, flow cytometry, tumor xenografts, and scratch assay, respectively. In addition, we found that enforced expression of miR-211 in HCT-116 cells was able to alter p53 pathway-associated regulatory proteins, such as MDM2, Bcl-2, Bcl-xL, and Bax. Conclusion/Significance: Our results demonstrate that CHD5 is a direct target of miR-211 regulation. Enforced expression of miR-211 promotes tumor cell growth at least in part by downregulating the expression level of the CHD5 tumor suppressor. Our results provide a better understanding of the association of between miR-211-regulated CHD5 expression and CHD5 function in colorectal tumorigenesis.

Citation Format: Chunxiao Cai, Hassan Ashktorab, Xiaowu Pang, Yuan Zhao, Wei Sha, Yulan Liu, Xinbin Gu. The microRNA-200 family overcomes cisplatin resistance by targeting ceramide glycosylation [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A13.
Abstract A14: microRNA-mediated interactions regulate established oncongenic pathways in cancer
Authors: Sumazin Pavel , Chiu Hua-Sheng , Califano Andrea
Published: April 2013

By analyzing gene expression data in gliobastoma in combination with matched microRNA profiles, we have uncovered a post-transcriptional regulation layer of surprising magnitude, comprising hundreds of thousands of microRNA -mediated interactions. These include ~7,000 genes whose transcripts act as microRNA ‘sponges’ and 148 genes that act through alternative, non-sponge interactions. Biochemical analyses in cell lines confirmed that this network regulates established drivers of tumor initiation and subtype, including PTEN, PDGFRA, RB1, VEGFA, STAT3, and RUNX1, suggesting that these interactions mediate crosstalk between canonical oncogenic pathways. RNA silencing of 13 microRNA-mediated PTEN regulators, whose locus deletions are predictive of PTEN expression variability, was sufficient to downregulate PTEN in a 3′ UTR-dependent manner and to increase tumor-cell growth rates. Thus, this microRNA-mediated network provides a mechanistic, experimentally validated rationale for the loss of PTEN expression in a large number of glioma samples with an intact PTEN locus. Recently, we extended this work to three other tumor types, showing that microRNA-mediated interactions propagate the effects of genetic alterations to regulate distal oncogenes and tumor suppressors in multiple cancers. Our results suggest that, although implemented by context-specific factors, hundreds of thousands of these interactions are context-independent.

Note: This abstract was not presented at the conference because the presenter was unable to attend.

Citation Format: Pavel Sumazin, Hua-Sheng Chiu, Andrea Califano. microRNA-mediated interactions regulate established oncongenic pathways in cancer [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A14.
Abstract A16: MiR-22 down-regulation via epigenetic control in oral cancer cells
Authors: Wu Li-Wha
Published: April 2013

The deregulation of certain microRNAs has been associated with the progression and metastasis of various cancer types. DNA methylation in the CpG islands plays a crucial role in the down-regulation of tumor suppressor genes, including miRNAs. MiR-22 has been shown to be deregulated in several cancer types, including breast cancer and multiple myeloma. Using real-time RT-PCR analysis, we also found that miR22 was down-regulated in the majority of tested oral cancer cell lines and 70% of the clinical specimens when compared with their normal counterparts. Consistent with the notion that DNA methylation might play a role in the gene silencing, we did detect a putative CpG island (~ 1.2 kb in length) located upstream from the putative miR-22 transcription start site (+1) using two independent CpG island prediction softwares. Two oral cancer lines with low miR−22 expression were treated for 3–5 days with the indicated dose of 5′-azaC together with or without trichostatin A. Total RNA was isolated from the treated cells for real-time quantitative PCR analysis of miR-22 expression. The expression of miR-22 was significantly induced by either inhibitor. Combined treatment further enhanced the expression, suggesting the involvement of epigenetic control in the decreased expression of miR-22 in oral cancer cells. We first divided the putative CpG island into 5 regions and designed nested PCR primers for bisulfate sequencing PCR. We found that only regions 3 to 5 in the putative CpG island were subjected to be influenced by methylation in certain oral cancer lines. Since MeCP2 selectively binds to methylated CpG dinucleotides, chromatin immunoprecipition together with qPCR will be used to examine if MeCP2 would have increased binding to the identified methylated CpG sites. Second, quantitative methylation specific PCR (qMSP) will be used to measure the methylation levels of miR-22 genes in oral cancer tissues and their normal control using SYBR Green–based detection technology. Third, in vitro methylation and promoter-driven luciferase assay will be used to investigate whether DNA methylation plays a direct role in regulating miR-22 promoter activity and whether CpG island deletion affects the relative luciferase activity. Together, this study would implicate that the expression of miR-22 is controlled by epigenetic control in oral cancer cells. However, the exact nature of miR-22 in oral carcinogenesis remains to be characterized.

Citation Format: Li-Wha Wu. MiR-22 down-regulation via epigenetic control in oral cancer cells [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A16.
Abstract A3: miR-31 and its host gene lncRNA LOC554202 are regulated by promoter hypermethylation in triple-negative breast cancer
Authors: Augoff Katarzyna , McCue Brian , Plow Edward F. , Sossey-Alaoui Khalid
Published: April 2013

Background: microRNAs have been established as powerful regulators of gene expression in normal physiological as well as in pathological conditions, including cancer progression and metastasis. Recent studies have demonstrated a key role of miR-31 in the progression and metastasis of breast cancer. Downregulation of miR-31 enhances several steps of the invasion-metastasis cascade in breast cancer, i.e., local invasion, extravasation and survival in the circulation system, and metastatic colonization of distant sites. miR-31 exerts its metastasis-suppressor activity by targeting a cohort of pro-metastatic genes, including RhoA and WAVE3. The molecular mechanisms that lead to the loss of miR-31 and the activation of its pro-metastatic target genes during these specific steps of the invasion-metastasis cascade are however unknown.

Results: In the present report, we identify promoter hypermethylation as one of the major mechanisms for silencing miR-31 in breast cancer, and in the triple-negative breast cancer (TNBC) cell lines of basal subtype, in particular. miR-31 maps to the intronic sequence of a novel long non-coding (lnc)RNA, LOC554202 and the regulation of its transcriptional activity is under control of LOC554202. Both miR-31 and the host gene LOC554202 are down-regulated in the TNBC cell lines of basal subtype and over-expressed in the luminal counterparts. Treatment of the TNBC cell lines with either a de-methylating agent alone or in combination with a de-acetylating agent resulted in a significant increase of both miR-31 and its host gene, suggesting an epigenetic mechanism for the silencing of these two genes by promoter hypermethylation. Finally, both methylation-specific PCR and sequencing of bisulfite-converted DNA demonstrated that the LOC554202 promoter-associated CpG island is heavily methylated in the TNBC cell lines and hypomethylated in the luminal subtypes.

Conclusion: Loss of miR-31 expression in TNBC cell lines is attributed to hypermethylation of its promoter-associated CpG island. Together, our results provide the initial evidence for a mechanism by which miR-31, an important determinant of the invasion metastasis cascade, is regulated in breast cancer.

Citation Format: Katarzyna Augoff, Brian McCue, Edward F. Plow, Khalid Sossey-Alaoui. miR-31 and its host gene lncRNA LOC554202 are regulated by promoter hypermethylation in triple-negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A3.
Abstract A33: The role of microRNA-181a in TGF-β-mediated breast cancer progression
Authors: Taylor Molly A. , Schiemann William P.
Published: April 2013

Transforming growth factor-beta (TGF-β) is a multifunctional cytokine that functions to inhibit breast cancer development in the normal mammary epithelium by inducing cell cycle arrest, and maintaining microenvironmental homeostasis through extracellular matrix (ECM) deposition and remodeling. Mammary tumorigenesis causes a loss in TGF-β-mediated cytostasis and leads to a switch in TGF-β function, whereby TGF-β promotes epithelial-mesenchymal transition (EMT), proliferation, invasion and metastasis. This switch in TGF-β function, from tumor suppressor to tumor promoter, is referred to as the “TGF-β paradox” and occurs through molecular mechanisms that remain incompletely understood. Moreover, this switch in TGF-β function is often accompanied by desmoplastic and fibrotic reactions, leading to the formation of a more rigid microenvironment, which in and of itself has been associated with tumor progression. We have shown that tissue compliance and extracellular matrix rigidity mediate how cells sense and respond to TGF-β. Indeed, we can recapitulate the “TGF-β paradox” by exposing metastatic breast cancer cells to compliant ECM signals, which reinstates the cytostatic activities of TGF-β. As a possible mechanism for the influence of matrix rigidity on TGF-β signaling, we sought to define the miRNA expression profiles induced by TGF-β in metastatic cells as compared to their non-metastatic counterparts when grown in either compliant or rigid conditions. We show that ECM rigidity regulates the miRNA expression signature induced by TGF-β in breast cancer cells. From this miRNA signature, we have identified the miR-181 family as a miR family that is highly upregulated in metastatic cells in response to TGF-β. Additionally, over-expression of a miR-181a mimic enhances TGF-β-mediated invasion. Conversely, treating cells with a hairpin inhibitor directed against miR-181a inhibits TGF-β-mediated invasion, EMT, and survival signaling. Furthermore, inhibition of miR-181a abrogates pulmonary outgrowth and enhances overall survival in vivo. Collectively, our findings identify the miR-181a family as a novel effector of TGF-β-driven tumor progression and suggest that measures capable of diminishing miR-181a levels may alleviate breast cancer progression.

[FY09-DOD-BCRP-Predoctoral Traineeship Award].

Citation Format: Molly A. Taylor, William P. Schiemann. The role of microRNA-181a in TGF-β-mediated breast cancer progression [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A33.
Abstract A6: microRNA sequencing of AKXD recombinant inbred panel identifies miR-216b as a candidate metastasis suppressor in a murine model of breast cancer
Authors: Faraji Farhoud , Hu Ying , Goldberger Natalie , Wu Gang , Buetow Ken H. , Zhang Jinghui , Hunter Kent W.
Published: April 2013

Metastatic disease continues to be the primary cause of mortality in cancer. Using a combination of complex genetics, mouse models of breast cancer, and human epidemiology, our laboratory has demonstrated that germline polymorphism contributes to an individual's susceptibility to metastasis. In the current study, we have used the AKXD recombinant inbred panel, which is derived from inbred mice of metastasis resistant, DBA, and metastasis-prone, AKR, genetic backgrounds, to identify microRNAs whose expression is associated with metastasis. microRNA sequencing of tumor tissue from the progeny of AKXD x Polyoma Middle-T mice demonstrated that the expression of the miR-216/217 cluster is significantly negatively correlated with pulmonary metastases in the AKXD panel. Linkage analysis demonstrated a significant association between the miR-216/217 locus and the DBA allele, suggesting that the difference in expression is inherited rather than somatically acquired. Finally, we show that ectopic expression of miR-216b in murine mammary tumor cells suppresses pulmonary metastasis without significantly impacting primary tumor growth in vivo. These findings suggest that miR-216b is an inherited modifier of metastasis with metastasis suppressing activity in a mouse model of breast cancer.

Citation Format: Farhoud Faraji, Ying Hu, Natalie Goldberger, Gang Wu, Ken H. Buetow, Jinghui Zhang, Kent W. Hunter. microRNA sequencing of AKXD recombinant inbred panel identifies miR-216b as a candidate metastasis suppressor in a murine model of breast cancer [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A6.
Abstract B4: MicroRNAs differentially expressed in preoperative human serum of ovarian cancer
Authors: Chao Angel , Wang Tzu Hao , Chen Hua-Chien , Chen Shu-Jen , Lai Chyong-Huey
Published: April 2013

MicroRNAs (miRNAs) have been reported to play important regulatory roles in many biological processes and tumorigenesis. To investigate the roles of serum miRNAs in patients before tumor bulk was surgically removed from ovarian cancer patients, we utilized miRNA real-time QPCR profiling technology to characterize the miRNAs in pre-operative and postoperative sera. Six pairs of sera were analyzed using 270 miRNA SyberGreen probes. Upregulation of miR187, miR499-3p, miR548c-5p, miR1, miR107, miR125a-5p, miR18b were identified in the preoperative sera. Targetscan was utilized to identify Dab2 as the target gene of miR187. In vitro studies of SKOV3 cells showed that ectopic expression of miR187 suppressed Dab2 and resulted in increased cell proliferation. We concluded that miR187 may be a potential biomarker in sera of ovarian cancer patients. Further studies with larger sample sizes are warranted to validate our results.

Citation Format: Angel Chao, Tzu Hao Wang, Hua-Chien Chen, Shu-Jen Chen, Chyong-Huey Lai. MicroRNAs differentially expressed in preoperative human serum of ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr B4.
Abstract IA10: Spreading of X-chromosome inactivation via a hierarchy of defined Polycomb stations
Authors: Pinter Stefan F. , Pinter Stefan F. , Pinter Stefan F. , Jeon Yesu , Jeon Yesu , Jeon Yesu , Ohsumi Toshiro K. , Ohsumi Toshiro K. , Borowsky Mark , Borowsky Mark , Lee Jeannie T. , Lee Jeannie T. , Lee Jeannie T. , Sadreyev Ruslan I. , Sadreyev Ruslan I. , Sadreyev Ruslan I. , Yildirim Eda , Yildirim Eda , Yildirim Eda
Published: April 2013

X-chromosome inactivation (XCI) achieves dosage balance in mammals by repressing one of two X-chromosomes in females. During XCI, the long noncoding Xist RNA and Polycomb proteins spread along the inactive X (Xi) to initiate chromosome-wide silencing. Although inactivation is known to commence at the X-inactivation center (Xic), how it propagates remains unknown. We have examined allele-specific binding of Polycomb repressive complex 2 (PRC2) and chromatin composition during XCI, and generate a chromosome-wide profile of Xi and Xa (active X) at nucleosome-resolution. Initially, Polycomb proteins are localized to a limited number of sites along the X. As Xist RNA spreads in cis during the XCI process, thousands of additional sites are recruited. PRC2 and H3K27 methylation spread along a gradient in an Xi-specific manner not seen on autosomes. Our findings suggest that XCI is governed by a hierarchy of defined Polycomb stations that spread H3K27 methylation in cis.

Citation Format: Stefan F. Pinter, Yesu Jeon, Toshiro K. Ohsumi, Mark Borowsky, Jeannie T. Lee, Ruslan I. Sadreyev, Eda Yildirim. Spreading of X-chromosome inactivation via a hierarchy of defined Polycomb stations [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA10.
Abstract IA17: Functional genomics, small RNAs and cancer
Authors: Hahn William C.
Published: April 2013

Efforts to sequence cancer genomes have begun to uncover comprehensive lists of genes altered in cancer. Unfortunately, the complexity and sheer volume of data that emerges from these efforts has made dissecting the underlying biology of cancer difficult. In addition, the number and types of candidate targets that require functional validation in vivo represent a significant barrier to using this information as a starting point for drug development programs, since many do not represent targets amenable to traditional small molecule or antibody-based therapeutic approaches. To address this problem, we have combined comprehensive analyses of cancer genomes with novel materials science to develop a platform that enables the ready in vivo validation of cancer targets. Specifically, we have developed a screening platform to perform loss of function screens at genome scale and have applied this in a massively parallel manner to screen several hundred full characterized cancer cell lines. We have combined the outputs of these screens with data emerging from the study of cancer genomes to identify candidate oncogenes. To credential these targets in vivo, we have helped develop novel nanocomplexes formed from siRNA bound to tandem peptides containing tumor-penetrating, endosomal escape and siRNA-binding domains that permit deep penetration in tumor. We use these nanoparticles to target a hitherto undiscovered ovarian cancer oncogene, ID4, an undruggable transcriptional regulator, and show that these tumor-penetrating nanocomplexes induced complete suppression of tumor growth and significant improvement of survival. Taken together, these studies provide a platform for the discovery and initial validation of candidate cancer targets.

Citation Format: William C. Hahn. Functional genomics, small RNAs and cancer [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA17.
Abstract IA18: Mechanisms of miRNA mediated cellular reprogramming
Authors: Morrisey Edward
Published: April 2013

Recent evidence has indicated that miRNAs have the ability to promote dramatic changes in cell fate including pluripotent stem cell reprogramming. Certain miRNA clusters including miR302/367 are highly expressed in embryonic stem cells and when over-expressed can convert fibroblasts to induced pluripotent stem cells. Moreover, recent publications have shown that certain miRNAs can directly convert fibroblasts to neurons indicating that this technique may be widely applicable to other cell lineages. Despite these intriguing results, little is understood about the molecular mechanism underlying miRNA mediated reprogramming. Since miRNAs can target hundreds of mRNAs, identification of specific targets as well as molecular pathways affected will require multiple approaches. Data will be presented on how our lab is using systems biology and genomic approaches to decipher the underlying mechanism of miRNA-mediated cellular reprogramming.

Citation Format: Edward Morrisey. Mechanisms of miRNA mediated cellular reprogramming [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA18.
Abstract IA21: Long noncoding RNAs as drug targets
Authors: Wahlestedt Claes Robert
Published: April 2013

Much of the mammalian genome is transcribed into non-coding RNAs of different categories. This lecture will primarily be concerned with natural antisense transcripts (NATs) most of which are long noncoding RNAs. NATs are found in most gene loci and regulate gene expression through several distinct mechanisms including chromatin modifications. Inhibition/perturbation of endogenous NATs by modified oligonucleotides called AntagoNATs, in vitro or in vivo, reveals concordant or discordant regulation and results in down- or up-regulation of conventional (protein-coding) gene expression, respectively. Evidence will be presented that AntagoNATs can potently induce locus-specific and reversible modulation of gene expression associated with alterations in chromatin marks.

Citation Format: Claes Robert Wahlestedt. Long noncoding RNAs as drug targets [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA21.
Abstract IA4: Linking RNA to human health and disease
Authors: Cabili Moran , Lander Eric , Sabeti Pardis , Regev Aviv , Rinn John L. , Rinn John L. , Rinn John L. , Trapnell Cole , Trapnell Cole , Goff Loyal , Goff Loyal , Broadbent Kate , Broadbent Kate , Guttman Mitchell
Published: April 2013

In the 50 years since RNA was identified as a central component in the flow of genetic information, it has become increasingly clear that RNA is more than a mere messenger and instead performs vast and diverse functions. Numerous studies have revealed that the mammalian genome is pervasively transcribed, giving rise to many thousands of non-coding transcripts including a class of long intergenic noncoding RNAs (lincRNAs). Raising the question of what do lincRNAs do?

To address this question we have developed a ‘guilt by association’ to ‘predict’ lincRNA functions leading to hypothesis driven experimentation. Our guilt by association method pointed to a clear connection of lincRNAs and numerous cellular pathways ranging from pluripotency, cancer, adipogenesis to parasitology. Experimental perturbation experiments have unraveled a myriad of functional roles for lincRNAs in these pathways. Together, these results point to key regulatory roles for lincRNAs across diverse biological pathways and diseases, with a common theme of interfacing with and modulating protein regulatory complexes.

Citation Format: Moran Cabili, Eric Lander, Pardis Sabeti, Aviv Regev, John L. Rinn, Cole Trapnell, Loyal Goff, Kate Broadbent, Mitchell Guttman. Linking RNA to human health and disease [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA4.
Abstract IA7: Unraveling the complexities of p63 in cancer and stem cells
Authors: Flores Elsa R.
Published: April 2013

Aberrant expression of microRNAs (miRNAs) and the enzymes that control their processing have been reported in multiple biological processes including in cancer and the regulation of stem cells, but the mechanisms governing this are not clearly understood. We have generated conditional knockout mice that allow the functional separation of TAp63 and ΔNp63. Using the TAp63 conditional knock out mouse model, we found that TAp63 suppresses tumorigenesis and metastasis through coordinate transcriptional regulation of Dicer and miR-130b. Interestingly, we have recently found that ΔNp63 also plays an important role in miRNA processing by transcriptionally activating DGCR8. In turn, DGCR8 is required for processing of key miRNAs that repress genes required for stem cell pluripotency, Oct4, Sox2, and Nanog. Strikingly, epidermal cells derived from ΔNp63 deficient mice express markers of pluripotency at levels comparable to mouse embryonic stem cells. Moreover, these cells exhibit characteristics of stem cells that can self-renew and can differentiate into multiple cell fates in vitro and in vivo. Our data reveal a novel role for ΔNp63 in the commitment to epidermal differentiation through transcriptional regulation of DGCR8 and downstream modulation of key miRNAs required to maintain stem cell pluripotency. Taken together, our data show that p63 plays critical roles in regulating miRNAs in multiple biological processes.

Citation Format: Elsa R. Flores. Unraveling the complexities of p63 in cancer and stem cells [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA7.
Abstract PR5: Treatment of ovarian cancer with targeted tumor-penetrating siRNA nanocomplexes
Authors: Ren Yin , Cheung Hiu Wing , Drapkin Ronny , Root David , Lo Justin , Fogal Valentina , Ruoslahti Erkki , Hahn William , Bhatia Sangeeta , von Maltzahn Geoffrey , Agrawal Amit , Cowley Glenn , Weir Barbara , Boehm Jesse , Tamayo Pablo , Mesirov Jill , Karst Alison
Published: April 2013

Whole-genome analysis of cancer samples is identifying many potential therapeutic targets, by virtue of their being frequently mutated or functionally essential in specific types of cancer. However, we lack efficient ways to test the therapeutic benefit of modulating targets in vivo. RNAi offers one potential solution; however, approaches to deliver siRNA in vivo have been challenging due to their susceptibility to serum nucleases, endosomal entrapment, and stimulation of innate immunity. Furthermore, nanoparticle- and antibody-based siRNA delivery approaches have historically suffered from limited tumor penetration and low transvascular transit, thereby limiting the applicability of parenchymal siRNA targets. Here we describe a tumor penetrating nanocomplex (TPN) comprised of siRNA complexed to a tandem tumor-penetrating and membrane-translocating peptide, which enables the homing of siRNA deep into tumor parenchyma. Upon complexation with siRNA, the resulting nanocomplex is stable, non-immunostimulatory, displays homing peptides in a multivalent fashion that increases their binding avidity and delivers siRNA to the cytosol of tumor cells through receptor-specific interactions and membrane translocation. Upon systemic administration into mice, this nanocomplex penetrates into the parenchyma of metastatic peritoneal tumors and silences target genes in cells of interest in a receptor-specific manner. We employed TPNs in vivo to evaluate ID4, a novel candidate oncogene in ovarian cancer, which we identified by combining genome-scale RNAi screening of cancer cell lines with genome-scale sequence analysis of patient tumors. We show that treatment of tumor-bearing mice with ID4-specific TPNs suppresses tumor growth and significantly improved survival. These findings provide a framework for the identification, credentialing, and understanding of novel cancer targets as well as validating a specific therapeutic target in ovarian cancer.

This abstract is also presented as Poster B2.

Citation Format: Yin Ren, Hiu Wing Cheung, Ronny Drapkin, David Root, Justin Lo, Valentina Fogal, Erkki Ruoslahti, William Hahn, Sangeeta Bhatia, Geoffrey von Maltzahn, Amit Agrawal, Glenn Cowley, Barbara Weir, Jesse Boehm, Pablo Tamayo, Jill Mesirov, Alison Karst. Treatment of ovarian cancer with targeted tumor-penetrating siRNA nanocomplexes [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr PR5.
Introducing The Productive Operating Theatre Programme in Urology Theatre Suites
Authors: Ahmed Kamran , Khan Nuzhath , Anderson Deirdre , Watkiss Jonathan , Challacombe Ben , Khan Mohammed Shamim , Dasgupta Prokar , Cahill Declan
Published: April 2013

Background: The Productive Operating Theatre (TPOT) is a theatre improvement programme designed by the UK National Health Service. The aim of this study was to evaluate the implementation of TPOT in urology operating theatres and identify obstacles to running an ideal operating list. Method: TPOT was introduced in two urology operating theatres in September 2010. A multidisciplinary team identified and audited obstacles to the running of an ideal operating list. A brief/debrief system was introduced and patient satisfaction was recorded via a structured questionnaire. The primary outcome measure was the effect of TPOT on start and overrun times. Results: Start times: 39-41% increase in operating lists starting on time from September 2010 to June 2011, involving 1,365 cases. Overrun times: Declined by 832 min between March 2010 and March 2011. The cost of monthly overrun decreased from September 2010 to June 2011 by GBP 510-3,030. Patient experience: A high degree of satisfaction regarding level of care (77%), staff hygiene (71%) and information provided (72%), while negative comments regarding staff shortages and environment/facilities were recorded. Conclusions: TPOT has helped identify key obstacles and shown improvements in efficiency measures such as start/overrun times.
Clinical Characteristics and Time Trends in Etiology of Hepatocellular Cancer in Germany
Authors: Schütte Kerstin , Kipper Matthias , Kahl Stefan , Bornschein Jan , Götze Tobias , Adolf Daniela , Arend Jörg , Seidensticker Ricarda , Lippert Hans , Ricke Jens , Malfertheiner Peter
Published: April 2013

Introduction: The incidence of hepatocellular cancer (HCC) continues to rise in Europe with a shift of the primary cause towards alcoholic and non-alcoholic fatty liver disease. Metabolic factors like diabetes mellitus and overweight have been identified as significant risk factors for HCC development. Patients and Methods: A retrospective analysis in a large single-center cohort of 650 patients diagnosed with HCC was performed. Demographic characteristics, risk factors, tumor stage at diagnosis and survival were evaluated. Results: Among 650 patients (aged 17-87 years, with a male: female ratio of 4:1), 80.8% had underlying liver cirrhosis. Alcohol abuse was identified as the only risk factor for liver cirrhosis in 52.2% of patients. Viral infection with hepatitis C and hepatitis B was present in 13.7 and 3.6% of patients, respectively. 66.1% of patients with HCC were overweight with a body mass index exceeding 25, 25.5% even exceeding 30; 52% of patients had diabetes mellitus. Conclusion: Strategies aiming at prevention and surveillance of patients at risk to develop HCC in the future need to widen the focus from patients with chronic viral hepatitis and a history of alcohol abuse to patients with metabolic risk factors.
Topical Retinoids in Oral Lichen Planus Treatment: An Overview
Authors: Petruzzi Massimo , Lucchese Alberta , Lajolo Carlo , Campus Guglielmo , Lauritano Dorina , Serpico Rosario
Published: April 2013

Background: Treatment of oral lichen planus (OLP) is a major challenge for clinicians and patients. There is limited scientific evidence about topical treatment with retinoids. We conducted a literature review of data on the effectiveness and safety of topical retinoids in OLP patients. Materials and Methods: We searched the MEDLINE, Embase and Cochrane databases for articles on topical retinoids treatment on OLP patients (searches from 1970 to February 2012). Results: Sixteen studies (280 OLP patients topically treated with different classes of retinoids) met the inclusion criteria. Isotretinoin was the most frequently employed retinoid in the treatment of OLP. The clinical and/or histopathological efficacy of retinoids was recorded in the majority of the selected studies. A transient and moderate burning sensation was the most frequently reported side effect. Conclusions: Topical retinoids appear as an alternative choice in OLP treatment. Whether keratotic OLP better responds to topical retinoids than erosive OLP is still an open question that deserves further comparative and controlled clinical trials. The benefits and harms of using topical retinoids in people with OLP require thorough evaluation in properly designed controlled studies.
Atrichia with Papular Lesions in a Chinese Family Caused by Novel Compound Heterozygous Mutations and Literature Review
Authors: Wang Shuang , Tu Chen , Feng Yiguo , Wang Xiaopeng , Zhang Dingwei , Xiao Shengxiang
Published: April 2013

Background: Congenital atrichia with papular lesions (APL) is characterized by complete absence of body hair shortly after birth, along with papules, and caused by mutations in the hairless gene (HR). Objective: To investigate whether APL with HR mutations might also be found among patients in non-consanguineous Chinese families and to discuss the phenotypic variations with the same mutations. Methods: DNA sequencing of the HR was performed in the Chinese pedigree and in 100 controls. Results: A nonsense mutation c.T2265A in the patient and his father as well as a 2bp deletion (3482delCT) in the patient and his mother were detected. Conclusion: Our study identified the first mutation in exon 10 in HR as well as the second novel compound heterozygous mutations in a Chinese family, also adding new variants to the knowledge of HR mutations in APL. Phenotypic heterogeneity in congenital atrichia might be subject to the founder genes or modifier genes.
Quantitative Comparison of CDKN2B Methylation in Pediatric and Adult Myelodysplastic Syndromes
Authors: Kim Miyoung , Kook Hoon , Park Hyeon Jin , Ahn Hyo Seop , Lee Kwang Chul , Lee Kun Soo , Park Sang Kyu , Lim Jae Young , Kim Hyun Kyung , Han Dong Kyun , Lee Dong Soon ,   The Korean Pediatric MDS Working Party
Published: April 2013

Background/Aims: Transcriptional repression of tumor suppressor genes is determined by the quantity of promoter hypermethylation. We analyzed the methylation quantity of CDKN2B in pediatric myelodysplastic syndromes (MDS). Methods: Quantitative measurement of CDKN2B methylation was performed in 25 pediatric MDS patients and 12 controls using pyrosequencing, and the result was compared with those from 74 adult MDS cases and 31 adult controls. The association between CDKN2B methylation quantity and factors related to prognosis including bone marrow blast percentage and karyotype was analyzed. Results: Pediatric MDS patients showed a higher methylation level (MtL) of CDKN2B than pediatric controls (2.94 vs. 1.62; p = 0.031) but a lower level than adult MDS patients (8.76; p < 0.001). MtL was higher in pediatric MDS cases with >5% blasts than in pediatric controls (3.78 vs. 1.62; p = 0.052). Pediatric MDS cases with abnormal karyotype showed a higher MtL than pediatric controls (5.95 vs. 1.62; p = 0.045). Conclusions: We confirmed that methylation of CDKN2B is associated with the pathogenesis and prognosis in pediatric MDS. The difference in MtLs between pediatric and adult MDS might be related to the physiological hypermethylation of tumor suppressor genes in aging.
The Relationship of NT-proBNP and Dialysis Parameters with Outcome of Incident Haemodialysis Patients: Results from the Membrane Permeability Outcome Study
Authors: Locatelli Francesco , Hannedouche Thierry , Martin-Malo Alejandro , Jacobson Stefan H. , Vanholder Raymond , Ronco Claudio , La Milia Vincenzo , Lopez Gomez Juan M. , Stefoni Sergio , Maheut Hervé , Klinger Marian , Krummel Thierry , Dhondt Annemie , Berdud Isabel , Gauly Adelheid ,   for the Membrane Permeability Outcome (MPO) Study Group
Published: April 2013

Background/Aims: The association of raised levels of natriuretic peptides with elevated risk of mortality was investigated in the present analysis of the Membrane Permeability Outcome study. Methods: N-terminal probrain type natriuretic peptide (NT-proBNP) was measured in 618 incident haemodialysis patients, randomised to either high-flux or low-flux. Characteristics of patients with NT-proBNP levels below or above the median were descriptively analysed and survival analysis was performed. Results: Median NT-proBNP value was 2,124 pg/ml, with 1,854 pg/ml in the high-flux and 2,919 pg/ml in the low-flux group. Survival probability was lowest in patients with both a history of cardiovascular disease and NT-proBNP values above the median (p < 0.001). A multivariate Cox proportional hazard model showed interaction between presence of cardiovascular diseases and NT-proBNP levels above the median. Conclusions: NT-proBNP is an independent predictor of mortality also in incident haemodialysis patients. Lower concentrations associated with high-flux dialysis suggest a possible biological link to improved survival in this group.
Comparison of Three Versions of Partin Tables to Predict Final Pathologic Stage in a Chinese Cohort: A Decision Curve Analysis
Authors: Xiao Wen-Jun , Ye Ding-Wei , Yao Xu-Dong , Zhang Shi-Lin , Dai Bo
Published: April 2013

Purpose: To compare Partin tables (PTs) 1997, 2001, and 2007 for their clinical applicability in a Chinese cohort based upon a decision curve analysis (DCA). Methods: Clinical and pathologic data of 264 consecutive Chinese patients with clinically localized prostate cancer were used. These patients underwent open radical prostatectomy between 2005 and 2011. DCA quantified the net benefit of different PT versions relating to specific threshold probabilities of established capsular penetration (ECP), seminal vesicle involvement (SVI), and lymph node involvement (LNI). Results: Overall, ECP, SVI, and LNI were recorded in 23.1, 10.2, and 6.1%, respectively. When the threshold probability was below the prevalence for LNI and ECP predictions, the DCA favored the 2007 version versus the 1997 version for SVI. Conclusions: DCA indicates that for low threshold probability, decision models are useful to discriminate the performance differences of three PT versions, although net benefit differences were not apparent. For high threshold probability, there may not be an important benefit from the use of PTs and the current analysis cannot translate into meaningful net gains differences.