bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-185: Oxidative damage targets complexes containing DNA methyltransferases, SIRT1 and polycomb members to promoter CpG islands
Authors: O'Hagan Heather M. , Wang Wei , Sen Subhojit , Lee Stella S. , Clements Eriko G. , Cai Yi , Van Neste Leander , Easwaran Hariharan , Baylin Stephen B.
Published: August 2014

A key question in cancer epigenetics is how cancers of multiple types simultaneously acquire global losses and gains of DNA methylation. The increases often occur in promoter CpG islands and can be associated with transcriptional inactivation of key tumor suppressor genes. Here we demonstrate a molecular response to oxidative damage, a key factor in cancer risk states, which could help explain the gains and losses of DNA methylation that occur during tumor progression. Within 30 minutes of exposing cells to the reactive oxygen species, hydrogen peroxide (H2O2), the major maintenance enzyme for DNA methylation, DNMT1, becomes notably more tightly bound to chromatin. Concomitantly, DNMT1 targets SIRT1 to chromatin and both proteins become part of a large multi-protein complex(es) which also contains the de novo DNA methyltransferase, DNMT3B. This oxidative damage-induced complex also contains specific polycomb group members, which, in the context of SIRT1, define the Polycomb Repressive Complex 4 (PRC4), previously found only in embryonic and adult stem cells and cancer cells. By examining chromatin on a genome-wide scale, we demonstrate that H2O2 treatment preferentially damages GC-rich regions of DNA. This damage causes a shift in localization of the above complex(es) from non-GC-rich to GC-rich regions of the genome including promoter CpG islands of which some are DNA hypermethylated in cancer cells. Additionally, this treatment causes a decrease in nascent RNA transcript levels of these genes that have oxidative damage-induced enrichment of the silencing complex in their CpG island-containing promoters. Thus, oxidative damage induces formation and localization of a silencing complex that may in part explain cancer specific aberrant losses and gains in DNA methylation associated with gene transcriptional silencing.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-185. doi:10.1158/1538-7445.AM2011-LB-185
Abstract 103: A prospective study of plasma inflammatory markers and risk of colorectal cancer in men.
Authors: Song Mingyang , Wu Kana , Ogino Shuji , Fuchs Charles S. , Giovannucci Edward L. , Chan Andrew T.
Published: August 2014

Chronic inflammation may mediate risk of colorectal cancer (CRC); however, the association between circulating inflammatory markers and risk of CRC has been inconsistent. We prospectively evaluated the association of plasma C-reactive protein (CRP), interleukin-6 (IL-6), and the soluble tumor necrosis factor receptor 2 (sTNFR-2) with incident CRC among 18,225 men in the Health Professionals Follow-up Study who provided blood samples in 1994. Through 2008, we documented 274 CRC cases and matched up to 2 controls by age and date of blood draw. We used conditional logistic regression to estimate relative risks (RRs) and confidence intervals (CIs). Compared to men in the lowest quartile of plasma IL-6 (Q1), men in the highest quartile (Q4) had a multivariate RR for CRC of 1.54 (95% CI, 0.99-2.40; Ptrend = .02). However, after excluding cases diagnosed within 2 years of blood draw, the association was substantially attenuated (Q4 versus Q1, RR = 1.26, 95% CI = 0.78-2.05; Ptrend = .21). In analyses restricted to cases diagnosed at least 2 years after blood draw, the association of IL-6 with CRC appeared to differ by body mass index such that the significantly positive association was only present among lean individuals (Pinteraction = .03). We did not observe any significant association between CRP or sTNFR-2 and CRC. Taken together, plasma inflammatory markers are not generally associated with risk of CRC among men. However, the possibility that plasma IL-6 is associated with increased risk of CRC among lean men requires further investigation.

Citation Format: Mingyang Song, Kana Wu, Shuji Ogino, Charles S. Fuchs, Edward L. Giovannucci, Andrew T. Chan. A prospective study of plasma inflammatory markers and risk of colorectal cancer in men. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 103. doi:10.1158/1538-7445.AM2013-103
Abstract 1068: Keratinocyte-specific deletion in mice reveals gene dose-dependent function of SIRT1 in tumorigenesis.
Authors: Ming Mei , Soltani Keyoumars , Shea Christopher R. , Li Xiaoling , He Yu-ying
Published: August 2014

The protein deacetylase SIRT1, a mammalian counterpart of the yeast silent information regulator 2 (Sir2) and a proto member of the sirtuin family, regulates various pathways in metabolism, DNA repair, and cell survival. However, the role of SIRT1 in cancer is still under debate. Here we show that the role of SIRT1 in skin cancer development induced by the human skin carcinogen UVB radiation is dependent on its gene dose. Keratinocyte-specific heterozygous deletion of SIRT1 increases UVB-induced skin tumorigenesis, whereas homozygous deletion of SIRT1 decreases skin tumorigenesis. In mouse skin, SIRT1 is haploinsufficient for DNA repair and the expression of xeroderma pigmentosum C (XPC), a protein critical for repairing UVB-induced DNA damage. Similar to homozygous SIRT1 deletion, heterozygous SIRT1 deletion reduces the XPC protein levels and UVB-induced DNA damage repair. As compared with normal human skin, down-regulation of SIRT1 is in parallel with down-regulation of XPC in human cutaneous squamous cell carcinoma at both the protein and mRNA levels. In contrast, homozygous SIRT1 deletion in mouse skin augments p53 acetylation, and the expression of its transcriptional target Noxa, and sensitizes epidermis to UVB-induced apoptosis in vivo, while heterozygous SIRT1 deletion has no effect. Although mice with homozygous SIRT1 deletion do not develop tumors, these mice suffer severe sunburn. The gene dose-dependent function of SIRT1 in DNA repair and cell survival is consistent with its role in UVB-induced skin tumorigenesis and injury. Taken together, our results indicate that, depending on the SIRT1 levels, SIRT1 acts as a tumor suppressor and as an oncogene.

Citation Format: Mei Ming, Keyoumars Soltani, Christopher R. Shea, Xiaoling Li, Yu-ying He. Keratinocyte-specific deletion in mice reveals gene dose-dependent function of SIRT1 in tumorigenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1068. doi:10.1158/1538-7445.AM2013-1068
Abstract 1070: New potent inhibitors of the androgen receptor that target its BF3 surface binding site.
Authors: Munuganti Ravi , Ban Fuqiang , Li Huifang , LeBlanc Eric , Axerio Peter , Frewin Kate , Tomlinson Guns Emma , Cherkasov Artem , Rennie Paul S.
Published: August 2014

In the development and progression of prostate cancer, the androgen receptor (AR) plays a critical role and its hormone/ligand-binding site is the primary therapeutic target for all antiandrogens (eg Bicalutamide, MDV3100) currently used to treat advanced, metastatic forms of this disease. While treatment with these AR inhibitors initially suppresses prostate tumor growth, resistance to these drugs invariably emerges. Accordingly, there exists a clinical need for the development of new AR antagonists with different chemical structures and different mechanisms of action for targeting and inhibiting AR transactivation. To this end, we have focused on a surface pocket on the AR called Binding Function 3 (BF3). Applying iterative in silico screening to millions of chemicals in the ZINC database, coupled with biological screening for AR binding and activity, we identified several compounds that can bind directly to the BF3 pocket and inhibit AR transactivation. Cell-based screening assays for inhibition of a fluorescent ARE-reporter and PSA expression, together with Biolayer Interferometry analysis for measuring binding to the AR, revealed several chemically distinct BF-3 binders that showed significant IC50 inhibitions of the AR in the nano-molar to low micro-molar range. Validation for binding to the BF3 site was performed by x-ray crystallography. Furthermore, none of these compounds were able to displace DHT from the hormone binding site even at concentrations more than 10-fold higher than their IC50 values. In addition to wild type LNCaP prostate cancer cells, these BF3 binders effectively inhibited cell proliferation (MTS assay) and PSA expression in derived MDV3100-resistant prostate cancer cell lines, but had no effect on cell viability of AR-negative prostate cancer cell lines. In summary, we have identified an entirely new class of anti-androgens that bind to the BF3 surface site of the AR and inhibit its transactivation by a mechanism which does not involve binding to its hormone/ligand binding site and thereby bypasses the treatment resistance seen with conventional antiandrogens. (Supported by funds from the PCF, Canada Safeway, and CIHR).

Citation Format: Ravi Munuganti, Fuqiang Ban, Huifang Li, Eric LeBlanc, Peter Axerio, Kate Frewin, Emma Tomlinson Guns, Artem Cherkasov, Paul S. Rennie. New potent inhibitors of the androgen receptor that target its BF3 surface binding site. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1070. doi:10.1158/1538-7445.AM2013-1070
Abstract 1083: The pivotal role of IKKalpha in the development of spontaneous lung squamous cell carcinomas.
Authors: Xiao Zuoxiang , Jiang Qun , Willette-Brown Jami , Zhu Feng , Xi Sichuan , Burkett Sandra , Lin Fanching , Back Timothy , Datla Mahesh , Sun Zhonghe , Goldszmid Romina , Wu Xiaolin , Schrump David , Young Howard , Trinchieri Georgio , Wiltrout Robert , Hu Yinling
Published: August 2014

During the last decades lung cancer has become the leading cause of cancer deaths in the world, and the need to develop better diagnostic techniques and therapies is urgent. To advance the understanding of this disease, various genetically engineered and chemical induced mouse models have been established. However, there are no robust animal models of lung squamous cell carcinomas (SCCs), one of the major types of lung cancer. Here, we generated Ikkα-KA/KA knock-in mice (KA/KA) in which an ATP binding site of IKKα, Lys 44 was replaced by alanine. All the knock-in mice at 4 to 6 months of age developed spontaneous lethal lung SCCs associated with markedly increased leukocyte infiltration and expression of cytokines, and chemokines in the lungs. Furthermore, we identified deregulated c-myc, Nanog, Oct3/4, p53, Rb, EGFR, MAPK, Jun-B, p63, Trim29, Rhov, CDK1, and IGF1 in mouse lung SCCs, and identified reduced IKKα and IκBα and increased ROS1 in mutant lungs and SCCs, some of which were found in human lung SCCs. Lung cancers were prevented by reintroducing epithelial-cell IKKα, depleting macrophages or depleting lymphocytes. This study not only provides a novel model for studying the pathogenesis, treatment, early detection, and prevention of human lung SCCs, but also demonstrates how a single mutation in IKKα elicits malignancy through the combined epithelial-cell-autonomous and immune mechanisms.

Citation Format: Zuoxiang Xiao, Qun Jiang, Jami Willette-Brown, Feng Zhu, Sichuan Xi, Sandra Burkett, Fanching Lin, Timothy Back, Mahesh Datla, Zhonghe Sun, Romina Goldszmid, Xiaolin Wu, David Schrump, Howard Young, Georgio Trinchieri, Robert Wiltrout, Yinling Hu. The pivotal role of IKKalpha in the development of spontaneous lung squamous cell carcinomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1083. doi:10.1158/1538-7445.AM2013-1083
Abstract 1088: HOXB13 inhibition of succinate dehydrogenase leads to epithelial-to-mesenchymal transition in mouse ovarian cancer cell lines.
Authors: Aspuria Paul-Joseph , Cheon Dong-Joo , Gozo Maricel , Salumbides Brenda , Vergnes Laurent , Asara John , Reue Karen , Kensicki Elizabeth , Karlan Beth , Orsulic Sandra
Published: August 2014

HOXB13 is a homeobox gene whose dysregulation has been implicated in cancer. We have previously shown that HOXB13 plays an oncogenic role in ovarian cancer by driving epithelial-to-mesenchymal transition (EMT); however the mechanism by which this occurs has not been established. Global metabolomics profiling revealed that overexpression of HOXB13 in genetically defined mouse ovarian cancer cell lines inhibits succinate dehydrogenase (SDH) activity. Targeted-knockdown of the SDH subunit SdhB by shRNA results in mislocalization of E-cadherin and a spindle-shaped morphology suggestive of EMT. Metabolomics and real-time flux analysis showed that knockdown of SdhB results in elevated levels of succinate as well as defective mitochondrial respiration. Despite the mitochondrial respiration defect, SdhB knockdown cells display increased anchorage-independent growth in soft agar and enhanced xenograft tumor formation. Elevated levels of succinate have been shown to inhibit α-ketoglutarate requiring enzymes such as the Jumanji C (JmjC)-domain containing H3K27 demethylases, UTX and JMJD3. Indeed, knockdown of SdhB results in a hypermethylated epigenome as evidenced by increased levels of H3K27me2 and H3K27me3. Both the epigenetic and EMT phenotypes can be recapitulated by pharmacological inhibition of UTX and JMJD3 in control cells. These data point to a mechanism wherein modulation of oncometabolite levels can affect the epigenome, thereby influencing cancer cell morphology and tumorigenic properties.

Citation Format: Paul-Joseph Aspuria, Dong-Joo Cheon, Maricel Gozo, Brenda Salumbides, Laurent Vergnes, John Asara, Karen Reue, Elizabeth Kensicki, Beth Karlan, Sandra Orsulic. HOXB13 inhibition of succinate dehydrogenase leads to epithelial-to-mesenchymal transition in mouse ovarian cancer cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1088. doi:10.1158/1538-7445.AM2013-1088
Abstract 1103: An abnormally stiff microenvironment supports the overabundance of fibroblasts in non-small cell lung cancer.
Authors: Puig Marta , Giménez Alícia , Galgoczy Roland , Lugo Roberto , Ramírez Josep , Gómez-Caro Abel , Gascón Pere , Reguart Noemí , Alcaraz Jordi
Published: August 2014

Breathing demands our lungs to be soft and elastic. In contrast, lung tumors exhibit an abnormal tissue hardening concomitantly with an altered lung architecture and function, which brings the mechanical microenvironment of the tumor closer to that of muscle or bone. This tissue hardening has been associated with the abundant reactive stroma rich in activated fibroblasts (also referred to as tumor associated fibroblasts or TAFs) that is a hallmark of non-small cell lung cancer (NSCLC). However, it remains unknown whether tissue hardening alone is sufficient to drive the abnormal abundance of fibroblasts in the stroma of NSCLC. To address this question, we cultured the human lung fibroblast cell line CCD-19Lu or primary human lung fibroblasts on collagen-coated polyacrylamide gels exhibiting normal- or tumor-like stiffness in the absence (0%) or presence (0.1%) of serum for 5 days. Primary cells were isolated from both tumor-free regions (referred to as control fibroblasts) or tumors of NSCLC patients diagnosed with either Adenocarcinoma (ADC, n=5) or Squamous Cell Carcinoma (SCC, n=5) histological subtypes. We observed a significantly higher density of CCD-19Lu fibroblasts in tumor-like gels compared to normal-like gels regardless the presence of serum. Similar results were obtained in both primary control fibroblasts and SCC-TAFs. In contrast, tumor-like gels induced a weaker density increase in ADC-TAFs. The increased fibroblast density in the tumor-like gels was associated with increased survival rather than proliferation, as revealed by a downregulation of caspase-3 and a rise in AKT phosphorylation. Our results indicate that extracellular hardening alone is sufficient to induce an increased density in lung fibroblasts by activating pro-survival pathways and suggest an abnormal response of ADC-TAFs to extracellular mechanical cues. Collectively these findings underline a major role of tissue hardening in the abnormal abundance of TAFs in NSCLC, particularly in the SCC subtype. These data may be useful in developing novel targeted therapies against the pro-survival effects of tissue hardening in SCC-TAFs, which act as co-conspirators of tumor progression.

Citation Format: Marta Puig, Alícia Giménez, Roland Galgoczy, Roberto Lugo, Josep Ramírez, Abel Gómez-Caro, Pere Gascón, Noemí Reguart, Jordi Alcaraz. An abnormally stiff microenvironment supports the overabundance of fibroblasts in non-small cell lung cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1103. doi:10.1158/1538-7445.AM2013-1103
Abstract 1113: The comprehensive mutational profiling of lung adenocarcinoma through large-scale RNA sequencing analysis.
Authors: Lee Won-Chul , Ju Young Seok , Shin Jong-Yeon , Lee June Koo , Bleazard Thomas , Lee Jun-Ho , Kim Jung-Oh , Yu Saet-Byeol , Kim Jihye , Rhee Hwanseok , Lee Se-Hoon , Kim Jong-Il , Kang Jin-Hyoung , Kim Young Tae , Seo Jeong-Sun
Published: August 2014

All cancers harbor molecular alterations in their genomes. The transcriptional consequences of these somatic mutations have not yet been comprehensively explored in lung cancer. Here we present the first large scale RNA sequencing study of lung adenocarcinoma, demonstrating its power to identify somatic point mutations as well as transcriptional variants such as gene fusions, alternative splicing events and expression outliers. Our results reveal the genetic basis of 200 lung adenocarcinomas in Koreans including deep characterization of 87 surgical specimens by transcriptome sequencing. We identified driver somatic mutations in cancer genes including EGFR, KRAS, NRAS, BRAF, PIK3CA, MET and CTNNB1. Candidates for novel driver mutations were also identified in genes newly implicated in lung adenocarcinoma such as LMTK2, ARID1A, NOTCH2 and SMARCA4. We found 45 fusion genes, 8 of which were chimeric tyrosine kinases involving ALK, RET, ROS1, FGFR2, AXL and PDGFRA. Among 17 recurrent alternative splicing events, we identified exon 14 skipping in the proto-oncogene MET as highly likely to be a cancer driver. The number of somatic mutations and expression outliers varied markedly between individual cancers and was strongly correlated with smoking history of patients. We identified genomic blocks within which gene expression levels were consistently increased or decreased that could be explained by copy number alterations in samples. We also found an association between lymph node metastasis and somatic mutations in TP53. These findings broaden our understanding of lung adenocarcinoma and may also lead to new diagnostic and therapeutic approaches.

Citation Format: Won-Chul Lee, Young Seok Ju, Jong-Yeon Shin, June Koo Lee, Thomas Bleazard, Jun-Ho Lee, Jung-Oh Kim, Saet-Byeol Yu, Jihye Kim, Hwanseok Rhee, Se-Hoon Lee, Jong-Il Kim, Jin-Hyoung Kang, Young Tae Kim, Jeong-Sun Seo. The comprehensive mutational profiling of lung adenocarcinoma through large-scale RNA sequencing analysis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1113. doi:10.1158/1538-7445.AM2013-1113
Abstract 1120: Identification and characterization of a novel androgen-regulated long non-coding RNA in prostate cancer.
Authors: Malik Rohit , Iyer Matthew K. , Prensner John R. , Patel Lalit , Han Sumin , Chen Wei , Feng Felix , Chinnaiyan Arul M.
Published: August 2014

Long non-coding RNAs (lncRNAs) have recently been associated with the development and progression of a variety of cancers, including prostate cancer. However, to date very few prostate cancer lncRNAs have been characterized by functional studies as bona fide oncogenes and tumor suppressors. Previously, transcriptome sequencing (RNA-Seq) of prostate tumors and benign adjacency tissues revealed a set of putative lncRNAs termed Prostate Cancer Associated Transcripts (PCATs) with significantly altered expression levels in cancer. Intriguingly, a subset of these PCATs were strikingly upregulated in treatment-resistant metastatic prostate cancer samples, suggesting that they may play a role in the development of castrate resistant disease. To explore this possibility we stimulated prostate cancer cell lines with synthetic androgen and monitored the responsiveness of several PCATs. We found that PCAT29, a six-exon nuclear transcript located in a gene desert on chromosome 15, was suppressed by androgen in a time-dependent fashion. Furthermore, androgen receptor (AR) ChIP-Seq data revealed a strong binding site upstream of the PCAT29 promoter suggesting that PCAT29 may be a direct androgen receptor target. Supporting this notion, physical castration of a mouse Xenograft model led to profound upregulation of PCAT29 suggesting that AR signaling suppresses its transcription. Knockdown of PCAT29 using two independent shRNA leads to significant increase in the proliferation of LNCaP cells. Consistently, overexpression of PCAT29 in DU145 cells suppresses proliferation. Finally, we show that in prostate cancer patients, high PCAT29 expression correlates with better overall survival. Taken together our study suggests that PCAT29 may have a tumor suppressor like function in prostate cancer. Ongoing studies are focused on understanding the potential mechanism of PCAT29 function and its relationship with androgen signaling.

Citation Format: Rohit Malik, Matthew K. Iyer, John R. Prensner, Lalit Patel, Sumin Han, Wei Chen, Felix Feng, Arul M. Chinnaiyan. Identification and characterization of a novel androgen-regulated long non-coding RNA in prostate cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1120. doi:10.1158/1538-7445.AM2013-1120
Abstract 1121: The long non-coding RNA MALAT1 is an essential gene regulator for lung cancer metastasis in a novel human knockout model .
Authors: Gutschner Tony , Hämmerle Monika , Eißmann Moritz , Hsu Jeff , Kim Youngsoo , Hung Gene , Revenko Alexey , Arun Gayatri , Stentrup Marion , Groß Matthias , Zörnig Martin , MacLeod A. Robert , Spector David L. , Diederichs Sven
Published: August 2014

The long non-coding RNA MALAT1 was one of the first lncRNAs associated with cancer: it is a highly conserved nuclear ncRNA and a predictive marker for metastasis development in lung cancer. However, its high abundance and nuclear localization have greatly hampered its functional analysis since it is only inefficiently knocked down by RNA interference (RNAi).

To uncover its functional importance, we developed a MALAT1 knockout model in human lung tumor cells by genomically integrating RNA destabilizing elements site-specifically into the MALAT1 locus using Zinc Finger Nucleases (ZFN).This approach yielded a more than 1000-fold silencing of MALAT1 providing a unique loss-of-function model.

Proposed mechanisms of action of MALAT1 include regulation of splicing or gene expression. In lung cancer, MALAT1 does not alter alternative splicing but actively regulates gene expression inducing a signature of metastasis-associated genes. Consequently, MALAT1-deficient cells are impaired in migration and form fewer tumor nodules in a mouse xenograft model.

Encouraged by this discovery of the essential function of MALAT1 in lung cancer metastasis, we wanted to analyze whether MALAT1 could also be therapeutically targeted: We developed Antisense oligonucleotides (ASOs) effectively blocking MALAT1 expression in the cell culture and in the animal. Notably, MALAT1-ASO treatment prevents metastasis formation after tumor implantation. Thus, targeting MALAT1 with antisense oligonucleotides provides a potential therapeutic approach to prevent lung cancer metastasis with MALAT1 serving as both, predictive marker and therapeutic target.

Lastly, regulating gene expression, but not alternative splicing is the critical function of MALAT1 in lung cancer metastasis.

In summary, ten years after the discovery of the lncRNA MALAT1 as a biomarker for lung cancer metastasis, our loss-of-function model unravels the active function of MALAT1 as a regulator of gene expression governing hallmarks of lung cancer metastasis.

Citation Format: Tony Gutschner, Monika Hämmerle, Moritz Eißmann, Jeff Hsu, Youngsoo Kim, Gene Hung, Alexey Revenko, Gayatri Arun, Marion Stentrup, Matthias Groß, Martin Zörnig, A. Robert MacLeod, David L. Spector, Sven Diederichs. The long non-coding RNA MALAT1 is an essential gene regulator for lung cancer metastasis in a novel human knockout model . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1121. doi:10.1158/1538-7445.AM2013-1121
Abstract 113: Gamma-H2AX level in peripheral blood lymphocytes as a risk predictor for bladder cancer.
Authors: Fernandez Mario I. , Gong Yilei , Ye Yuanqing , Lin Jie , Chang David , Wu Xifeng
Published: August 2014

Introduction: Identification of susceptibility to double-strand breaks (DSB) may provide valuable information about genomic instability and cancer risk. The formation of gamma-H2AX foci is a highly sensitive marker for DNA DSBs induction. We assessed whether levels of gamma-H2AX in peripheral blood lymphocytes (PBL) obtained after stimulation by ionizing radiation (IR) are associated with bladder cancer risk in a bladder cancer case-control study.

Material and Methods: Patients and controls were enrolled from an ongoing bladder cancer case-control study. Epidemiologic data were collected during an in-person interview using a structured questionnaire. Baseline and IR induced H2AX-phosphorylation was assessed in PBL from 174 newly diagnosed, previously untreated bladder cancer patients and from 174 age, sex and ethnicity matched, healthy control subjects by a novel, image-based, high-throughput phenotypic assay. The ratio of gamma-H2AX level of IR-treated cells to that of non-treated cells (baseline) derived from the same blood sample was used as the parameter to assess the sensitivity to the mutagen. Logistic regression analysis was used to estimate odds ratios associated with gamma-H2AX. We also compared the discriminatory ability of a model with only demographic variables and a model including gamma-H2AX ratio.

Results: The mean gamma-H2AX ratios were significantly higher for cases than for controls (1.43±0.14 vs. 1.35±0.12; p=1.44E-08). This trend was irrespective of age, sex or smoking status. The risk estimates of bladder cancer for induced DNA DSBs showed a significant trend for increased risk at the highest tertiles for the whole cohort (OR=3.09; 95%CI 1.76-5.40; p=8.15E-05 for the second tertile and OR=3.78; 95%CI 2.26-6.33; p=4.18E-07 for the third tertile) as well as for each category. Discrimination ability of the epidemiological model was moderate, with an area under curve (AUC) of 0.64. However, the AUC increased significantly to 0.74 when gamma-H2AX ratio was incorporated.

Conclusions: Our findings suggest that a higher susceptibility to induction of DSBs as measured by the gamma-H2AX assay is significantly associated with an increased risk for bladder cancer. This might help to identify individuals at high risk for this cancer, adding new perspectives to established epidemiological and genetic risk factors. Further research of the role of gamma-H2AX in biological processes of bladder cancer is warranted.

Citation Format: Mario I. Fernandez, Yilei Gong, Yuanqing Ye, Jie Lin, David Chang, Xifeng Wu. Gamma-H2AX level in peripheral blood lymphocytes as a risk predictor for bladder cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 113. doi:10.1158/1538-7445.AM2013-113
Abstract 1158: Detection of clonally expanded HBV DNA integration sites as a marker for early detection of HBV related HCC.
Authors: Lin Selena , Jain Surbhi , Block Timothy , Song Frank , Su Ying Hsiu
Published: August 2014

Hepatocellular carcinoma (HCC), the 5th most frequent cancer worldwide, has a 5-year survival rate of 14% because it is difficult to diagnose at its curative stages. The goal of this project is to determine if the detection of clonally expanded HBV DNA integration sites can be used as a marker for early detection of HBV related HCC (HBV-HCC) in order to improve its prognosis

Hepatitis B virus (HBV) infections are associated with over 80% of HCC cases worldwide. Upon infection, the HBV genome integrates into the host chromosome at a random site, thus creating a unique genetic signature for each HBV infected cell. Certain HBV infected cells undergo progressive “uncontrolled clonal expansion” leading to the development of tumors, resulting in an over expansion of the unique HBV integration sites making them the predominant or “major HBV integration sites” (MIS).

Cell-free circulating DNA from cancer patients reflects the characteristics of the tumor DNA. We and others have shown that urine contains DNA from the circulation and can be used as a source for cell-free circulating DNA. Successful detection of HBV integration sites in the circulation of HBV-HCC patients has not been demonstrated. In order to detect cell free circulating HBV DNA integration sites, a targeted enriched Next Generation Sequencing (NGS) assay was developed. Targeted enrichment was performed using an in-solution hybridization platform with biotinylated HBV RNA baits surrounding the HBV DNA nucleotide positions 1571 to 1960, the most frequent HBV breakpoint region. The assay was tested using library constructed DNA controls: Hep3B, which contains integrated DNA, and HepG2, which contains no HBV DNA. To determine the amount of captured DNA containing HBV DNA, the captured DNA was quantified for HBV containing DNA and total captured DNA. Almost all captured DNA contained HBV DNA. To confirm targeted capture of integrated HBV DNA, the captured DNA was cloned followed by sequencing. 3 out of 3 clones that were sequenced contain integrated HBV DNA. This assay demonstrated targeted capture and enrichment of HBV integration sites. This assay will be tested for sensitivity in detecting HBV integration sites and used to establish the criteria for the appearance of MIS as a biomarker for HBV-HCC. Overall, if successful, this cancer related HBV DNA marker would offer a high specificity and sensitivity in screening for HBV-HCC.

Citation Format: Selena Lin, Surbhi Jain, Timothy Block, Frank Song, Ying Hsiu Su. Detection of clonally expanded HBV DNA integration sites as a marker for early detection of HBV related HCC. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1158. doi:10.1158/1538-7445.AM2013-1158
Abstract 1200: Molecular subtypes of gastric cancer show systematic differences in response to PI3K inhibitors and fluorouracil.
Authors: Lei Zengdeng , Deng Nian Tao , Zouridis Hermioni , Tan Iain Beehaut , Ooi Chia Huey , Ivanova Tatiana , Zhang Shenli , Lee Minghui , Wu Jeanie , Ngo Anna , Manesh Sravanthy , Boussioutas Alex , Teh Bin Tean , Goh Liang Kee , Flotow Horst , Tan Patrick , Rozen Steven G.
Published: August 2014

Background & Aims: Gastric cancer is the second leading cause of cancer death worldwide, killing >730,000 people every year. Almost all gastric cancers are adenocarcinomas, which exhibit considerable heterogeneity between patients. We sought to identify subtypes of gastric adenocarcinomas that have particular biological properties and responses to cytotoxic drugs. Methods: Robust unsupervised clustering of 248 gastric tumors based on global gene expression revealed three major subtypes. We developed a classifier, GC-Class ("Gastric Cancer Classifier") for the three subtypes and validated it in a second set of 70 tumors. We then determined the distinct genomic and epigenomic properties and drug sensitivities of the subtypes. We determined drug sensitivities of primary tumors by multivariate Cox proportional hazard modeling using clinical survival data. We determined drug sensitivities in cell lines using previously reported data and high-throughput screening of 158 compounds in 23 gastric cancer cell lines. Results: There are three major subtypes of gastric adenocarcinoma: “invasive," “proliferative," and “metabolic”. The subtypes show systematic differences in genomic and epigenetic characteristics and in drug response. Proliferative-subtype tumors show high genomic instability and DNA hypomethylation. Metabolic-subtype cancer cell lines are preferentially sensitive to fluorouracil, and, in two independent groups, patients with the metabolic-subtype tumors benefited significantly from fluorouracil treatment. Invasive-subtype tumors have characteristics in common with cancer stem cells, and cell lines in this subtype are particularly sensitive to PI3K/AKT/mTOR inhibitors. Conclusions: The molecular classification of gastric cancers reported here is reproducible and biologically and therapeutically meaningful, and it holds promise as a basis for selecting and developing therapies tailored to particular subtypes.

Citation Format: Zengdeng Lei, Nian Tao Deng, Hermioni Zouridis, Iain Beehaut Tan, Chia Huey Ooi, Tatiana Ivanova, Shenli Zhang, Minghui Lee, Jeanie Wu, Anna Ngo, Sravanthy Manesh, Alex Boussioutas, Bin Tean Teh, Liang Kee Goh, Horst Flotow, Patrick Tan, Steven G. Rozen. Molecular subtypes of gastric cancer show systematic differences in response to PI3K inhibitors and fluorouracil. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1200. doi:10.1158/1538-7445.AM2013-1200
Abstract 1277: Utilizing uterine cancer models to study malignant transformation driven by Lkb1 loss.
Authors: Peña Christopher G. , Nakada Yuji , Castrillon Diego
Published: August 2014

The serine-threonine kinase LKB1 is an upstream component of the AMPK-mTOR pathway and regulates cell survival and growth. Inherited germline mutations in LKB1 predispose women to endocervical malignancies whereas somatic mutations in LKB1 promote cervical cancer progression. Our lab has shown that tissue specific knockout of Lkb1 in the endometrial epithelium of mice facilitates growth of highly invasive, lethal tumors that are well differentiated and retain structural polarity. Additionally, stable shRNA mediated knockdown of LKB1 in human immortalized endocervical cells drives anchorage-independent growth. To investigate potential pathways involved in LKB1 mediated oncogenic transformation, we have employed a microarray based approach comparing hits from human immortalized endocervical cell lines and mouse tissue to identify specific genes that are differentially regulated when LKB1 function is absent. Preliminary data suggests that pro-angiogenic and inflammatory mediators are upregulated in LKB1 deficient cells. We are currently assessing the overall contribution of these factors to growth and invasiveness in our model systems and the mechanisms by which Lkb1 loss facilitates their activation. These pathways can be potential therapeutic targets in other cancers characterized by Lkb1 loss of function mutations.

Citation Format: Christopher G. Peña, Yuji Nakada, Diego Castrillon. Utilizing uterine cancer models to study malignant transformation driven by Lkb1 loss. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1277. doi:10.1158/1538-7445.AM2013-1277
Abstract 1292: β-catenin is activated in arsenic-transformed human bronchialepithelial cells and promotes angiogenesis .
Authors: Wang Zhishan , Humphries Brock , Yang Chengfeng
Published: August 2014

Arsenic exposure represents a major health concern causing human cancers, yet the mechanism of arsenic carcinogenesis has not been elucidated. We and others recently reported that cell malignant transformation by arsenic is accompanied by epithelial to mesenchymal transition (EMT). However, the role of EMT in arsenic carcinogenesis is not well understood. Although previous studies showed that acute short term arsenic treatment stimulates angiogenesis, it remains to be determined whether cells that were malignantly transformed by long term arsenic exposure have a pro-angiogenic effect. The objective of this study was to investigate the effect of arsenic-transformed human bronchial epithelial cells that underwent EMT on angiogenesis and the underlying mechanism. It was found that the conditioned medium from arsenic-transformed cells strongly stimulated tube formation by human umbilical vein endothelial cells (HUVECs). Moreover, enhanced angiogenesis was detected in mouse xenograft tumor tissues resulting from inoculation of arsenic-transformed cells. Mechanistic studies revealed that β-catenin was activated in arsenic-transformed cells up-regulating its target gene expression including angiogenic-stimulating vascular endothelial growth factor (VEGF). Stably expressing microRNA-200b in arsenic-transformed cells that reversed EMT inhibited β-catenin activation, decreased VEGF expression and reduced tube formation by HUVECs. SiRNA knocking down β-catenin decreased VEGF expression. Adding a VEGF neutralizing antibody into the conditioned medium from arsenic-transformed cells impaired tube formation by HUVECs. It was further determined that the canonical Wnt signaling was not increased in arsenic-transformed cells. These findings suggest that EMT in arsenic-transformed cells promotes angiogenesis through activating β-catenin-VEGF pathway in the absence of elevated-canonical Wnt signaling.

Citation Format: Zhishan Wang, Brock Humphries, Chengfeng Yang. β-catenin is activated in arsenic-transformed human bronchialepithelial cells and promotes angiogenesis . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1292. doi:10.1158/1538-7445.AM2013-1292
Abstract 1295: Inhibition of clonogenicity and xenograft tumor growth by activation and/or over-expression of peroxisome proliferator-activated receptor-β/δ (PPARβ/δ).
Authors: Yao Pei-Li , Borland Michael G. , Krishnan Prasad , Zhu Bokai , Gonzalez Frank J. , Peters Jeffrey M.
Published: August 2014

The peroxisome proliferator-activated receptor-β/δ (PPARβ/δ) regulates a variety of biological processes but the function of PPARβ/δ in carcinogenesis remains controversial. Stable human cancer cell lines (A431, MDA-MB-231 and MCF7) that constitutively over-express PPARβ/δ were produced to effectively examine the role of this receptor in human cancer models. Ligand activation of PPARβ/δ both in MDA-MB-231 (ER-negative) and MCF7 (ER-positive) cells over-expressing PPARβ/δ cells caused significantly decreased clonogenicity compared to controls. Over-expression of PPARβ/δ reduced tumor volumes and tumor weights of ectopic xenografts from both MDA-MB-231 and MCF7cells compared to controls. Ligand activation of PPARβ/δ caused an even greater reduction of tumor volumes and tumor weights compared to controls. Interestingly, similar results were observed in the human epidermoid carcinoma cell line A431 and other human cancer cell lines. Ligand activation of PPARβ/δ strongly inhibited clonogenicity in A431 cells over-expressing PPARβ/δ. Xenografts from A431 control cells rapidly developed tumors while tumors were barely detectable in A431 cells over-expressing PPARβ/δ. These observations demonstrate the inhibitory effect of activating or over-expressing PPARβ/δ on tumorigenesis in human cancer cell lines. This suggests that PPARβ/δ suppression of tumorigenicity may be mediated through common mechanisms.

Citation Format: Pei-Li Yao, Michael G. Borland, Prasad Krishnan, Bokai Zhu, Frank J. Gonzalez, Jeffrey M. Peters. Inhibition of clonogenicity and xenograft tumor growth by activation and/or over-expression of peroxisome proliferator-activated receptor-β/δ (PPARβ/δ). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1295. doi:10.1158/1538-7445.AM2013-1295
Abstract 1339: Mitochondrial DNA copy number is prospectively associated with breast cancer risk.
Authors: Thyagarajan Bharat , Wang Renwei , Barcelo Helene , Nelson Heather , Koh Woon Puay , Yuan Jian Min
Published: August 2014

A previous case-control study reported a positive association between mitochondrial DNA (mtDNA) copy number in peripheral blood and breast cancer risk. However, data on mtDNA copy number and breast cancer risk in prospective cohorts is lacking. We evaluated the prospective association between mtDNA copy number and breast cancer risk in the Singapore Chinese Health Study. We conducted a nested case-control study of 183 incident breast cancer cases with pre-diagnostic blood samples and 529 individually matched control women who were free of breast cancer. The mtDNA copy number was measured using real time PCR. Conditional logistic regression methods were employed to examine the association between mtDNA copy number and breast cancer risk. Overall, there was no association between mtDNA copy number and breast cancer after adjustment for potential confounders (p=0.37). Among participants who donated a blood sample within 3 years of breast cancer diagnosis women in the second and third tertile of mtDNA copy number had a significantly increased breast cancer risk as compared to those in the lowest mtDNA copy number tertile (odds ratio (95% confidence interval): 1.84 (0.93-3.64) and 2.13 (1.09-4.17) respectively; p for trend = 0.03). There was no association between mtDNA copy number and breast cancer risk among women who donated a blood sample ≥ 3 years before breast cancer diagnosis (p for trend = 0.73). This study supports a prospective association between increased mtDNA copy number and breast cancer risk that is dependent on the time interval between blood collection and breast cancer diagnosis.

Citation Format: Bharat Thyagarajan, Renwei Wang, Helene Barcelo, Heather Nelson, Woon Puay Koh, Jian Min Yuan. Mitochondrial DNA copy number is prospectively associated with breast cancer risk. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1339. doi:10.1158/1538-7445.AM2013-1339
Abstract 1341: Identification of significant linkage evidence for lethal prostate cancer on chromosome arm 11p15.
Authors: Cannon-Albright Lisa A. , Teerlink Craig C. , Agarwal Neeraj
Published: August 2014

We performed genome wide linkage analysis in a set of high-risk prostate cancer pedigrees, each with 3 or more sampled cases whose death certificate indicated a contribution of prostate cancer to death (lethal prostate cancer). All prostate cancer cases were present in the Utah SEER Cancer Registry (pathology confirmed); all “lethal” prostate cancer cases were also required to have a Utah death certificate indicating prostate cancer as a contributing cause of death.

A set of markers with no linkage disequilibrium was selected for linkage analysis. We took the intersection of SNP markers from five Illumina genotyping platforms used (550K, 610K, 1M,Omni_express (720k), and Omni_1M), resulting in selection of 301,646 markers. We began with the first marker on each chromosome and then skipped markers until one satisfied all criteria (min 0.1 cM distance, heterozygosity 0.35, R-squared < 0.16 -using HapMap's LD files based on CEPH). This resulted in selection of a set of 25,436 SNP LD-free genome wide markers for linkage.

We have performed genome-wide linkage analysis for 21 of the genotyped high-risk lethal prostate cancer pedigrees with the 25,436 selected SNP markers. Genome wide hetLODs showed one significant linkage peak for the recessive model on chromosome 14 (LOD = 4.20). The pedigree with the highest LOD in this region has a +2.69; we are attempting to expand sampling for other pedigrees with linkage evidence in this region.

A single pedigree with 16 prostate cancer cases, at least 4 of whom have already died from prostate cancer and were sampled, provided a LOD score = +3.56 on chromosome arm 11p15. An 11p15 haplotype inherited in common from the founder to 6 generations of descendants is shared in at least 9 of the prostate cancer cases, 3 of whom died from prostate cancer.

The 1-LOD drop defined support interval for the pedigree linked to chromosome 11 occurs at approximately 34-46 cM and contains 13 currently documented genomic features, several of which may be reasonable candidates for lethal prostate cancer including the gene PRMT3 (arginine methyltransferase 3), DAL-1, NELL1, FANCF (Fanconi anemia, complementation group F), and GAS2 (growth arrest-specific 2).

Sequencing of multiple haplotype sharing cases in the pedigree is underway.

Citation Format: Lisa A. Cannon-Albright, Craig C. Teerlink, Neeraj Agarwal. Identification of significant linkage evidence for lethal prostate cancer on chromosome arm 11p15. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1341. doi:10.1158/1538-7445.AM2013-1341