bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1281: Germline mutations in NBN conferring DNA damage response defects are found in patients with multiple cancer types
Authors: Topka Sabine , Walsh Michael F. , Maria Ann , Lincoln Annie , Mandelker Diana , Zhang Liying , Ladanyi Marc , Berger Michael F. , Robson Mark E. , Vijai Joseph , Offit Kenneth 
Published: July 2017

Abstract
Nibrin, the protein encoded by the NBN gene forms a complex with Mre11 and Rad51 (MRN complex) that is crucial for DNA damage repair. Mutations in NBN are found in &gt;90% of patients with Nimjegen breakage syndrome (NBS), an autosomal recessive disorder characterized by growth retardation, microcephaly, radiosensitivity, immunodeficiency and increased cancer risk. Most of NBS patients harbor the common founder mutation c.657del5 that leads to expression of a hypomorphic 70kDa C-terminal fragment produced by alternative translation initiation. Cell lines derived from these patients show increased sensitivity to DNA-damaging agents, chromosome instability, and abnormal cell cycle checkpoint function. Several studies have addressed cancer incidence in individuals with germline NBN mutations, showing increased cancer risk for individuals harboring the c.657del5 founder mutation and for carriers of the R215W missense mutation across multiple cancer types. For other NBN mutations conflicting reports exist as to their association with cancer risk. Here, we report newly identified NBN germline frameshift and truncating mutations in patients with multiple cancer types, including prostate, lung, breast cancer, acute lymphocytic leukemia, and chronic lymphocytic leukemia. Modeling these mutations in an NBN-deficient cellular background showed expression of a novel C-terminal truncated fragment that can bind to Mre11. Cells expressing these mutant proteins display attenuated DNA damage repair function and decreased overall survival following induction of DNA damage. Impaired Chk2 phosphorylation was also observed, indicating cell cycle checkpoint deficiencies. Thus, the NBN germline mutations identified here could contribute to genomic instability predisposing to tumorigenesis. Further in vitro studies with these and additional germline mutations occurring in cancer patients are ongoing, in order to better understand the role of this pathway of DNA damage repair in susceptibility to malignancies.
Citation Format: Sabine Topka, Michael F. Walsh, Ann Maria, Annie Lincoln, Diana Mandelker, Liying Zhang, Marc Ladanyi, Michael F. Berger, Mark E. Robson, Joseph Vijai, Kenneth Offit. Germline mutations in NBN conferring DNA damage response defects are found in patients with multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1281. doi:10.1158/1538-7445.AM2017-1281
Abstract 1284: Identification of potential cancer regulatory germline single-nucleotide polymorphisms in the non-coding genome
Authors: Kulkarni Diptee A. , Song Kijoung , Guo Karl 
Published: July 2017

Abstract
Tumorigenesis in sporadic cancers is mainly driven by somatic genetic alterations such as driver mutations in protein coding genes or chromosomal changes comprising deletions, amplifications or translocations resulting in loss of tumor suppressor proteins, gain of oncogenic proteins or expression of aberrant fusion proteins, respectively. Some cancers lack such somatic changes, but are addicted to expression of certain genes for their sustained proliferation and survival. There is evidence of such oncogenic addiction to LIM domain only 1 (LMO1) expression in neuroblastoma (NB). Genome-wide association studies (GWAS) have identified robust associations between germline single-nucleotide polymorphisms (SNPs) within LMO1 and NB susceptibility with the causal SNP being rs2168101. Investigation of the mechanism of NB dependency on LMO1 showed that LMO1 expression in NB cells is regulated by rs2168101, which resides within a highly conserved tissue-specific super enhancer in LMO1 intron 1 and drives LMO1 expression through GATA3 transcription factor binding. This makes LMO1-dependent NB a unique example of sporadic cancer driven by germline genetic variation. Numerous GWAS have identified significant associations between germline SNPs in the non-coding genome and cancer risk or outcomes. To identify additional examples of regulatory SNPs as cancer drivers, we merged published genome-wide significant associations from cancer GWAS with genome regulatory data from ENCODE (Encyclopedia of DNA Elements; Nature. 2012 Sep 6; 489 (7414): 57-74)) and searched for clusters of cancer associated SNPs that resided within gene regulatory elements. Gene regulatory elements were defined as those marked by active epigenetic features and chromatin accessibility in cancer cell lines. Of the ~1,600 unique, genome-wide significant SNPs from cancer GWAS with regulatory evidence, we identified 46 clusters of 3 or more putative regulatory SNPs near 28 genes. These clusters were particularly enriched within ovarian cancer associated loci. Mechanistic studies such as reporter assays and genome editing in relevant cell types are being considered to identify the causal SNPs from these clusters regulating gene expression and driving tumorigenesis, which in turn may lead us to new cancer targets.
Citation Format: Diptee A. Kulkarni, Kijoung Song, Karl Guo. Identification of potential cancer regulatory germline single-nucleotide polymorphisms in the non-coding genome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1284. doi:10.1158/1538-7445.AM2017-1284
Abstract 1287: Multigene panel testing and risk estimates in 10,233 ovarian cancer cases
Authors: Lilyquist Jenna , LaDuca Holly , Polley Eric , Shimelis Hermela , Hu Chunling , Moore Raymond , Hart Steven N. , Couch Fergus J. , Dolinsky Jill , Goldgar David E. 
Published: July 2017

Abstract
Germline pathogenic variants in BRCA1 and BRCA2 account for 10% of ovarian cancer (OC), including ovarian, fallopian tube, and primary peritoneal carcinomas. Pathogenic variants in BRIP1, RAD51C, RAD51D, and other cancer predisposition genes have been observed in another 2% to 5% of OCs. However, the specific genes associated with OC and estimates of risk associated with pathogenic variants in the individual genes are not well defined. We sought to determine the relevance of multigene panel testing results for OC cases. The study was focused on 140,449 individuals, including 10,233 OC cases, receiving clinical panel testing of cancer predisposition genes. Standardized relative risks (SRR) for pathogenic variants in 18 cancer predisposition genes were estimated using reference controls from the Exome Aggregation Consortium (ExAC). The median (range) age at diagnosis of OC was 57 (21-90) years. OC cases were 76.2% Caucasian, 3.6% African American, 4.6% Asian, 4.7% Hispanic, and 10.9% unknown/other. Among the 10,233 OC cases, 1391 (13.6%) had pathogenic mutations, including 1032 pathogenic mutations among the 7793 Caucasian OC cases (13.2%). Using the non-Finnish European ExAC (excluding TCGA samples) reference controls, the allele frequency for all pathogenic variants in each gene was summed and compared to the frequency of mutations in the Caucasian OC cases. Pathogenic variants in the known OC predisposition genes: BRCA1, BRCA2, BRIP1, MSH2, MSH6, RAD51C, and RAD51D were associated with a high risk of OC (SRR&gt;4.0). Additionally, significant associations were observed for pathogenic variants in suspected OC risk genes ATM and PALB2 (SRR=2.06 and 2.78, respectively). This study identified several genes routinely screened on multigene panel testing that confer high or moderate risks of OC. Associations with known OC predisposition genes were confirmed. In addition, this study provides evidence that PALB2 is a moderate risk OC gene, and that ATM may confer lower to moderate risks of OC. If confirmed in future studies, these risks should be carefully considered in future screening and management of OC patients. In contrast, BARD1 and genes in the MRN complex were not associated with clinically relevant risks of OC.
Citation Format: Jenna Lilyquist, Holly LaDuca, Eric Polley, Hermela Shimelis, Chunling Hu, Raymond Moore, Steven N. Hart, Fergus J. Couch, Jill Dolinsky, David E. Goldgar. Multigene panel testing and risk estimates in 10,233 ovarian cancer cases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1287. doi:10.1158/1538-7445.AM2017-1287
Abstract 1291: Mutation analysis of endometrial cancer in a population-based study by targeted next-generation sequencing
Authors: Chen Maxine , Crous-Bou Marta , Downing Michael J. , Busch Evan L. , Glass Kimberley , Prescott Jennifer , Mutter George L. , Vivo Immaculata De 
Published: July 2017

Abstract
Endometrial carcinoma (EC), a malignancy that arises from the epithelial lining of the uterus, is heterogeneous at histologic and molecular levels. Risk factors and outcomes also differ by type. Though prior studies characterized the genomic landscape of endometrial carcinoma, few integrated histologic, clinical, and prospectively collected epidemiologic data into the analysis. We collected formalin-fixed paraffin embedded tumor tissue from women enrolled in the Nurses’ Health Study who were diagnosed with EC between 1976 and 2012. We targeted 50 cancer related genes for high-throughput sequencing to identify genetic variants in 37 ECs and correlate findings with immunohistochemical, histologic, and epidemiologic data. Case selection was designed to include maximal power to discover genetic changes associated with p53 immunohistochemical status and clinical stage of disease at diagnosis. Mutations most frequently occurred in TP53 (57%), PTEN (46%), and PIK3CA (38%). TP53 mutations were seen in 83% of ECs that immunostained positive for mutant p53, with the most frequent TP53 mutations occurring in R248. Well-differentiated endometrioid tumors had elevated frequencies of PTEN and PIK3CA mutations compared to less differentiated tumors (p &lt; 0.05). The mutation profiles of these samples are consistent with previous studies, supporting the viability of archival paraffin-embedded tissue in mutation detection. This study’s interdisciplinary approach to tumor characterization may help inform future development of personalized models for EC.
Citation Format: Maxine Chen, Marta Crous-Bou, Michael J. Downing, Evan L. Busch, Kimberley Glass, Jennifer Prescott, George L. Mutter, Immaculata De Vivo. Mutation analysis of endometrial cancer in a population-based study by targeted next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1291. doi:10.1158/1538-7445.AM2017-1291
Abstract 1303: A genome-wide association study of prostate cancer in Latinos
Authors: Hopp Hannah , Ingles Sue , Huff Chad , Sheng Xin , Weaver Brandi , Stern Mariana , Strom Sara , Thompson Ian , Conti David , Haiman Christopher A. 
Published: July 2017

Abstract
Recent studies estimate that individuals of African or Latin American ancestry represent less than 4% of samples analyzed to date in genome-wide association studies. The clinical value of genetic information in guiding personalized medicine in populations of non-European ancestry will require additional discovery and risk locus characterization efforts in these populations. Here, we performed a genome-wide association study (GWAS) meta-analysis of prostate cancer in Latino men to search for risk loci that may be important in this population. We combined GWAS data for 1034 cases and 1046 controls genotyped with the Illumina 660 Beadarray with GWAS data for 1235 cases and 1053 controls genotyped with the Illumina Oncoarray as part of the ELLIPSE U19 GAME-ON Consortium. A total of ~11 million genotyped and imputed SNPs of ≥1% frequency were tested for association with prostate cancer risk in logistic regression models controlling for age, study and genetic ancestry. Genome-wide significant associations were observed with 24 variants all located at 8q24 (128.484-128.548), and which capture the first reported prostate cancer susceptibility locus in ‘region 1’ of 8q24. The most significant association genome-wide was with SNP rs7824776 (risk allele frequency, 0.35; OR=1.69, p=3.4x10-11). No novel genome-wide significant associations were noted outside of 8q24. We observed a high degree of generalizability of known prostate cancer risk loci, with 78 (76%) of the 103 known risk variants having effects that were directionally consistent in their association with prostate cancer risk as previously reported, of which 31 (30%) were statistically significant with p &lt; 0.05. In addition to these findings from the largest GWAS of prostate cancer in Latinos conducted to date, we will also present the results investigating effect heterogeneity by local ancestry (i.e. proportion Native American vs. European). In addition, we will present a comparison of polygenic risk models between Latinos, African Africans and men of European ancestry that incorporate the known risk loci to better understand how genetic risk tracks with population differences in prostate cancer incidence.
Citation Format: Hannah Hopp, Sue Ingles, Chad Huff, Xin Sheng, Brandi Weaver, Mariana Stern, Sara Strom, Ian Thompson, David Conti, Christopher A. Haiman. A genome-wide association study of prostate cancer in Latinos [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1303. doi:10.1158/1538-7445.AM2017-1303
Abstract 1306: Two distinct regulatory mechanisms underlie estrogen receptor negative breast cancer susceptibility at the 2p23.2 locus
Authors: Harro Carly M. , Mendoza-Fandino Gustavo , Woods Nicholas T. , Li Xueli , Couch Fergus J. , Monteiro Alvaro N. 
Published: July 2017

Abstract
Genome Wide Association Studies (GWAS) are designed to identify single nucleotide polymorphisms (SNPs) mapping to genomic regions associated with a particular trait or disease. Currently, 19 genomic loci associated with risk for estrogen receptor negative breast cancer have been identified. However, for most of these loci the mechanisms driving susceptibility have remained elusive. The 2p23.2 locus, defined by SNP rs67073037 (p = 4.76 x 10-9), contains 79 SNPs exhibiting genome-wide significant associations as well as four candidate genes: SPDYA, TRMT61B, WDR43, and FAM179A. Post-GWAS functional analysis revealed two candidate causal regulatory elements: an enhancer-like element defined by SNP rs44017214 located in the first intron of the WDR43 gene; and a segment in the 3’-UTR region of WDR43 defined by SNPs rs11680458 and rs11331880 which are predicted to have allele specific binding of non-coding microRNAs miR-548 and miR-376, respectively. We validated allele specific transcription factor binding to rs44017214 using competitive binding of USF1/USF2 to the risk allele in both MCF10A and CAL51 cell lines in Electrophoretic Mobility Shift Assays (EMSA). Additionally, rs44017214 was removed using CRISPR-cas9, and expression of neighboring genes was evaluated by qRT-PCR. No change in expression was found for any gene in a 2 Mb region surrounding the SNP, with the exception of PLB1. This suggests that the enhancer element in the intron of WDR43 has PLB1 as its target. To assess the miRNA binding site impact on WDR43 expression the pMIR-REPORT Luciferase allele-specific vector was co-transfected with miR-141/200, miR548, or miR-376 in MCF10A cells. The rs1131880 allele C in the WDR43 3’-UTR lead to the suppression of luciferase expression by miR-376 compared to the G allele. This study reveals two independent regulatory mechanisms within the 2p23.2 locus; (i) modulation of enhancer activity by allele specific binding of transcription factors USF1/USF2 to rs4401714, and (ii) decreasing the expression of WDR43 through the formation of a miR-376 binding site at the 3’-UTR of the WDR43 gene. Elucidating the functional significance of these common variants in the novel susceptibility loci 2p23.2 furthers our knowledge of the etiology of estrogen receptor negative breast cancer.
Citation Format: Carly M. Harro, Gustavo Mendoza-Fandino, Nicholas T. Woods, Xueli Li, Fergus J. Couch, Alvaro N. Monteiro. Two distinct regulatory mechanisms underlie estrogen receptor negative breast cancer susceptibility at the 2p23.2 locus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1306. doi:10.1158/1538-7445.AM2017-1306
Abstract 1324: Profile of common prostate cancer risk variants in an unscreened Romanian population
Authors: Iordache Paul D. , Halldórsson Bjarni , Manolescu Andrei , Mates Dana , Ursu Radu , Jinga Viorel 
Published: July 2017

Abstract
In the present study we investigated for the first time the profile of common prostate cancer risk variants in an unscreened Romanian population. The study population consisted of 990 unrelated histopathologically confirmed prostate cancer (PCa) cases and 1,034 male controls consisting of patients admitted for urological and surgical conditions, excluding cancer. DNA was extracted from whole blood at deCODE Genetics (Reykjavik, Iceland) and genotyped using Illumina SNP arrays, 24.295.558 variants were imputed using the 1000 Genomes dataset in the 2,024 Romanian subjects. A systematic literature review for variants associated with prostate cancer identified in previous GWAS‘ was done using the NHGRI catalog as a starting point, identifying 238 unique variants from 28 studies. None of the tested variants in a Romanian only GWAS reached a genome wide significance (p-value lower than 5x10-8) but 807 markers reached p-values of 1x10-6. Thirty-one of the previously-reported SNPs replicated in the Romanian cohort, with the strongest associations seen at: 8q24.21, 11q13.3, 6q25.3, 5p15.33, 22q13.2, 17q12 and 3q13.2. The most signficantly replicated variants in Romania are rs1016343 at 8q24.21 (P = 2.2x10-4), rs7929962 at 11q13.3 (P = 2.7x10-4) and rs9364554 at 6q25.2 (P = 4.7x10-4). Our present study is the first GWAS on prostate cancer performed on a Romanian cohort. The high proportion of clinically significant disease in the Romanian prostate cancer cases will allow the dissection of the association between genetic variation and severe disease. Acknowledgements: This study was funded in part by the European Union FP7 Program (ProMark project 202059) and by the EEA grant (ROMCAN project RO14-0017; EEA-JRP-RO-NO-20131-10191).
Citation Format: Paul D. Iordache, Bjarni Halldórsson, Andrei Manolescu, Dana Mates, Radu Ursu, Viorel Jinga. Profile of common prostate cancer risk variants in an unscreened Romanian population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1324. doi:10.1158/1538-7445.AM2017-1324
Abstract 134: A dual mTOR-PI3K inhibitor DCB-HDG2-57 with Hedgehog signaling pathway antagonist activity
Authors: Lee Ying-Shuan , Kuo Mann-Yan , Liu Chia Wei , Tseng Yu-Wen , Wei Win Yin , Chiou Shian-Yi , Lin Her Sheng , Lu Y.-Y. , Liao Chu-Bin , Pen Shao-Zheng 
Published: July 2017

Abstract
The Hedgehog (Hh) signaling pathway is a critical regulator of embryonic patterning, and aberrant Hh pathway activation has been implicated in a diverse spectrum of cancers. Therefore, components of the Shh pathway (such as Shh, SMO, and GLI1/2) are viable therapeutic targets for anti-tumor strategy. Smo antagonists such as GDC-0449 and NVP-LDE225 have received FDA approval for treating basal cell carcinoma. However, acquired resistance has emerged as a challenge to targeted therapeutics and may limit their anti-cancer efficacy. Studies have linked the hyperactive phosphatidylinositol-3-kinase (PI3K)/AKT/mTOR signaling pathway in a variety of human cancers and drug resistance condition. The synergistic role of PI3K/AKT/mTOR in Hh signaling in embryonic development and Hh-dependent tumors has been reported. Both the PI3K/Akt/mTOR and Hh pathway also play important role in maintaining the stem cell-like properties of cancer stem cell (CSCs). We report here the development of a potent dual mTOR-PI3K inhibitor designated DCB-HDG2-57 with Hh signaling pathway antagonist activity. In vitro biochemical assays showed that DCB-HDG2-57 inhibited recombinant pI3Kα and mTOR kinase with IC50 of 27.2 and 133 nM, respectively. DCB-HDG2-57 is also highly active in cellular assays, as evidenced by inhibition of phosphorylation of cellular downstream targets of PI3K-mTOR kinases ribosomal protein S6 kinase (S6K1, Ser240/24) in the colon (LS-180) and pancreatic cancer (MiaPaCa2 and PANC1) cell lines. Interestingly, DCB-HDG2-57 demonstrated Hh signaling pathway antagonist activity in a 293 cell-based Gli-luciferase inhibition assay upon agonist treatment, and retains inhibition activity against the Smo wild-type and D473H mutant co-transfection with IC50 of 261.8 and 327.7 nM, respectively. In addition, DCB-HDG2-57 can significantly decrease the cancer stem cell liked side population of PANC1 pancreatic cell, and inhibited the migration of E3LZ10.7 pancreatic cancer cell. DCB-HDG2-57 demonstrated in vivo tumor growth inhibition activity in LS-180 colon cancer xenograft model and reduced the Gli-1 RNA abundance in the tumor. Taken together, our data demonstrate that combined pharmacological blockade of mTOR-PI3K and Hh pathway of DCB-HDG2-57 can provide a therapeutic strategy for targeting ligand-dependent Hh cancer.
Citation Format: Ying-Shuan Lee, Mann-Yan Kuo, Chia Wei Liu, Yu-Wen Tseng, Win Yin Wei, Shian-Yi Chiou, Her Sheng Lin, Y.-Y. Lu, Chu-Bin Liao, Shao-Zheng Pen. A dual mTOR-PI3K inhibitor DCB-HDG2-57 with Hedgehog signaling pathway antagonist activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 134. doi:10.1158/1538-7445.AM2017-134
Abstract 1341: Talin plays an important role in cell-cell interactions
Authors: Patel Devang M. , Kumar Akhilesh , Morgan William , Birnbaum Michael D. , Jiang Chaunhua , Zhang Fangliang 
Published: July 2017

Abstract
Appropriate cell adhesion is necessary for numerous physiological processes and can be deranged in many diseases, including cancer. It has long been recognized that the cadherins mediated cell-cell adhesion receptor is an important determinant of tumor progression, serving as a suppressor of invasion and metastasis. Recently a role for the C-terminal region of talin (the VAD fragment) in cadherin mediated cell-cell attachment has been suggested, but its molecular mechanism remained unclear. Here, we identified a small region of the VAD fragment required for its localization to cadherin-mediated cell-cell junctions and also found that its localization to cell-cell junctions is independent of its actin binding properties. To identify the binding partner of the VAD fragment at cell-cell junctions we utilized immune-pulldown and found that it interacts with catenins, an important component of cadherin-mediated cell-cell junction. Based on our data, we proposed that the VAD-fragment of talin stabilized and/or stimulated the cell-cell junction by interacting with catenins.
Citation Format: Devang M. Patel, Akhilesh Kumar, William Morgan, Michael D. Birnbaum, Chaunhua Jiang, Fangliang Zhang. Talin plays an important role in cell-cell interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1341. doi:10.1158/1538-7445.AM2017-1341