bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1319: Epigenome-wide association study reveals differential DNA methylation consistent with progression of multiple myeloma
Authors: Gragg Stephen D. , Absher Devin , Cui Xiangqin , Pillion Christina , Myers Richard , Kumar Shaji , Costa Luciano , Chiu Brian , Vachon Celine , Brown Elizabeth
Published: July 2017

Purpose: Multiple myeloma (MM) is the second most common hematological malignancy in the US. It is characterized by a clonal expansion of plasma cells in the bone marrow and extramedullary sites and is preceded by two precursor conditions including monoclonal gammopathy of undetermined significance (MGUS) and smoldering myeloma (SMM). Strong evidence suggests a germline and environmental etiology. However, efforts to characterize heritable changes in gene activity, such as DNA methylation, have not been widely reported.

Methods: We examined epigenome-wide DNA methylation as markers of MGUS, SMM and MM in peripheral blood obtained from treatment-naïve European American cases with heavy-chain IgG or IgA MGUS (n=60), SMM (n=31) and MM (n=54) and age- and sex-matched controls (n=79) included from the University of Alabama at Birmingham, University of Chicago and the Mayo Clinic, Rochester [54.5% males; mean age, 64 years (range, 36 to 86)]. We quantified DNA methylation of over 450,000 CpG and non-CpG loci using the Infinium HumanMethylation450 array (Illumina). Differentially methylated positions were calculated using a general linear model framework adjusted for confounders and cellular heterogeneity.

Results: A total of 6 CpGs were differentially methylated in MM cases compared to controls at a level of genome-wide statistical significance. MM was associated with hypomethylation at differentially methylated positions inside SBNO2 (P=3.37x10-10), WIZ (P=1.12x10-8), CA6 (P=4.29x10-8) and ADORA1 (P=3.68x10-8) as well as intergenic positions proximal to TNFRSF8 (Chr 1p36.22; P=2.24x10-9) and ENDOV (Chr 17q25.3; P=2.74x10-8). Each of these loci, with the exception of CA6 and ADORA1, were hypomethylated in each of the 3 plasma cell dyscrasia phenotypes including MGUS and SMM and MM cases compared to controls (P<0.03), albeit not at a level of genome-wide statistical significance.

Conclusions: These preliminary findings suggest that differences in DNA methylation may contribute to altered risk of MM, as well as its precursor conditions, and may play a role in plasma cell dyscrasia progression as a consequence of heritable changes in gene activity due to past exposures. Replication in a large yet similarly well-characterized population is warranted.

Citation Format: Stephen D. Gragg, Devin Absher, Xiangqin Cui, Christina Pillion, Richard Myers, Shaji Kumar, Luciano Costa, Brian Chiu, Celine Vachon, Elizabeth Brown. Epigenome-wide association study reveals differential DNA methylation consistent with progression of multiple myeloma [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 1319. doi:10.1158/1538-7445.AM2017-1319
Abstract 1320: Non-additive and interaction effects of HLA class 2 polymorphism contributing to risk of glioma
Authors: Zhang Chenan , Walsh Kyle
Published: July 2017

Although genome-wide association studies have identified a number of susceptibility loci for adult glioma, little is still known regarding whether polymorphisms in the human leukocyte antigen (HLA) region contribute risk. HLA associations have previously been reported for a number of malignancies, with selected HLA polymorphisms investigated in a subset of glioma studies. However, no systematic analysis has been conducted to date, and no investigation into potential non-additive effects of such associations has been described. In this study, we conducted comprehensive genetic analyses of HLA variants in the major histocompatibility complex (MHC) region among 1,746 adult glioma patients and 2,312 controls from the GliomaScan Consortium. Genotype data were generated with the Illumina 660-Quad array, containing 1,822 SNP probes across the MHC region. We imputed HLA alleles using a reference panel of 5,225 individuals in the Type 1 Diabetes Genetics Consortium who underwent high-resolution HLA typing via next-generation sequencing. Subjects were of European-ancestry, and case-control comparisons were adjusted for population stratification using ancestry-informative principal components. Because alleles in different loci across the MHC region are linked, we created multi-locus haplotypes consisting of genes DRB1, DQA1, and DQB1. Although none of the haplotypes were associated with glioma in additive models, DRB1*15:01-DQA1*01:02-DQB1*06:02 showed an improvement in model fit after the inclusion of a non-additive term, which was significant after Bonferroni correction (P = 2.5x10-3). Furthermore, the interaction of DRB1*15:01-DQA1*01:02-DQB1*06:02 with haplotype DRB1*04:01-DQA1*03:01- DQB1*03:01 resulted in a 3.80-fold increase in the odds of glioma (P = 8.8x10-3). Our results indicate that the DRB1*15:01-DQA1*01:02-DQB1*06:02 haplotype contributes to the risk of glioma via a dominant effect, with heterozygosity conferring greater risk of glioma than expected from homozygote disease risk in an additive model.

Citation Format: Chenan Zhang, Kyle Walsh. Non-additive and interaction effects of HLA class 2 polymorphism contributing to risk of glioma [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 1320. doi:10.1158/1538-7445.AM2017-1320
Abstract 1325: Genome-wide association study of thyroid nodule in Korean population
Authors: Lee Eun Kyung , Hwangbo Yul , Park Young Joo , Kim Jong-Il , Jung Yuh-Seog , Ryu Jun Sun
Published: July 2017

Thyroid nodule is very common. Several autopsy surveys reported that 30% or more of patients had thyroid nodule. However, inherited genetic risk factors for thyroid nodule remain unknown. Genome-wide association studies (GWAS) are widely used in human genetics to identify genes associated with various diseases. We aimed to find genetic factors for thyroid nodule and conducted case-control GWAS.

Objective: To identify genetic variants associated with susceptibility to thyroid nodules

Methods: We performed a two-stage GWAS for thyroid nodule. The discovery stage involved a genome-wide scan of 713 subjects with thyroid nodule and 591 subjects with normal thyroid from a population-based cohort. replication testing was conducted in an additional 600 cases and 600 controls from the participants of a health check-up.

Results In discovery stage, 21 candidate single nucleotide polymorphisms (SNP) in 20 loci including NKX2-1, ITGB1 and ZBTB25 were selected for replication. The strongest signal located in NKX2-1 (P = 9x10-7), which is known susceptibility locus for differentiated thyroid cancer. However, no SNP showed significant association in replication test. In joint analysis, no association signals reaching genome-wide significance (P <5x10-8) were detected.

Conclusion GWAS for thyroid nodule have failed to identify susceptibility locus. Therefore, genetic effect for development of thyroid nodule could be negligible.

Citation Format: Eun Kyung Lee, Yul Hwangbo, Young Joo Park, Jong-Il Kim, Yuh-Seog Jung, Jun Sun Ryu. Genome-wide association study of thyroid nodule in Korean 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 1325. doi:10.1158/1538-7445.AM2017-1325
Abstract 1327: CD147 contributes to extracellular matrix remodeling and degradation
Authors: Tan Tiffany , Kosmider Beata , Marchetti Nathaniel , Bolla Sudhir , Mandapati Chenna , Criner Gerard , Bahmed Karim
Published: July 2017

Chronic obstructive pulmonary disease (COPD) is an incurable, progressive lung disease characterized by shortness and difficulty in breathing. Patients with COPD are at higher risk of developing lung cancer and often are associated with poor outcome of lung cancer diagnosis and treatment. Extracellular matrix (ECM) remodeling and degradation is one of the common hallmarks between cancer and COPD. It contributes to degradation of air sacs (emphysema) or small airways (obstructive bronchiolitis). It is also involved in cancer initiation and progression to assist tumor expansion and cancer cell migration. In this study, we analyzed lung tissue and primary alveolar type II (ATII) cells isolated from patients with emphysema and control organ donors. ATII cells secrete and store pulmonary surfactant and restore the epithelium after damage. We performed RNA sequencing in ATII cells to identify dysregulated proteins, which are involved in ECM degradation in emphysema. To further study the mechanism involved in the ECM degradation in this disease, we analyzed the expression of selected proteins and we focused on the role of extracellular matrix metalloproteinase inducer (CD147). CD147 is a cell membrane protein involved in inducing the production of extracellular matrix metalloproteinases (MMPs). First, we found that cells isolated from patients with emphysema have higher expression of CD147 in ATII cells in comparison with controls as detected by western blotting and RT-PCR. This may explain high ECM degradation in this disease. Second, we observed higher MMPs levels in plasma obtained from individuals with this disease. Third, we found significantly higher expression of cathepsin B in ATII cells isolated from emphysema in comparison with controls. Cathepsin B is an enzyme that facilitates a direct degradation of ECM proteins and activate other proteases capable of degrading ECM. Fourth, our data indicate that CD147 interacts with cathepsin B, which may lead to the activation of MMPs and emphysema progression. In summary, our results show for the first time the important role of CD147 in emphysema development. Moreover, we found that cathepsin B may contribute to CD147-mediated disease progression. Further studies will elucidate its role in lung cancer development in patients with emphysema.

Note: This abstract was not presented at the meeting.

Citation Format: Tiffany Tan, Beata Kosmider, Nathaniel Marchetti, Sudhir Bolla, Chenna Mandapati, Gerard Criner, Karim Bahmed. CD147 contributes to extracellular matrix remodeling and degradation [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 1327. doi:10.1158/1538-7445.AM2017-1327
Abstract 1332: NOTCH - HEY1 pathway induces EMT in head and neck squamous cell carcinoma
Authors: Fukusumi Takahito , Guo Theresa W. , Ren Shuling , Sakai Akihiro , Ando Mizuo , Haft Sunny , Liu Chao , Califano Joseph A.
Published: July 2017

Background

Head and neck squamous cell carcinoma (HNSCC) is noted to have a NOTCH mutation rate of 20% within the Cancer Genome Atlas (TCGA) dataset consistent with tumor suppressor gene status. However, NOTCH genes are also upregulated in wild type HNSCC and show signs of downstream activation in a substantial proportion of HNSCC. In this study, we aimed to further explore the potential for NOTCH pathways to be activated in HNSCC.

Material and Methods

mRNA sequence of TCGA data includes 520 HNSCC tumors and 46 normal tissues. We used 447 HNSCC excluding 73 tumors with NOTCH mutations. The activated groups of NOTCH downstream genes were defined as tumors with expression 1 standard deviation above the mean of normal tissue. We used four HNSCC cell lines (SKN3, Cal27, SCC61, SCC090) to ascertain the results of the TCGA analysis in vitro.

Result

In TCGA analysis, HEY1 activated HNSCC had significant more expression of NOTCH pathway genes. In particular NOTCH4 had the most significant correlation with HEY1 activation among NOTCH receptors. To confirm this result in vitro, HEY1 expression was compared between si-control and si-NOTCH4 of SKN3, Cal27, SCC61 and SCC090. As expected, HEY1 expression in all si-NOTCH4 treated cell lines were significant decreased. Next, we examined the relationship about NOTCH4 and an epithelial mesenchymal transition phenotype (EMT). Using TCGA data, we found that mesenchymal marker genes were significantly increased in high NOTCH4 group. In vitro experiments, si-NOTCH4 cells decreased mesenchymal marker gene expression such as Fibronectin and TWIST1. We also examined HEY1 function. Similar to NOTCH4, it was found that HEY1 is significantly related to EMT in silico and in vitro.

Conclusion

The NOTCH4-HEY1 pathway is significantly upregulated in HNSCC and induces EMT.

Citation Format: Takahito Fukusumi, Theresa W. Guo, Shuling Ren, Akihiro Sakai, Mizuo Ando, Sunny Haft, Chao Liu, Joseph A. Califano. NOTCH - HEY1 pathway induces EMT in head and neck squamous cell carcinoma [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 1332. doi:10.1158/1538-7445.AM2017-1332
Abstract 1334: Mesenchymal cell sub-populations selectively modulate paracrine hedgehog signaling in triple negative breast cancer
Authors: Ramos Karla P. , Domenech Maribella
Published: July 2017

Recent studies correlate Hedgehog (Hh) signaling with reduced survival rates in triple negative breast cancer (TNBC) patients. Activation of hedgehog signaling in the adjacent mesenchyme has been shown to promote tumor growth and it is a poor prognosis factor for TNBC. We developed a novel tumor-mesenchymal in vitro model of hedgehog signaling in TNBC to evaluate the role of mesenchymal cell sub-populations in the proliferative potential and stem cell markers of breast cancer cells using a custom designed multiwell array. As a source of mesenchymal cell sub-populations we evaluated myofibroblasts, mesenchymal stem cells derived from bone marrow or adipose tissue and tumor cells that undergo epithelial-mesenchymal transition (EMT). Tumor cells were culture with 1 or 2 mesenchymal cell sub-populations in adjacent compartments +/- SHH ligand for 72-96hrs. Active Hh signaling was confirmed by up-regulation of main Hh target genes (e.g. Gli1, Patch1). Paracrine Hh signaling only in bone marrow-derived mesenchymal stem cell and EMT significantly increased proliferation (10-15%) of TNBC and normal breast cancer cell lines. Addition of adipose-derived mesenchymal stem cells or pharmacological Hh inhibitors (Cyclopamine and Gant61) partially abolished tumor growth indicating that other non-canonical signals are involve in paracrine Hh-driven tumors. Cancer stem cell markers were selectively modulated in co-cultures. Our results suggest that paracrine Hh signaling-driven by bone marrow and EMT mesenchymal are potential therapeutic targets to treating TNBC.

Citation Format: Karla P. Ramos, Maribella Domenech. Mesenchymal cell sub-populations selectively modulate paracrine hedgehog signaling in triple negative breast cancer [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 1334. doi:10.1158/1538-7445.AM2017-1334
Abstract 1335: Deubiquitinase OTUD6B isoforms are important regulators of growth and proliferation
Authors: Bocchetta Maurizio , Osipo Clodia , Sobol Anna
Published: July 2017

Deubiquitinases (DUBs) are increasingly linked to the regulation of fundamental processes in normal and cancer cells, including DNA replication and repair, programmed cell death, and oncogenes and tumor suppressors signaling. Here evidence is presented that the deubiquitinase OTUD6B regulates protein synthesis in non-small cell lung cancer (NSCLC) cells, operating downstream from mTORC1. OTUD6B associates with the protein synthesis initiation complex and modifies components of the 48S preinitiation complex. The two main OTUD6B splicing isoforms seem to regulate protein synthesis in opposing fashions: the long OTUD6B-1 isoform is inhibitory, while the short OTUD6B-2 isoform stimulates protein synthesis. These properties affect NSCLC cell proliferation, since OTUD6B-1 represses DNA synthesis while OTUD6B-2 promotes it. Mutational analysis and downstream mediators suggest that the two OTUD6B isoforms modify different cellular targets. OTUD6B-2 influences the expression of cyclin D1 by promoting its translation while regulating (directly or indirectly) c-Myc protein stability. This phenomenon appears to have clinical relevance as NSCLC cells and human tumor specimens have a reduced OTUD6B-1/OTUD6B-2 mRNA ratio compared to normal samples. The global OTUD6B expression level does not change significantly between non-neoplastic and malignant tissues, suggesting that modifications of splicing factors during the process of transformation are responsible for this isoform switch. Because protein synthesis inhibition is a viable treatment strategy for NSCLC, these data indicate that OTUD6B isoform 2, being specifically linked to NSCLC growth, represents an attractive, novel therapeutic target and potential biomarker for early diagnosis of malignant NSCLC.

Note: This abstract was not presented at the meeting.

Citation Format: Maurizio Bocchetta, Clodia Osipo, Anna Sobol. Deubiquitinase OTUD6B isoforms are important regulators of growth and proliferation [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 1335. doi:10.1158/1538-7445.AM2017-1335
Abstract 1348: GDC-0032, a p110 beta sparing PI3K inhibitor is highly efficient on PIK3CA-mutated and HER2-amplified breast cancer model
Authors: De Pradip , Sun Yuliang , Carlson Jennifer , Friedman Lori , Williams Casey , Dey Nandini , Leyland-Jones Brian
Published: July 2017

Background: HER2 amplification/overexpression frequently co-occurs with PI3K pathway activation in breast tumors. Mutations in PIK3CA are known to be involved in a wide range of human cancers including HER2+ breast cancer, and mutant PIK3CA is thought to act as an oncogene. Here, we evaluate the efficacy of GDC0032, a p110 beta-sparing PI3K inhibitor against HER2+ or HER2+/PIK3CA mutated breast cancer cells. MATERIALS AND METHODS: Four HER2+ breast cancer (BC) cell lines consisting of three activating (either helical or kinase domain) PIK3CA mutation (HER2+/ER+ and HER2+/ER-) were analyzed for proliferation, apoptosis, cell cycle and signaling pathway activation assays. Preclinical efficacy of GDC-0032 was also evaluated in vivo in a mouse model. RESULTS: 1) All HER2+ and HER2+/PIK3CA mutant cell lines exhibited low IC50 values (ranging from 0.1 µM-1.5 µM) irrespective of ER-positive or not. 2) GDC-0032 caused a strong differential growth inhibition in both HER2+ and HER2+/ /PIK3CA mutated breast cancer cell lines when compared to lines that were HER2- and PIK3CA wild type by 3D-ON-TOP clonogenic assay. 3) Administration of GDC-0032 induced cell cycle G0/G1 arrest and resulted in increased apoptosis in a dose-dependent manner. Furthermore, induction of apoptosis was more with GDC-0032 when combined with RAD001. 4) GDC0032 also blocked expression of CYCLIN D1. 5) Investigation of the signal transduction revealed that the treatment of GDC-0032 reduced the level of p-AKT (Ser473 and Thr308), and p-S6 expression is indicating the down-regulation of downstream signaling of PI3K and mTOR pathway. 6) GDC-0032 was highly active at reducing established tumor growth in vivo in BC mouse xenografts harboring PIK3CA mutation and HER2 amplification. CONCLUSION: Our in vitro or in vivo data showed that GDC-0032 was highly efficient either as a single agent as well as with RAD001 in HER2+/PIK3CA mutated breast cancer cell lines. Our data suggest that GDC-0032 represents a novel therapeutic option in patients harboring PIK3CA mutations and/or HER2/neu gene amplification in breast cancer.

Citation Format: Pradip De, Yuliang Sun, Jennifer Carlson, Lori Friedman, Casey Williams, Nandini Dey, Brian Leyland-Jones. GDC-0032, a p110 beta sparing PI3K inhibitor is highly efficient on PIK3CA-mutated and HER2-amplified breast cancer model [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 1348. doi:10.1158/1538-7445.AM2017-1348
Abstract 1349: NSAIDs: Multiple roles in multiple environments
Authors: Calaf Gloria M. , Roy Debasish
Published: July 2017

Non steroidal drugs are mainly known for their activities and use as anti-inflammatory, antipyretic compounds. But, in recent observations, they are exposed to use as an effective alternative compounds to prevent or stimulate different metabolic activities and help in preventing various neoplastic progression. They have specific role in controlling estrogen metabolism during breast cancer progression. Sometimes, they are used as an apoptotic induction in various cancers. Their role in hypoxia induced proliferation is also showing promising results. Different NSAIDs will help to induce the activities of various tumor suppressor genes. As chronic inflammation increases the risk for various cancers, therefore, it is important to eliminate inflammation through anti-Inflammatory compounds where NSAIDs are playing a vital role. Most of them are acting to prevent inflammation either via selective or non-selective COX based mechanism. The non-selective COX inhibitor sulindac and the COX-2 selective inhibitor etodolac etc. have been shown to prevent the formation and cause regression of adenomas in patients with familial polyposis. Unfortunately, COX-1 and/or COX-2 inhibition and depletion of physiologically important prostaglandins is associated with gastrointestinal, renal and cardiovascular toxicities that limit the use of NSAIDs and COX-2 inhibitors for cancer chemoprevention In this particular study, we are using various NSAIDs in a radiation-induced estogren treated breast cancer model to establish their role in differential expression of various cancer related genes selected from different cell cycle pathways microarray. Selection of biomarkers from these altered genes will help to develop a valid strategy for cancer prevention through precision based molecular targeted therapy.

Supported by Office of Academic Affairs, Honors Program, COBI, Hostos-CUNY, NY, USA (DR) and Tarapacá University, Arica, Chile (GMC).

Citation Format: Gloria M. Calaf, Debasish Roy. NSAIDs: Multiple roles in multiple environments [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 1349. doi:10.1158/1538-7445.AM2017-1349
Abstract 1353: Polyisoprenylated cysteinyl amide inhibitors disrupt actin cytoskeleton organization, induce cell rounding, and block invasion of NSCLC
Authors: Ntantie Elizabeth , Fletcher Jerrine , Amissah Felix , Salako Olufisayo O. , Nkembo Augustine T. , Poku Rosemary A. , Lamango Nazarius S.
Published: July 2017

Non-small Cell Lung Cancer (NSCLC) malignancy is dependent on cellular processes that promote metastasis. F-actin organization is central to cell migration, invasion, adhesion and angiogenesis which are all processes involved in metastasis. F-actin remodeling is enhanced by the overexpression and/or hyper-activation of some members of the Rho family of small GTPases. Therefore agents that mitigate hyperactive Rho proteins may be clinically relevant for controlling metastasis. We previously reported the synthesis and characterization of polyisoprenylated cysteinyl amide inhibitors (PCAIs) as potential inhibitors of the cancer phenotype. In this report, we investigate the potential role of PCAIs against NSCLC malignancy and show that as low as 0.5 µM PCAIs significantly inhibit 2D and 3D NCI-H1299 cell migration by 48% and 45%, respectively. PCAIs at 1 µM inhibited 2D and 3D NCI-H1299 cell invasion through Matrigel by 50% and 85%, respectively. Additionally, exposure to 5 µM of the PCAIs, NSL-BA-040 caused a 38% drop in F-actin intensity at the cell membrane 24 h post treatment. Importantly, this drop in F-actin was accompanied by a 73% reduction in the number of filopodia per cell. Interestingly, the polyisoprenyl group of the PCAIs is essential for these effects, as NSL-100, an analog that lacks the farnesyl moiety, does not elicit similar effects on F-actin assembly and organization. Put together, our findings indicate that PCAIs disrupt F-actin assembly and organization to suppress cell motility and invasion and point towards a potential role of PCAIs as effective therapies for NSCLC metastasis and invasion.

Citation Format: Elizabeth Ntantie, Jerrine Fletcher, Felix Amissah, Olufisayo O. Salako, Augustine T. Nkembo, Rosemary A. Poku, Nazarius S. Lamango. Polyisoprenylated cysteinyl amide inhibitors disrupt actin cytoskeleton organization, induce cell rounding, and block invasion of NSCLC [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 1353. doi:10.1158/1538-7445.AM2017-1353
Abstract 1383: Histone H3 lysine 9 methyltransferase SUV39H1 is associated with clinical outcome of renal clear cell carcinoma patients
Authors: Meng Wei , Cui Ri , Haque Saikh Jaharul , Croce Carlo M. , Chakravarti Arnab
Published: July 2017

Background: Epigenetic alternations have three important components including DNA methylation, histione modifications, and non-coding RNA. The epigenetic changes are highly dynamic and also reversible, which regulate a variety of biological processes. Euchromatin which is a loosely packed form of chromatin is highly associated with active gene expression. In contrast, heterochromatin is associated with high histone methylation and DNA methylation but low RNA transcription. SUV39H1 catalyzes the histone 3 lysine 9 trimethylation (H3K9me3) in heterochromatin regions, which also mediates DNA methylation at pericentric heterochromatin. Currently, the oncogenic role of SUV39H1 in renal cell carcinoma (RCC) pathogenesis is poorly understood. To this end, we assessed the role of SUV39H1 in renal RCC cells and association with clinical outcome of RCC patients.

Results: In SUV39H1 knocked down cells, we observed global H3K9me3 level reduction and cell growth inhibition. Proximal ligation assay was used to determine the H3K9me3 and 5-methylcytosine (5mC) interaction in RCC cells. Knocking down of SUV39H1 gene significantly reduced the co-localization of H3K9me3 and 5mC in pericentric repetitive sequences. Moreover, Southern blot demonstrated that expansion of a pentanucleotide (GGAAT) repeats was associated with upregulation of SUV39H1, which is linked to SUV39H1 function with microsatellite instability and rearrangement. In The Cancer Genome Atlas (TCGA) database, we found that SUV39H1 gene expression was upregulated in RCC tissues compared to normal tissues, and high SUV39H1 expression predicted a worse overall survival outcome (p = 0.002) in RCC patients.

Conclusion: SUV39H1 upregulation promotes cell proliferation and microsatellite instability. SUV39H1 expression could serve as a prognostic biomarker for RCC patients.

Citation Format: Wei Meng, Ri Cui, Saikh Jaharul Haque, Carlo M. Croce, Arnab Chakravarti. Histone H3 lysine 9 methyltransferase SUV39H1 is associated with clinical outcome of renal clear cell carcinoma patients [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 1383. doi:10.1158/1538-7445.AM2017-1383
Abstract 1389: Effects of geinstein on histone modifying enzyme expression in prostate cancer
Authors: Aquila Lanni , Smothermon Nick , Morey Lisa
Published: July 2017

The present study sought to examine the expression of two histone modifying enzymes, SET8 and SIRT1, in human prostate cancer cell model when exposed to increasing concentrations of genistein. Genistein is a phytoestrogen found mainly in soy-based foods and is of importance due to the varying intake levels worldwide. This compound is thought to have chemopreventive properties and it is hypothesized to exert its affects by epigenetically modifying chromatin organization within cells. As an estrogen-like compound, genistein may exert effects similar to that of estrogen. For this reason, SET8, a histone methyltransferase, and, SIRT1, a histone deacetylase, were studied. Previously, these histone modifying enzymes were found to play a role in estrogen signaling. In the present study, cells were treated either for 24 hours (acute) or 5 days (chronic), total RNA was extracted, followed by an RT-PCR, and amplification of the genes of interest via PCR. Changes in gene expression were quantitated using ImageJ. Overall, it was concluded that the exposure to genistein impacts the gene expression of both SET8 and SIRT1 within human prostate cancer cells.

Note: This abstract was not presented at the meeting.

Citation Format: Lanni Aquila, Nick Smothermon, Lisa Morey. Effects of geinstein on histone modifying enzyme expression in prostate cancer [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 1389. doi:10.1158/1538-7445.AM2017-1389
Abstract 14: Anticancer activities of terpenoid compounds isolated from the plant centipeda minma against nasopharyngeal carcinoma cells
Authors: Liu Bei-bei , Zhu Kui-yuan , Chan Chi-on , Zhang Ling-Hua , Mok Daniel Kam-Wah , Chen Si-bao
Published: July 2017

Nasopharyngeal carcinoma (NPC) is one of common cancers throughout south-east Asia, southern China and other regions. Radiotherapy and chemotherapy are the standard treatments for NPC with severe adverse effects, multi-drug resistance, and insensitivity to advanced NPC. Complementary and novel treatments for NPC gain considerable interest around the world. The medicinal plant Centipeda minma is traditionally used in China for the treatment of various nasal diseases such as allergy, rhinitis, sinusitis and nasopharyngeal carcinoma. In the current study, we studied the anticancer potential of an ethanol extract (CME) and 3 pure sesquiterpenoids (A1, A2, A3) extracts from Centipeda minma against NPC cells in vitro and some underlying mechanisms of actions. The NPC cell lines CNE-1 and CNE-2 cells were treated with either CME or 3 pure compounds (A1, A2, A3). Proliferation of NPC cells was inhibited in a concentration- and time-dependent manner. For 48 h treatment, the IC50 values were 41.57 to 24.98 μg/mL for CME, and 2.3 to 7.5 μM for A1 to A3. While these extracts showed no appreciable effect on normal human LO2 hepatocytes, significant numbers of NPC cells underwent apoptotic morphological changes following treatments. Cytometric analysis demonstrated that treatments with CME and compounds results in NPC cell cycle arrest at the G2/M phase and eventually apoptosis in a concentration and time-dependent manner. Western blot analysis showed that these extracts could down-regulate Bcl-2 expression, up-regulate Bax expression and caspase-8, 9, 3 activities. In addition, the potential anti-NPC actions might be also associated with the marked inhibition of multiple signal transduction pathways including EGFR, VEGFR, HER2, FGFR, IGF-1R, PI3K/AKT/mTOR, MAP/ERK and Jan/Stat3 pathways. In summary, the Centipeda minma extract and terpenoids are potential apoptosis inducing agents to kill NPC cells and may be promising anti-cancer drug leads against nasopharyngeal carcinoma. The exact mechanism of actions remains further study.

Note: This abstract was not presented at the meeting.

Citation Format: Bei-bei Liu, Kui-yuan Zhu, Chi-on Chan, Ling-Hua Zhang, Daniel Kam-Wah Mok, Si-bao Chen. Anticancer activities of terpenoid compounds isolated from the plant centipeda minma against nasopharyngeal carcinoma cells [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 14. doi:10.1158/1538-7445.AM2017-14
Abstract 1403: PCNA-dependent cleavage and degradation of SDE2 regulates response to replication stress
Authors: Jo Ukhyun , Cai Winson , Wang Jingming , Kwon Yoojin , D’Andrea Alan D. , Kim Hyungjin
Published: July 2017

Maintaining genomic integrity during DNA replication is essential for cellular survival and for preventing tumorigenesis. Proliferating cell nuclear antigen (PCNA) functions as a processivity factor for DNA replication, and posttranslational modification of PCNA plays a key role in coordinating DNA repair against replication-blocking lesions by providing a platform to recruit factors required for DNA repair and cell cycle control. Here, we identify human SDE2 as a new genome surveillance factor regulated by PCNA interaction. SDE2 contains an N-terminal ubiquitin-like (UBL) fold, which is cleaved at a diglycine motif via a PCNA-interacting peptide (PIP) box and deubiquitinating enzyme activity. The cleaved SDE2 is required for negatively regulating ultraviolet damage-inducible PCNA monoubiquitination and counteracting replication stress. The cleaved SDE2 products need to be degraded by the CRL4CDT2 ubiquitin E3 ligase in a cell cycle- and DNA damage-dependent manner, and failure to degrade SDE2 impairs S phase progression and cellular survival. Collectively, this study uncovers a new role for CRL4CDT2 in protecting genomic integrity against replication stress via regulated proteolysis of PCNA-associated SDE2 and provides insights into how an integrated UBL domain within linear polypeptide sequence controls protein stability and function. Knowledge on such mechanism will be useful to identify novel cancer therapeutic interventions exploiting deregulated ubiquitin signaling and SDE2 activities in cancer.

Citation Format: Ukhyun Jo, Winson Cai, Jingming Wang, Yoojin Kwon, Alan D. D’Andrea, Hyungjin Kim. PCNA-dependent cleavage and degradation of SDE2 regulates response to replication stress [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 1403. doi:10.1158/1538-7445.AM2017-1403
Abstract 1404: Regulation of 53BP1 by the structural nuclear protein NuMA
Authors: Moreno Naike Salvador
Published: July 2017

Cells repair DNA double-strand breaks (DSB) through two major pathways: homologous recombination (HR) and non-homologous end joining (NHEJ). The choice between these two pathways is critical to cell survival and is altered in cancers. 53BP1 is a protein with an important role in this choice: it promotes NHEJ by blocking CtIP-dependent DNA resection. Here, we present a new negative regulation mechanism of 53BP1 that relies on the structural protein NuMA. This protein participates in mitotic spindle assembly, influences chromatin organization during the interphase and modulates the chromatin response to DNA damage. We identified NuMA in a proteomics analysis of a 53BP1-interacting proteins. The interaction was confirmed by reciprocal immunoprecipitation and with a FRET assay. In response to DSB, we measured greater than 50% decreased 53BP1-NuMA binding, which suggests that NuMA may restrain 53BP1 diffusion in the absence of DNA damage. Fluorescence correlation spectroscopy (FCS) measurements in cells expressing GFP-tagged 53BP1 support this hypothesis. Moreover, NuMA overexpression inhibited 53BP1 recruitment at DNA damage sites in laser microirradiation assays, whereas NuMA silencing had the opposite effect. 53BP1 plays an essential role in B cell class switch recombination and mediates PARP inhibitor sensitivity in BRCA1-null cells. NuMA overexpression prevented immunoglobulin switching, and overwrote cancer cell sensitivity to PARP inhibitors to the same extent as 53BP1 loss of function. Our results help understand how 53BP1 is controlled, and shed light on the mechanisms regulating PARPi sensitivity.

Citation Format: Naike Salvador Moreno. Regulation of 53BP1 by the structural nuclear protein NuMA [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 1404. doi:10.1158/1538-7445.AM2017-1404
Abstract 1405: A novel chemotherapeutic agent to treat tumors with DNA mismatch repair deficiencies
Authors: Myung Kyungjae , Zhang Yongliang , Park Young-Un
Published: July 2017

Impairing the division of cancer cells with genotoxic small molecules has been a primary goal to develop chemotherapeutic agents. However, DNA mismatch repair (MMR)-deficient cancer cells, are resistant to most conventional chemotherapeutic agents. Here we have identified baicalein as a small molecule that selectively kills MutSα-deficient cancer cells. Baicalein binds preferentially to mismatched DNA and induces a DNA damage response in a mismatch repair-dependent manner. In MutSα-proficient cells, baicalein binds to MutSα to dissociate CHK2 from MutSα leading to S phase arrest and cell survival. In contrast, continued replication in the presence of baicalein in MutSα-deficient cells results in a high number of DNA double-strand breaks and ultimately leads to apoptosis. Consistently, baicalein specifically shrinks MutSα-deficient xenograft tumors and inhibits the growth of AOM-DSS-induced colon tumors in colon-specific MSH2 knockout mice. Collectively, baicalein offers the potential of an improved treatment option for patients with tumors with a DNA MMR deficiency.

Citation Format: Kyungjae Myung, Yongliang Zhang, Young-Un Park. A novel chemotherapeutic agent to treat tumors with DNA mismatch repair deficiencies [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 1405. doi:10.1158/1538-7445.AM2017-1405
Abstract 1408: LIM protein Ajuba participates in the ATR response by direct interaction with RPA70
Authors: Fowler Sandy Wan S. , Loayza Diego , Maguin Pascal
Published: July 2017

DNA damage response (DDR) pathways are essential for genome stability and cell survival. Specifically, the ATR kinase is activated by DNA replication stress or UV irradiation. An early event in this activation is the phosphorylation and local recruitment of RPA, a single strand DNA binding protein. Our lab has shown that the LIM protein Ajuba associates with RPA, an OB fold-containing protein, and this interaction prevents an unscheduled ATR response. We hypothesize that Ajuba represses the ATR pathway through direct interaction with RPA, thereby preventing activation of ATR. To test this hypothesis, we employed E. coli and in vitro translation system for the production of recombinant proteins. Our data show that Ajuba directly associates with the large subunit of RPA, RPA70. The domains involved in the interaction were the C-terminal OB folds of RPA70, and the region between the PreLIM and LIM domains in Ajuba. We speculate that this interaction mediates the association of Ajuba with the RPA complex in cells. Understanding the implication of the Ajuba and RPA interaction will allow us to gain insights on the regulation of DDR, which is involved in early events of cellular transformation and tumorigenesis in human cells.

Citation Format: Sandy Wan S. Fowler, Diego Loayza, Pascal Maguin. LIM protein Ajuba participates in the ATR response by direct interaction with RPA70 [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 1408. doi:10.1158/1538-7445.AM2017-1408
Abstract 141: CD44 positive and sorafenib resistant hepatocellular carcinomas respond to the ATP-competitive mTOR inhibitor INK128
Authors: Badawi Mohamed , Kim Jihye , Sutaria Dhruvitkumar , Motiwala Tasneem , Reyes Ryan , Wani Nissar , Jacob Samson , Phelps Mitch , Schmittgen Thomas
Published: July 2017

The PI3K/AKT/mTOR pathway is activated in about 50% of patients with hepatocellular carcinoma (HCC). Allosteric mTOR inhibitors, also known as rapalogs, fail to show any significant clinical utility. In an effort to identify new pathways and compounds to treat advanced HCC, we considered the ATP-competitive mTOR inhibitor INK128. ATP-competitive mTOR inhibitors attenuate both mTORC1 and mTORC2. We evaluated INK128 in sorafenib sensitive and insensitive HCC cell lines, CD44low and CD44high HCC and those cell lines with acquired sorafenib resistance. CD44 was significantly increased in Huh7 cells made resistant to sorafenib. Forced expression of CD44 enhanced cellular proliferation and migration, and rendered the cells more sensitive to the anti-proliferative effects of INK128. INK128 suppressed CD44 expression by blocking phosphorylation of eukaryotic translation initiation factor 4EBP1 in HCC cells while allosteric mTOR inhibitors do not. Moreover, INK128 exhibited potent anti-proliferative and anti-migration effects on the mesenchymal-like HCC cells, CD44high and sorafenib resistant HCC cells compared to the allosteric mTOR inhibitor everolimus. Combination studies of INK128 and sorafenib showed an additive to synergistic anti-proliferative effect in CD44high HCC cells. Our findings suggest that ATP-competitive mTOR inhibitors are effective in treating advanced HCC patients who express CD44, and are insensitive or resistant to sorafenib. It also highlights the potential use of CD44 as a biomarker of response in these patients.

Citation Format: Mohamed Badawi, Jihye Kim, Dhruvitkumar Sutaria, Tasneem Motiwala, Ryan Reyes, Nissar Wani, Samson Jacob, Mitch Phelps, Thomas Schmittgen. CD44 positive and sorafenib resistant hepatocellular carcinomas respond to the ATP-competitive mTOR inhibitor INK128 [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 141. doi:10.1158/1538-7445.AM2017-141
Abstract 1411: Differential mismatch repair-dependent damage responses in subpopulations of cells from human intestinal organoids
Authors: Lin Bo , Yang Qingfen , Rath Abhijit , Heinen Christopher D.
Published: July 2017

Hereditary mutations in DNA mismatch repair (MMR) genes cause the cancer predisposition syndrome called Lynch syndrome. Patients predominantly develop colorectal cancer and some extracolonic cancers at a young age. The MMR pathway repairs mismatches created during DNA replication, but also can induce apoptosis and cell cycle arrest in response to certain DNA damaging agents as a protective mechanism to eliminate cells at risk of accumulating mutations. Our understanding of this MMR-directed DNA damage response has come primarily from studies in human cancer cell lines. We wished to examine the role of the MMR-dependent damage response in a model that may be more relevant to the human intestine. Therefore, we have created human intestinal organoids (HIOs) in vitro either by directing the differentiation of human embryonic stem cells (hESCs) or through culturing of adult intestinal tissue samples. We have used these HIOs to specifically study the MMR dependent damage response to DNA alkylation damage. We have found that whereas hESCs undergo rapid apoptosis in response to alkylation damage, the differentiated HIOs or those created from adult tissues undergo not only apoptosis, but also senescence and accelerated differentiation following damage. Using CRISPR-Cas9 gene editing in hESCs, we also created MMR-deficient HIOs that failed to respond to the drug indicating that these responses are MMR-dependent. We then determined that the cells undergoing apoptosis following DNA damage are most likely the intestinal stem cells suggesting that different cell types in the intestine have different MMR-dependent responses to damage. Together these results suggest that loss of MMR function in the intestinal crypts may provide a selective advantage particularly in an environment conducive with DNA damage that promotes tumorigenesis.

Note: This abstract was not presented at the meeting.

Citation Format: Bo Lin, Qingfen Yang, Abhijit Rath, Christopher D. Heinen. Differential mismatch repair-dependent damage responses in subpopulations of cells from human intestinal organoids [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 1411. doi:10.1158/1538-7445.AM2017-1411
Abstract 1419: Role of a novel Senataxin-associated nuclease in DNA repair
Authors: McCartney Heather , Macara Ian
Published: July 2017

Yeast two-hybrid analysis has identified a novel, uncharacterized Senataxin-interacting protein with 5’ exonuclease activity, and homology to the FEN1 nuclease domain. Senataxin is an RNA/DNA helicase that functions in resolving R loop structures which occur as a result of normal replication and transcription but can also persist resulting in genomic instability. We found that SAN1 (Senataxin-Associated Nuclease 1) is unable to cut dsDNA or bubbles, but is active against 5’ overhangs and against ssDNAs of greater than 15 nucleotides. SAN1 cleaves 3 or 8 nt fragments from the 5’ end of ssDNA and utilizes magnesium as a cofactor. As the definitive 5’ nuclease responsible for unhooking ICLs has yet to be identified we speculate that SAN1 might function in excising crosslinked nucleotides that result from interstrand crosslink (ICL) damage. We generated a SAN1 -/- HeLa cell line through CRISPR/Cas gene editing and found that SAN1 -/- cells are sensitized to ICL agents mitomycin-c and cisplatin. Interestingly, colony survival assays have shown that SAN1 does not appear to be epistatic of FANCD2, a key component of the classical pathway for resolving ICLs, the Fanconi Anemia pathway. Additionally, although the nuclease domain of SAN1 is homologous to the FEN1 family of structure-specific nucleases, SAN1 also possesses a unique and conserved C terminus of unknown function. Our goal is to understand the relationship between the structure and nuclease activity of SAN1 in DNA repair and how SAN1 relates to other known ICL-repair pathways. Understanding the components that regulate genome stability is crucial in understanding how cancer occurs and what protein targets will be the most advantageous to pursue in developing potential therapeutics. This study may also provide a better understanding of a novel factor in resistance to ICL-inducing chemotherapeutics such as cisplatin and MMC which are still widely used in the treatment of breast and ovarian cancers.

Citation Format: Heather McCartney, Ian Macara. Role of a novel Senataxin-associated nuclease in DNA repair [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 1419. doi:10.1158/1538-7445.AM2017-1419