bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4273: Identification of RNA-seq shape abnormality
Authors: Choi Hyo Young , Hayes David N. , Marron James S.
Published: August 2018

A substantial proportion of human genes differ in function through different forms of shape changes in read coverage of RNA-seq. For example, tumor-suppressor genes lose their function through various changes in expression such as aberrant splicing, frameshift indel, large deletions, or overexpression of noncoding RNAs. Although previous studies have examined mutational effect on such shape changes, it has been observed that a large fraction of shape aberration occurs in the absence of mutations. We hypothesize that read coverage shapes would show rich information on various forms of abnormality in RNA-seq data, which may have been missed in current mutation callers. We have developed a statistical method to systematically detect abnormal RNA-seq samples using read coverage data alone independently of mutational analysis. We model the underlying mechanism possibly generating aberrant shapes by multiple unknown mixture distributions, recasting the problem as high-dimensional latent variables framework. Based on this underlying mechanism, we normalize the read coverage to adjust different library sizes, extract the latent information in a robust way, and determine the cases that are strongly involved in abnormality. This approach allows us to detect not only local changes in expression such as alternative splicing events and frameshift indel but also landscape changes such as fusion and a wide range of deletions. This methodology can be applied genome-widely to detect key genes with strong shape aberrations, prioritizing genes for further investigation. We analyzed 522 TCGA head and neck squamous cell carcinomas RNA-seq tumor samples. At several known tumor-suppressor genes, we identified the cases with novel structural changes including alternative splicing, intragenic deletion, and fusion with/without mutations reported as well as the cases with no evidence of changes despite presence of mutations known for altering shapes. Notably, some of the identified shape changes in TP53 and CDKN2A were confirmed as being the outcomes of missing genetic variants near splice sites (exon-intron junctions). The genome-wide study with carefully chosen significance level provided a set of key genes with strong evidence of shape abnormality including TP53, CDKN2A, and FAT1 that are known for the most alternative splicing events. We also analyzed how often such shape changes arise with or without certain mutations in genome-wide scans. To conclude, our results provide a new statistical framework for various forms of RNA-seq shape changes and a tool for systematic discovery of such abnormal samples, and give insights into mutational effect on shape aberration.

Citation Format: Hyo Young Choi, David N. Hayes, James S. Marron. Identification of RNA-seq shape abnormality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4273.
Abstract 4280: Improving the sensitivity of wide targeted cancer gene panels via novel genome analysis tools
Authors: Kermani Bahram G. , Roberts Evans L. , Boyle Theresa A. , Magliocco Anthony M.
Published: August 2018

In the recent years, wide targeted gene panels have gained popularity, due to their ability to interrogate many genes at the same time. In cancer, particularly, there is a set of ~600 genes known as Cancer Gene Census for which mutations have been causally implicated. Many of the wide cancer panels, therefore, target a subset of these genes. As targeted panels widen, the average coverage of them reduces, if the total budget of the DNA reads remains constant. Therefore, wide panels usually have a more modest coverage, as compared to narrow panels. The reduction in coverage, along with the biases that exist in targeted enrichment approaches make a challenging environment for genome assembly pipelines. We argue that, in such systems, false negatives are prone to increase to non-trivial values, primarily due to: 1) inefficiencies in the enrichment methods, especially if they are hybridization-based; 2) sporadic insufficiency of coverage; 3) biases in the analysis pipelines; 4) filtering operations that take place, in attempt to reduce false positives. As much of the losses are due to the dependency of the assays and the pipelines to the reference genome, we have approached this issue by designing a tandem set of tools: 1) A hybrid-denovo genome assembly pipeline, which has significantly less bias to the reference genome, as compared to the conventional align-to-reference methods. This pipeline can be used in lieu of or in combination with the conventional pipelines; 2) An in-silico verification (ISV) tool that provides the experts with a multifaceted visual and textual information, to gauge the evidence (or lack thereof) for the variants of interest. While not meant to necessarily be a replacement to wet validation, ISV provides the ability to identify the errors that may otherwise seep through the system. In order to show feasibility of this approach, a small set of FFPE TruSight Tumor 170 samples including cases of lung and breast cancer was used. The comparisons were done for all RefSeq exonic bases on a hereditary cancer gene subset. Our preliminary analysis using this data shows that by using our proprietary genome analysis pipeline and ISV tool, the sensitivity of the reported variants could be improved from ~80% to ~98% or higher, without impairing the specificity. If we consider intronic bases which have reasonable coverage, including those involved in splicing, the sensitivity improvements could be even larger.

Citation Format: Bahram G. Kermani, Evans L. Roberts, Theresa A. Boyle, Anthony M. Magliocco. Improving the sensitivity of wide targeted cancer gene panels via novel genome analysis tools [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4280.
Abstract 4283: A structure network approach to predict the dynamics and structural stability effects of germline PTEN mutations associated with cancer versus autism phenotypes
Authors: Smith Iris N. , Thacker Stetson , Eng Charis
Published: August 2018

Individuals with germline mutations in the tumor suppressor gene phosphatase and tensin homolog (PTEN), irrespective of clinical presentation, are referred to as PTEN hamartoma tumor syndrome (PHTS). PHTS confers a high risk of breast, thyroid and other cancers. Yet, PTEN mutations are found in up to 20% of individuals with autism spectrum disorder (ASD) and macrocephaly. What remains unclear is why mutations in one gene can lead to seemingly disparate phenotypes. Thus, we sought to identify differences in cancer- vs. ASD-associated PTEN mutations by investigating putative structural effects. We utilized a computational theoretical approach combining protein structure network (PSN), normal mode analysis (NMA), and elastic network models (ENMs) to interrogate 6 PTEN mutations from patients with PHTS-associated cancer, 6 mutations from those with ASD only, 4 mutations shared across both phenotypes, and 1 mutation with both ASD and cancer. Combined with in silico prediction methods we calculated structural stability changes induced by each mutation. All 6 cancer-associated mutations showed decreases in structure stability and increased dynamics across domain interface. In contrast, 5 of 6 ASD-associated mutations showed only localized destabilization. We coupled ENM-NMA with PSN and found PTEN R130G (cancer only) and R173C (shared in patients with both ASD and cancer), play a role in inter-residue signal propagation, indicating both residue positions are crucial to structural stability. Our data suggest that ASD-associated mutations affect local structural dynamics, whereas cancer-associated mutations mediate long-range perturbations significantly altering structural stability and salient communication pathways. These approaches lend insight into altered structural effects of germline PTEN mutations associated with PTEN-ASD and PTEN-cancer, potentially aiding in identification of specific mutations that contribute to each phenotype. Moreover, this work may illuminate the shared and separate molecular features that contribute to autism or cancer – providing a deeper understanding of genotype-phenotype relationships for germline PTEN mutations. The ability to accurately predict PTEN-ASD may spare patients the need to undergo high-risk cancer surveillance that is now performed in all with PHTS.

Citation Format: Iris N. Smith, Stetson Thacker, Charis Eng. A structure network approach to predict the dynamics and structural stability effects of germline PTEN mutations associated with cancer versus autism phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4283.
Abstract 4293: Glycogen synthase kinase 3 b maintains mitotic arrest by regulating mitotic checkpoint complex levels
Authors: Rashid Maisha S. , Taylor William R.
Published: August 2018

The cell cycle is regulated by checkpoints that ensure genomic integrity and proper cell division. We are investigating the role of a multifunctional ser/thr kinase, glycogen synthase kinase 3 (GSK3), in the regulation of the mitotic checkpoint. Our data show that spindle toxin-induced mitotic arrest is relieved in multiple cancer cell lines by the GSK3 inhibitors, SB 415286 (SB), RO-81220 (RO) and lithium chloride. Additionally, the mitotic index is reduced in CRISPR-generated GSK3β knockout human cells and GSK3β knockout mouse embryo fibroblasts compared to wild type cells in the presence of taxol. Mitotic arrest is dependent on the mitotic checkpoint complex (MCC), composed of Mad2, BubR1, Cdc20 and Bub1. GSK3 appears to target the MCC to regulate mitotic arrest. For example, Mad2, BubR1 and Bub1 localization at kinetochores and MCC assembly were both reduced by co-treatment of GSK3 inhibitors and spindle toxin compared to spindle toxin alone. These data imply that GSK3β plays a role in maintaining the mitotic checkpoint. The strength of the checkpoint was determined to act like a rheostat rather than a toggle-switch, as cells undergo mitotic slippage after prolonged arrest in spindle toxins. Our data indicates that GSK3 regulates the strength of the checkpoint, as illustrated by time lapse-imaging. GSK3-inhibition induced exit was observed to be dependent on how long the cells were arrested in mitosis prior to GSK3-inhibitor addition. GSK3 inhibition in taxol also decreases the amount of KnL1, part of the KMN network forming the kinetochore, at the centromeres. This indicates a regulatory role of GSK3 in kinetochore assembly and function. The Wnt-signaling pathway and the PI3K/Akt signaling pathway are known upstream regulators of GSK3β, negatively regulating GSK3β activity. Our data shows that inhibiting Wnt-signaling and PI3K/Akt-signaling in the presence of taxol, induces a longer mitotic arrest compared to taxol alone. This suggests that GSK3β is regulated upstream by the Wnt- and the PI3K/Akt signaling archs to control mitosis. Finally, our data implicated that de-acetylase sirtuin2 is a downstream target of GSK3 in its mitotic regulatory role. Our observations indicate a novel regulator of the checkpoint and novel insight in connecting growth-signaling pathways with mitosis.

Citation Format: Maisha S. Rashid, William R. Taylor. Glycogen synthase kinase 3 b maintains mitotic arrest by regulating mitotic checkpoint complex levels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4293.
Abstract 4296: Cofilin-1 is associated with replicative origins licensing through regulation of MCM2-7 helicase
Authors: Lee Yi-Jang , Chang Chun-Yuan
Published: August 2018

G1 to S phase transition is strictly regulated to avoid uncontrolled growth in mammalian cells. Although DNA replication initiates in S phase, licensing of DNA replicative origins substantially begins from late M to G1 phase. Interference of replicative origins licensing will lead to genomic instability and cell death. In addition, integral actin organization is required for G1 phase to S phase transition. Whether actin architectures will influence the licensing of DNA replicative origins is unclear. Previously, we found that over-expression of cofilin-1, a member of actin depolymerizing factor (ADF)/cofilin family could destabilize actin cytoskeleton and cause G1 phase arrest. The microarray assay further showed that minichromosome maintenance complex 2-7 (MCM2-7) helicase involved in the establishment of licensing was regulated by cofilin-1. In this study, we aim to investigate whether cofilin-1 would affect the expression of MCM2-7 complexes and the initiation of replicative origins licensing. First, we exploited a double thymidine blockage assay to demonstrate that the cofilin-1 expression was down-regulated during G1 to S phase transition. Use of H1299/tet-on-cofilin-1 cells, we also found that doxycycline induced exogenous cofilin-1 could inhibit the expression of MCM2-7 complex in both dose and time-dependent manners. Chromatin fractionation for analyzing the replicative origin licensing was performed to confirm these observations. DNA fiber analysis for determining the interorigin distance (IOD) was applied to investigate the IOD after the overexpression of cofilin-1 in H1299/tet-on-cofilin-1 cells. Taken together, current results revealed a novel finding that cofilin-1 could regulate MCM2-7 complex for mediating the replicative origin licensing and cell cycle progression. Since MCM2-7 complex has been regarded a prognostic marker of several human cancers, this study may contribute to designing of new therapeutic strategy for cancer treatment.

Citation Format: Yi-Jang Lee, Chun-Yuan Chang. Cofilin-1 is associated with replicative origins licensing through regulation of MCM2-7 helicase [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4296.
Abstract 4301: Mechanisms underlying the inhibitory effect of CRT0066101 on bladder cancer growth in vitro and in vivo
Authors: Li Quentin , Hsu Iawen , Railkar Reema , Sanford Thomas , Agarwal Piyush K.
Published: August 2018

CRT0066101 is an inhibitor of protein kinase D with anti-tumor activity in several types of human carcinomas. However, the effect and mechanism of CRT0066101 in bladder cancer remain unknown. In this study, we show that CRT0066101 inhibited the proliferation and migration of bladder cancer cells, but had only a marginal effect in human uroepithelial cells, indicating a differential inhibitory effect on cell growth between bladder cancer and normal urothelium. We also demonstrate that CRT0066101 blocked bladder cancer growth in a xenograft flank mouse model. Our cell cycle analysis revealed that CRT0066101 arrested bladder tumor cells at the G2-M phase, the arrest being accompanied by decreases in the levels of cyclin B1 and CDK1 and increases in the levels of p27kip1 and phospho-CDK1 (Thr14/Tyr15). Moreover, CRT0066101 reduced the expression of Cdc25C, which dephosphorylates/activates CDK1, but enhanced the activity of the checkpoint kinase Chk1, which phosphorylates/ inactivates Cdc25C. Finally, CRT0066101 was found to elevate the levels of Myt1, Wee1, phospho-Cdc25C (Ser216), Gadd45α, and 14-3-3 proteins, all of which cause a reduction in CDK1-cyclin B1 activity. Together, these data suggest that CRT0066101 suppresses bladder cancer growth partly through modulating the cell cycle G2 checkpoint and inducing G2-M phase arrest, leading to the blockade of cell cycle progression.

Citation Format: Quentin Li, Iawen Hsu, Reema Railkar, Thomas Sanford, Piyush K. Agarwal. Mechanisms underlying the inhibitory effect of CRT0066101 on bladder cancer growth in vitro and in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4301.
Abstract 4308: RBBP6 expressional effects on cell proliferation and apoptosis in breast cancer cell lines with distinct p53 statuses
Authors: Motadi lesetja R. , Moela pontsho
Published: August 2018

Breast cancer incidence rate has increased beyond that of lung cancer, making it the most common malignancy among women. Breast tumour progression is partly as a result of p53 inactivation by overexpressed ubiquitous regulatory proteins that possess p53 binding domain. RBBP6 forms a member of such protein since it has an E3 ligase activity due to its RING finger-like domain. Moreover, its overexpression in several malignancies makes it a potential target in cancer management. However, it is not clearly defined whether RBBP6 effect on cell growth and apoptosis is cell line dependent, more especially in breast cancer cell lines that have distinct p53 expression profiles. The present study therefore aims at evaluating RBBP6 effects on cell growth and apoptosis in breast cancer cell lines with different p53 expression profiles. Following analysis at mRNA and protein levels in breast cancer tissue, RBBP6 expression was successfully manipulated using gene silencing and protein overexpression techniques in MCF-7 and MDA-MB-231 cell lines. Transfection efficiencies were confirmed using qPCR and western blot, followed by monitoring of cell proliferation in the presence of transfection using xCELLigence system. The cells were then co-treated with anti-cancer agents followed by apoptosis detection using confocal microscopy and flow cytometry, which was further confirmed by caspase 3/7 activity and quantification of apoptotic genes. RBBP6 was overexpressed in breast cancer tissues that were classified as stage 3 and 4 while in stage 1 it was expressed but at much lower levels. The wt. p53-expressing MCF-7 cell line was more susceptible to apoptosis induction as opposed to the mt. p53-expressing MDA-MB-231. RBBP6 silencing led to a significant accumulation of p53 expression in MCF-7 as compared to MDA-MB-231. Co-treatment with GABA and camptothecin seemed to sensitize the cells to apoptosis induction. These data suggest that RBBP6 silencing triggers significant levels of intrinsic apoptosis and over-expression appears to promote cell proliferation in wild type p53-expressing MCF-7 rather than in MDA-MB-231 cells. Insignificant changes in the expression of mt. TP53 in MDA-MB-231 cell line following RBBP6 silencing and over-expression suggests that RBBP6 is highly likely to interact with wt-p53 rather than mutated p53. In conclusion, the effect of RBBP6 on cell proliferation and apoptosis induction in breast cancer seem to be cell line dependent based on p53 status

Citation Format: lesetja R. Motadi, pontsho Moela. RBBP6 expressional effects on cell proliferation and apoptosis in breast cancer cell lines with distinct p53 statuses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4308.
Abstract 4311: Rb may play a key role in green tea-induced growth inhibition of human myeloid leukemia cells
Authors: Henry Darrell , Brumaire Sebastien , Hu Xiaotang
Published: August 2018

Although the benefits of green tea to human health including preventing cancer have been widely reported in recent years, the specific effect and action mechanisms of green tea on cancer cells are largely unclear. In this study, we presented evidence that green tea extract and its major chemical component, Epigallocatechin-3-gallate (EGCG), inhibit both suspension and adherence cancer cells through the regulation of pRb-CDK complexes. Addition of green tea extract to the culture of myeloid leukemia TF-1a and MV4-11 cells significantly inhibited their proliferation measured by XTT and BrdU assays. The inhibition is dose dependent with more than 35% inhibition being observed at a concentration of 4% (v/v) of the tea extracts derived from 8% (g/ml) green tealeaf in distilled water. The tea extract also markedly reduced the numbers of stem/progenitors derived from TF-1a, MV4-11, and Hep-G2 cells, determined by counting colony-forming cells in semi-solid clonal culture. EGCG showed a similar inhibitory effect on TF-1a, MV4-11, and Hep-G2 cells and their stem/progenitors. Next, we investigated what mechanism(s) is responsible for the green tea-induced growth inhibition of the cells. Surprised to us the expression of Rb was significantly upregualted with a maximal enhancement being observed when 0.00001% of EGCG (g/ml) or 4% (v/v) of green tea extracts were added to the cell culture. The upregulation of Rb was significantly blocked by pre-treatment with cycloheximade, a protein synthesis inhibitor. In contrast, green tea extract and EGCG downregulated dramatically phosphorylation of pRb. Addition of cycloheximade had no effect on the phosphorylation of Rb in the absence or presence of green tea extract or EGCG analyzed by Western blotting. We also found that green tea extract and EGCG had no significant effect on the expression of CDC2, CDK2, CDK4, CDK6, and CDK inhibitors, p21 and p27, but the formation of CDK4-pRb and CDK6-pRb complexes were significantly downregulated detected by immunoprecipitation. Taken together, our data suggest that green tea (the extract and EGCG) regulate Rb protein at both translation and post-translation levels. The upregulation of Rb synthesis, downregulation of Rb phosphorylation and CDK-Rb complexes all promote the binding of Rb to E2F transcription factors and inhibit the E2F-dependent transcription, leading to cell growth inhibition (supported by Barry Faculty Stimulating Grant 2017-2018).

Citation Format: Darrell Henry, Sebastien Brumaire, Xiaotang Hu. Rb may play a key role in green tea-induced growth inhibition of human myeloid leukemia cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4311.
Abstract 4315: Colorectal cancer epigenomic landscape
Authors: Orouji Elias , Raman Ayush , Tang Ming , Dhamdhere Mayura , Rai Kunal
Published: August 2018

Cancer cells utilize genetic and epigenetic aberrations for their excessive growth. Although we have sufficient understanding of the genomic alterations in colorectal cancer, we have incomplete knowledge of epigenomic aberrations and their impact on tumor growth. In order to comprehensively define the epigenetic patterns specific to colorectal cancer, we generated profiles for 6 histone modification marks, including H3K4me1 (enhancer), H3K27Ac (active enhancer), H3K9me3 (heterochromatin), H3K27me3 (polycomb repression), H3K79me2 (transcription) and H3K4me3 (promoter), using a high-throughput ChIP-Seq methodology developed in house applicable to frozen tumors. Chromatin state transitions specifically pointed to drastic changes in enhancer patterns, consistent with some prior studies. Furthermore, using similarity network fusion (SNF) we identified the best singular mark and are currently developing a tool to identify combinatorial chromatin states that could most efficiently distinguish and eventually predict CRC from normal colon. In a more detailed investigation into patterns of active enhancers using normal colon, adenomas and colorectal cancers, we identified specific changes in enhancers from normal tissue to these neoplastic lesions. Importantly, we noted gains of enhancers in a large number of genomic loci in colon cancer compared to adjacent normal tissues. These enhancers are enriched in important signaling components including Notch, Wnt, and stem cell regulators. We specifically noted changes in enhancer regions in the proximity of ASCL2 (intestinal cancer stem cell gene), SALL4 (early pluripotency marker) as well as FZD10 and CTNNB1 (Wnt signaling). A preliminary Cas9-based deletion study suggested these enhancers to be functional in regulating gene expression, and currently its effect on cell proliferation and other cancer properties is being investigated. Further, we reasoned that blocking aberrantly gained enhancers using BRD inhibitor in combination with pathway inhibitors could be a useful strategy in this cancer. Our data supported this hypothesis, and we are currently performing a systematic study to identify most effective combinations. In summary, we have identified aberrant enhancer gains as a major feature of colorectal cancer and propose this to be utilized as a therapeutic approach.

Citation Format: Elias Orouji, Ayush Raman, Ming Tang, Mayura Dhamdhere, Kunal Rai. Colorectal cancer epigenomic landscape [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4315.
Abstract 4317: Cell-type specific epigenetic effects of tobacco smoking on the immune cell methylome
Authors: Wang Xuting , Wan Ma , Bennett Brian D. , Pittman Gary S. , Campbell Michelle , Su Dan , Thompson Isabel J. , Martos Suzanne N. , Bell Douglas A.
Published: August 2018

Exposure to tobacco smoke dramatically alters DNA methylation in blood cells and this immune cell modulation may mediate smoking-associated complex diseases. To identify cell-type specific, smoking-associated differentially methylated regions (SM-DMRs) in hematopoietic cells from smokers and non-smokers, we used Illumina 450/850K arrays, reduced representation (RRBS) and whole genome bisulfite sequencing (WGBS) to measure methylation on DNA extracted from whole blood and 7 leukocyte subtypes (CD4+, CD8+, CD14+ monocytes, CD15+ granulocytes, B cells, NK cells and CD34+ progenitor cells). SM-DMRs preferentially occurred at enhancers (H3K27ac), and/or CpG island shores and were enriched for transcription factor (TF) binding suggesting crosstalk between TFs, DNA methylation, and tobacco smoke exposure. SM-DMRs in or near genes AHRR, ALPPL2, and GFI1 were highly significant in CD34+, CD14+, CD15+, B cells and NK cells but were absent in CD4+ and CD8+ T cells. We also identified genomic regions with distinct cell-type and lineage-specific differences in smoking-associated methylation and gene expression. AHRR displayed increased levels of both noncoding RNA and mRNA gene expression only in CD14+ monocytes. The SM-DMR in GPR15 was highly significant in CD4+ and CD8+ T cells, B cells, and NK cells but absent in myeloid cells. To explore possible links between smoking, DNA methylation/gene expression and immune cell functions, we carried out pathway analysis on smoking-affected methylomes and transcriptomes in each cell type. The smokers' transcriptome of CD56+ NK cells showed perturbation of genes either altered in leukemias, linked with leukemia GWAS SNPs, or under various types of innate immune stimulation. In particular, the locus containing HLA-DQA1 and HLA-DQB1 is highly significantly linked with chronic lymphocytic leukemia and these genes were strongly down-regulated in NK cells of smokers. The NK cell methylome of smokers also displayed perturbation of genes altered in leukemia cell lines. To identify and characterize rare blood cells among cell-type subsets that have smoking-altered transcriptomes, we are carrying out single cell RNA-seq. These studies may reveal new biological connections between tobacco smoke exposure and smoking-associated disease etiology.

Citation Format: Xuting Wang, Ma Wan, Brian D. Bennett, Gary S. Pittman, Michelle Campbell, Dan Su, Isabel J. Thompson, Suzanne N. Martos, Douglas A. Bell. Cell-type specific epigenetic effects of tobacco smoking on the immune cell methylome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4317.
Abstract 4320: p53 binding sites in normal and cancer cells are characterized by distinct chromatin context
Authors: Cui Feng
Published: August 2018

The tumor suppressor protein p53 interacts with DNA in a sequence-dependent manner. Thousands of p53 binding sites have been mapped genome-wide in normal and cancer cells. However, the way p53 selectively binds its cognate sites in different types of cells is not fully understood. Here, we performed a comprehensive analysis of 25 published p53 cistromes and identified 3,551 and 6,039 "high-confidence" binding sites in normal and cancer cells, respectively. Our analysis revealed two distinct epigenetic features underlying p53-DNA interactions in vivo. First, p53 binding sites are associated with transcriptionally active histone marks (H3K4me3 and H3K36me3) in normal-cell chromatin, but with repressive histone marks (H3K27me3) in cancer-cell chromatin. Second, p53 binding sites in cancer cells are characterized by a lower level of DNA methylation than their counterparts in normal cells, probably related to global hypomethylation in cancers. Intriguingly, regardless of the cell type, p53 sites are highly enriched in the endogenous retroviral elements of the ERV1 family, highlighting the importance of this repeat family in shaping the transcriptional network of p53. Moreover, the p53 sites exhibit an unusual combination of chromatin patterns: high nucleosome occupancy and, at the same time, high sensitivity to DNase I. Our results suggest that p53 can access its target sites in a chromatin environment that is nonpermissive to most DNA-binding transcription factors, which may allow p53 to act as a pioneer transcription factor in the context of chromatin.

Citation Format: Feng Cui. p53 binding sites in normal and cancer cells are characterized by distinct chromatin context [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4320.
Abstract 4326: The chromatin context and consequence of cisplatin-adduct DNA damage
Authors: Gallon John , Loomis Erick , Martin Nicholas , Flanagan James , Brown Robert
Published: August 2018

Improvements in survival rates for ovarian cancer lag behind those of other cancers. The combination of paclitaxel and carboplatin, along with debulking surgery, form the primary mode of treatment, however, the majority of patients eventually develop resistance. Epigenetic mechanisms have been implicated in the emergence of drug resistance, with platinum based therapies shown to induce DNA methylation changes at relapse which are associated with overall survival. Using a next generation sequencing approach, including a novel NGS method to map platinum adducts, we sought to investigate the association between platinum-DNA adduct formation and changes to chromatin conformation in the emergence of resistance to platinum therapy. We found chromatin conformation changes at the transcription start sites (TSS) of genes differentially expressed between platinum sensitive and resistant cell lines (p<0.05, n=3 pairs). Furthermore, we found non-TSS associated chromatin conformation changes which distinguish sensitive from resistant lines, and occur primarily in the direction of reduced accessibility in resistant lines (FDR <0.05, log2FC >±1.5). Finally, we found that 2kb windows enriched for platinum-DNA adducts are significantly more accessible than an equal number of random windows on the same chromosome (p<0.05, 1000 permutations). Taken together, these data suggest that platinum treatment may induce epigenetic changes, which reduce chromatin accessibility, rendering cells less susceptible to the formation of platinum-DNA adducts in subsequent treatments, resulting in cells becoming less sensitive to the drug.

Citation Format: John Gallon, Erick Loomis, Nicholas Martin, James Flanagan, Robert Brown. The chromatin context and consequence of cisplatin-adduct DNA damage [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4326.
Abstract 4328: hTERT protein expression, hTERT methylation and HPV infection in uterine cervical cancer
Authors: Moreno-Acosta Pablo , Molano Mónica , Morales Nicolas , Romero-Rojas Alfredo , Gamboa Oscar , Acosta Jinneth , Alvarez Raynner , Magné Nicolas , Muñoz Nubia
Published: August 2018

The analysis of expression of the hTERT protein, the methylation status of the hTERT gene as the type of HPV infection, will contribute to deepen the role played by HPV infection in the expression and methylation of hTERT. The study included a group of one hundred fifty-five samples of women with squamous cell carcinomas of the uterine cervix in stage FIGO IIB-IIIB treated at the National Cancer Institute in Bogotá, Colombia. The expression of the hTERT protein was detected by immunohistochemistry both at the nuclear level and at the cytoplasmic level. In 79.7% of the cases, the protein was expressed at the nuclear level and 78% at the cytoplasmic level. HPV16, the most frequent viral type found, was detected by means of a GP5+/GP6+ mediated PCR- RLB in 84.4% and in 82.2% of the cases that expressed hTERT at the nuclear level and at the cytoplasmic level, respectively; with respect to HPV species, both at the nuclear level and at the cytoplasmic level, the species most frequently found was the alpha 9 species (HPVs 16, 31, 35, 52.58) followed by alpha 7 (HPVs 18, 45.59) and alpha 6 (HPVs 56, 66). In the multiple correspondence analyzes, a close relationship was observed between the cytoplasmic expression as nuclear of hTERT and the alpha species 9. A distant relationship was also observed between the expression of the protein and methylation, as well as between the non-methylation and the alpha 7 family of HPV; likewise, a distant relationship was observed between the non-methylation of hTERT and the alpha 9 species. The analyzes carried out show a possible relationship between the expression of the hTERT protein and the alpha 9 HPV species.

Citation Format: Pablo Moreno-Acosta, Mónica Molano, Nicolas Morales, Alfredo Romero-Rojas, Oscar Gamboa, Jinneth Acosta, Raynner Alvarez, Nicolas Magné, Nubia Muñoz. hTERT protein expression, hTERT methylation and HPV infection in uterine cervical cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4328.
Abstract 4331: High-throughput whole-genome sequencing of formalin fixed, paraffin-embedded tissues from colorectal cancer patients
Authors: Kubit Matthew , Wood-Bouwens Christina , Grimes Sue , Bell John , Shin GiWon , Lau Billy , Miller Mickey , Day Kenneth , Escobar Helaman , Ji Hanlee , Nadauld Lincoln , Hummelen Paul Van
Published: August 2018

Formalin-fixed, paraffin-embedded (FFPE) storage is a universally-adopted, cost-effective and long-term solution for tissue storage. Given the abundance of FFPE clinical samples, they provide a good source of tissue for genome sequencing studies. However, the extraction of nucleic acids from FFPE tissues yield highly fragmented DNA of variable quality. The poor quality and low yield make it difficult to generate adequate sequencing libraries for genomic studies.

For a population cancer genome study, we optimized a procedure for whole-genome sequencing on FFPE tumor and normal tissue of colorectal cancer patients. This pilot study aimed to first identify changes in DNA copy number using low-pass sequencing, with the additional goal of later adding structural variant and gene fusion detection and single nucleotide variant analysis with deeper sequencing. We processed, sequenced and analyzed 193 patients. These FFPE samples had varying storage characteristics. We optimized the initial extraction quality thresholds, DNA extraction and library preparation to generate high quality sequencing data.

We identified an initial sample quality and library threshold to hold the best correlation for sequencing quality. Optimal yield and DNA size from extracted FFPE was achieved by using Promega's LEV DNA FFPE Extraction Kit. Library prep optimization involved using mechanical shearing of DNA to increase overall library size for structural variant detection as well as using unique dual index adapters to identify index swapping artifacts during sequencing. An additional cleanup was also performed post-fragmentation to increase overall library size. Overall, we successfully developed a robust protocol for conducting whole genome sequencing on FFPE tumor samples.

Citation Format: Matthew Kubit, Christina Wood-Bouwens, Sue Grimes, John Bell, GiWon Shin, Billy Lau, Mickey Miller, Kenneth Day, Helaman Escobar, Hanlee Ji, Lincoln Nadauld, Paul Van Hummelen. High-throughput whole-genome sequencing of formalin fixed, paraffin-embedded tissues from colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4331.
Abstract 4334: Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer
Authors: Xia Li C. , Bell John M. , Wood-Bouwens Christina , King Daniel A. , Shin GiWon , Greer Stephanie , Connolly Ian D. , Gephart Melanie H. , Ji Hanlee P.
Published: August 2018

Little is known about the genomic features of brain metastases from colorectal cancer (CRC) and the contributing genetic factors. We conducted an analysis of large-scale structural aberrations, including chromosome aneuploidies, with a method called linked-read whole genome sequencing and a new somatic rearrangement detection software tool (ZoomX) to better understand the genomic architecture of brain metastases from CRC. We resolved on average 145 distal inter- and intra-chromosomal somatic junctions per sample with their exact haplotype information and basepair level breakpoints. In addition, we used a new haplotyping method based on these imbalances to generate cancer chromosome haplotypes of up to 146 Mbp long. We identified extensive chromosomal-level instability (CIN) in these cancer genomes, with an average of 90 large-scale copy number aberrations per sample in sizes ranging from hundreds of Kbp to hundreds of Mbp. A substantial fraction of CIN is likely attributable to earlier chromothripsis events. For example, we identified multiple chromothripsis events disrupting the loci of known cancer genes such as TP53, an essential colon cancer driver. We identified novel rearrangements including an oncogenic gene fusion; e.g. SET/DPP10 among these metastatic samples. A majority of chromosome arms demonstrated an allelic imbalance across all of the samples. In summary, the analysis revealed pervasive chromosome-level genome instability as a potential contributor to devastating brain invasion by CRC. It also demonstrated the advantages of linked-read whole genome sequencing. This approach is cost-effective and represents a high-resolution tool to assess genome-wide rearrangements and to generate megabase-scale haplotypes.

Citation Format: Li C. Xia, John M. Bell, Christina Wood-Bouwens, Daniel A. King, GiWon Shin, Stephanie Greer, Ian D. Connolly, Melanie H. Gephart, Hanlee P. Ji. Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4334.
Abstract 4352: High caveolin-1 expression in African American women with early-stage triple-negative breast cancer
Authors: Baumbach-Reardon Lisa L. , Getz Julie , Ahearn Mary E. , Carpten John , Pegram Mark
Published: August 2018

In the U.S., the incidence rates of breast cancer (BC) among Caucasian (CA) women are lower than those of African American (AA); however, AA women have a significantly higher mortality rate. It is imperative that we continue to investigate the underlying molecular biology that may contribute to the cause of health disparities between AA and CA with TNBC. In this study, gene expression profiling, using the Almac BC DSA Research Tool, was performed on archived FFPE samples, obtained from CA and AA women diagnosed with early-stage (Node 0) TNBC. Unsupervised hierarchical clustering revealed a pattern of differential gene expression in the AA cohort compared to CA. Using a subtyping Tool for TNBC, we found a distinct distribution pattern of TNBC molecular subtypes in the AA cohort, which was very different than the CA cohort: basal-like (14%), immunomodulatory (43%) and mesenchymal (43%). Gene expression analyses, comparing the AA and CA cohort (fold change > 2.0, p-value <.05), resulted in 190 differentially expressed genes (DEG). Pathway enrichment analysis conducted in MetaCore GeneGo revealed that the DEGs were over-represented in cytoskeletal remodeling, cell adhesion, tight junctions, and immune response in the AA TNBC cohort. Furthermore, several genes in the Wnt/β-catenin pathways were overexpressed in the top 10 enrichment pathways. We validated our results using RT-qPCR and identified Caveolin-1 (CAV1) as being significantly expressed in the AA-TNBC cohort (p-value 1.22 x 10-05). An independent cohort of FFPE samples, from AA and CA women with early stage TNBC, was used to create a tissue microarray (TMA). Immunohistochemistry results showed no difference in subcelluar localization of Cav1 between the AA and CA cohorts; however, the AA cohort had significantly higher levels of Cav1 staining (p-value 0.04). Additionally, using RT-qPCR, we demonstrated that CAV1 mRNA was significantly higher in the AA TNBC cohort (p-value 0.48). Furthermore, endogenous Cav1 was shown to be highly expressed in a cell line panel of TNBC, in particular, those of the mesenchymal and basal-like molecular subtypes. Finally, using siRNA, we demonstrated that CAV1 silencing resulted in a significant decrease in cell proliferation for each of the TNBC cell lines while it showed no effect on the luminal ER+ cell lines. Our combined study results suggest that CAV1 overexpression may be a biologic contributor to the observed health disparity between AA women and CA diagnosed with early-stage TNBC.

Citation Format: Lisa L. Baumbach-Reardon, Julie Getz, Mary E. Ahearn, John Carpten, Mark Pegram. High caveolin-1 expression in African American women with early-stage triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4352.
Abstract 4359: Several cancer types are associated with increased expression and activity of the ECT2 RhoGEF and decreased expression and activity of the DLC1 RhoGAP, leading to increased RhoA activity
Authors: Wang Dunrui , Qian Xiaolan , Durkin Marian E. , Papageorge Alexander G. , Lowy Douglas R.
Published: August 2018

RhoA, which is a member of the Ras family of small GTPases, whose proteins cycle between an active GTP-bound form and an inactive GDP-bound form, frequently has high activity in advanced cancer. The RhoA protein is activated by RhoGEFs, which catalyze replacement of bound-GDP with bound-GTP, and inactivated by RhoGAPs, which hydrolyze bound-GTP to bound-GDP. In this study, we have used the The Cancer Genome Atlas (TCGA) and the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) databases to examine the relationship between a specific RhoGEF, ECT2, and a specific RhoGAP, DLC1, and experimentally tested the biological relevance of some key findings. Using the TCGA dabase, we have found increased expression of the ECT2 RhoGEF frequently occurs in synchrony with decreased expression of the DLC1 RhoGAP in several tumor types, including lung adenocarcinoma, lung squamous cell carcinoma, and hepatocellular cancer. In lung adenocarcinoma, the combination of high ECT2 expression and low DLC1 expression level is more common in poorly differentiated tumors than in well differentiated ones. Using other publicly available datasets from NCBI Gene Expression Omnibus (GEO), the expression DLC1 and ECT2 was found to be cell cycle related, with higher DLC1 being observed exclusively in the G0 phase, while ECT2 was higher during the cell cycle, relative to G0, and peaked in the G2/M phase. In CPTAC, phosphorylation of a specific ECT2 amino acid (S861) is correlated with a poor prognosis in breast cancer. Consistent with this observation, experimental mutation of ECT2 S861 to A861 results in an ECT2 gene with loss-of-function. Point mutation of ECT2 and DLC1 were found at overall frequencies of 1.7% and 4.7%, respectively, in the tumors of the TCGA database. These cancer-associated mutations occur along the entire length of the ECT2 and DLC1 proteins, rather than being located primarily in the Rho-GEF domain of ECT2 or the Rho-GAP domain of DLC1, and experimental analysis of a subset of these mutants indicates that most of the ECT2 mutants are gain-of-function, while most of the DLC1 mutants are loss-of-function. Our results imply that ECT2 and DLC1 frequently act in concert, but in opposite directions, in cancer to increase RhoA activity.

* Authors contributed equally to this abstract

Citation Format: Dunrui Wang, Xiaolan Qian, Marian E. Durkin, Alexander G. Papageorge, Douglas R. Lowy. Several cancer types are associated with increased expression and activity of the ECT2 RhoGEF and decreased expression and activity of the DLC1 RhoGAP, leading to increased RhoA activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4359.