bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 335: Variable off-target effects of clinically advanced PARP inhibitors
Authors: Wielgos Monica E. , Patibandla Jay , Firlit Michelle , Oudenhove Elke Van , Cybulska Paulina , Jelinic Petar , Levine Douglas A.
Published: August 2018

High-grade serous ovarian carcinoma (HGSOC) is the most common subtype of ovarian cancer with low 5-year survival rates. Inhibitors of poly (ADP-ribose) polymerase (PARP) are promising novel agents that uniquely target HGSOCs with DNA repair deficiencies. The majority of patients with DNA repair proficient HGSOCs do not respond to PARP inhibitor monotherapy, highlighting the need for novel treatment approaches for these women. The goal of this study was to expand the patient population that could benefit from PARP inhibition by identifying the off-target effects that are favorable in combination with CHK1 inhibitors among the five most clinically advanced PARP inhibitors.

Cell cycle and western blot analysis revealed that the four most potent PARP trappers (rucaparib, olaparib, niraparib, and talazoparib) have a strong effect on the cell cycle. The PARP trappers in particular activated CHK1 through phosphorylation at the serine 345 residue, decreased total protein levels of CDC25C, and arrested cells in the S/G2 phase of the cell cycle. These results were not observed after treatment with veliparib, the least potent PARP trapper. We created phospo-CHK1 mutants to confirm CHK1 activation at serine 345 and to further investigate whether potent PARP trappers activate CHK1 on serine 317, another residue that is also phosphorylated in response to replication stress. The data suggest that PARP trappers activate CHK1 at both the serine 317 and 345 phosphorylation sites.

Next, we examined whether PARP inhibition-induced activation of CHK1 is a determinant of synergy between PARP and CHK1 inhibitors. We exposed one of our established BRCA wild-type, TP53 mutant HGSOC patient-derived xenograft models to a PARP1 inhibitor (veliparib or talazoparib) or to the CHK1 inhibitor (MK-8776) or a combination of PARP and CHK1 inhibitors. CHK1 inhibition slightly increased sensitivity to talazoparib compared to single agent therapy. However, the tumor volume was significantly reduced by the combination of CHK1 inhibition and veliparib treatment compared to either single agent alone. This study suggests that there are off-target cell cycle effects that vary among the five most clinically-advanced PARP inhibitors that likely influence the response to combinatorial treatment. We propose the use of PARP and CHK1 inhibition as a strategy for HGSOC patients who would otherwise have minimal benefit to PARP inhibitor monotherapy.

Citation Format: Monica E. Wielgos, Jay Patibandla, Michelle Firlit, Elke Van Oudenhove, Paulina Cybulska, Petar Jelinic, Douglas A. Levine. Variable off-target effects of clinically advanced PARP inhibitors [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 335.
Abstract 3351: Myc inhibition by Omomyc impairs melanoma growth and progression through genome-wide gene expression reprogramming
Authors: Zacarias-Fluck Mariano F. , Martín Génesis , Massó-Vallés Daniel , Foradada Laia , Whitfield Jonathan R. , Beaulieu Marie-Eve , Soucek Laura
Published: August 2018

Myc encodes for a transcription factor deregulated in the vast majority of human cancers, mainly by amplification or constant upstream oncogenic signaling. Previous work from our laboratory showed that targeting Myc by transgenic expression of the Myc inhibitor Omomyc is an effective strategy to inhibit tumor progression and cause tumor regression in a wide array of mouse cancer models, without any evidence of toxicity in normal tissues. Our goal now is to assess whether Myc inhibition can be an effective approach to treat melanoma, the most dangerous form of skin cancer. For this purpose, we transfected human melanoma cell lines with a doxycycline-dependent vector expressing Omomyc-RFP and characterized the effect of Myc inhibition on proliferation and colony formation, as well as the expression of different cell cycle related proteins. We observed that Omomyc significantly reduced proliferation of a wide variety of cell lines, regardless of their driving mutations. In p53 wild type cells, Omomyc expression was accompanied by p53 stabilization and concomitant p21 upregulation, and in BRaf or NF1 mutated melanoma cells, by downregulation of cyclin D1. In order to elucidate the mechanism of action underlying this anti-tumorigenic effect, we performed a microarray analysis of A375 melanoma cells in the presence or absence of Omomyc-RFP expression. This analysis showed that Omomyc affected genome-wide gene expression. More in detail, Gene Set Enrichment Analysis showed that Omomyc significantly blunts the expression of both Myc and E2F targets, as well as RNA biogenesis, DNA replication and different cell cycle checkpoints, among many others relevant gene sets. Importantly, Omomyc significantly reduced the expression of genes related to melanoma metastases. Finally, in order to validate Omomyc therapeutic impact in vivo, A375 and SkMel147 cells were s.c. implanted into nude mice and the effect of Omomyc expression on tumor progression was evaluated. Our results show that Omomyc expression significantly impairs the growth of both cell lines, increasing the survival of tumor-bearing mice. These results combined clearly show that Omomyc-mediated Myc inhibition is an effective means to impair melanoma progression, by directly targeting Myc, inhibiting cell cycle and decreasing melanoma aggressiveness.

Citation Format: Mariano F. Zacarias-Fluck, Génesis Martín, Daniel Massó-Vallés, Laia Foradada, Jonathan R. Whitfield, Marie-Eve Beaulieu, Laura Soucek. Myc inhibition by Omomyc impairs melanoma growth and progression through genome-wide gene expression reprogramming [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 3351.
Abstract 3358: FOXF1 defines the core-regulatory circuitry in gastrointestinal stromal tumor (GIST)
Authors: Ran Leili , Chen Yuedan , Wong Wai Pung E. , Li Dan , Cao Zhen , Shukla Shipra , Xie Yuanyuan , Zheng Deyou , Koche Richard P. , Antonescu Cristina R. , Chen Yu , Chi Ping
Published: August 2018

The cellular context that integrates upstream signaling and downstream nuclear response dictates the oncogenic behaviour and shapes treatment responses in distinct cancer types. Here, we uncover that in GIST, the forkhead family member, FOXF1, directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal (ICC) lineage-specification and GIST tumorigenesis. Further, FOXF1 co-localizes with ETV1 at enhancers and functions as a pioneer factor that regulates the ETV1-dependent GIST-lineage specific transcriptome through modulation of the local chromatin context, including chromatin accessibility, enhancer maintenance and ETV1 binding. Functionally, FOXF1 is required for human GIST cell growth in vitro and murine GIST tumor growth and maintenance in vivo. The simultaneous control of the upstream signaling and nuclear response sets up a unique regulatory paradigm and highlights the critical role of FOXF1 in enforcing the GIST cellular context for highly lineage-restricted clinical behaviour and treatment response.

Citation Format: Leili Ran, Yuedan Chen, Wai Pung E. Wong, Dan Li, Zhen Cao, Shipra Shukla, Yuanyuan Xie, Deyou Zheng, Richard P. Koche, Cristina R. Antonescu, Yu Chen, Ping Chi. FOXF1 defines the core-regulatory circuitry in gastrointestinal stromal tumor (GIST) [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 3358.
Abstract 3360: Origins of mutations in colorectal cancer
Authors: Gold Barry
Published: August 2018

The origins of most human cancers remain unclear. In selected cases, exposure to potent environmental mutagens or familial germ line mutations, which affect tumor suppressor genes or oncogenes, have been identified with specific cancers. Wnt signaling due to mutations in APC is compromised as an early event in 75% of human colorectal cancer (CRC), with truncating nonsense mutations (65%) dominating the mutation spectrum. Because 43% of the nonsense mutations occur at Arg CGA codons, the C→T mutation is attributed to hydrolytic deamination of 5-methylC. The enhanced incidence of colorectal cancer (CRC) associated with the Western diet has been epidemiologically linked to heterocyclic aromatic amines (HAA) produced by high temperature cooking of meat. Analysis of the mutation spectra in CRC indicated that the G→T transversions, which are produced by this class of mutagens were not enriched but were actually lower than what would be statistically anticipated based on random mutations. Moreover, the APC mutation patterns in the U.S.A. vs. China are indistinguishable despite differences in diet. However, dissection of the APC mutation pattern in tumors that arise in the different anatomical regions of the large intestine shows that the nonsense mutation pattern in APC differ in the different regions: there is a statistically significant increase in G→T transversions in the rectum vs. the other regions, albeit, the percent of G→T mutations still remains lower than predicted based on random mutagenesis. Therefore, it appears that HAA's may contribute to the incidence of rectal cancer.

Citation Format: Barry Gold. Origins of mutations in 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 3360.
Abstract 3362: Mice with a “deletor” phenotype allow high resolution detection of lymphoid leukemia tumor suppressor genes
Authors: Yin Mianmian , Baslan Timour , Freeland Amy , Pruitt Steven C. , Aplan Peter D.
Published: August 2018

Mice that are homozygous for a deficiency allele of the DNA replication factor minichromosome maintenance protein 2 (designated Mcm2def) are born viable and are healthy for the first 2 months of life. Beginning at three months, these mice develop precursor T-cell lymphoblastic leukemia/lymphoma (pre-T LBL). Copy number aberration (CNA) analysis showed that these pre-T LBL samples had 8-14 small (100-1000 kb) interstitial deletions per sample. Remarkably, all mice had two or more deletions that encompassed genes known to be relevant for human pre-T LBL, including Pten, Cdkn1a, Tcf3, and Tcf12.

Mice that express a NUP98-HOXD13 (NHD13) transgene develop a wide array of leukemias, most commonly myeloid, less commonly T-cell, and, rarely, B-lineage. To identify myeloid tumor suppressor genes, we crossed the NHD13 transgene onto the Mcm2def background. All Mcm2def:NHD13+ mice developed pre-T LBL by 3 months of age, reflecting the highly penetrant nature of the Mcm2def phenotype. None of the Mcm2def:NHD13+ mice developed myeloid leukemia. Surprisingly, approximately 30% of the Mcm2def:NHD13+ mice developed concurrent B-cell precursor acute lymphoblastic leukemia (BCP-ALL) and pre-T LBL. The thymus was typically infiltrated with pre-T LBL cells, whereas the bone marrow and spleen were infiltrated with BCP-ALL cells, characterized by clonal VDJ rearrangement and CD19 staining. Parenchymal organs (lung, kidney, liver) were variably infiltrated with pre-T LBL, BCP-ALL, or both. CNA analysis showed that the pre-T LBL were characterized by Pten, CDkn1a, Tcf3, and Tcf12 deletions, similar to the Mcm2def pre-T LBL, whereas the BCP-ALL were characterized by homozygous or heterozygous deletions of Pax5 and a 400 kb region encompassing Cebpb and Ptpn1. There were no shared deletions present in both BCP-ALL and pre-T LBL from the same mouse, indicating that the BCP-ALL and pre-T LBL arose independently, and not from a common precursor. The high frequency (5/7 samples) of acquired Pax5 deletions in the BCP-ALL samples serves to validate the model; whereas the finding of Cebpb/Ptpn1 deletions (5/7 samples) suggests an unanticipated role of either Cebpb or Ptpn1 in BCP-ALL.

Citation Format: Mianmian Yin, Timour Baslan, Amy Freeland, Steven C. Pruitt, Peter D. Aplan. Mice with a “deletor” phenotype allow high resolution detection of lymphoid leukemia tumor suppressor genes [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 3362.
Abstract 3370: Mad2l2 inhibits colorectal cancer growth by promoting ncoa3 ubiquitination and degradation
Authors: li yixin , qin ge , long qian , zhang changlin , shi dingbo , chen miao , deng wuguo
Published: August 2018

Nuclear receptor coactivator 3 (NCOA3) is a transcriptional coactivator that has elevated expression in multiple tumor types, including colorectal cancer (CRC). However, the molecular mechanisms that regulate the tumorigenic functions of NCOA3 in CRC remain largely unknown. In this study, we aimed to discover and identify the novel regulatory proteins of NCOA3 and explore their mechanisms of action. Immunoprecipitation coupled with mass spectrometry analysis was used to detect, identify and verify the proteins that interacted with NCOA3 in CRC cells. The biological functions of the candidate proteins and the underlying molecular mechanism were investigated in CRC cell lines and a mouse model in vitro and in vivo. The clinical significance of NCOA3 and its interaction partner protein in CRC patients was also studied. We discovered and identified mitotic arrest deficient 2-like protein 2 (MAD2L2, also known as MAD2B or REV7) as an interaction partner of NCOA3 by immunoprecipitation coupled with mass spectrometry analysis. Overexpression of MAD2L2 suppressed the cell proliferation, migration and clonogenecity in CRC cell lines and a mouse model by inducing the degradation of NCOA3. We also found that increased MAD2L2 expression in CRC cells activated p38, which was required for the phosphorylation of NCOA3 that led to its ubiquitination and degradation by the proteasome. Moreover, we demonstrated that MAD2L2 predicted favorable prognosis in CRC patients. These results indicate that MAD2L2 inhibits colorectal cancer growth by promoting NCOA3 ubiquitination and degradation. Our study have discovered a novel role of MAD2L2 in the regulation of NCOA3 degradation, and proposed that MAD2L2 serves as a potential tumor suppressor in CRC.

Citation Format: yixin li, ge qin, qian long, changlin zhang, dingbo shi, miao chen, wuguo deng. Mad2l2 inhibits colorectal cancer growth by promoting ncoa3 ubiquitination and degradation [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 3370.
Abstract 3372: Mutations of mismatch repair genes in Her2 overexpressed breast cancer
Authors: Baghdadi Mohammed A. , Sobahy Turki M. , Alardati Hosam A. , Zekri Jamal E.
Published: August 2018

The importance of Mismatch Repair (MMR) in therapeutic selection is an area of recent research. Minority of unselected breast tumors exhibit mutations indicative of deficient MMR. Here, we present our preliminary data investigating 7 MMR genes exclusively in Her2-overexpressed (Her2OE) breast cancer (BC). Twenty-five archival formalin-fixed paraffin-embedded samples from 25 Her2OE BC patients underwent targeted next generation sequencing for 7 MMR genes (MLH1, MLH3, MSH2, MSH6, PMS2, POLD1 and EPCAM). The analysis was performed through the Saudi Human Genome Project bioinformatics pipeline. Data filtration was performed to rank genetic variants based on their predicted pathogenicity. Methods of filtration included mutation effect, ClinVar findings, ExAC loss of function index (pLI) and collective proteomics index. Twenty-four out of 25 (96%) tumors contained significant mutations in one or more MMR genes. Three cases (12%) contained mutations in 3-4 MMR genes while 21 (84%) had 1-2 alteration(s) in these gene(s). Only one case showed no significant mutations in any of the studied MMR genes. MLH1, MLH3, MSH2, MSH6, PMS2, POLD1 and EPCAM were mutated in 6(24%), 1(4%), 5(20%), 18(72%), 2(8%), 6(24%) and 3(12%) respectively. In this preliminary report, mutations in MMR genes affect up to 96% of Her2OE BC tumors. Such result may impact on therapeutic choices. This result is to be confirmed in larger cohort.

Citation Format: Mohammed A. Baghdadi, Turki M. Sobahy, Hosam A. Alardati, Jamal E. Zekri. Mutations of mismatch repair genes in Her2 overexpressed 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 3372.
Abstract 3397: Clinical significance of 3q amplification in squamous cell carcinoma of lung
Authors: Lee Eunjung , Kim Chungyeul , Kim Han-Kyeom , Kim Baek-hui
Published: August 2018

Squamous cell carcinoma (SqCC) is major subtype of non-small cell lung cancer (NSCLC). One of the molecular characteristic of SqCC is amplification of distal portion of 3q. The aim of this study is to find out the clinical significance of the 3q amplification in SqCC of lung. Method : We extracted DNA from 90 cases of FFPE blocks of lung SqCC tissue. Ten genes (PIK3CA, SOX2, KLHL6, MCF2L2, LAMP3, MCCC1, ABCC5, ATP11B, TP63, YEATS2) included in 3q were selected and the amplification of each gene was analyzed by using NanoString nCounter analysis system (PhileKorea). The hierarchical clustering was performed with the resulting values. Results : We identified two groups in all 90 cases of SqCC by hierarchical clustering. One group with 3q amplification was 50 cases, and the other group without 3q amplification was 40 cases. There was no significant difference in sex, age, stage, smoking history, histologic grade and the results of immunohistochemical staining (p63, p40 and p53) between the two groups. It showed the tendency that the group with 3q amplification presented poor disease free survival (P=0.193) and overall survival (P=0.34) than the group without 3q amplification. Among the ten genes, PIK3CA and YEATS2 were significantly associated with survival. Each genes with amplification showed poor disease free survival (PIK3CA; P=0.036, YEATS2; P=0.025). Conclusion : The amplification of 3q can help sorting out two subsets of SqCC of lung whose clinical outcomes are likely to diverge. Among the genes included in 3q, PIK3CA and YEATS2 were associated with prognosis. These finding demonstrate the role of these genes in biologic behavior of tumor and suggest opportunities for targeted therapies.

Citation Format: Eunjung Lee, Chungyeul Kim, Han-Kyeom Kim, Baek-hui Kim. Clinical significance of 3q amplification in squamous cell carcinoma of lung [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 3397.
Abstract 3415: Cytogenetics of renal oncocytomas identify three distinct and mutually exclusive diagnostic classes of chromosome aberrations
Authors: Anderson Christopher B. , Lipsky Michael , Nandula Subhadra V. , Christopher Freeman E. , Thomas Matthews , Walsh Caitlin E. , Li Gen , Szabolcs Matthias , Mansukhani Mahesh M. , McKiernan James M. , Vundavalli Murty V.
Published: August 2018

Christopher B. Anderson1, Michael Lipsky1, Subhadra V. Nandula2,3, Christopher E. Freeman2, Thomas Matthews2, Catlin Walsh2, Gen Li1, Matthias Szabolcs2, Mahesh M. Mansukhani 2, James M. McKiernan1, Vundavalli V. Murty 2 1Departments of Urology, 2Pathology and Cell Biology, Columbia University Medical Center, New York, New York; 3Cancer Genetics Inc, Rutherford, New Jersey

The cytogenetic alterations in renal oncocytoma (RO) are poorly understood. We analyzed 130 consecutive RO for karyotypic alterations. Clonal chromosome abnormalities were identified in 63 (48.5%) cases, which could be categorized into 3 classes of mutually exclusive cytogenetic categories. Class 1 RO had diploid karyotypes with 11q13 rearrangement in balanced translocations with ten or more different chromosome partners in all 20 (31.7%) cases. We identified recurrent translocation partners at 5q35, 6p21, 9p24, 11p13-14 and 11q23, and confirmed that CCND1 gene rearrangement at 11q13 utilizing fluorescence in situ hybridization (FISH). Class 2 RO exhibited hypodiploid karyotypes with loss of chromosome 1 and concurrent losses of Y in males and X in females in 25 (39.7%) cases. The class 3 tumors comprising of 18 (30.2%) cases showed diverse types of abnormalities with the involvement of 2 or more chromosomes exclusive of abnormalities seen in Class 1 and 2 tumors. Furthermore, karyotypically uninformative cases were subjected to FISH analysis to identify class 1 and 2 abnormalities. In this group we found similar frequencies of CCND1 rearrangement, loss of 1 or Y as with karyotypically abnormal cases. We validated our results against 91 tumors from the Mittleman database. Correlation of clinical data with all the 3 classes of RO showed no clear evidence of overall patient survival. Our findings support the hypothesis that RO exhibit 3 principal cytogenetic categories, which may have different roles in initiation and/or progression. These cytogenetic markers provide a key tool in the diagnostic evaluation of RO.

Citation Format: Christopher B. Anderson, Michael Lipsky, Subhadra V. Nandula, Freeman E. Christopher, Matthews Thomas, Caitlin E. Walsh, Gen Li, Matthias Szabolcs, Mahesh M. Mansukhani, James M. McKiernan, Murty V. Vundavalli. Cytogenetics of renal oncocytomas identify three distinct and mutually exclusive diagnostic classes of chromosome aberrations [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 3415.
Abstract 3416: Customizable gene panels overcome challenges associated with targeted resequencing
Authors: Barry Andrew John , Patel Kruti M. , Emerman Amy B. , Adams Scott , Bowman Sarah , Mauceli Evan , Stewart Fiona , Dimalanta Eileen , Russello Salvatore , Elfe Charles , Davis Theodore , Hendrickson Cynthia
Published: August 2018

Efficient utilization of targeted gene panels for clinical research is challenged by the wide variation in gene constituents specific to a given study. While focused gene panels efficiently provide the necessary depth of coverage for low-frequency variant detection, the high costs and technical requirements associated with panel design present obstacles to delivering assays that are focused on the specific targets of interest. The NEBNext DirectTM technology utilizes a novel approach to selectively enrich nucleic acid targets ranging from a single gene to several hundred genes, without sacrificing specificity. The approach rapidly hybridizes both strands of genomic DNA with biotinylated probes prior to streptavidin bead capture, enzymatic removal of off-target sequences, and conversion of captured molecules into sequence-ready libraries. This results in an exceptionally uniform coverage profile for a given target. Unlike alternative hybridization methods, this 1-day workflow does not necessitate upfront library preparation, and instead converts the captured molecules into libraries compatible with Illumina sequencing. We have designed and optimized baits specific to the full exonic content of >800 genes associated with cancer as well as a variety of other disease areas. These are designed, balanced, and pooled on a per gene basis, and can be readily combined into customized panels, allowing rapid turnaround of specific custom gene subsets. Here, we present the ability to rapidly deploy custom gene panels across a variety of panel sizes and content, while maintaining high specificity, uniformity of coverage across target content, and sensitivity to detect nucleic acid variants from clinically relevant samples.

Citation Format: Andrew John Barry, Kruti M. Patel, Amy B. Emerman, Scott Adams, Sarah Bowman, Evan Mauceli, Fiona Stewart, Eileen Dimalanta, Salvatore Russello, Charles Elfe, Theodore Davis, Cynthia Hendrickson. Customizable gene panels overcome challenges associated with targeted resequencing [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 3416.
Abstract 3424: Genomic alterations in clonal hematopoiesis
Authors: Huang Kuan-Lin , Xie Mingchao , Wu Yige , Jayasinghe Reyka , Varghese Rajees , Mashl R. Jay , Cao Song , Wyczalkowski Matthew , Liang Wen-wei , Wendel Michael C. , Fields Ryan , McLellan Michael D. , Link Daniel C. , Chen Feng , Ding Li
Published: August 2018

Cancer development is an incremental process. Mutations that initiate clonal hematopoiesis often arise in individuals many years before disease symptoms are apparent. We discovered blood somatic mutations in 8,612 germline blood samples in The Cancer Genome Atlas, drawing fundamental distinctions between these events and germline variants. In a preliminary scan of 5,949 samples, 13,345 blood-specific mutations were identified, preferentially distributed across 26 genes, including ones frequently mutated in hematologic malignancies (e.g., DNMT3A, ASXL1, TET2, JAK2, IDH2, SF3B1, MLL3, and KDM6A) and genes rarely mutated in primary hematologic tumors, including EGFR, PIK3CA, NOTCH2, and PPM1D. Further, we utilized both exome sequencing and SNP array data to conduct the first large-scale survey of blood somatic copy number variation, discovering potentially oncogenic events such as JAK2 amplification. Finally, elderly individuals and smokers have increased likelihoods of undergoing clonal expansion. Our analysis of genomic alterations reveals the origins of hematologic malignancies and can facilitate advancement in early detection and prevention.

Citation Format: Kuan-Lin Huang, Mingchao Xie, Yige Wu, Reyka Jayasinghe, Rajees Varghese, R. Jay Mashl, Song Cao, Matthew Wyczalkowski, Wen-wei Liang, Michael C. Wendel, Ryan Fields, Michael D. McLellan, Daniel C. Link, Feng Chen, Li Ding. Genomic alterations in clonal hematopoiesis [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 3424.
Abstract 3429: Genome and epigenome profiling of high stage neuroblastoma
Authors: Ohira-Ichikawa Miki , Sugino Ryuichi P. , Takenobu Hisanori , Li Zhenghao , Haruta Masayuki , Nagae Genta , Renard-Guillet Claire , Nakagawara Akira , Aburatani Hiroyuki , Kamijo Takehiko
Published: August 2018

Neuroblastoma (NB) is the most common pediatric extracranial solid tumor with a wide range of clinical phenotypes from spontaneous regression to highly resistant to chemotherapy. Loss of 1p and 11q and genomic alterations of MYCN, ALK, ATRX and TERT have been known to be involved in oncogenesis and unfavorable phenotype of NB, however, only small numbers of recurrent driver mutations have been observed by NGS-based studies. This implies epigenetic alterations also influence the pathogenesis of NB. In this study, to elucidate the molecular basis of malignant subtype of NB, we conducted methylome analysis for 145 primary NBs (stage 1:3; stage 2:8; stage 3:16; stage 4:105; stage 4s:13) by Infinium Human Methylation 450 BeadChip. By hierarchical clustering of methylome signature, the tumors were classified into four clusters. Cluster-1 shows good similarity with nerve cell controls and, together with cluster-3 (very young, early tumor stage), exhibited favorable prognosis. Unfavorable cluster-2 and -4 exhibited hyper-methylation phenotypes in CpG islands (CGI) and the former was enriched by MYCN-amplified tumors. These two clusters (n=73) showed strong correlation with poor patient prognosis (p=0.0055). 1400 hyper-methylated CGI locus which corresponded 550 genes were picked up and annotated by GO database. The term “cell adhesion”, “cell-cell signaling”, “transmission of nerve impulse” and “cellular component morphogenesis” were enriched. No 1p or 11q genes were enriched in hyper-methylated genes but several genes such as ANKK1 on chr11q whose lower expression levels are strongly correlated with unfavorable prognosis of the patient (p=4.0e-07) were included. Further analyses by comparing the influences in gene expression profiles by methylation and by histone modification of PRC2 are ongoing. Our recent data indicated that NTRK1, whose higher expression is a strong favorable marker, is transcriptionally downregulated in MYCN-amplified tumors by both methylation and H3K27me3 on distinct promoter regions (Li Z et al). Since application of epigenetic drugs are one of the possible therapeutic choices for NB, transcriptional regulation by the epigenetic alterations are needed to be intensively studied.

Citation Format: Miki Ohira-Ichikawa, Ryuichi P. Sugino, Hisanori Takenobu, Zhenghao Li, Masayuki Haruta, Genta Nagae, Claire Renard-Guillet, Akira Nakagawara, Hiroyuki Aburatani, Takehiko Kamijo. Genome and epigenome profiling of high stage neuroblastoma [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 3429.
Abstract 3435: Differential genomics and transcriptomics between tyrosine kinase inhibitor sensitive versus resistant BCR-ABL dependent chronic myeloid leukemia
Authors: Singh Neetu , Tripathi Anil Kumar , Sahu Dinesh Kumar , Mishra Archana , Linan Margaret , Argente Bianca , Varkey Julia , Chowdhry Rebecca , Agarwal Avinash , Yoo Chris , Kant Ravi , Bhatt Madan Lal
Published: August 2018

Previously it has been stated that BCR-ABL1 fusion protein is sufficient to induce CML, but additional genomic changes are required for disease progression. Based on this notion, we profiled control and Tyrosine Kinase Inhibitors (TKI)-treated-CML-samples in different-phases supported by copies of BCR-ABL-transcripts. Molecular-profiling was done through Molecular Inversion Probe (MIP) based array, Human Transcriptomics Array2.0, and Axiom Biobank genotyping-arrays. Transcriptionally, clusters of control, TKI-resistant and -sensitive cases were identified which showed correlation with BCR-ABL transcript-levels with the involvement of 228 pathways. On a comparison between TKI-sensitive versus resistant cases, at the exonic level Cassette Exon splicing event was observed in LAPTM4B (0.46), PIEZO2 (0.32), ANGPT1 (0.29), CFH (0.28), HLTF (0.28), SPTLC3 (0.26); Alternative 3' Acceptor Site splicing (0.22); and Junctional splicing in CD109 and ZNF711. These splicing events led to up-regulation of these transcripts. On further processing through Reactome Pathway, we identified over-expression of Hemostasis pathway in CML-resistant cases with specific involvement of Tie2 and Basigin signalling pathway. Based on CNV profiling, we identified low CNVs in CP-new and CP-UT-TKIs-sensitive cases with undetectable or <10% BCR-ABL copies. While, high CNVs (previously reported gain of 9q34) was observed in BCR-ABL-independent and -dependent TKIs-non-sensitive-CP-UT/AP-UT/B-UT and B-new samples. Further, genotyping CML-CP-UT cases with BCR-ABL 10 to 77.02% copies, we identified and validated rsIDs, rsID239798 and rsID9475077 in linkage with FAM83B which may act as potential therapeutic resistance candidate. BCR-ABL1, additional genetic events, over-expression of Tie-2 and Basigin signalling pathway and rsIDs in linkage with FAM83B in TKI resistant cases can be used for developing a signature profile which may help in monitoring therapy.

Citation Format: Neetu Singh, Anil Kumar Tripathi, Dinesh Kumar Sahu, Archana Mishra, Margaret Linan, Bianca Argente, Julia Varkey, Rebecca Chowdhry, Avinash Agarwal, Chris Yoo, Ravi Kant, Madan Lal Bhatt. Differential genomics and transcriptomics between tyrosine kinase inhibitor sensitive versus resistant BCR-ABL dependent chronic myeloid leukemia [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 3435.
Abstract 344: A high-throughput functional screen reveals synthetic lethal interactions associated with replication stress in HORMAD1-expressing triple-negative breast cancers
Authors: Tarantino Dalia , Walker Callum , Weekes Daniel , Pemberton Helen , Frankum Jessica , Brough Rachel , Lord Christopher J. , Grigoriadis Anita , Tutt Andrew
Published: August 2018

HORMAD1, expression of which is usually restricted to germline cells, is expressed in ~60% of triple-negative breast cancers (TNBCs) where it is associated with higher levels of allelic imbalance. In experimental systems, HORMAD1 also drives Homologous Recombination (HR) deficiency, PARP inhibitor and cisplatin sensitivity. To provide further insights into the role of HORMAD1 in TNBC, we generated a doxycycline-inducible HORMAD1 expression system in the copy number stable, HORMAD1-negative, TNBC cell line SUM159. Clonal, HORMAD1-positive, populations were established which displayed increased levels of genomic instability and reduced levels of homologous recombination. To identify synthetic lethal therapeutic targets associated with HORMAD1 expression in TNBC, we performed an RNAi library screen, in which the viability of HORMAD1-expressing SUM159 clonal cell populations was assessed following the targeted depletion of 1743 genes. Candidate synthetic lethal (SL) genes were validated in a secondary screen using 3 additional HORMAD1-expressing SUM159 clones. The primary siRNA screen identified 63 genes which were SL with elevated HORMAD1 expression, including XRCC1, TDP1, Pol η, BRIP1 and ATR - genes with a known function in mitigating replication stress. DNA polymerase η (POLH) is a Y-family DNA polymerase involved in translesion synthesis (TLS), a DNA damage tolerance pathway employed by proliferating cells to bypass replication fork stalling DNA lesions and to prevent replication fork collapse. We hypothesised that HORMAD1 expression leads to Pol η localisation to replication factories, to mediate lesion bypass. Consistent with this, we found an enrichment in Pol η and monoubiquitylated-PCNA in the chromatin fraction of HORMAD1-expressing SUM159 cells, suggesting that Pol η and TLS might buffer the effect of elevated HORMAD1 expression in TNBC. Our data suggest that HORMAD1 expression in mitotic cells leads to a dependency on pathways implicated in preventing or resolving replication stress, such as TLS, and suggests that vulnerabilities associated with specific DNA repair processes could be used to target HORMAD1-positive TNBCs.

Citation Format: Dalia Tarantino, Callum Walker, Daniel Weekes, Helen Pemberton, Jessica Frankum, Rachel Brough, Christopher J. Lord, Anita Grigoriadis, Andrew Tutt. A high-throughput functional screen reveals synthetic lethal interactions associated with replication stress in HORMAD1-expressing triple-negative breast cancers [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 344.
Abstract 3444: EGFR-dependent matriptase activation in ErbB2-amplified breast cancer
Authors: Gaymon Darius
Published: August 2018

Of the nearly 250,000 new breast cancer cases expected annually, nearly 25% will have ErbB2 (HER2) gene amplification, which is associated with increased growth signaling, more aggressive disease, and poor patient prognosis. Matriptase is a type II transmembrane serine protease that plays a role in normal epithelial cell biology. The expression and activation of matriptase are tightly regulated in normal cells partly through co-expression with endogenous inhibitor, HAI-1, which rapidly inhibits the protease, once activated, by the formation of a high affinity complex. Matriptase has oncogenic potential when its regulation is deranged and it activates downstream substrates known to play a role in tumor progression such as pro-HGF. ErbB2 activity can regulate matriptase activity in prostate cancer and so we set out to elucidate the relationship between ErbB2 and matriptase in ErbB2-amplified breast cancer. SKBR3, AU565, and ErbB2 transfected MCF7 cells (MB7) were used to explore the relationship between ErbB2 levels and matriptase activation as they express higher levels of ErbB2 compared with MCF7 cells. Under standard growth conditions, high level of ErbB2 activation was associated with extensive matriptase activation. Activation of ErbB2 by stimulating EGFR with EGF resulted in increased matriptase activation. Inhibition of ErbB2 activity by serum deprivation or Lapatinib (a dual ErbB2 and EGFR kinase inhibitor) treatment resulted in decreased matriptase activation. Treatment with Lapatinib or the EGFR-specific inhibitor, Gefitinib, blocked matriptase activation whereas the ErbB2 inhibitor, AG825, has no effect. Using inhibitors of downstream signaling pathways, EGFR-induced matriptase activation was shown to be mediated by PI3K signaling. Further elucidation of the pathway is ongoing. In summary, our data suggest that EGFR signaling in this context modulates matriptase activation, which may also contribute to breast cancer progression.

Citation Format: Darius Gaymon. EGFR-dependent matriptase activation in ErbB2-amplified 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 3444.
Abstract 3449: AGL loss promotes anchorage independent growth of non-small cell lung cancer by activating FAK
Authors: Guin Sunny , Richmond Craig
Published: August 2018

Loss of glycogen debranching enzyme (AGL) has been shown to promote growth of bladder and non-small cell lung cancer. AGL loss predominantly assists anchorage independent growth of non-small cell lung cancer (NSCLC) cells. However the mechanism driving this anchorage independent growth with AGL loss is not well understood. To identify the driver pathways which contributions to increased anchorage independent growth with AGL loss, we carried out a phospho-kinase screen in A549 NSCLC cells with and without AGL expression. The kinase screen identified an increase in phospho-FAK (Tyr 576/577) levels with loss of AGL. The result of the screen was validated using separate independent Western blot experiments in A549 and other NSCLC cell lines which showed an increase in FAK activation at Tyr 576/577 with loss of AGL. We next treated NSCLC cells with and without AGL with FAK specific inhibitor (FAK inhibitor 14). Treatment with FAK inhibitor 14 had a greater cytotoxic effect (p<0.05) on NSCLC cells that have AGL loss. These data suggest that activation of FAK is a major driver of anchorage independent growth in NSCLC cells that have lost AGL expression and inhibition of FAK activity can serve as a therapeutic avenue for NSCLC patients with low tumor AGL expression.

Citation Format: Sunny Guin, Craig Richmond. AGL loss promotes anchorage independent growth of non-small cell lung cancer by activating FAK [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 3449.
Abstract 345: Characterizing and therapeutically targeting G-quadruplex DNA in ATRX-mutant glioma
Authors: Wang Yuxiang , Danussi Carla , Kannan Kasthuri , Chan Timothy A. , Huse Jason T.
Published: August 2018

Inactivating ATRX mutations are defining molecular alterations in several cancer variants, including large subsets of malignant glioma. ATRX encodes a chromatin binding protein widely implicated in epigenetic and transcriptional regulation. However, ATRX is also thought to guard against genomic instability, in part by mitigating the formation of deleterious G-quadruplex (G4) DNA secondary structures. G4s have been shown to stall DNA replication leading to single-strand breaks and, potentially, DNA damage and genomic instability. To study this biology in a glioma-relevant context, we generated an isogenic astrocyte model featuring intact or deficient ATRX. While ATRX deficiency had no effect on baseline proliferation, cell cycle progression, and apoptosis, it led to markedly increased G4 formation, DNA damage, and replication stress signaling. These effects were reversed by ATRX re-expression. Moreover, ATRX-deficient astrocytes acquired copy number alterations over time, unlike ATRX-intact counterparts. Given these findings, we hypothesized that therapeutically targeting G4s might serve to exploit the inherent genomic vulnerabilities of ATRX-deficient cancer. Remarkably, treatment with a G4 stabilizing compound (CX3543) selectively inhibited growth and colony formation in ATRX-deficient astrocytes at nanomolar concentrations, and synergistically potentiated the effects of ionizing radiation and hydroxyurea. Finally, CX3543 significantly inhibited the growth of patient-derived, ATRX-deficient glioma xenografts in mice, with only minimal effects on ATRX-intact glioma xenografts. These results confirm and characterize a novel functionality for ATRX in the mitigation of genomic instability and point towards a viable strategy for therapeutically targeting ATRX deficiency in cancer.

Citation Format: Yuxiang Wang, Carla Danussi, Kasthuri Kannan, Timothy A. Chan, Jason T. Huse. Characterizing and therapeutically targeting G-quadruplex DNA in ATRX-mutant glioma [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 345.
Abstract 3454: HIV-1 envelope protein gp120 promotes glioma tumor growth through the Akt and MAP kinase pathways
Authors: Valentin-Guillama Gabriel , Kucheryavykh Yuriy , Kucheryavykh Lilia
Published: August 2018

The median survival of glioblastoma (GBM) patients with HIV is significantly shorter compared to HIV-negative GBM patients, despite the fact that they receive the same treatments. This indicates that HIV infection is associated with more aggressive tumor behavior. Earlier we shown that gp120, a glycoprotein found in the HIV shell, stimulates up-regulation of glycolysis in glioma cells. The purpose of this study was to evaluate the underlying signaling mechanisms of gp120 dependent up-regulation of glycolysis in glioma cells.

Using antibody array and western blot we have identified that U87 glioma cells treated with gp120 (200 ng/ml) for 5 consequent days showed increased activation of MAP kinase and Akt/mTOR pathways. Increase of pAkt(pS473), pGSK3b(pS9), pMKK3(S189), pmTOR(S2448), p38(T180/Y182), pJNK(T183) has been identified. This data coincides with previously obtained results showing that glioma cells treated with gp120 exhibit higher proliferation rates and increased cell survival compared to un-treated glioma cells.

In summary, we conclude that gp120 triggers activation of regulatory kinases Akt and MAPK involved in cell growth, cell proliferation, cell survival, protein synthesis, transcription, glycolysis, and cell migration.

Citation Format: Gabriel Valentin-Guillama, Yuriy Kucheryavykh, Lilia Kucheryavykh. HIV-1 envelope protein gp120 promotes glioma tumor growth through the Akt and MAP kinase pathways [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 3454.
Abstract 3456: Molecular mechanisms of RSK2-ELK3 signaling axis in neoplastic cell transformation
Authors: Cho Seon-Yeon , Lee Cheol-Jung , Yoo Sun-Mi , Kim Seung-Min , Park Juhee , Cho Yong-Yeon
Published: August 2018

Constitutive active Ras mutation (RasG12V) plays a key role in cell proliferation and transformation in many solid human cancers. RSK2, a member of p90RSK superfamily, controlled by ERKs is an intermediate signaling molecule transducing Ras activation signal to downstream substrates including transcription factors, epigenetic factors and some kinases. Since RSK2 shows wide range of substrate spectrum, identification of RSK2's novel substrates is important to understand the role of RSK2 in cancer. We found that ELKs including ELK1, ELK3 and ELK4 are novel interaction partners of RSK2 by mammalian two-hybrid assay. In vitro kinase assay and immunoprecipitation assay indicated that ELK3 is a major binding partner of RSK2. Luciferase reporter assay demonstrated that ELK3 transactivation activity was increased by RSK2, resulted in the increase of c-fos promoter activity. Importantly, constitutive active (CA)-RasG12V-mediated foci formation in NIH3T3 cells were more increased by ectopic co-expression of CA-RasG12V and RSK2. Additionally, signaling blockage of the CA-RasG12V/ELK3 by RSK2 knockdown suppressed foci formation. These results demonstrated that RSK2-ELK3 signaling axis plays an important role in RasG12V-mediated neoplastic cell transformation.

Key words : MAPK, RSK2, ELKs, cell proliferation, cell transformation

Citation Format: Seon-Yeon Cho, Cheol-Jung Lee, Sun-Mi Yoo, Seung-Min Kim, Juhee Park, Yong-Yeon Cho. Molecular mechanisms of RSK2-ELK3 signaling axis in neoplastic cell transformation [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 3456.