bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2997: Epigenomic signatures of acquired platinum resistance in high grade serous ovarian cancer
Authors: Fang Fang , Cardenas Horacio , Jiang Guanglong , Perkins Susan M. , Zhang Chi , Keer Harold , Liu Yunlong , Matei Daniela , Nephew Kenneth
Published: August 2018

Epithelial ovarian cancer (OC) is the most lethal gynecologic malignancy. The majority of advanced stage patients develop uniformly fatal resistance to standard platinum-based treatments. Epigenetic changes, particularly DNA methylation aberrations have been implicated in acquired resistance to platinum in OC. The goal of the current study was to identify methylation changes associated with the development of acquired resistance to platinum-based chemotherapy. We hypothesized that OC tumors harboring an aberrant DNA methylome could be reversed by DNMTi and re-sensitized to platinum treatment. To achieve our objective, we generated and compared tumor DNA methylation profiles from patients with recurrent platinum-resistant OC treated on a clinical trial with a DNA methyl transferase inhibitor, guadecitabine, before (n=65) and after (n=19) treatment (NCT01696032), and patients with primary (platinum-naïve) OC (n=20). Human ovarian surface epithelial cells (HOSE) were used as controls (n=5). We examined methylation levels across the genome using the Infinium Human Methylation 450 Bead Chip (Illumina). By comparing the methylome of platinum naive and platinum resistant ovarian tumors, normalized to HOSE, we identified 444 CpG island-containing gene promoters that became hypermethylated in resistant tumors. Of those, 45 gene promoters were hypermethylated at an FDR<0.05 and 19 genes at an FDR<0.05 and Δβ>0.1. Among those significantly hypermethylated genes, acquired promoter CpG island methylation of Ras Association Domain Family 1A (RASSF1A; a tumor suppressor gene in multiple cancer types) was observed. Of the 444 hypermethylated promoters in tumor resistant samples, 93 CpG islands became hypomethylated after guadecitabine treatment, suggesting that these promoters may be associated with reversal of resistance. Of those were the IFNA8 promoter, a gene known to be associated with anti-tumor effects in ovarian and other solid malignancies, and DEFB124, which is involved in the innate immune response. Pathways associated with immune reactivation were highly enriched by guadecitabine treatment, including IL-12 signaling and production of macrophages and MAPK and apoptosis signaling. Together, these results support that aberrant DNA methylation affecting gene networks associate with immune response plays a role in platinum resistant development and could be a therapeutic target.

Citation Format: Fang Fang, Horacio Cardenas, Guanglong Jiang, Susan M. Perkins, Chi Zhang, Harold Keer, Yunlong Liu, Daniela Matei, Kenneth Nephew. Epigenomic signatures of acquired platinum resistance in high grade serous ovarian 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 2997.
Abstract 3003: Loss of heterozygosity of essential genes represents a novel class of cancer vulnerabilities
Authors: Nichols Caitlin A. , Paolella Brenton R. , Gibson William J. , Brown Meredith S. , Urbanski Laura M. , Kosmicki Jack A. , Busanovich John P. , Berger Ashton C. , Gao Galen F. , Cherniack Andrew D. , Beroukhim Rameen
Published: August 2018

Despite progress in precision cancer drug discovery, few highly selective therapies exist in the clinic, creating the need for additional therapeutic targets. We have shown that copy number alterations (CNAs) in essential genes represent novel non-driver gene vulnerabilities in cancer. Here we interrogate loss of heterozygosity (LOH) of single nucleotide polymorphisms (SNPs) located in essential genes as a novel class of candidate therapeutic targets. We hypothesized that monoallelic inactivation of the single allele retained in tumors can selectively kill cancer cells, while somatic cells, which retain both alleles, will tolerate allele-specific knockout. We identified a list of over 1000 common missense SNPs in at least 1500 essential genes that undergo LOH in cancer and performed proof-of-concept allele-specific gene inactivation in two essential genes (PRIM1 and EXOSC8) using CRISPR-Cas9. We assessed the fidelity of allele-specific gene disruption and its cellular effects on gene expression, cell growth, and cell death in LOH and non-LOH genetic contexts. We determined that allele-specific knockout of PRIM1 and EXOSC8 selectively targets cells harboring only the single targeted allele of that gene. In cells retaining only the sensitive allele, we observed decreased target gene expression and cell viability that did not occur in cells retaining the resistant allele. We conclude that allele-selective inactivation of essential genes in regions of LOH (such as PRIM1 and EXOSC8) represents a novel candidate therapeutic strategy in cancer. The corresponding class of novel non-driver cancer vulnerabilities may provide a rich source of targets for future precision therapeutic development using gene editing, RNAi, or small-molecule approaches.

Citation Format: Caitlin A. Nichols, Brenton R. Paolella, William J. Gibson, Meredith S. Brown, Laura M. Urbanski, Jack A. Kosmicki, John P. Busanovich, Ashton C. Berger, Galen F. Gao, Andrew D. Cherniack, Rameen Beroukhim. Loss of heterozygosity of essential genes represents a novel class of cancer vulnerabilities [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 3003.
Abstract 3044: Label-free detection and identification of cancer-associated vesicles in human breast cancer
Authors: You Sixian , Sun Yi , Tu Haohua , Barkalifa Ronit , Chaney Eric J. , Marjanovic Marina , Higham Anna M. , Luckey Natasha N. , Cradock Kimberly A. , Liu Z. George , Boppart Stephen A.
Published: August 2018

Detection and identification of cancer-associated vesicles in their native tissue environment is essential to understand vesicle-mediated communication in cancer progression and potentially facilitate the treatment and management of cancer. Here we develop a label-free optical imaging method that can reliably detect cancer-associated vesicles in vitro, in vivo and in untreated human tissue ex vivo. Preliminary analysis conducted on fresh human breast tissue obtained from healthy and cancer subjects showed that a significant portion of vesicles from the cancer subjects have unique optical signatures in comparison with those from healthy subjects. Additionally, the spatial distribution of these vesicles with unique optical signatures in the tumor micro- and macro-environment appeared correlated with the staging of human breast cancer. These results suggest the potential capability of this methodology to identify and characterize the tumor associated vesicles in the authentic tumor microenvironment, which could open new windows in the explorations of their diagnostic values and physiological roles in cancer progression.

Citation Format: Sixian You, Yi Sun, Haohua Tu, Ronit Barkalifa, Eric J. Chaney, Marina Marjanovic, Anna M. Higham, Natasha N. Luckey, Kimberly A. Cradock, Z. George Liu, Stephen A. Boppart. Label-free detection and identification of cancer-associated vesicles in human 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 3044.
Abstract 3069: DSP-0692, a novel and selective stearoyl-CoA desaturase (SCD) inhibitor targeting cancer stem cells
Authors: Sugaru Eiji , Furuta Yudai , Fukunaga Yuichi , Umehara Hiroki , Otsubo Tsuguteru , Watanabe Manabu , Hasegawa Futoshi , Tojo Shingo , Hashizume Miki , Ban Hitoshi
Published: August 2018

In recent years evidence has accumulated in support of the cancer stem cells (CSCs) model in cancer chemotherapy resistance, highlighting the urgency and necessity of identifying CSC-specific targets for new cancer therapeutics.

SCD, a key enzyme for lipid metabolism, is overexpressed in various types of cancer and plays an important role in cancer cell proliferation. In particular, recent studies have implicated SCD involved also in the maintenance of CSCs.

Here, the identification and the functional characterization of DSP-0692, a novel and selective SCD inhibitor, is reported, using various pharmacological approaches to address the mechanism of SCD inhibition in cancer cells and its efficacy in preclinical tumor models. In these preclinical models, DSP-0692 inhibited human SCD activity with low nanomolar IC50 values. SCD expression was induced in tumor cells cultured in sphere conditions, which were resistant to conventional agents within therapeutic concentration. DSP-0692 showed strong growth inhibition when tumor cells were cultured in sphere conditions, but had little impact on cells cultured under normal two-dimensional conditions. In addition, DSP-0692 inhibited the CSC-related signaling pathway and decreased CSC markers expression in tumor cells as well as in tumor tissues. Treatment of DSP-0692 as single agent suppressed tumor growth in multiple models. Furthermore, this efficacy was enhanced in combination with conventional chemotherapies in those tumor models. Of note, SCD protein expression in tumor tissues was useful as a predictive marker for the susceptibility to DSP-0692 treatment.

Taken together, these data suggest that inhibition of fatty acid desaturation by DSP-0692 could be a new therapeutic strategy in SCD-positive cancer, with potential to overcome resistance to standard chemotherapies.

Citation Format: Eiji Sugaru, Yudai Furuta, Yuichi Fukunaga, Hiroki Umehara, Tsuguteru Otsubo, Manabu Watanabe, Futoshi Hasegawa, Shingo Tojo, Miki Hashizume, Hitoshi Ban. DSP-0692, a novel and selective stearoyl-CoA desaturase (SCD) inhibitor targeting cancer stem 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 3069.
Abstract 3070: Cancer stem cells in field cancerization of oral squamous cell carcinoma
Authors: Mohanta Simple , DR Ravindra , Kekatpure Vikram , Hedne Naveen , Pillai Vijay , Chauhan Shubhra , BS Naveen , Ramakrishnan Athira , Jacob Bichu , Surendra Vishak , Mohanty Leeky , Muralidharan Anjana , Suresh Amritha , Kuriakose Moni Abraham
Published: August 2018

Introduction: Field cancerization, the occurrence of transformed cells in the area adjacent to the tumor, has been attributed to the probable reasons of local recurrence of oral squamous cell carcinoma. Cancer stem cells (CSCs) have properties of tumor initiation, migration, and metastasis. The objective of the study was to evaluate their role in field cancerization.

Experimental Procedure: A panel of CSCs and its related markers was established from literature and validated in i) samples from surgical margins, ii) samples from 1 cm and 2 cm distance from margin around the tumor and in additional sides. First-phase validation was done in retrospective surgical margins of tumor (N=23) by qPCR and immunohistochemistry. The best marker subset from qPCR to predict recurrence was identified by ROC curve and logistic regression analysis and validated by immunohistochemistry. The final validation is being carried out in prospective samples from tumor-adjacent normal area as mentioned above. The marker profiles were correlated with the histology of the samples and the clinical outcome of the patients on follow-up.

Summary of Data: Out of 18 markers selected from literature CD44, CD147, SOX2, Snail, ATR, CyclinD1, MMP9 were selected from gene expression of first-phase validation. Among these SOX2, ATR, Cyclin D1, CD44 and CD147 were selected from IHC of first phase for second-phase validation in prospective samples (n=10) collected from 27 patients, which were clinically normal with varied grades of dysplasia; these samples were evaluated by the selected markers from the first set of validation. The correlation of markers expression with disease outcome of patients and with other clinical parameters is currently ongoing.

Conclusion: Our results suggest that CSCs have role in field cancerization and might be predictive of tumor recurrence/reinitiation and/or development of second primary tumor.

Citation Format: Simple Mohanta, Ravindra DR, Vikram Kekatpure, Naveen Hedne, Vijay Pillai, Shubhra Chauhan, Naveen BS, Athira Ramakrishnan, Bichu Jacob, Vishak Surendra, Leeky Mohanty, Anjana Muralidharan, Amritha Suresh, Moni Abraham Kuriakose. Cancer stem cells in field cancerization of oral squamous cell carcinoma [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 3070.
Abstract 3073: Low copy number of mtDNA is associated with cancer stemness in ESCC
Authors: Hara Takeo , Masuike Yasunori , Tanaka Koji , Makino Tomoki , Yamasaki Makoto , Miyazaki Yasuhiro , Takahashi Tsuyoshi , Kurokawa Yukinori , Eguchi Hidetoshi , Nakajima Kiyokazu , Mori Masaki , Doki Yuichiro
Published: August 2018

Alterations of mitochondrial DNA (mtDNA) copy numbers in various human cancers have been studied. However, those of esophageal squamous cell carcinoma (ESCC) is still unclear. In the present study, we investigated the correlation of mtDNA copy number with clinicopathologic features, prognosis and malignant potential of ESCC. MtDNA copy numbers of resected specimen from 80 patients treated with radical esophagectomy were measured by quantitative real-time PCR analyses. Human ESCC cells, TE8 and TE11, were cultured and depletion of mtDNA content was induced by knockdown of mitochondrial transcription factor A expression or treatment with ethidium bromide. The mRNA expression, proliferation, invasion and cell cycle were investigated. The results showed that mtDNA copy number of cancerous parts was 56.0 (37.4-234.5) % of non-cancerous parts and significantly lower (p<0.05). Low mtDNA copy number in resected cancerous tissues was significantly correlated with pathological depth of tumor invasion and pathological stage (p<0.05). The patients with lower mtDNA copy number had significantly poorer 5-year overall and recurrence-free survival than higher group (p<0.01). MtDNA depleted TE8 and TE11 cells proliferated more slowly than control cells under normoxia, but proliferated at almost the same rate even under hypoxic condition. In mtDNA depleted cells, the mRNA expression of cd44 were increased, and the sphere formation abilities were enhanced and the cell cycle arrest at G0/G1 phase was induced. In conclusion, low copy number of mtDNA is associated with cancer stemness in ESCC. MtDNA copy number may be a novel therapeutic target for esophageal squamous cell carcinoma.

Citation Format: Takeo Hara, Yasunori Masuike, Koji Tanaka, Tomoki Makino, Makoto Yamasaki, Yasuhiro Miyazaki, Tsuyoshi Takahashi, Yukinori Kurokawa, Hidetoshi Eguchi, Kiyokazu Nakajima, Masaki Mori, Yuichiro Doki. Low copy number of mtDNA is associated with cancer stemness in ESCC [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 3073.
Abstract 3074: CD95/Fas increases type I interferon expression through NF-κB activation
Authors: Syed Abdul Qadir , Peter Marcus
Published: August 2018

CD95/Fas, an apoptosis-inducing death receptor, has also been shown to be required for the proliferation and survival of cancer cells. Chronic stimulation through CD95 enhanced formation of cancer stem cell enriched spheres and it increased expression of cancer stem cell markers and a set of genes consistent with a Type I Interferon (IFN) signature. We reported that CD95 stimulation induces upregulation of Type I IFNs that bind to both Type I receptors IFNAR1 and IFNAR2, resulting in activation of JAK kinases, activation of STAT1, and induction of a number of STAT1-regulated genes. However, the mechanism through which CD95 induces Type I IFNs and STAT1 activation is unknown. In this study we have investigated the mechanism of CD95 stimulation of Type I IFN production in the context of breast cancer. We show that knockout of CD95, FADD or Caspase-8 in MCF7 cells using the CRIPSR/Cas9 gene editing system resulted in a loss of the ability of CD95 to increase IFNα, IFNβ, STAT1, STAT2 expression and the phosphorylation of STAT1 and STAT3. The caspase-8 selective inhibitor zIETD-fmk blocked phosphorylation of STAT1 and STAT3 and blocked Type I IFN expression following CD95 stimulation. This identifies caspase-8 as a critical mediator of the Type I IFN-inducing activity of CD95. On other hand, we also showed that CD95 stimulation induced an antiviral program through RIG-I signaling, which is known to induce NF-κB and IFN signaling. RIG-1, MDA5, IRF7 expression and phosphorylation of IRF3 were increased with prolonged CD95 stimulation. Knocking down IRF3 using a siIRF3 smart pool partially reduced the phosphorylation of STAT1 and STAT3 in response to CD95 stimulation. Finally, we show that NF-κB activation is a key regulator of CD95-mediated Type I IFN expression. A NF-κB inhibitor completely blocked STAT1, STAT2 expression and phosphorylation of STAT1 and STAT3 following CD95 stimulation. Knocking out CD95, FADD or Caspase-8 or knocking down IRF3 also reduced NF-κB activation in response to CD95 stimulation. We conclude that CD95 stimulation induces Type I IFN expression through activation of caspase-8 and NF-κB and identify RIG-1 as a possible mediator of NF-κB activation during CD95 stimulation.

Citation Format: Abdul Qadir Syed, Marcus Peter. CD95/Fas increases type I interferon expression through NF-κB activation [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 3074.
Abstract 3080: Chronic exposure to arsenic induces malignant transformation in human kidney epithelial cells
Authors: Chang Yu-Wei , Singh Kamaleshwar
Published: August 2018

Arsenic contamination is a significant environmental and public health issue worldwide including the United States. Accumulating evidence suggests that kidney is one of the target organ for arsenic-induced carcinogenesis and toxicological effects. However, the mechanism of arsenic-induced renal carcinogenesis is not well understood. Therefore, the objective of this study was to evaluate the carcinogenicity of chronic exposure to low dose arsenic on kidney epithelial cells, and identify the molecular mechanism underlying this process. HK-2 kidney epithelial cells derived from normal human kidney were treated with arsenic for acute, long-term and chronic durations and cellular response to arsenic exposure at these time points was determined by evaluating the changes in growth, morphology, and expression of genes. The results revealed a significant dose-dependent growth inhibition after acute exposure, whereas increased growth after long-term and chronic exposure to arsenic of HK-2 cells as compared to untreated control cells. The anchorage-independent growth assay for colony formation further confirmed malignant transformation of arsenic exposed cells. Additionally, the morphological changes of EMT and stemness were also observed in long-term arsenic exposed cells. These changes observed above were further confirmed by analysis of gene and protein expression. Our data suggest that cellular response of EMT and stemness act a driving factor and mechanistic basis for increased survival and malignant transformation in arsenic exposed cells. In summary, results of this study suggest that acute exposure to arsenic can cause loss of kidney epithelial cells with potential significance to acute kidney injury, whereas the chronic exposure to arsenic can increase the risk of kidney cancer through enhancing cell proliferation.

Citation Format: Yu-Wei Chang, Kamaleshwar Singh. Chronic exposure to arsenic induces malignant transformation in human kidney epithelial 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 3080.
Abstract 3119: Treatment prediction by subset analysis of tumor infiltrating lymphocytes (TILs) in combination therapy with trastuzumab, pertuzumab, and docetaxel for advanced HER2-positive breast cancer
Authors: Takada Koji , Kashiwagi Shinichiro , Asano Yuka , Wataru Goto , Morisaki Tamami , Noda Satoru , Takashima Tsutomu , Onoda Naoyoshi , Hirakawa Kosei , Ohira Masaichi
Published: August 2018

Background: The trastuzumab, pertuzumab, and docetaxel (TPD) regimen is strongly recommended as a treatment option for first-line therapy for advanced human epidermal growth factor receptor (HER) 2-positive breast cancer. The immune microenvironment in cancer is involved in many antitumor treatment effects, and tumor-infiltrating lymphocytes (TILs) is being established as a biomarker for therapeutic effect and prognosis. Recently, subset analysis of TILs is also under way. We have previously reported the clinical validity and benefits of evaluating TILs for neoadjuvant chemotherapy (NAC). Chemotherapy with a TPD regimen is garnering attention for its clinical outcomes and impact on cancer microenvironments. In this study, we evaluated the impact of chemotherapy with a TPD regimen, on immune micro environments in HER2-positive breast cancer using immune related proteins as indicators.

Methods: The subjects consisted of 30 patients who received the TPD regimen. The expression levels of estrogen receptor (ER), progesterone receptor (PgR), Ki67, CD8, forkhead box protein (FOXP) 3, programmed death (PD) 1, and programmed death ligand (PD-L) 1 were evaluated in biopsy specimens, by immunostaining. We also examined the ratio of CD8 and FOXP3 (CFR).

Results: The objective response rate (ORR) in the high CFR group was higher than in the low CFR group (p=0.013). The CD8 positive, high CFR and PD-L1 negative group had significantly longer PFS than the CD8 negative, low CFR and PDL1 positive group (p=0.045, log-rank) (p=0.007, log-rank) (p=0.040, log-rank), respectively. The high CFR group had significantly better OS than the low CFR group (p=0.034, log-rank). Receiver operating characteristic (ROC) analyses showed that, for advanced HER2-positive breast cancer patients, the CFR results [area under the curve (AUC): 0.708] were better than those for the other factors (AUC: CD8=0.681, FOXP3=0.639, PD1=0.528, PD-L1=0.681).

Conclusions: This study shows with the TPD regimen, a high CFR leads to a high ORR and long PFS in HER2-positive breast cancer. CFR, therefore, may be one of the important prognostic factors for this disease.

Citation Format: Koji Takada, Shinichiro Kashiwagi, Yuka Asano, Goto Wataru, Tamami Morisaki, Satoru Noda, Tsutomu Takashima, Naoyoshi Onoda, Kosei Hirakawa, Masaichi Ohira. Treatment prediction by subset analysis of tumor infiltrating lymphocytes (TILs) in combination therapy with trastuzumab, pertuzumab, and docetaxel for advanced HER2-positive 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 3119.
Abstract 3168A: S100A4 mediates paracrine interactions with breast tumor cells
Authors: Dulyaninova Natalya G. , Levine Adriana , Backer Jonathan M. , Bresnick Anne R.
Published: August 2018

S100A4, a member of the S100 family of Ca2+-binding proteins, has a direct and causative role in tumor metastasis. In murine models of breast cancer, S100A4 overexpression in tumor cells promotes an aggressive metastatic phenotype, while inhibition of S100A4 expression significantly reduces metastatic burden. We have now evaluated the contribution of stromal S100A4 to mammary tumor progression. The growth of E0771 orthotopic mammary tumors was reduced in S100A4-/- mice as compared to wild type mice. In addition, in a 3D collagen assay that recapitulates macrophage-tumor cell paracrine interactions that drive metastasis in vivo, S100A4-/- bone marrow-derived macrophages failed to stimulate breast tumor cell invasion. Our cell biological studies on bone marrow-derived macrophages from wild type and S100A4-/- mice show that loss of S100A4 produces two mechanistically distinct phenotypes in macrophages: a myosin-IIA-dependent defect in matrix degradation, due to an inhibition of podosome rosettes (actin-rich degradative structures that allow macrophages to penetrate through endothelial layers and their associated basement membranes), and a defect in invasion, due to a myosin-IIA-independent increase in microtubule acetylation and stability. These studies suggest that S100A4, which has well described pro-metastatic functions in tumor cells, also plays a critical role in immune cells in the tumor microenvironment.

Citation Format: Natalya G. Dulyaninova, Adriana Levine, Jonathan M. Backer, Anne R. Bresnick. S100A4 mediates paracrine interactions with breast tumor 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 3168A.
Abstract 3176: CD99 regulates ERK1/2-MSK1/2-CREB axis in Ewing sarcoma
Authors: Celik Haydar , Conn Erin J. , Allegakoen David V. , Petro Jeff R. , Toretsky Jeffrey A. , Uren Aykut
Published: August 2018

Ewing sarcoma (ES) is an aggressive malignancy of bone and soft tissue that affects predominantly children and young adults with a high propensity to metastasize and poor prognosis. ES cells express high levels of a cell surface protein CD99, which is routinely used as a marker antigen in the histological diagnosis of ES, and contributes to its pathogenesis. We performed a phospho-kinase array to uncover specific cellular responses evoked by CD99 inhibition in ES cells. The treatment of ES cells with CD99 antibody or a small molecule CD99 inhibitor (clofarabine) resulted in strong activation of mitogen- and stress-activated kinases 1 and 2 (MSK1/2) as well as its substrate CREB and its upstream kinase ERK1/2. These findings were further confirmed with western blot analysis in ES cells treated with either different CD99 antibodies or clofarabine. The treatment of osteosarcoma (OS) cells with clofarabine or the forced expression of CD99 in OS cells did not change their phosphorylation levels, suggesting that CD99-mediated ERK1/2-MSK1/2-CREB signaling cascade is specific to ES cells. Interestingly, knock-down of the CD99 protein in ES cells led to a significant decrease in ERK1/2 phosphorylation without any effect on the downstream phosphorylation of MSK1/2 and CREB. Cytarabine, a structurally similar pyrimidine analog that has been identified as an inhibitor of EWS/FLI1 transcriptional activity but failed in clinical trials on ES patients, did not activate ERK1/2-MSK1/2-CREB axis unlike clofarabine in ES cells. These findings suggest that clofarabine functions through alternative mechanisms on ES cells that are different than cytarabine. Clofarabine induced a significant increase in phosphorylation levels of MSK1/2 in a small cohort of TC-71 xenografts, supporting its use as a potential pharmacodynamic marker of CD99 inhibitor activity. In conclusion, our findings suggest that CD99 regulates ERK1/2-MSK1/2-CREB axis in ES, which represents an intracellular pathway that may be responsible for CD99's biological activities in ES.

Citation Format: Haydar Celik, Erin J. Conn, David V. Allegakoen, Jeff R. Petro, Jeffrey A. Toretsky, Aykut Uren. CD99 regulates ERK1/2-MSK1/2-CREB axis in Ewing sarcoma [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 3176.
Abstract 3177: mTOR inhibitor augments the antitumor effect of p53-expressing oncolytic adenovirus in human neuroblastoma cells
Authors: Tanimoto Terutaka , Tazawa Hiroshi , Noso Hiroshi , Tani Morimichi , Oyama Takanori , Urata Yasuo , Kagawa Shunsuke , Noda Takuo , Fujiwara Toshiyoshi
Published: August 2018

Background: Neuroblastoma (NB) is a primary malignant tumor of the peripheral sympathetic nervous system. High-risk NB patients show an unfavorable clinical outcome, even after treatment with intensive chemotherapy and aggressive surgical resection. Therefore, a novel therapeutic strategy is needed for the treatment of high-risk NB patients. We developed a tumor-specific replication-competent oncolytic adenovirus OBP-702, in which the hTERT promoter drives the expression of the viral E1A and E1B genes for tumor-specific viral replication and the Egr-1 promoter induces p53 expression. Preclinical studies demonstrated that OBP-702 induces autophagy-related cell death in human NB cell lines. To enhance OBP-702-induced autophagy-related cell death, we hypothesized that a mTOR inhibitor temsirolimus, which is well-known autophagy inducer, may promote autophagy-related cell death by OBP-702 infection. In this study, we investigated the antitumor effect of OBP-702 in combination with temsirolimus in human NB cell lines.

Methods: We used 3 human NB cell lines, including IMR-32, CHP-134 and SK-N-SH. The antitumor effect of OBP-702 and temsirolimus was evaluated using XTT assay. In vitro synergistic effect was calculated with CalcuSyn software (BioSoft, Inc.). Virus-mediated cell death and p53 expression were analyzed by Western blot analysis. Ad-p53, a replication-defective adenovirus expressing p53 gene, was used to assess the effect of p53 in combination with temsirolimus. The combined effect of OBP-702 and temsirolimus was further evaluated using a subcutaneous CHP-134 xenograft tumor model.

Results: Combination with OBP-702 and temsirolimus exhibited a synergistic antitumor effect in all NB cell lines in vitro. We confirmed that combination with these drugs enhanced autophagy. In addition, temsirolimus showed an effect to stabilize p53 protein induced by OBP-702. Ad-p53 also showed synergistic effect in combination with temsirolimus. The combination treatment significantly inhibited tumor growth, as compared to monotherapy, in NB xenograft tumor model.

Conclusions: These results suggest that p53-expressing oncolytic adenovirus and mTOR inhibitor synergistically induce autophagic cell death and may be a promising strategy in NB patients.

Citation Format: Terutaka Tanimoto, Hiroshi Tazawa, Hiroshi Noso, Morimichi Tani, Takanori Oyama, Yasuo Urata, Shunsuke Kagawa, Takuo Noda, Toshiyoshi Fujiwara. mTOR inhibitor augments the antitumor effect of p53-expressing oncolytic adenovirus in human neuroblastoma 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 3177.
Abstract 318: Inhibition of FASN induces apoptosis and senescence in breast cancer
Authors: Steen Travis Vander , Lupu Ruth
Published: August 2018

Fatty Acid Synthase (FASN), the key multienzyme in de novo lipogenesis, is upregulated and activated in numerous carcinomas, including breast cancer. Fatty acids play a fundamental role in cellular structure, energy production and storage and are intermediates in the biosynthesis of hormones and other biologic molecules. Therefore, FASN is a novel therapeutic target for treatment in cancer cells that have upregulated FASN protein. BT474 breast cancer cells, which overexpress FASN, were treated with a pharmacologic FASN inhibitor and resulted in apoptosis in a dose-dependent manner. Inhibition of FASN simultaneously upregulates the pro-apoptotic BCL2 family members Bim, Puma, and Noxa; additionally, FASN inhibition alters the NDAPH/NADP+ balance and induces reactive oxygen species (ROS) production. Most significantly, FASN inhibition induces sensitization of breast cancer cells to the BH3 mimetic navitoclax, a potential opportunity to use BH3 mimetics for the treatment of breast carcinomas. These results support further preclinical and potentially clinical development of a dual FASN and Bcl-2 treatment for breast cancer tumors that express FASN. In addition to apoptosis, there is an increase in cellular senescence in breast cancer cells overexpressing FASN when treated with FASN inhibitors. The increase in ROS, a known effect of FASN inhibition, is known to induce cellular stress, resulting in both apoptosis and senescence. Increased senescence was initially observed by x-gal staining of BT474 cells treated with FASN inhibitors via microscopy and FLOW. We also observed an increased expression of several pro-senescent genes both at the protein and mRNA levels, including p16/INK4a, p14ARF/p19ARF, p15, and p21. A hallmark of age-induced cellular senescence is the shortening of telomeres. However, telomere shortening was not observed, suggesting that senescence was a result of FASN inhibition and activation of senescence-induced genes. Therefore, inhibition of FASN appears to be an ideal target for therapeutic treatment of breast cancers that overexpress FASN through both apoptosis and senescence.

Citation Format: Travis Vander Steen, Ruth Lupu. Inhibition of FASN induces apoptosis and senescence in 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 318.
Abstract 3220: Preliminary evaluation of 212Pb BB2r targeted radiotherapy in prostate cancer
Authors: Rold Tammy L. , Okoye Nkemakonam C. , Timothy Hoffman
Published: August 2018

Introduction: Treating castration resistant prostate cancer (CRPC) continues to be a challenge for clinicians. We have recently shown that gamma emitting 203Pb-RM2 (DOTA-4-amino-1-carboxymethyl-piperidine-D-Phe-Gln-Trp-Ala-Val-Gly-His-Sta-Leu-NH2) efficiently targets the BB2r expressed on CRPC cells in vivo. We are now exploring the potential of using the alpha-emitting radioisotope 212Pb to generate the radiotherapeutic 212Pb-RM2. Using 212Pb-RM2, we have performed in vitro cell studies to examine treatment effects in terms of DNA damage, clonogenic potential, and cell viability and preliminary in vivo xenograft targeting proof of principle studies.

Methods: 212Pb-RM2 was prepared using an automated radiosynthesizer using 212Pb eluted from a 212Ra/212Pb generator. DNA damage, colony formation, and cell viability were evaluated in PC-3 cells following treatment with 212Pb-RM2 at 0.51, 1, 2, and 4uCi/160uL. DNA damage was assessed using 53BP1 foci following a 4hr incubation with 212Pb-RM2 (T0) and at 24hrs and 48hrs. Colony formation assays were performed on cells treated with TRT for 4hrs, and analyzed at 12-14 days. The MTT assay was conducted up to 144hrs. All cell experiments were performed in triplicate on different occurrences. PC-3 xenografted SCID mice were administered 212Pb-RM2 and organs/tissues were harvested and counted at 15 min, 1hr, 4hr, and 24hrs post injection.

Results: DNA damage was found to be sustained over time with 53BP1 foci/cell at 48hrs of 14.8+1.6, 33.8+2. 6, 29.6+1.1, and 40.6+1.6 (avg+SEM) at 0.51, 1, 2, and 4uCi of 212Pb-RM2/160uL, respectively. Colony formation followed a dose dependent response with surviving fraction decreasing as TRT increased with 17.7+3.2, 4.4+2.9, 0.5+0.5, and 0.0+0.0 (avg+SEM) at 0.51, 1, 2, and 4uCi of 212Pb-RM2/160uL, respectively. 212Pb-RM2 tumor uptake in PC-3 xenografts was found to be 5.2+0.7, 5.0+0.9, 3.9+0.7, and 2.6+0.3 %ID/g at 15min, 1hr, 4hr, and 24hrs respectively. In vivo BB2r blocking studies confirmed 212Pb-RM2 targeting of the BB2r with > 72% blocking of normal pancreas uptake measured at 4hr post injection.

Conclusions: Treatment with alpha emitting 212Pb-RM2 TRT showed sustained levels of DNA damage which was confirmed by impaired colony formation at all dose levels of 212Pb-RM2 TRT studied. Preliminary in vivo tumor targeting and retention of 212Pb-RM2 was observed out to 24hrs post injection warranting further evaluation of 212Pb-RM2 in multiple CRPC cell line models assessing potential therapeutic efficacy.

Acknowledgements: US Veterans Administration (VA) BX001699 and USVA Research Career Scientist (TJH)

Citation Format: Tammy L. Rold, Nkemakonam C. Okoye, Hoffman Timothy. Preliminary evaluation of 212Pb BB2r targeted radiotherapy in prostate 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 3220.
Abstract 3257: Polygenic risk score, stage, and mode of detection in relation to breast cancer risk
Authors: Trentham-Dietz Amy , Hampton John M. , Ong Irene M. , Page C David , Gould Michael N. , Haag Jill D. , Newcomb Polly A. , Shull James D. , Burnside Elizabeth S.
Published: August 2018

Identification of increasing numbers of breast cancer risk variants holds promise to improve risk prediction and identify population subgroups that could benefit from targeted prevention and early detection. We aimed to examine whether women with increased polygenic risk are more likely to be diagnosed with symptomatic breast cancer. A case-control study including data collected from interviews, DNA from saliva, and cancer registry data collected between 2001-2007 (4,315 cases, 3,919 controls) was used to construct a polygenic risk score (PRS). Single nucleotide polymorphisms (SNPs, N=98) were selected from recently published genome-wide association studies of breast cancer and breast density, and comparative rat genome studies. Logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CI) associated with the SNPs. SNPs with p-values ≤0.10 (N=24) were used to construct quintiles of the PRS by multiplying the log-odds of the SNPs by the number of risk alleles; multivariable logistic regression models evaluated all women and strata of women defined by method of detection and stage at diagnosis. Odds ratios were adjusted for age, family history of breast cancer, age at menopause/menopausal status, body mass index, parity, and age at first birth. Overall, PRS quintile categories were associated with breast cancer risk in a dose response manner (Q1: OR=1, reference; Q2 OR=1.36, 95% CI 1.16-1.58; Q3 OR=1.66, 95% CI 1.43-1.93; Q4 OR=1.83, 95% CI 1.58-2.12; Q5 OR=2.58, 95% CI 2.23-2.98). Evaluated on a continuous scale, the PRS was associated with an OR=1.38 for a 1-unit change in the standard deviation (SD), 95% CI 1.32-1.45. Odds ratios were essentially unchanged when stratified by method of detection (p-value=0.40). The odds ratio of breast cancer associated with the continuous PRS was elevated among women diagnosed with advanced breast cancer: DCIS, OR=1.36, 95% CI 1.26-1.47 per 1 SD; localized OR=1.37, 95% CI 1.30-1.45 per 1 SD; regional OR=1.38, 95% CI 1.28-1.48 per 1 SD; and distant OR=1.82, 95% CI 1.39-2.40. These results suggest that polygenic risk scores are strongly related to breast cancer risk, that the association does not vary by method of breast cancer detection, but that the association is strongest for metastatic breast cancer.

Citation Format: Amy Trentham-Dietz, John M. Hampton, Irene M. Ong, C David Page, Michael N. Gould, Jill D. Haag, Polly A. Newcomb, James D. Shull, Elizabeth S. Burnside. Polygenic risk score, stage, and mode of detection in relation to breast cancer risk [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 3257.
Abstract 3267: Cervical microbiota and the urinary metabolome in patients with high-risk and low-risk HPV infections
Authors: Ortiz Gilmary , Chorna Natalyia , Romaguera-Agrait Josefina , Martinez-Ferrer Magaly , Sanchez Maria , Ortiz Ana P. , Guerrero-Preston Rafael , White James R. , Godoy-Vitorino Filipa
Published: August 2018

Genital human papillomavirus (HPV) is the world's most commonly diagnosed sexually transmitted infection, and high-risk HPV types are strongly linked to cervical dysplasia and carcinoma. The microbiota of the human cervico-vaginal tract is the interface between the host and environment, and its constituents may act as determinants of susceptibility for HPV infection. There exists the potential for reliable diagnostic biomarkers for cervical cancer in the cervical microbiome as well as in urine, which would be an important biospecimen due to its abundance and non-invasive collection strategy. In this study, we performed comprehensive metabolomic analysis on urine samples from 65 women (54 HPV+, 38 of whom have cervical intraepithelial neoplasia (CIN), and 11 HPV-) and discuss the potential diagnostic implication and metabolic description of high-risk and low-risk HPV infected patients.

The experimental procedure employed gas chromatography mass spectrometry (GC-MS) on the urine-derived products and HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. We further characterized resident cervical bacteria in these patients using Illumina sequencing of the V4 region of the 16S ribosomal RNA with a high-resolution bioinformatics methodology (Resphera Insight v2.2) for species-level taxonomic assignment.

The hybridization assay detected 11 low-risk and 10 high-risk HPV types many of them co-occurring in the cervical samples. Lactobacillus iners OTUs were shared by all samples but were significantly more dominant in women with low-risk HPV strains (p-value=0.05), while G. vaginalis, S. sanguinegens and L. jensenii were associated with high-risk strains. CIN1 and CIN3 dysplasic biopsies, detected significant enrichments of Gardnerella vaginalis, L.crispatus and Prevotella amnii (p-values <0.05). Preliminary GC-MS analysis identified elevated levels of palmitic (C16:0) and stearic fatty acids (C18:0) as well as lactic acid, abundant in the HPV+ samples while 5-oxo-proline and Neu5Ac (N-Acetylneuraminic acid) were abundant in the HPV- samples.

Our preliminary data identifies possible microbial and metabolic biomarkers associated with oncogenic HPV and cervical intraepithelial neoplasia in women living in Puerto Rico.

Citation Format: Gilmary Ortiz, Natalyia Chorna, Josefina Romaguera-Agrait, Magaly Martinez-Ferrer, Maria Sanchez, Ana P. Ortiz, Rafael Guerrero-Preston, James R. White, Filipa Godoy-Vitorino. Cervical microbiota and the urinary metabolome in patients with high-risk and low-risk HPV infections [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 3267.
Abstract 3271: A machine learning approach for somatic mutation discovery
Authors: Wood Derrick , White James , Georgiadis Andrew , Emburgh Beth Van , Parpart-Li Sonya , Mitchell Jason , Anagnostou Valsamo , Niknafs Noushin , Karchin Rachel , Papp Eniko , McCord Christine , Loverso Peter , Riley David , Diaz Luis A. , Jones Sian , Sausen Mark , Velculescu Victor E. , Angiuoli Samuel
Published: August 2018

Variability in the accuracy for somatic mutation detection may affect discovery of alterations and therapeutic management of cancer patients. To address this issue, we developed a somatic mutation discovery method based on machine learning approaches that outperformed other methods using tumor alterations that were experimentally validated (sensitivity of 97% vs 90-99%; positive predictive value of 98% vs 34-92%). Analysis of tumor-normal exome data from 1,376 TCGA samples using this method revealed concordance for 74% of mutation calls but also identified likely false positive and negative changes in TCGA data, including in clinically actionable genes. For melanoma and lung cancer patients treated with immune checkpoint inhibitors, determination of high-quality somatic mutation calls improved mutation load-based predictions of clinical outcome. Integration of high-quality mutation detection in clinical NGS analyses improved the accuracy of test results compared to other clinical sequencing analyses not using these approaches (sensitivity of 100% vs 50-97%; positive predictive value of 100% vs 9-66%). These analyses provide an approach for improved identification of tumor-specific mutations and have important implications for research and clinical management of patients with cancer.

Citation Format: Derrick Wood, James White, Andrew Georgiadis, Beth Van Emburgh, Sonya Parpart-Li, Jason Mitchell, Valsamo Anagnostou, Noushin Niknafs, Rachel Karchin, Eniko Papp, Christine McCord, Peter Loverso, David Riley, Luis A. Diaz, Sian Jones, Mark Sausen, Victor E. Velculescu, Samuel Angiuoli. A machine learning approach for somatic mutation discovery [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 3271.
Abstract 3272: A graph remapping framework for in silico adjudication of SNVs, INDELs, and structural variants from genetic sequencing data
Authors: Lee Dillon , Qiao Yi , Marth Gabor
Published: August 2018

Several state-of-the-art, easy to use tools are available both for short-variant detection (e.g. GATK, FREEBAYES), and structural variant (SV) detection (e.g. LUMPY, MANTRA, DELLY), but these tools often produce divergent variant calls, especially INDELs, and it is very difficult to reconcile such variants into a single, accurate set. Furthermore, while it would be highly desirable to also detect larger, structural variants (SV), existing SV detector packages are typically difficult to integrate, highly resource-intensive to run, and result in call sets that require expert manual review to reduce false positive detection rate.

Our algorithm, GRAPHITE (https://github.com/dillonl/graphite) requires as input a collection of variant calls, made by one or more short-variant or SV detection tools. Typically, this starting set is high sensitivity (i.e. inclusive), but low specificity (i.e. have a high false discovery rate). We then apply a novel “variant adjudication” procedure to discard false positives, while keeping true positive calls. This is accomplished by constructing a graph from these variants (the Variant Graph) representing allelic variants as graph branches, in addition to the branches formed by the current, linear genome reference sequence. Using a graph mapping algorithm (GSSW, a graph extension of the Smith-Waterman alignment algorithm) we developed earlier, we re-map all reads from each of the samples contributing to the candidate calls. We retain candidate variants confirmed by mappings to those branches in the graph that represent the corresponding variant allele, and discard those candidates that were not confirmed by such mappings. This procedure results in a highly specific callset that also maintains the high sensitivity of the inclusive starting callset constructed by multiple primary variant calling methods. Because the graph construction and mapping approach works for most types of SVs in addition to all short variants, variants of all different types can be integrated in a single step.

Here we present the application of this method for cross-validating structural variants calls from Pacific Biosciences data by remapping deep Illumina WGS read sets to Variant Graphs constructed using the candidate Pacific Biosciences variants, as part of the Human Genome Structural Variation Consortium (HGSVC) data analysis project. We also present GRAPHITE's application to improving the accuracy of allele frequency measurement in tumor sequencing data, which is essential for the accurate reconstruction of subclonal evolution in longitudinal tumor samples.

Citation Format: Dillon Lee, Yi Qiao, Gabor Marth. A graph remapping framework for in silico adjudication of SNVs, INDELs, and structural variants from genetic sequencing data [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 3272.