bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2549: A long non-coding RNA regulates the androgen receptor and mediates prostate cancer progression
Authors: Pitchiaya Sethuramasundaram , Malik Rohit , Cieslik Marcin , Zhang Yajia , Jiang Xia , Chinnaiyan Arul M.
Published: July 2017

The pervasive expression of long non-coding RNAs (lncRNAs) and their roles in a plethora of cellular processes has revolutionized our understanding of functional genetic elements. Emerging evidence suggest that lncRNAs are promising cancer biomarkers and dysregulation of lncRNAs results in attenuated or accelerated oncogenic phenotypes. In support of these findings, recent reports from the Chinnaiyan lab suggest that lncRNAs can potentially drive and act as independent predictors of aggressive prostate cancer (PCa). Central to PCa progression is the androgen receptor (AR), a nuclear hormone receptor, and the dysregulated transcription program it mediates. Consequently, androgen deprivation therapy (ADT) supplemented with anti-androgens is the initial standard-of-care in treating advanced PCa. Yet, the disease often manifests as a lethal, hormone-refractory castration-resistant prostate cancer (CRPC) after initial ADT and this phenomenon is linked to the resumption of AR activity. Therefore, we sought to identify novel and therapeutically actionable targets of AR that can detect the onset of PCa or stratify PCa variants. To this end, our lab recently characterized the transcriptional landscape of cancer and discovered > 50,000 novel transcripts, a significant fraction of which were tissue- and cancer-specific lncRNAs. Using this updated transcriptome as a reference and performing RNA-seq on PCa cells stimulated with dihydrotestosterone (an androgen), we identified Androgen Receptor regulated lncRNA-1 (ARlnc1) as an important PCa-specific, AR-regulated lncRNA that reciprocally regulates AR. By employing single-molecule fluorescence in situ hybridization (smFISH), we find that ARlnc1 and AR transcripts colocalize within the nucleus of PCa cells and that ARlnc1 promotes transcription of AR. Moreover, we found that ARlnc1 interacts with anti-apoptotic, stress-granule related proteins and regulates PCa cell proliferation in vitro and in mouse xenografts. We have additionally found that anti-sense oligonucleotides (ASOs) that target this lncRNA can reduce tumor growth in xenograft models. Taken together, our data suggests that ARlnc1 and AR reciprocally and positively modulate each other to promote PCa progression and that ARlnc1 may serve as an enhancer RNA that regulates AR transcription. Our data suggests that ARlnc1 can be therapeutically targeted to orthogonally modulate the AR signaling axis for PCa treatment.

Citation Format: Sethuramasundaram Pitchiaya, Rohit Malik, Marcin Cieslik, Yajia Zhang, Xia Jiang, Arul M. Chinnaiyan. A long non-coding RNA regulates the androgen receptor and mediates prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2549. doi:10.1158/1538-7445.AM2017-2549
Abstract 2554: PRR14, a novel regulator of Ras signaling pathway
Authors: Yang Mei , Long Meijun , Shi Xiaoliu , Yuan Zhi-Min , Su Hang
Published: July 2017

PRR14, a component of nuclear lamina, has recently been identified as a novel oncogene in lung cancer. Frequently upregulated in lung cancers, PRR14 promotes tumorigenesis through activating the PI3-kinase/Akt/mTOR signal pathway. The regulatory effect is mediated by direct interaction with GRB2, a docking protein upstream of both PI3K and Ras. Indeed, PRR14 is commonly elevated in many cancer types including lung cancer and breast cancer, but our understanding of the underlying molecular mechanism is still very elusive. Given the complicated interplay between PI3K and Ras signal pathways and their importance in carcinogenesis and optimal treatment, we further explored the effect of PRR14 on Ras activation. We used MCF10A human mammary epithelial cells and its K-RasV12-induced cancerous counterparts to establish isogenic cell lines that express different levels of PRR14. Colony formation and growth curves were monitored simultaneously. Western blot and Ras pull-down activation assay were employed to examine protein level and Ras activity. Cell fractionation was performed to detect protein location. We found that the expression level of PRR14 positively correlated with both Ras protein level and its activity, resulting in consequent changes in cell proliferation and colony formation. Remarkably, elevated PRR14 promoted translocation of Ras from cytoplasm into the cell nucleus and its stabilization. In conclusion, PRR14 sequesters, stabilizes and activates Ras in cell nuclei. When upregulated, PRR14 promotes tumorigenesis, and Ras signaling pathway presents one of the complex underlying mechanisms.

Citation Format: Mei Yang, Meijun Long, Xiaoliu Shi, Zhi-Min Yuan, Hang Su. PRR14, a novel regulator of Ras signaling pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2554. doi:10.1158/1538-7445.AM2017-2554
Abstract 2557: Role of microRNAs in breast cancer
Authors: El-Mahdy Hesham Abbas , Mansour Ossama Abdelmotaal , Badr Mohamed Mohamed , Elshimy Reham Aly
Published: July 2017

Background: Breast cancer (BC) is one of the most common cancer in women around the world and the second leading cause of death worldwide. MicroRNAs (miRNAs) expression participates in breast cancer.

Objectives: The purpose of this study is to investigate the expression of miR-133a and miR-155 in breast cancer serum and study their correlation with tumor suppressor protein (p53), carcinoembryonic antigen (CEA) and cancer antigen-15.3 (CA-15.3) concentrations in serum of breast cancer patients and also study their correlations with clinicopathological features.

Material and methods: In this study the expression of miR-133a and miR-155 in serum were measured using quantitative real-time polymerase chain reaction (qRT-PCR), P53 concentration was measured by enzyme-linked immunosorbent assays (ELISA), CEA and CA-15.3 concentration were measured using ARCHITECT immunoassay in women with breast cancer (n=60) and controls (n = 80).

Results: In this study miRNA-155 was significantly overexpressed (P<0.001) while miR-133a had significant down expression (P<0.001) in the serum of breast cancer patients compared to control serum. P53 had no significant correlations with any of the studied miRNAs. Carcinoembryonic antigen and CA-15.3 have significant higher concentration in the serum of breast cancer patients compared to control serum. A significant association was observed between miR-133a with tumor grade (P<0.05) and miR-155 with lymph node involvement (P<0.05). A significant correlation between miR-155 and CEA (P<0.05). No correlations between miR-133a and P53, CEA, CA-15.3. By using receiver operating characteristic (ROC) curve, the two miRNAs showed higher sensitivity, specificity, positive predictive value and negative predictive value than routine markers.

Our Conclusion: These miRNAs have a significant signature in the pathogenesis of breast cancer and can be used as non-invasive potential biomarkers for breast cancer detection.

Note: This abstract was not presented at the meeting.

Citation Format: Hesham Abbas El-Mahdy, Ossama Abdelmotaal Mansour, Mohamed Mohamed Badr, Reham Aly Elshimy. Role of microRNAs in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2557. doi:10.1158/1538-7445.AM2017-2557
Abstract 256: Delta tocopherol inhibits urothelial tumorigenesis in the UPII mutant Ha-ras transgenic mouse model and induces apoptosis via activation of the ATF4/CHOP-DR5 pathway
Authors: Blair Christopher A. , Wu Maggie , Huynh Tim , Hu Hanze , Walia Arman , Yang Chung S. , Zi Xiaolin
Published: July 2017

Epidemiological studies have reported that Vitamin E intake was inversely related to the risk of multiple cancers including human urinary bladder cancer. Tocopherols (T) are the major forms of vitamin E in the U.S. diet, exist as α-T, β-T, γ-T and δ-T. Compared to α-T, the anti-cancer effect of other Ts and their mechanisms of action remain largely unknown. We have shown that δ-T is the most effective one among the Ts in reducing the viabilities of bladder cancer cell lines with IC50s of under 10 μM, whereas there is no or minimal effect of α-T at a concentration of up to 50 μM on the viability of bladder cancer cell lines. δ-T treatment of bladder cancer cell lines, RT4 and UMUC-3, resulted in apoptosis via marked induction of death receptor-5 (DR5) expression and then activation of caspase 3, 8, and 9 leading to PARP cleavage and apoptotic morphology. siRNA knockdown of DR5 expression significantly attenuated the apoptotic effects of δ-T in bladder cancer cells. Consistent with the above results, δ-T treatment significantly upregulated the expression of ER stress sensors PERK and IRE1α, as well as downstream components GRP78, ATF4, and CHOP. These results suggested that δ-T can induce endoplasmic reticulum stress and the Unfolded Protein Response, triggering its apoptotic effect. Furthermore, homozygous male UPII mutant Ha-ras transgenic mice that mimic the development and progression of human urothelial cell carcinoma (UCC) with H-ras activation were fed with vehicle control diet (n=20) or diet supplemented with δ-T (0.2% in diet) for 150 days (n=18). The δ-T diet significantly decreased the mean bladder weights (serves as a surrogate of tumor weight) of survived Ha-ras mutant mice by 56% (control vs δ-T, 0.259 ± 0.015 gram vs. 0.114 ± 0.012 gram, P<0.0001) with no significant difference in overall body mass and no detectable indication of toxicity. Our results suggest that δ-T is a potent anti-cancer agent and deserves further investigation in preventing the recurrence and progression of non-muscle-invasive UCC.

Citation Format: Christopher A. Blair, Maggie Wu, Tim Huynh, Hanze Hu, Arman Walia, Chung S. Yang, Xiaolin Zi. Delta tocopherol inhibits urothelial tumorigenesis in the UPII mutant Ha-ras transgenic mouse model and induces apoptosis via activation of the ATF4/CHOP-DR5 pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 256. doi:10.1158/1538-7445.AM2017-256
Abstract 2566: Positive cross-regulatory loop links ZBTB7A to estrogen receptor alpha expression in breast cancer
Authors: Molloy Mary Ellen , Lewinska Monika , Nguyen ThanhThao , Yuan Zhi-Min
Published: July 2017

In breast development and tumorigenesis the biological functions of estrogen are mediated by estrogen receptor alpha (ERα). Approximately 70% of breast cancers are classified as ERα positive and are therefore candidates to receive various forms of endocrine therapy. De novo or acquired resistance to endocrine therapies limits their clinical effectiveness. Identification of novel targets is critical to combat disease progression. Our lab has recently discovered that ZBTB7A suppresses glycolysis by transcriptionally repressing key genes within the glycolytic pathway in various cancer types (Liu, X.S., et al. 2014). Currently, ZBTB7A is proposed to be an oncogene in breast cancer (Zu, X., et al. 2011), however its function in ERα positive breast cancers has yet to be fully addressed. Using publically available datasets, we found that in luminal breast cancers relapse free survival was improved for patients whose tumors expressed high levels of ZBTB7A. Gene expression analysis of TCGA datasets revealed that ZBTB7A and ERα are highly correlated in human breast tumors prompting us to evaluate their potential cross regulation. ERα mRNA and protein levels were significantly decreased upon ZBTB7A silencing both in MCF-7 and T47D breast cancer cell lines. Upon estradiol stimulation, ZBTB7A silencing reduced ERα target gene expression and estrogen response element driven luciferase reporter activity. Additionally, silencing of ZBTB7A inhibited estradiol-induced proliferation and decreased sensitivity to tamoxifen in MCF-7 and T47D cells. These data suggest that ZBTB7A may be required to mediate the pro-proliferative signal of estradiol through its regulation of ERα expression in breast cancer cell lines. To evaluate the potential regulation of ERα on ZBTB7A, ERα was silenced and ZBTB7A mRNA and protein expression were determined. ERα silencing had no effect on ZBTB7A mRNA levels, but led to decreased ZBTB7A protein expression. These effects on ZBTB7A protein expression were attenuated by the presence of the proteasomal inhibitor MG132. Together, these data suggest a model in which ZBTB7A promotes ERα expression at the transcript level while ERα stabilizes ZBTB7A post-transcriptionally conferring a positive feedback loop and sensitivity to estradiol and endocrine therapies. ZBTB7A may contribute to the transcriptional program maintaining a hormone and endocrine therapy responsive phenotype in breast cancer.

Citation Format: Mary Ellen Molloy, Monika Lewinska, ThanhThao Nguyen, Zhi-Min Yuan. Positive cross-regulatory loop links ZBTB7A to estrogen receptor alpha expression in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2566. doi:10.1158/1538-7445.AM2017-2566
Abstract 2569: BCL6 promotes glioma and serves as a novel therapeutic target
Authors: Xu Liang , CHEN Ye , Dutra-Clarke Marina , Mayakonda Anand , Hazawa Masaharu , Savinoff Steve E. , Doan Ngan , Said Jonathan W. , Yong William H. , Yang Henry , Ding Ling-Wen , Jiang Yan-Yi , Tyner Jeffrey W. , Ching Jianhong , Kovalik Jean-Paul , Müschen Markus , Breunig Joshua J. , Lin De-Chen , Koeffler Phillip
Published: July 2017

ZBTB transcription factors orchestrate gene transcription during tissue development. However, their roles in glioblastoma multiforme (GBM) remain unexplored. Here, through a functional screening of ZBTB genes, we identify that BCL6 is required for GBM cell proliferation and is overexpressed in GBM samples. Using a somatic transgenic mouse model, Bcl6 confers the proliferative and invasive stimuli to glioma cells in vivo. Moreover, we discover AXL as a novel downstream target of BCL6. Through AXL, BCL6 enhances both MEK-ERK and S6K-RPS6 axes. Pharmacological inhibition of BCL6 activity effectively blocks GBM growth and inhibits AXL expression. Together, these findings uncover a novel glioma-promoting role of BCL6, and provide the rationale of targeting BCL6 as a potential therapeutic approach.

Citation Format: Liang Xu, Ye CHEN, Marina Dutra-Clarke, Anand Mayakonda, Masaharu Hazawa, Steve E. Savinoff, Ngan Doan, Jonathan W. Said, William H. Yong, Henry Yang, Ling-Wen Ding, Yan-Yi Jiang, Jeffrey W. Tyner, Jianhong Ching, Jean-Paul Kovalik, Markus Müschen, Joshua J. Breunig, De-Chen Lin, Phillip Koeffler. BCL6 promotes glioma and serves as a novel therapeutic target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2569. doi:10.1158/1538-7445.AM2017-2569
Abstract 2574: The PICT-1 is required for USP7 to effectively stabilize p53 protein, and codon 389 polymorphism is a risk factor for ovarian cancer
Authors: Yoshimoto Masafumi , Tokuda Aoi , Yaginuma Yuji
Published: July 2017

The ovarian cancers causes the deaths of more than 100,000 women per year worldwide, and it is a complex disease, with multiple both histological subtypes and molecular characteristics recognized; therefore, overall survival rates have improved little in the last 30 years. We have to precisely identify genetic and molecular events which could serve as markers for early diagnosis or targets for new therapeutics for ovarian cancers.

The PICT-1 (also named GLTSCR2), one of the nucleolar proteins, has several tumor suppressor functions, such as the stabilization of PTEN and p53. Some studies reported that the loss of or low PICT-1 expression is the common alteration in many cancers, such as brain, skin, lung, esophageal, prostate, kidney, breast, and cervix, but its association with ovarian carcinogenesis has been unknown. Therefore, we investigated its alteration, regulation mechanism, and the effect for p53 stabilization in ovarian cancer.

We found that polymorphism on codon 389 (rs184994) was a statistically significant association with the risk of ovarian cancers. Furthermore, ectopic expression of PICT-1 was required for USP7 to effectively stabilize p53 protein. Because PICT-1 was reported to bind both p53 and MDM2 that enabled to form USP7-p53-MDM2 complex, we investigated whether PICT-1 was regulated by USP7-p53-MDM2 complex. Our results suggested that this complex was the important regulator for PICT-1. In the investigation of the role of PICT-1 that played in the ovarian carcinogenesis using immunohistochemical stainig, we found that PICT-1 protein levels decreased in ovarian cancer tissues compared to normal ovary, and there was a positive correlation between PICT-1 and USP7 protein expression. Our findings suggested that PICT-1 involved in exactly p53 regulation along with MDM2 and USP7, and PICT-1 should be considered as a potential target for therapeutic human cancers.

Citation Format: Masafumi Yoshimoto, Aoi Tokuda, Yuji Yaginuma. The PICT-1 is required for USP7 to effectively stabilize p53 protein, and codon 389 polymorphism is a risk factor for ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2574. doi:10.1158/1538-7445.AM2017-2574
Abstract 2576: Benzyl isothiocyanate potentiates p53 signaling and antitumor effects against breast cancer through activation of p53-LKB1 and p73-LKB1 axes
Authors: Nagalingam Arumugam , Xie Bei , Kuppusamy Panjamurthy , Muniraj Nethaji , Langford Peter , Győrffy Balázs , Saxena Neeraj , Sharma Dipali
Published: July 2017

Functional reactivation of p53 pathway, although arduous, can potentially provide a broad-based strategy for cancer therapy owing to frequent p53 inactivation in human cancer. Using a phosphoprotein-screening array, we found that Benzyl Isothiocynate, (BITC) increases p53 phosphorylation in breast cancer cells and reveal an important role of ERK and PRAS40/MDM2 in BITC-mediated p53 activation. We show that BITC rescues and activates p53-signaling network and inhibits growth of p53-mutant cells. Mechanistically, BITC induces p73 expression in p53-mutant cells, disrupts the interaction of p73 and mutant-p53, thereby releasing p73 from sequestration and allowing it to be transcriptionally active. Furthermore, BITC-induced p53 and p73 axes converge on tumor-suppressor LKB1 which is transcriptionally upregulated by p53 and p73 in p53-wild-type and p53-mutant cells respectively; and in a feed-forward mechanism, LKB1 tethers with p53 and p73 to get recruited to p53-responsive promoters. Analyses of BITC-treated xenografts using LKB1-null cells corroborate in vitro mechanistic findings and establish LKB1 as the key node whereby BITC potentiates as well as rescues p53-pathway in p53-wild-type as well as p53-mutant cells. These data provide first in vitro and in vivo evidence of the integral role of previously unrecognized crosstalk between BITC, p53/LKB1 and p73/LKB1 axes in breast tumor growth-inhibition.

Citation Format: Arumugam Nagalingam, Bei Xie, Panjamurthy Kuppusamy, Nethaji Muniraj, Peter Langford, Balázs Győrffy, Neeraj Saxena, Dipali Sharma. Benzyl isothiocyanate potentiates p53 signaling and antitumor effects against breast cancer through activation of p53-LKB1 and p73-LKB1 axes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2576. doi:10.1158/1538-7445.AM2017-2576
Abstract 2580: Ceramide-rubusoside nano-micelles restores p53-mediated tumor suppression in p53R248W mutant ovarian cancer cells
Authors: khiste sachin K. , Liu Zhijun , Liu Yong-Yu
Published: July 2017

Ceramide (Cer), a sphingolipid metabolite, has crucial functions in anti-proliferation, cell differentiation and apoptosis. Cellular Cer levels highly correlates to therapeutic efficacy of anticancer drugs, however, the hydrophobicity Cer has limits to develop it as a therapeutic agent. Here, we report that Cer-rubusoside (Cer-RUB) nanomicelles enhanced Cer bioavailability and restored p53-mediated tumor suppression. These nanomicelles significantly increased the levels of NBD-C6-Cer by more than 50-fold in serum, 40-fold in tumor and 70-fold in lung of tumor-bearing mice (1 mg/kg, i.p., 24 hr), respectively. Cer-RUB (3 µM) significantly increased OVCAR-3 (p53 R248W) cell sensitivity to cisplatin, and the IC50 values decreased by 3-fold, even though these values were no significant changes in A2780 (wt p53) cells. Furthermore, Cer-RUB treatments (1 mg/kg, i.p. every 3 days for 24 days) significantly increased cisplatin efficacy in tumor growth-arrest in OVCAR-3 tumor-mice, and the tumor volumes reduced by 52% (1653 vs. 805 mm3) in combination with cisplatin, compared to cisplatin alone. We found that ovarian cancer stem cells (CD44+/CD133+) decreased by 10-fold (0.85 vs. 0.08% of total cells) in OVCAR-3 tumors treated with Cer-RUB combined with cisplatin, as compared to cisplatin alone, respectively. Western blotting showed that Cer-RUB treatments selectively increased the expression levels of phosphorylated p53 (Ser15), BAX and p21 in OVCAR-3 cancer cells and tumors, respectively. These studies indicates that the gain-of-function (GOF) of p53 R248W leads OVCAR-3 cell resistance to cisplatin and tumor growth. Cer-RUB can restore p53 and eliminates the GOF of p53 R248W in cancers.

Citation Format: sachin K. khiste, Zhijun Liu, Yong-Yu Liu. Ceramide-rubusoside nano-micelles restores p53-mediated tumor suppression in p53R248W mutant ovarian cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2580. doi:10.1158/1538-7445.AM2017-2580
Abstract 2582: KIRnome: KIR genotyping for whole genome/exome sequencing data
Authors: Kim Daeyoon , Yoon Sung-Soo , Koh Youngil , Lee Su Yeon , Yun Hongseok , Cho Sunghoon , Kim Hyung-Lae
Published: July 2017

In this study, we tried to develop valid KIR calling algorithm from WES/WGS data. As a consequence, here we suggest KIRnome (KIR typing for whole genome and exome sequencing) which is a KIR typing method for applying sequencing data such as WES/WGS. A total of 71 sequencing data (18 WES and 53 WGS data, respectively) and matched experimentally validated KIR genotype data are used to train and validate. Before developing this method, two types of allele references (genomic and coding, here after called gSeq and cSeq) are constructed by allele sequence of IPD/KIR. KIRnome consists of two part, first part is calculating normalized depth (here after called depth) of 16 KIR genes and considering allele reference length and second is estimating KIR type based on depth. In general, we get higher normalized depth when using genomic references for WGS data and using coding references for WES data. This coincides with scheme KIRnome and the characteristics of WGS and WES data. Given 71 samples of 3 data sets, we evaluated KIR genotyping performance of KIRnome per each KIR gene. For all 16 KIR genes, KIRnome shows >=98.5% accuracy. When KIRnome performance was tested only in 13 WES samples, the accuracy slightly drops to 94%. We assume this is attributable to relatively small number of the samples. In conclusion, we developed a novel and unique method named KIRnome for KIR typing from NGS data. KIRnome could determine KIR genotype accurately from WES and WGS data respectively. We expect KIRnome would facilitate revealation of immunogenetic facts in various disease. Moreover, future generation of KIR specific NGS data and improved reference sequence information of KIR would enable KIRnome to type KIR at allele level in a near future.

Citation Format: Daeyoon Kim, Sung-Soo Yoon, Youngil Koh, Su Yeon Lee, Hongseok Yun, Sunghoon Cho, Hyung-Lae Kim. KIRnome: KIR genotyping for whole genome/exome sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2582. doi:10.1158/1538-7445.AM2017-2582
Abstract 2587: VCF2CNA: a tool for efficiently detecting copy number alteration using VCF genotype data
Authors: Putnam Daniel K. , Ma Xiaotu , Rice Stephen V. , Liu Yu , Zhang Jinghui , Chen Xiang
Published: July 2017

Whole genome sequencing (WGS) is increasingly used in both research and clinical settings. The Variant Call Format (VCF) specification is a widely adopted file format for genetic variation data exchange partially due to its smaller file size compared to raw WGS BAMs. Each variant in a typical VCF file contains its chromosome position, reference/alternative alleles and corresponding allele counts. This makes it possible to identify copy number alterations (CNAs). To this end, we developed VCF2CNA (http://vcf2cna.stjude.org), a web interface tool for CNA analysis from VCF files.

A user of VCF2CNA, uploads a VCF file via the provided web interface. The entire analysis runs remotely with an average run time of 23 minutes. Results are emailed to the user as either a downloadable link or file attachments. VCF2CNA also accepts input in the Mutation Annotation Format (MAF) and the variant file format produced by the Bambino program.

We analyzed 22 TCGA glioblastoma tumor/normal pairs by Illumina technology to evaluate VCF2CNA’s performance. It achieved high consistency (average F1-score: 0.952 ± 0.082) with CONSERTING, a tool that incorporated read-depth and SV data from raw BAMs for CNA detection. A segment-by-segment comparison between results from CONSERTING and VCF2CNA indicated that the latter was less sensitive to focal CNAs. This is expected because there is less information in the VCF input than in raw BAMs. Further analysis using samples with a “fractured genome” pattern revealed that VCF2CNA was more robust to library artifacts and produced relatively clean CNA profiles (on average 76.2-fold reduction compared to the number of segments reported by CONSERTING).

Finally, we analyzed 137 pediatric neuroblastoma samples from the TARGET project, sequenced by Complete Genomics, Inc. (CGI) technology. MYCN amplification has been clinically validated in 33 samples. VCF2CNA identified high amplitude MYCN gains in 32 samples and the remaining sample carried a low-level broad gain covering MYCN. For comparison, CGI’s HMM-based method reported MYCN gains in only 15 out of the 33 samples. VCF2CNA further identified two additional MYCN amplifications among the remaining samples. Collectively, our analysis suggests that VCF2CNA is a platform-independent, efficient, robust and accurate tool for general WGS-based CNA analysis. It further complements CONSERTING, which produces more accurate result in focal CNAs at the cost of significantly higher computational burden.

Citation Format: Daniel K. Putnam, Xiaotu Ma, Stephen V. Rice, Yu Liu, Jinghui Zhang, Xiang Chen. VCF2CNA: a tool for efficiently detecting copy number alteration using VCF genotype data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2587. doi:10.1158/1538-7445.AM2017-2587
Abstract 2601: COSMIC-3D: exploring cancer mutations in three dimensions for drug design and discovery
Authors: Jubb Harry C. , Saini Harpreet , Verdonk Marcel , Forbes Simon
Published: July 2017

Explosions in the availability of cancer genomic data and protein structure data give us the potential to explore cancer molecular biology at an unprecedented scale, and in atomic detail. We present COSMIC-3D, which combines COSMIC, the most comprehensive cancer mutation database available (http://cancer.sanger.ac.uk), with the wealth of publicly available 3D protein structure data, to create a resource with which the protein-structural nature of cancer can be probed.

COSMIC-3D will help us understand which cancer mutations drive the progression of cancers, by identifying which are in functional sites that have an effect on driving cell growth and proliferation, and where they are clustered in protein structures across the proteome, for specific cancer types. Through understanding the effects of cancer mutations on known and predicted drug binding sites, we aim to predict potential new drug targets in cancers, and improve the specificity and efficacy of new or existing drugs, by using protein structure with cancer mutation data to guide mutation-specific drug design.

COSMIC-3D is available as a web interface at http://cancer.sanger.ac.uk/cosmic3d, and enables interactive exploration of the cancer mutome in a 3D peptide environment, showing all forms of exonic point mutation. Individual mutant locations can be highlighted as molecular surfaces, while recurrence across nonsynonymous substitutions is visualized as 3D heat-maps. Cancer mutations can also be visualised in combination with precalculated small-molecule “druggable” binding sites, providing a powerful visual approach for development of hypotheses across structural, functional, and drug-resistance impacts of cancer variants. COSMIC-3D shows, for example, the steric occlusion of the binding site of ATP-competitive small-molecule inhibitors in the EGFR kinase domain by the mutation of L858 to arginine; these kinds of insights can be applied to novel cancer targets for any protein-structural mutation of interest.

The human cancer structural proteome comprising COSMIC-3D extends to nearly 8,500 human genes; 1/3rd of genes in COSMIC. Over 30,000 human protein structures are available across these genes, to which over 345,000 cancer mutations are mapped. From structure based druggability prediction, over 6,500 proteins in COSMIC are predicted to have small-molecule druggable binding sites, making COSMIC-3D a powerful and exciting resource for the exploration and guidance of drug design and discovery in oncology.

Citation Format: Harry C. Jubb, Harpreet Saini, Marcel Verdonk, Simon Forbes. COSMIC-3D: exploring cancer mutations in three dimensions for drug design and discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2601. doi:10.1158/1538-7445.AM2017-2601
Abstract 2611: A crowdsourcing-based clinical trial information curation and searching system
Authors: Yu Pengfei , Song Qingxuan , Han Yang , Hu Guanghui
Published: July 2017

Targeted cancer therapies based on actionable mutations identified are the future of cancer treatment. Besides those approved by the Food and Drug Administration (FDA) for different types of cancers, many other target therapy drugs are in development under different phases of clinical trials. Access to information about these clinical trials is important to health care professionals and patients. Public clinical trials database (www.clinicaltrials.gov) provides a very comprehensive resource for clinicians and researches to search for relevant clinical trials based on different kinds of searching criteria. However, due to the complexity of wording and phasing upon submission, some of the searching results returned by native search engine did not perfectly match the search criteria. Many undesired results are presented with false positives and false negatives when users are searching for clinical trials targeting specific actionable mutations. To tackle this problem, we developed a crowd-sourcing based clinical trial curation and searching system on top of the information extracted from public database. We divide the information extracted from clinicaltrials.gov into three different levels: standard, easy-to-clean and unstructured. With the crowdsourcing approach, our online system can harness the brainpower of biological scientists to translate the most unstructured information such as cancer types, gene mutations into standard format that is easy to be queried. In the searching phase, we combine the aspects of actionable mutation, cancer type, location, and clinical trial phase to select the best matches between patient conditions and clinical trials in our curated database. With the same searching criteria, our system can provide more relevant clinical trials compared with those provided by clinicaltrials.gov. The curation system is currently open to reviewers with eligibility check. And the search engine is publicly available at: https://agis.admerahealth.com/AGIS/ClinTrials/.

Citation Format: Pengfei Yu, Qingxuan Song, Yang Han, Guanghui Hu. A crowdsourcing-based clinical trial information curation and searching system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2611. doi:10.1158/1538-7445.AM2017-2611
Abstract 2633: Identification of novel T cell co-inhibitory and co-stimulatory receptors from screening a comprehensive library of extracellular proteins
Authors: Brace Arthur , Sallee Nathan , Chou Justin , Garrenton Lindsay , Chen Diana , Liang Ryan , Kemper Greg , Yang David , Jaquez Marina , Powers Janine , Mkrtichyan Mikayel , Brennan Thomas , Borges Luis
Published: July 2017

Antibody blockade of immune checkpoint regulators such as PD-1 and CTLA-4 has been shown to be an effective cancer treatment strategy; however, a large percentage of patients still do not respond to existing therapies. Discovery of additional immune checkpoints and co-stimulatory receptors and development of antibody therapeutics against them are likely critical to address this unmet patient need. We generated a comprehensive library of essentially all human extracellular proteins and have used this library to screen for new agents that modulate the function of various immune cell subsets both in vitro and in vivo. Using primary T effector and regulatory T cells, we have identified new targets that modulate the activities of these T cell populations in vitro and are currently evaluating these proteins as possible targets for cancer immunotherapy. In addition, we have expressed a subset of the library in three different models of tumor-bearing mice and have identified several proteins that modulate anti-tumor immunity in vivo. Several of the proteins identified in these screens have activity across multiple primary cell and in vivo tumor model screens and we are rapidly evaluating them as possible targets for novel immuno-oncology therapeutics. Taken together, we believe that we have developed robust in vitro and in vivo platforms that will allow us to discover novel cancer immuno-therapeutics that will help address the needs of cancer patients that fail to respond to current immunomodulatory therapies.

Citation Format: Arthur Brace, Nathan Sallee, Justin Chou, Lindsay Garrenton, Diana Chen, Ryan Liang, Greg Kemper, David Yang, Marina Jaquez, Janine Powers, Mikayel Mkrtichyan, Thomas Brennan, Luis Borges. Identification of novel T cell co-inhibitory and co-stimulatory receptors from screening a comprehensive library of extracellular proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2633. doi:10.1158/1538-7445.AM2017-2633
Abstract 265: Global transition in cardia and non-cardia gastric cancer incidence, 1998-2007
Authors: Shin Aesun , Kim Dalis Seungeun , Woo Hyungtaek
Published: July 2017

Gastric cardia and non-cardia cancer differs in their descriptive patterns and risk factors. The objective of this study was to determine the global trends in incidence of cardiac and non-cardiac gastric cancer. Ninety two high quality registries with the proportion of Not Otherwise Specified (NOS) gastric cancer (ICD-10 code C16.8-9) below 50% and the total number of gastric cancer cases above 300 were selected from 225 registries in Cancer Incidence of Five Continent (CI5) volume 9 and 262 registries from CI5 volume 10. The NOS cases were re-distributed to cardia and non-cardia according to the registry-specific proportion. Age-standardized incidence rates (ASRs) per 100,000 population and incidence rate ratios (IRR) from 1998-2002 to 2003-2007 were calculated. Non-cardia cancer incidence was significantly decreased in 5 out of 10 Asian registries, 17 out of 18 European registries, 27 out of 56 North American registries, and all 5 Oceanian registries in men. Only two registries in Asia showed a significant increase in non-cardia cancer incidence. In contrast, cardia cancer significantly increased in one Asian registry, two European registries, and two North American registries. Significant decrease in cardia cancer was observed in 3 Asian registries, 6 European registries, 11 North American registries, and 3 Oceanian registries in men. In women, six registries (1 Asian, 2 European, and 3 North American) showed significant increase in non-cardia cancer, whereas registries 25 (3 Asian, 13 European, 8 North American, and 1 Oceanian) showed significant decrease in non-cardia cancer incidence. Cardia cancer in women increased in 16 registries (2 Asian and 14 North American) and decreased in 9 registries (1 Asian, 5 European, and 3 North American). In conclusion, non-cardia cancer incidence decreased in most registries, whereas decrease in cardia cancer is more prominent in men but not in women.

Citation Format: Aesun Shin, Dalis Seungeun Kim, Hyungtaek Woo. Global transition in cardia and non-cardia gastric cancer incidence, 1998-2007 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 265. doi:10.1158/1538-7445.AM2017-265
Abstract 2657: PD-L1 blockade enhances T cell cytotoxicity against primary mediastinal B cell lymphoma
Authors: Shah Tishi , Luo Wen , Awasthi Aradhana , Ayello Janet , Hochberg Jessica , Cairo Mitchell
Published: July 2017

Background:

Primary Mediastinal B cell Lymphoma (PMBL) represents 2-4% of Non-Hodgkin Lymphomas (NHL) in adolescents and young adults (AYA) (Gerrard/Cairo et al., Blood, 2013). Disease progression, relapse and long-term toxicity remain a concern for patients treated on current chemo-immunotherapy and mediastinal radiotherapy. Alternative therapeutic regimens are urgently needed, especially in patients without an early response to therapy. Programmed Death 1 (PD-1) is a negative co-stimulatory receptor critical for suppression of T-cell activation, with binding of PD-1 and Programmed Death Ligand 1 (PD-L1) resulting in T cell exhaustion (Postow/Wolchok et al., J Clin Oncol, 2015). Gain in 9p associated with amplification of PD-L1 has been reported in up to 60% of PMBL specimens, leading to overexpression of PD-L1 and potential immune cell evasion of PMBL (Rosenwald/Staudt et al., J Exp Med, 2003; Twa/Steidl et al., Blood, 2014). Blockade of PD-1/PD-L1 interaction, therefore, constitute a potentially promising alternative for treatment of resistant PMBL.

Objective:

In the current study, we sought to investigate whether PD-L1 blockade enhances T cell responses in PD-L1 expressing PMBL.

Methods:

PD-L1 expression on Karpas 1106p PMBL treated with or without IFN γ was investigated by western blotting and flow cytometry analyses. T cells were isolated from human PBMC followed by activation and expansion using anti-CD2, anti-CD3 and anti-CD28 Biotinylated MACSiBead particles. T cell activation was confirmed by CD25 and CD69 expression using flow cytometry. Activated T cells were incubated with or without anti-PD-L1 (Clone 6E11, Genentech) at a dose of 10 ug/ml together with Karpas 1106p cells treated with or without IFN γ. Cell proliferation was assessed with MTS assays after incubation for 24 hours.

Results:

We demonstrated that Karpas 1106p cells express a low level of PD-L1. However, following IFN γ treatment (48 hours) there was a significant increase in PD-L1 expression. Anti-PD-L1 had no significant effect on T cell mediated inhibition of cell proliferation in Karpas 1106p cells with low PD-L1 expression. However, anti-PD-L1 and T cell treatment significantly inhibited cell proliferation in IFN γ treated Karpas 1106p cells when compared to T cell treatment alone (32±18% vs. 3±3% at E:T=5:1, p=0.048).

Conclusion:

PD-L1 blockade enhances T cell cytotoxicity against PMBL, which is dependent on PD-L1 expression level on PMBL cells. Future in-vivo NSG xenograft studies are ongoing.

Citation Format: Tishi Shah, Wen Luo, Aradhana Awasthi, Janet Ayello, Jessica Hochberg, Mitchell Cairo. PD-L1 blockade enhances T cell cytotoxicity against primary mediastinal B cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2657. doi:10.1158/1538-7445.AM2017-2657
Abstract 2660: PD-1 blockade in combination with zoledronic acid to enhance the antitumor efficacy in the breast cancer mouse model
Authors: Li Yuan , Du Yang , Sun Ting , Xue Huadan , Tian Jie , Jin Zhengyu
Published: July 2017

Purpose: Blockade of PD-1 receptor may provide proof of concepts for the activity of an immune-modulation approach for the treatment of a breast cancer (BC). Zoledronic acid (ZA) has been proven to inhibit angiogenesis, invasion, and adhesion of tumor cells. The aim of this study was to investigate the potential of antibody treatment towards the T-cell checkpoint inhibitor PD-1 alone or in combination with ZA in BC mouse model.

Experimental Design: The 4T1-Luc mouse mammary tumor model was used in this study. The anti-tumor efficacy of anti-PD-1 antibody alone or in combination with ZA was monitored by measuring tumor volume and bioluminescence imaging (BLI). At the end of study, the tumor immunohistochemistry was performed to confirm the in vivo observation and flow cytometry was used to determine the immune cell population in tumors. The survival rate was also calculated to evaluate the treatment efficacy.

Results: The results showed that mice treated with the combination therapy exhibited the best antitumor response compared to untreated controls or single therapy. Furthermore, Combination therapy inhibited tumor regrowth as determined by BLI imaging, and thus significantly improved the median overall survival compared to other groups.

Conclusions: Our study provides evidence for enhanced clinical BC treatment benefit from targeting co-signal molecules by combining PD-1 blockade with ZA treatment.

Citation Format: Yuan Li, Yang Du, Ting Sun, Huadan Xue, Jie Tian, Zhengyu Jin. PD-1 blockade in combination with zoledronic acid to enhance the antitumor efficacy in the breast cancer mouse model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2660. doi:10.1158/1538-7445.AM2017-2660
Abstract 2665: Green tea catechin, EGCG, enhances antitumor immunity by down-regulation of PD-L1 expression in non-small human lung cancer cell lines
Authors: Rawangkan Anchalee , Iida Keisuke , Sakai Ryo , Fujiki Hirota , Suganuma Masami
Published: July 2017

(-)-Epigallocatechin gallate (EGCG) is now widely accepted as a non-toxic, effective cancer preventive compound. EGCG also acts as a synergist with anti-cancer drugs for cancer treatment. Considering the wide beneficial effects of EGCG, we think EGCG might have antitumor immunity. Programmed death-ligand 1 (PD-L1) expression on tumor cells is involved in PD-L1/PD-1 pathway. PD-L1 protein levels varied among 6 non-small human lung cancer cell lines (NSCLCs): LC-AI and Lu99 cell lines showed the highest PD-L1 expression, A549 and H322 cell lines were medium, and H1703 and H1299 were very low, independent on cancer cell lines. Since PD-L1 expression is induced by various cytokines and growth factors, we studied the effects of IFN-γ and EGF on cell-surface PD-L1 level using flow cytometry, and its gene expression using RT-PCR. Treatment with IFN-γ dose-dependently stimulated PD-L1 expression in both A549 and H1299 cells, and not effective on Lu99 cells, whereas treatment with EGF stimulated PD-L1 in Lu99 cells only.

Pretreatment with EGCG for 3 h, dose-dependently inhibited INF-γ-induced PD-L1 gene expression and protein level on cell-surface in both A549 and H1299. It is important to note that EGCG also inhibited phosphorylation of STAT1. In addition, EGCG inhibited EGF-induced PD-L1 gene expression and protein level in Lu99 cells via inhibition of phosphorylation of Akt. In order to study the effects of EGCG in between rodent carcinogenesis experiment and antitumor immunity, green tea extract (GTE) was given to NNK-induced lung tumors in A/J mice, which showed significant reduction of PD-L1 protein level, determined by immunohistochemical analysis using anti-PD-L1 antibody. Furthermore, the group treated with NNK + GTE significantly showed reduced number of tumors per mouse from 3.2 to 2.2, and decreased tumor size. Treatment with Wortmannin, a PI3K inhibitor, as a control, did not inhibit PD-L1 expression in A549 and H1299 cells. The results strongly suggest that EGCG enhances antitumor immunity via inhibition of PD-L1 expression in cancer cells, resulting in significant cancer preventive activity.

Citation Format: Anchalee Rawangkan, Keisuke Iida, Ryo Sakai, Hirota Fujiki, Masami Suganuma. Green tea catechin, EGCG, enhances antitumor immunity by down-regulation of PD-L1 expression in non-small human lung cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2665. doi:10.1158/1538-7445.AM2017-2665