bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4395: Somatic genomic alteration of 412 cancer-targeted genes of periampullary and pancreatic ductal adenocarcinoma in Indian patient population
Authors: Sikdar Nilabja , Saha Gourab , Singh Richa , Anchlia Dhiraj , Roy Paromita , Ghatak Supriyo , Banerjee Sudeep , Gulati Sumit , Ghosh Shibajyoti
Published: July 2017

Introduction: Pancreatic Ductal Adenocarcinoma (PDAC), the most common primary malignant disease of the pancreas and the periampullary region, accounts for about 75% of all nonendocrine tumors arising in this region. It is 4th most lethal malignancies. The 5 year survivability rate is below 5%. At the beginning of the 21st century, the estimated number of PC worldwide was 110,000, with an estimated global mortality rate of 98%. Incidence of periampullary adenocarinoma (PACs) is low, approximately 0.5-2% of all gastrointestinal malignancies and 20% of all tumors of the extrahepatic biliary tree.

Aims & Objectives: To identify the somatic single nucleotide variants (SNV’s) in 412 cancer related genes in PDAC & PAC’s. To identify possible altered biological pathways enriched in these cancers.

Methodology: DNA samples from Tissue and blood were sequenced for exon sequencing of 412 cancer related genes (NIMBLGNE panel, Custom). Raw fastq files processed using GATK tools and variants identified by Varscan2, & MuTect. Altered pathways identified by KEEG.

Result: A total 105 Somatic exonic Single Nucleotide Variants (SNV’s), 9 somatic exonic Indels, 22 LOH mutations (both Indel and SNV’s) were identified in our sample set. Among the candidate genes of PDAC somatic SNV’s were found in TP53, SMAD4 in some patient whereas frequency of KRAS mutation was less frequent. Fourteen SNV’s were reported in cosmic database which includes 5 pathogenic variants, whereas 91 SNV’s were novel. A total 75 non-synonymous, 6 stopgain, and 24 synonymous SNV’s were observed among 105 SNV’s. Fifty eight percent of transversion and 52% of transition observed from all SNVs. Among all transversion fifty five percent SNV’s were C>T, G>T. PI3-Akt, Proteoglycans in cancer, Transcription misregulation, Rap1, ErbB, Neurotrophin pathways were found to be most commonly enriched in our patient population. Our data strongly suggest PI3-Akt, Proteoglycans in cancer pathways play a critical role in the disease.

Conclusion: This study implicates a landscape of somatic SNV’s in PDAC’s and PAC’s and alteration of biological pathways in our patient population. We also observeed ERBB2 and KMT2C genes are predominantly alerted in PDAC’s and PAC’s. P53, KRAS and SMAD4 are the known mutated genes contributes very similar mutational pattern.

Citation Format: Nilabja Sikdar, Gourab Saha, Richa Singh, Dhiraj Anchlia, Paromita Roy, Supriyo Ghatak, Sudeep Banerjee, Sumit Gulati, Shibajyoti Ghosh. Somatic genomic alteration of 412 cancer-targeted genes of periampullary and pancreatic ductal adenocarcinoma in Indian patient population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4395. doi:10.1158/1538-7445.AM2017-4395
Abstract 440: The oncogenic activity of a pro-oxidant intracellular milieu is associated with redox dependent activation of NF-kB
Authors: Yee Michelle Y. , Chong Stephen J. , Pervaiz Shazib
Published: July 2017

Evidence over the years has highlighted that intracellular redox status plays a critical role in determining cell fate. To date, we have shown that a pro-oxidant milieu, specifically a mild elevation of intracellular superoxide, promotes cancer cell survival and chemoresistance. To that end, we demonstrated in vitro that elevated superoxide, upon silencing of superoxide dismutase (SOD1), resulted in sustained phosphorylation of Bcl-2 at serine 70, thereby stabilizing its anti-apoptotic activity. These findings were corroborated by the abundance of Serine 70 Bcl2-phosphorylation and low SOD1 expression in lysates of patients with aggressive lymphomas and/or disease with poor prognosis. In addition to the anti-apoptotic protein Bcl-2, the pro-inflammatory transcription factor nuclear factor kappa B (NF-κB)- mediated signaling was also shown to be modulated by intracellular redox milieu. As constitutive activation of NF-κB has been reported in various human tumors, which is often associated with malignant progression and chemotherapeutic resistance, here we set out to investigate whether a pro-oxidant environment, specifically the upregulation of intracellular superoxide, was associated with the induction of NF-κB transcriptional activity. Indeed, we demonstrate that elevated intracellular superoxide via the pharmacological inhibition and genetic silencing of SOD1 results in enhanced activation of canonical NF-κB signalling. This is accompanied by increased p65 nuclear localization and transcription of NF-κB regulated genes, which potentially confer survival advantages to tumour cells upon chemotherapeutic treatments. Considering the association between NF-kB activation, chronic inflammation and the process of carcinogenesis, these preliminary data provide a novel mechanism of activation of this master transcriptional factor with potential therapeutic implications.

Citation Format: Michelle Y. Yee, Stephen J. Chong, Shazib Pervaiz. The oncogenic activity of a pro-oxidant intracellular milieu is associated with redox dependent activation of NF-kB [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 440. doi:10.1158/1538-7445.AM2017-440
Abstract 441: GOT1 regulates anaplerotic glutamine metabolism under chronic acidosis stress in pancreatic cancer
Authors: Abrego Jaime , Gunda Venugopal , Vernucci Enza , Shukla Surendra , King Ryan J. , Dasgupta Aneesha , Chaika Nina , Singh Pankaj Kumar
Published: July 2017

Epithelial-cell derived tumors exhibit the Warburg effect that is characterized by an increased rate of glycolysis and lactate release, as well as, reduced oxidative metabolism. It is known that these metabolic alterations of cancer cells result in a tumor microenvironment with a lower pH than that of the plasma. However, little is known regarding the physiology and metabolism of cancer cells enduring chronic acidosis. Here, we cultured pancreatic cancer cells in chronic acidosis, i.e. pH 6.9 to 7.0, and observed a shift from glycolytic metabolism to oxidative metabolism that also results in reduced cell growth and increased intracellular ROS levels. We identified that this is due to an increase in glutamine uptake and increased expression of the transaminase enzyme GOT1 that enhances glutamine metabolism. Survival in low pH is reduced upon depletion of GOT1 due to further increased intracellular ROS levels. Thus, GOT1 plays an important role in energy metabolism and ROS balance in chronic acidosis stress. Our studies suggest the therapeutic potential of targeting anaplerotic glutamine metabolism in pancreatic cancer.

Citation Format: Jaime Abrego, Venugopal Gunda, Enza Vernucci, Surendra Shukla, Ryan J. King, Aneesha Dasgupta, Nina Chaika, Pankaj Kumar Singh. GOT1 regulates anaplerotic glutamine metabolism under chronic acidosis stress in pancreatic 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 441. doi:10.1158/1538-7445.AM2017-441
Abstract 4417: The role of EBV infection in aerobic glycolysis in nasopharyngeal carcinoma
Authors: Tsao George S. , Zhang Jun , Xia Lin , Tsang C , Lin Weitao , Yip Y , Deng W , Lo K , Lung M
Published: July 2017

Accumulating evidence indicates that oncogenic viral protein exerts a crucial role in activating aerobic glycolysis during tumorigenesis, but the underlying mechanisms are largely undefined. The Epstein-Barr virus (EBV)-encoded latent membrane protein 1 (LMP1) is a trans-membrane protein with potent cell signaling properties and has tumorigenic transformation property. Activation of NF-κB is a major signaling pathway mediating many downstream transformation properties of LMP1. Here we report that activation of mTORC1 by LMP1 is a key modulator for activation of NF-κB signaling to mediate aerobic glycolysis. NF-κB activation is involved for LMP1-induced upregulation of glucose transptor-1 (Glut-1) transcription and growth of nasopharyngeal carcinoma (NPC) cells. Collectively, blocking the activity of mTORC1 signaling effectively suppressed LMP1-induced NF-κB activation and Glut-1 transcription. Interfering NF-κB signaling has no effect on mTORC1 activity but effectively altered Glut-1 transcription. Luciferase promoter assay of Glut-1 also confirmed that Glut-1 is a direct target gene of NF-κB signaling. Furthermore, we demonstrated that the LMP1 C-terminal activating region (CTAR) 2 is the key domain involved in mTORC1 activation, mainly through IKKβ-mediated phosphorylation of TSC2 at Ser939. Depletion of Glut-1 effectively led to suppression of aerobic glycolysis, inhibition of cell proliferation, colony formation, and attenuation of tumorigenic growth property of LMP1-expressing nasopharyngeal epithelial (NPE) cells. These findings suggest that targeting the signaling axis of mTORC1/NF-κB/Glut-1 represents a novel therapeutic target against NPC.

Acknowledgement: 96 800x600 This project was supported by the General Research Fund (HKU 779810M, 17120814 and 17161116), CRF equipment grant (1061402980, Health and Medical Research Fund of Hong Kong (12110782), AoE grant (AoE/M-06/08) and TBRS grant (T12-401/13-R). We thank Prof. Dongyan Jin (Department of Biochemistry, The University of Hong Kong) for the kind gifts of IKK related plasmids and Prof. Zhenguo Wu (Division of Life Science, The Hong Kong University of Science and Technology) for the discussion and interpretation of the data. We also thank Mr. Tony Chan for his technical support.

Note: This abstract was not presented at the meeting.

Citation Format: George S. Tsao, Jun Zhang, Lin Xia, C Tsang, Weitao Lin, Y Yip, W Deng, K Lo, M Lung. The role of EBV infection in aerobic glycolysis in nasopharyngeal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4417. doi:10.1158/1538-7445.AM2017-4417
Abstract 4427: An integrated analysis package of miRNA and mRNA expression dataAn integrated analysis package of miRNA and mRNA expression data
Authors: Wang Ti-Tai
Published: July 2017

MicroRNAs(miRNAs) are small and non-coding RNAs that can regulate gene expression by binding on the 3’UTR of target mRNAs and inhibiting mRNAs to translate protein, or even promoting mRNAs degradation. In various complex disease and pathological conditions, we can identify dysregulated which are the causative factors. Therefore, it is an essential approach to explore the interactions between miRNA and gene in certain diseases, such as cancers. However, challenge arises when we are trying to validate the interactions by doing bench experiments. The numbers of miRNA-gene interactions are too large to be validated. Currently, most prediction algorithms only provide its own result and low consistency rates across independent methods have been reported. Therefore, it is necessary to develop a systematic method to perform a comprehensive analysis by using the expression profiles from genes and miRNAs concurrently. To address these issues, we developed an R package named as anamiR. AnamiR is able to perform an integrated analysis of mRNA and miRNA with the phenotype information. The analysis procedures are briefly summarized as the follows. Initially, differential expression analysis would be applied to the raw data. Subsequently, the anamiR package can identify significant pairs of miRNAs and genes if their Pearson correlation coefficients are lower than the pre-defined threshold. Next, the significant pairs were compared to the embedded database in anamiR, which included two validated and several predicting miRNA-gene databases. Lastly, functional analysis is also available in this package to characterize the biological functions and signaling pathways of dysregulated miRNAs and genes. A breast cancer dataset was analyzed by using anamiR, which identified nine miRNA-gene interactions for deeper studying. Among these interactions, there are two miRNAs and nine genes included. miR-497-5p and miR-204-5p which both were mentioned in breast cancer frequently, are found by anamiR. The anamiR package is freely available at Bioconductor.

Citation Format: Ti-Tai Wang. An integrated analysis package of miRNA and mRNA expression dataAn integrated analysis package of miRNA and mRNA expression 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 4427. doi:10.1158/1538-7445.AM2017-4427
Abstract 4437: Small non-coding RNA profiling from prostate cancer plasma by deep sequencing
Authors: Liu Xianghua , Hunter Andrew , Zhang Qing , He Quanyuan , Benton Annemarie , Ortiz Gerri , Pannu Vaishali , Xiao Nick , Miglarese Mark , Spetzler David
Published: July 2017

Background: Prostate cancer (PCa) is the most common non-skin cancer among American men. MicroRNAs (miRNAs) are critical post-transcriptional regulators and involved in prostate cancer tumorigenesis. The aim of this study is to identify a PCa-specific expression profile of miRNAs from plasma to guide prostate cancer diagnosis and therapeutic treatment.

Methods: Plasma was collected from 5 PCa patients and 5 normal men. Circulating RNA was extracted from 1) 200ul plasma or 2) the pellets of anti-Ago2 immunoprecipitations from 500ul plasma using the miRNeasy Serum/Plasma kit (Qiagen), with addition of glycogen as a carrier. Small RNA libraries were constructed using the NEBNext Multiplex Small RNA Prep Set for Illumina® (New England. BioLabs). The cDNA library fragments were purified by Blue Pippin (Sage Science) for extraction of 140-160 bp size fraction containing small RNA inserts. Equimolar amounts of cDNA library samples were pooled and were sequenced in a single flowcell on an Illumina HiSeq2500 with 50 cycle kit and rapid run model.

Bioinformatics analysis: Adaptor was firstly removed from the raw reads, and the sequences were mapped to several small RNA databases by using bowtie1 with 1 mismatch. The multiple aligned reads were weighted to the mapped small RNAs based on their unique mapped reads counts. We then calculated the RPM (reads per million) as indicator of the expression levels of the small RNA. To get confident analysis results, we discarded the small RNAs whose averages of the raw reads counts in cancer and normal groups are smaller than 25 and only focus on the mature microRNAs. The moderate t-test is applied to find the differently expressed (DE) microRNAs between normal and cancer group.

Results: Two major small RNA classes identified from total plasma are miRNA (47.7%) and yRNA (35.0%). The percentage of miRNA increased to 85.3% by Ago2-IP method. The compositions of categories of small RNAs in cancer and normal samples are similar. We identified 28 and 22 differential miRNAs (>2 fold change between cancer and normal group) by total plasma and Ago-2 IP methods respectively.

Conclusions: We discovered a unique expression profile of miRNA detectable in the plasma from prostate cancer patients. Extracted RNA from the pellets of anti-Ago2 immunoprecipitations can enhance the detection of miRNA. Expand study to confirm these findings are needed.

Citation Format: Xianghua Liu, Andrew Hunter, Qing Zhang, Quanyuan He, Annemarie Benton, Gerri Ortiz, Vaishali Pannu, Nick Xiao, Mark Miglarese, David Spetzler. Small non-coding RNA profiling from prostate cancer plasma by deep sequencing [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 4437. doi:10.1158/1538-7445.AM2017-4437
Abstract 444: Monocarboxylate transporter 1 inhibition with AZD3965 increases cancer cell dependence on bioenergetic metabolism predicating combination therapy with mitochondrial inhibitors
Authors: Beloueche-Babari Mounia , Galobart Teresa Casals , Wantuch Slawomir , Smith Paul D. , Leach Martin O.
Published: July 2017

Monocarboxylate transporters (MCTs) are key mediators of lactate transport that have emerged as promising targets for anti-cancer therapy. The MCT1 inhibitor AZD3965 (AstraZeneca) has shown promising activity in various pre-clinical models and is currently in phase I/II clinical testing. Understanding the impact of this drug on tumour cell metabolism may unravel dependencies that could be exploited for combination therapy. Here we investigate changes in glucose metabolism induced by AZD3965 treatment using 13C NMR isotopomer analysis, and examine their significance for cell survival using mitochondrial metabolism inhibitors.

Exposure of Raji human lymphoma cells to AZD3965 in media supplemented with [1-13C]glucose led to a marked reduction in glucose uptake and lactate production in the cellular growth media alongside a build-up in intracellular [3- 13C]lactate and [1-13C]glucose levels, indicative of blockade of lactate excretion and inhibition of overall glycolytic activity. These effects were concomitant with increased [4-13C]glutamate levels, consistent with re-routing of pyruvate towards mitochondrial metabolism and enhanced flux through oxidative pyruvate dehydrogenase.

Further, AZD3965 treatment was paralleled with a significant increase in levels of steady state Krebs cycle-related metabolites (including succinate, fumarate, acetate and NAD+/NADH) and cellular ATP, as revealed by bioluminescent and 1H NMR analyses, indicating improved mitochondrial metabolism and cellular re-energization.

Co-administration of the mitochondrial complex I inhibitor metformin or the mitochondrial pyruvate carrier inhibitor UK5099 markedly potentiated the anti-proliferative effects of AZD3965 and led to significantly increased cell death, indicating that the observed upregulation in mitochondrial metabolism was necessary to maintain cell survival under MCT1 inhibitor-induced metabolic stress. Similar effects were observed with a second human lymphoma cell line, Hut78.

Our findings show that MCT1 inhibition leads to a shift in cellular metabolism towards mitochondrial bioenergetic metabolism, creating a metabolic vulnerability that could be exploited for combinatorial therapy to increase the efficacy of AZD3965.

Citation Format: Mounia Beloueche-Babari, Teresa Casals Galobart, Slawomir Wantuch, Paul D. Smith, Martin O. Leach. Monocarboxylate transporter 1 inhibition with AZD3965 increases cancer cell dependence on bioenergetic metabolism predicating combination therapy with mitochondrial inhibitors [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 444. doi:10.1158/1538-7445.AM2017-444
Abstract 4441: Unveil the role of cell-free circulating microRNA in lung cancer
Authors: Bianchi Fabrizio , Melocchi Valentina , Colangelo Tommaso , Cuttano Roberto , Muscarella Lucia Anna , Dama Elisa
Published: July 2017

We previously reported the identification of a signature composed by 34 serum circulating cell-free microRNAs (cf-miRNA) diagnostic for lung cancer. Using this signature, we developed a blood test (miR-test) which was capable of detecting asymptomatic lung cancer in a large cohort (N>1000) of high-risk individuals (>50years and smokers). Interestingly, we now found that a fraction (~30%) of these cf-miRNAs were preferentially expressed in cells of epithelial origin, while another ~30% were more expressed in hematopoietic cells. We reasoned that this cf-miRNA signature could result from the extracellular release of miRNAs from cancer epithelial cells as well as from immune/stromal cells composing the tumor microenvironment. We developed an integrated strategy for the identification of the origin of cf-miRNAs through combined analysis of published circulating and intracellular miRNAs expression datasets (microarray and qRT-PCR based) and of NGS analysis of cf-miRNAs in lung tumors. Our approach will contribute elucidating the biological role of cf-miRNAs in lung cancer and explore eventual therapeutic implications.

Citation Format: Fabrizio Bianchi, Valentina Melocchi, Tommaso Colangelo, Roberto Cuttano, Lucia Anna Muscarella, Elisa Dama. Unveil the role of cell-free circulating microRNA in lung 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 4441. doi:10.1158/1538-7445.AM2017-4441
Abstract 4442: micoRNA in FA defective tumor
Authors: Tang Shirley , Gao Li , Kathleen Kathleen , Fink Andrew , Kalvala Arjun , Aguila Brittany , Otterson Gregory , Villalona-Calero Miguel , Duan Wenrui
Published: July 2017

The Fanconi Anemia (FA) pathway is essential for human cells to maintain integrity following DNA damage. This pathway is involved in the endogenous repair of double stranded DNA breaks and homologous recombination as well as repair of DNA cross-linking caused by exogenous agents. Cancers with defective FA pathway are expected to be more sensitive to cross-link based therapy, or to treatments in which additional repair mechanisms are targeted. We have recently reported the detection of up to 20% of NSCLC to be FA functionally inactive (lack of FANCD2 foci formation in the nucleus of proliferating cells by triple stain immunofluorescence, FATSI negative). MicroRNAs (miRs, miRNA) are small, 19-25 nucleotide, single stranded, non-coding RNA molecules that have regulatory roles in humans by targeting mRNAs via cleaved or translational repression which can affect the output of protein coding genes and cause various changes in developmental and physiological processes including cancer. It has been published that some miRNAs are tumor suppressors, and others are oncogenes. However, microRNAs and the FA pathway in relationship to lung cancer progression remain unknown. In order to elucidate the role of FA related miRs in human lung cancer development or treatment, we analyzed miR expression in lung cancer cells and patient lung tumors. Several cell lines were generated using RNAi technology with FANCD2 deficiency and confirmed via reduction in FANCD2 protein expression. Using Nanostring counter technology, microRNA array analysis was performed on FANCD2 foci positive and foci negative tumors as well as matching normal lung tissues. A cluster of microRNAs (mir-431, 377, 376c, 200c, 26a, 135a, and let-7e) were found to be up-regulated, and miR-494,205, 630, 145,671 were found to be down-regulated in the foci negative tumors samples compared to matching non-tumor lung tissue. The same group of miRs were upregulated and its corresponding group were down-regulated in the foci negative tumors as compared to foci positive tumors. These findings indicate that the FA pathway may regulate downstream genes through regulation of microRNAs in lung cancer. In order to validate this hypothesis, specific miRs were be analyzed with Real-Time Quantitative PCR via foci positive and foci negative samples (cell and patient tissue) in hopes of finding significant and consistent regulation. This study contributes to further understanding in miRNA and cancer pathology that may be applicable to futuristic lung cancer treatment.

Citation Format: Shirley Tang, Li Gao, Kathleen Kathleen, Andrew Fink, Arjun Kalvala, Brittany Aguila, Gregory Otterson, Miguel Villalona-Calero, Wenrui Duan. micoRNA in FA defective tumor [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 4442. doi:10.1158/1538-7445.AM2017-4442
Abstract 4454: MED12 is recurrently mutated in Middle Eastern colorectal cancer
Authors: Siraj Abdul K. , Masoodi Tariq , Bu Rong , Al-Dayel Fouad , Al-Kuraya Khawla S.
Published: July 2017

Colorectal cancer (CRC) is a common cancer and a leading cause of cancer deaths. Previous studies have identified a number of key steps in the evolution of CRC but our knowledge of driver mutations in CRC remains incomplete. Recognizing the potential of studying different human populations to reveal novel insights in disease pathogenesis, we conducted genomic analysis of CRC in Saudi patients. In the discovery phase of the study, we conducted whole-genome sequencing of tumor and corresponding germline DNA in 27 CRC patients. In addition to known driver mutations, we identified three MED12 somatic mutations. In the replication phase, we employed a next-generation sequencing approach to capture and sequence MED12 and other candidate genes in a larger sample of 400 CRC patients and confirmed the enrichment for recurrent MED12 mutations. In order to gain insight into a plausible biological mechanism for the potential role of MED12 mutations in CRC, we studied CRC cell lines that differ substantially in the expression level of MED12, and found the latter to be correlated inversely with TGF-beta signaling and directly with apoptosis in response to chemotherapeutic agents. Importantly, these correlations were replicated when MED12 expression was experimentally manipulated. Our data expand the recently described role of MED12 as a tumor suppressor in other cancers to include CRC, and suggest TGF-beta signaling as a potential mediator of this effect.

Citation Format: Abdul K. Siraj, Tariq Masoodi, Rong Bu, Fouad Al-Dayel, Khawla S. Al-Kuraya. MED12 is recurrently mutated in Middle Eastern colorectal 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 4454. doi:10.1158/1538-7445.AM2017-4454
Abstract 4457: Inverse relationship between exon 8 single nucleotide polymorphism (c.1293 C>T) of gigaxonin and human tumor cell growth
Authors: Srivatsan Eri S. , Hwang Kimberly J. , Ko Albert , Chatoff Jenna R. , Basak Saroj K. , Venkatesan Natarajan , Palma-Diaz Fernando , Lewis Michael S. , Bomont Pascale , Wang Marilene B.
Published: July 2017

Gigaxonin, a product of the Giant Axonal Neuropathy (GAN) gene located on chromosome 16, is involved in intermediate filament processing of neural cells and vimentin fibers in fibroblasts. Previous studies have shown an interaction between p16 and gigaxonin in cisplatin mediated ubiquitination of NFkB. Genomic studies have indicated higher frequency (44.25%) of exon 8 single nucleotide polymorphism (SNP) (c.1293 C>T) of gigaxonin in the individuals of Caucasian population compared to normal population (22%). The polymorphism frequency is much lower in individuals of other ethnicities. To determine the relationship to tumors, we analyzed exon 8 polymorphism in HPV positive and negative cervical and head and tumors. Our studies showed a 47.25% polymorphic frequency in these tumors. There was no relationship between the presence of polypmorphism and HPV status. However, there was an inverse relationship between polymorphism and tumor recurrence. Our studies have further shown higher expression of gigaxonin protein in cancer cell lines containing the polymorphic T allele. Growth assays in vitro and in soft agar have shown a direct relationship between the presence of the T allele and slower cell line growth. Our results therefore indicate that in addition to p16 expression, exon 8 SNP could also serve as a diagnostic marker of chemo sensitivity in human tumors.

Citation Format: Eri S. Srivatsan, Kimberly J. Hwang, Albert Ko, Jenna R. Chatoff, Saroj K. Basak, Natarajan Venkatesan, Fernando Palma-Diaz, Michael S. Lewis, Pascale Bomont, Marilene B. Wang. Inverse relationship between exon 8 single nucleotide polymorphism (c.1293 C>T) of gigaxonin and human tumor cell growth [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 4457. doi:10.1158/1538-7445.AM2017-4457
Abstract 4458: Regulation of MYC protein stability by mutant KRAS in pancreatic ductal adenocarcinoma
Authors: Vaseva Angelina V. , Blake Devon R. , Azam Salma H. , Gilbert Karim T. , Pecot Chad V. , Pearce Kenneth H. , Herring Laura E. , Graves Lee M. , Houghton Peter J. , Der Channing J.
Published: July 2017

With the nearly 100% mutation frequency of KRAS in pancreatic ductal adenocarcinoma (PDAC), the development of therapeutic strategies to target KRAS is a high priority for the pancreatic cancer field. In the current study, we aimed to identify signaling changes caused by the acute suppression of mutant KRAS in PDAC cell lines. Strikingly, acute suppression of mutant KRAS in PDAC cell lines caused potent and rapid proteasome-dependent degradation of MYC protein. Ablation of MYC also suppressed PDAC growth both in vitro and in vivo, indicating a critical driver role for MYC in KRAS-dependent PDAC maintenance. A mechanism by which RAS effector signaling regulates MYC protein stability has been described, however we determined that this mechanism cannot fully account for how endogenous mutant KRAS stabilizes MYC protein in PDAC cells. We verified a role for the Raf-MEK-ERK but not the PI3K-AKT-GSK3β effector signaling pathway. Unexpectedly, we also excluded a role for MYC protein phosphorylation at MYC residue T58, and determined that ubiquitin ligases other than FBW7 are involved. These findings prompted us to search for additional KRAS-dependent protein kinases that facilitate MYC protein stability. We applied multiple screening strategies. First, we developed a novel fluorescence-based system to monitor real-time MYC protein degradation in PDAC cells and we adapted this system for use in a high-throughput flow-cytometry based assay. Second, we applied a mass spectrometry-based approach to profile the human kinome for KRAS-dependent changes in protein kinases. Finally, we applied gain-of-function (Cancer Toolkit) and loss-of-function (CRISPR/Cas9) genetic screens to identify signaling regulators of MYC protein stability. The results of these screens will be presented.

Citation Format: Angelina V. Vaseva, Devon R. Blake, Salma H. Azam, Karim T. Gilbert, Chad V. Pecot, Kenneth H. Pearce, Laura E. Herring, Lee M. Graves, Peter J. Houghton, Channing J. Der. Regulation of MYC protein stability by mutant KRAS in pancreatic ductal adenocarcinoma [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 4458. doi:10.1158/1538-7445.AM2017-4458
Abstract 4469: Targeting the tri-snRNP complex for triple-negative breast cancer therapy
Authors: Chan Stefanie , Sridhar Praveen , Lock Ying-Jie , Petrocca Fabio
Published: July 2017

Triple negative breast cancers (TNBC) account for ~15% of all breast cancers and the majority of breast cancers in women carrying a BRCA1 germline mutation. Due to the inadequacy of existing treatment, here we sought to identify shared genetic dependencies across different TNBC cell lines with the ultimate goal of uncovering novel therapeutic targets. To this end, we performed a targeted siRNA lethality screen across 11 human breast cell lines focusing on 154 genes, which we previously identified as selectively essential to a genetically-defined TNBC progenitor cell line (BPLER) relative to a myoepithelial-like isogenic cell line (HMLER). Thirty genes scored as recurrently and selectively required for survival of progenitor-like (or basal-A) TNBC lines compared to differentiated cell lines. Genes for proteins involved in RNA splicing were prominent shared dependencies among basal-A TNBC cell lines. Of particular note were those associated with the U4/U6.U5 tri-snRNP complex, including PRPF8 and PRPF38A. Transcriptome-wide RNA-seq analysis of the knockdown of either led to widespread intronic retention, expression of immune system genes and aberrant splicing of transcripts involved in protein translation, proteasome function, mitosis and apoptosis, including the TNBC dependency gene MCL1. As the proteasome and mitosis are also established TNBC vulnerabilities, we have identified specific classes of transcripts that are both particularly susceptible to perturbation of tri-snRNP activity and selectively essential for TNBC, making the tri-snRNP complex an attractive target for downstream drug development.

Citation Format: Stefanie Chan, Praveen Sridhar, Ying-Jie Lock, Fabio Petrocca. Targeting the tri-snRNP complex for triple-negative breast cancer therapy [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 4469. doi:10.1158/1538-7445.AM2017-4469
Abstract 4472: A subunit of splicing factor 3b, SF3B4, functions as driver of liver cancer via aberrant splicing activity on tumor suppressor KLF4
Authors: Shen Qingyu , Eun Jung Woo , Kim Hyung Seok , Yang Hee Doo , Kim Sang Yean , Nam Suk Woo
Published: July 2017

Alternative splicing is one of the crucial mechanism that contribute to proteome diversity and, as reported, up to 90% of genes are alternatively spliced in human. In the last few years, a large number of mRNA isoforms revealed to contribute many cellular development and disease, including cancer. SF3B4 is one of six subunits of the splicing factor 3b (SF3b) complex which is an important protein complex in U2 snRNP super complex. In this study, we show that SF3B4 expression was overexpressed in a large cohort of human hepatocellular carcinoma (HCC) patients. SF3B4 knockdown caused G1/S cell cycle arrest by recovering p27 expression and simultaneously suppressing cyclins, and CDKs in liver cancer cell. Consistently, Spliceostatin A, a SF3b complex inhibitor, also suppressed liver cancer cell growth with similar effect on cell cycle regulation. In addition, sustained suppression of SF3B4 reduced the in vivo tumor growth rate in mouse xenograft models. Furthermore, SF3B4 knockdown repressed in vitro tumor cell motility and invasion of liver cancer cells. Notably, we observed that SF3B4 knockdown increased alternative transcript splicing event of a large number of genes in liver cancer cells. From this, we found that SF3B4 knockdown caused induction of wildtype KLF4 transcript expression, and thereby exerted anti-tumor growth effect on liver cancer cells. Indeed, ectopic expression of KLF4 mimicked SF3B4 knockdown effect on same cells. Our results suggest that aberrant regulation of SF3B4 contribute to malignant transformation and growth of liver cancer cells by repression of tumor suppressor via unmodulated alternative splicing activity during liver tumorigenesis.

Citation Format: Qingyu Shen, Jung Woo Eun, Hyung Seok Kim, Hee Doo Yang, Sang Yean Kim, Suk Woo Nam. A subunit of splicing factor 3b, SF3B4, functions as driver of liver cancer via aberrant splicing activity on tumor suppressor KLF4 [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 4472. doi:10.1158/1538-7445.AM2017-4472
Abstract 4473: SRRM4 drives treatment-induced neuroendocrine transdifferentiation of prostate adenocarcinoma under androgen receptor pathway inhibition
Authors: Li Yinan
Published: July 2017

Treatment-induced neuroendocrine prostate cancer (t-NEPC) is an aggressive subtype of castration-resistant prostate cancer that typically does not respond to AR pathway inhibition (ARPI) and its diagnosis is increasing. To understand its development, we analyzed transcriptomes of prostate tumors to identify t-NEPC-specific RNA splicing. Interestingly, more than 66% of the splice events are predicted to be regulated by the RNA splicing factor, Serine/Arginine Repetitive Matrix 4 (SRRM4). We confirmed in vitro and in vivo that one SRRM4 target gene is the RE1-Silencer Factor (REST), a master regulator of neurogenesis. SRRM4 strongly stimulates adenocarcinoma cells to express t-NEPC biomarkers and this is exacerbated by ARPI. ARPI combined with gain of SRRM4 results in adenocarcinoma cells to assume multicellular spheroid morphology and establishes progressive NEPC xenografts. These SRRM4 actions are further enhanced by loss-of-function of TP53. We conclude that SRRM4 drives t-NEPC progression. This knowledge may guide the development of novel therapeutics aimed at t-NEPC.

Citation Format: Yinan Li. SRRM4 drives treatment-induced neuroendocrine transdifferentiation of prostate adenocarcinoma under androgen receptor pathway inhibition [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 4473. doi:10.1158/1538-7445.AM2017-4473
Abstract 4480: SerRS is a key inhibitor of VEGFA through both transcriptional and translational controls
Authors: Liu Ze , Shi Yi , Zhang Qian , Yang Xianglei
Published: July 2017

Vascular endothelial growth factor A (VEGFA) is the most important mediator of angiogenesis and a major target for cancer therapy. Recent studies from our lab revealed that seryl-tRNA synthetase (SerRS), by counteracting transcription factor c-Myc in the nucleus, is the crucial transcriptional repressor of VEGFA and a potent inhibitor of angiogenesis (1,2). Here we report that SerRS controls the expression of VEGFA not only in the nucleus but also in the cytoplasm through mediating its translational readthrough. Translational read-through of the VEGFA mRNA generates a novel isoform called VEGF-Ax that, compared with the non-readthrough isoform VEGF165, has a 22-amino acid C-terminal extension and much weakened angiogenic activity (3,4). Interestingly, serine was identified as the amino acid inserted in the place of the UGA stop codon during the read-through (3). In unpublished work, wWe findound that SerRS can bind to the 3’UTR region of the VEGFA mRNA. The binding anchors SerRS to charge serine onto tRNASec (the tRNA for the 21st amino acid selenocysteine that decodes the UGA stop codon), while preventing the charged serine from being modified into selenocysteine. SerRS binding also blocks the release factors (eRFs) from terminating translation at the stop codon. Therefore, SerRS is the key mediator of the translational readthrough that generates VEGF-Ax. Collectively, we have established that a member of the aminoacyl-tRNA synthetase family plays a critical role in regulating VEGF and angiogenesis through both transcriptional and translational controls.

References

1. Xu X, Shi Y, Zhang HM, Swindell EC, Marshall AG, Guo M, Kishi S, Yang XL*. Unique domain appended to vertebrate tRNA synthetase is essential for vascular development. Nat Commun. 2012 Feb 21;3:681.

2. Shi Y, Xu X, Zhang Q, Fu G, Mo Z, Wang GS, Kishi S, Yang XL*. tRNA synthetase counteracts c-Myc to develop functional vasculature. Elife. 2014 Jun 17;3:e02349.

3. Eswarappa SM, Potdar AA, Koch WJ, Fan Y, Vasu K, Lindner D, Willard B, Graham LM, DiCorleto PE, Fox PL. Programmed translational readthrough generates antiangiogenic VEGF-Ax. Cell. 2014 Jun 19;157(7):1605-18.

4. Xin H, Zhong C, Nudleman E, Ferrara N. Evidence for Pro-angiogenic Functions of VEGF-Ax. Cell. 2016 Sep 22;167(1):275-284.

Citation Format: Ze Liu, Yi Shi, Qian Zhang, Xianglei Yang. SerRS is a key inhibitor of VEGFA through both transcriptional and translational controls [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 4480. doi:10.1158/1538-7445.AM2017-4480
Abstract 4488: Tumor suppressor phosphatase PHLPP1 regulates transcription factor activity and gene expression in inflammation
Authors: Katsenelson Ksenya Cohen , Stender Joshua D. , Glass Christopher K. , Newton Alexandra C.
Published: July 2017

Epigenetic mechanisms play a key role in cancer and are a major contributor in driving the aberrantly high levels of oncogenic receptor tyrosine kinases (RTK) in cancer. Understanding mechanisms leading to altered transcription of oncogenes and tumor suppressors has the potential to provide new therapeutic targets. Here we show that the PH domain leucine-rich repeat protein phosphatase 1 (PHLPP1), a tumor suppressor that directly dephosphorylates and inactivates Akt, has an additional function of regulating approximately 10% of the transcriptome. Specifically, we used non-biased high-throughput RNA-sequencing and chromatin immunoprecipitation-sequencing techniques to analyze genome-wide mRNA levels and acetylation patterns of genes in cells from wild-type and PHLPP1 knockout mice. De novo motif analysis of the promoter for the genes regulated by PHLPP1 identified enrichment in the recognition motifs for a number of transcription factors, including ones involved in inflammatory signaling. Biochemical analysis revealed that PHLPP1 regulates the phosphorylation and activation of these transcription factors, such that loss of PHLPP1 leads to enhanced inflammatory signaling. Our data support a model in which PHLPP1 dephosphorylates specific transcription factors to act as the brakes to inflammatory signaling, a hallmark of cancer.

Citation Format: Ksenya Cohen Katsenelson, Joshua D. Stender, Christopher K. Glass, Alexandra C. Newton. Tumor suppressor phosphatase PHLPP1 regulates transcription factor activity and gene expression in inflammation [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 4488. doi:10.1158/1538-7445.AM2017-4488
Abstract 4491: Modulation of p63 expression by phosphorylation of RBM38 at S195 via miR-203
Authors: ZHANG YANHONG , YAN WENSHENG , ZHANG JIN , CHEN XINBIN
Published: July 2017

p63, a p53 family protein, acts as a sequence-specific DNA-binding transcriptional factor to regulate the expression of target genes involving in various cellular processes, including growth suppression and epithelial development. RBM38, a RNA-binding protein, is a target of p53 family and is known to interact with its target mRNAs and regulate their expression via mRNA stability. Previously, we found that RBM38 negatively regulates p63 mRNA stability through binding to the AU/U-rich element in 3′ untranslated region (3′-UTR). We also found that phosphorylation of RBM38 at Ser195 alters the conformation and function of RBM38 protein. However, it is unclear whether phosphorylation of RBM38 or miR-203 alters the ability of RBM38 to regulate p63 expression. In this study, we found that in both MCF7 and HaCaT cells, wild-type RBM38 and S195A mutant, but not phosphor-mimic S195D mutant, inhibit p63 mRNA stability, suggesting that Ser195 phosphorylation abrogates the ability of RBM38 to repress the expression of p63. Importantly, we found that phosphorylation of RBM38 disrupts the binding of RBM38 to the U-rich element in p63 3′-UTR. Additionally, we found that miR-203 inhibitor increases, whereas miR203 mimic decreases p63 expression through binding to p63 3′-UTR, consistent with a previous report. Interestingly, we found that the ability of RBM38 to repress p63 expression is disrupted by miR-203 inhibitor but enhanced by miR-203 mimic. Furthermore, we found that wild-type RBM38 protein, but not phosphor-mimic S195D mutant, physically interacts with Ago2, indicating that RBM38 may inhibit p63 mRNA stability by modulating Ago2-miR-203 complex to bind to the U-rich element in p63 3′-UTR. Together, we uncovered a novel mechanism by which RBM38 modulates p63 expression via miR-203.

Note: This abstract was not presented at the meeting.

Citation Format: YANHONG ZHANG, WENSHENG YAN, JIN ZHANG, XINBIN CHEN. Modulation of p63 expression by phosphorylation of RBM38 at S195 via miR-203 [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 4491. doi:10.1158/1538-7445.AM2017-4491
Abstract 451: Germ free mice accelerate cachexia-associated cancer
Authors: Neves Rodrigo Xavier das , Roy Soumen , Dzutsev Amiran , Huang April , Smith Loretta , Difilippantonio Simone , Misty Hawes , Seelaender Marília , Trinchieri Giorgio
Published: July 2017

The syndrome of cancer cachexia is currently defined as a state of ill health, malnutrition and physical wasting with marked white adipose tissue (WAT) and skeletal muscle mass wasting, representing the clinical consequence of a chronic and systemic inflammatory response. Over the last decade, WAT has been recognized as an important endocrine organ, and earning a lot of attention during cancer cachexia development. We investigated the role of microbiota along the cachexia associated cancer. We performed experiments with conventional and Germ Free mice (GF) (n=6 in each group) of 8-10 weeks old C57B/6, which were subcutaneously injected with LLC cells [4x106 cells in 0.2 mL; Tumor-bearing, (TB) or PBS control (C)]. We performed Immunohistochemistry, RT- qPCR, and Western Blot. We observed that GF Tumor-bearing mice have increased several symptoms of the cachexia compared to conventional TB mice. The WAT mass was decreased 50% in GF Tumor-bearing mice compared to all groups, which indicates a pathway related to lipolysis, as we found increased level of phosphorylated enzymes in GF Tumor-bearing mice. We also observed that GF Tumor bearing mice decreased skeletal muscle mass and gene expression that are related with atrophy were increased in GF Tumor bearing mice. Our data suggested that homeostasis of microbiota may impair the development of the cachexia syndrome.

Citation Format: Rodrigo Xavier das Neves, Soumen Roy, Amiran Dzutsev, April Huang, Loretta Smith, Simone Difilippantonio, Hawes Misty, Marília Seelaender, Giorgio Trinchieri. Germ free mice accelerate cachexia-associated 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 451. doi:10.1158/1538-7445.AM2017-451