bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5342: Somatic bi-allelic loss of TSC genes in eosinophilic solid and cystic renal cell carcinoma (ESC RCC)
Authors: Lee Nicole D. , Vats Pankaj , Cao Xuhong , Su Fengyun , Lonigro Robert , Premkumar Kumpati , Trpkov Kiril , McKenney Jesse K. , Mehra Rohit , Dhanasekaran Saravana M. , Chinnaiyan Arul M.
Published: August 2018

Renal cell carcinoma (RCC) subtypes with overlapping histomorphologic features pose diagnostic challenges. For instance, a unique category of sporadic renal tumors with eosinophilic cytoplasm and solid and cystic growth pattern (ESC RCC) may mimic a RCC subtype usually encountered in patients with germline aberrations of tuberous sclerosis complex (TSC) genes (TSC RCC). Here, we used next-generation sequencing (NGS) technology to interrogate the clinicopathologic and molecular profiles of ESC RCC tumors. Mutational and copy number analysis of NGS data from ESC RCC tumors revealed a somatic bi-allelic loss of TSC family genes, specifically TSC1 or TSC2, in six out of seven profiled cases. However, the corresponding background kidney showed only wild type alleles, thus excluding any germline involvement and differentiating ESC RCC from TSC RCC. Furthermore, bi-allelic loss of the TSC genes occurred in a mutually exclusively manner in this cohort. Our study clarifies the molecular identity of ESC RCC, and can thus guide future therapeutic strategies and provide a basis for the revision of current RCC classification.

Citation Format: Nicole D. Lee, Pankaj Vats, Xuhong Cao, Fengyun Su, Robert Lonigro, Kumpati Premkumar, Kiril Trpkov, Jesse K. McKenney, Rohit Mehra, Saravana M. Dhanasekaran, Arul M. Chinnaiyan. Somatic bi-allelic loss of TSC genes in eosinophilic solid and cystic renal cell carcinoma (ESC RCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5342.
Abstract 5343: Mutational signatures in EGFR sensitizing mutation positive lung adenocarcinoma
Authors: Kim Eun Young , Kim Arum , Chang Yoon Soo
Published: August 2018

Lung cancer has high mutational burden, which is featured by smoking signature. However, lung cancer with EGFR mutations is common in nonsmokers and women, which suggests that mutational stresses other than smoking are involved. We analyzed repeated deep sequencing data of EGFR sensitizing mutation positive lung adenocarcinoma tissue to identify characteristic mutational signatures, proposed by Alexandrov et al. Targeted next-generation sequencing was performed using Ion AmpliSeq Custom Panel of 0.6 Mb size containing 70 major genes including EGFR in 69 cases harboring sensitizing EGFR mutation. Publicly available data from EGFR sensitizing mutation were extracted from GDC data portal. Mutational signature was analyzed using maftools package. EGFR-TKI domain analysis revealed 53 mutations. C> T mutation was found in 26.4%, but C> T transition at CpG site that suggests aging effect was found in 2%, and C> T or C> G mutation in TCW motif reflecting APOBEC activity were found in 1.4%. C> A transversion corresponding to Signature 4 was also found in only one case, suggesting that the possibility of EGFR mutation by smoking effect is very low. The T> C substitution in ApT, indicating signature 5, was detected in 4%. The EGFR-TKI sensitizing mutation (E19del, L858R) has lower frequency of co-mutation while other EGFR-TKI domain mutations were frequently associated with multiple co-mutations. T>G substitution, indicating signature 28 and commonly found in Korean gastric cancer, was found in 39.1%. When the mutational signatures of a total 70 genes were analyzed, the C> T mutation was the most commonly detected (73.1%) and similarity with signature 5 was highest. These findings suggest that the mutational signature of EGFR sensitizing mutant lung cancer, which is frequent in Far East Asia, may be different from that of Western data. Additional data and analysis will be updated until the annual meeting.

Citation Format: Eun Young Kim, Arum Kim, Yoon Soo Chang. Mutational signatures in EGFR sensitizing mutation positive lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5343.
Abstract 5346: Recurrent genomic copy alterations deregulate the transcriptome and key signaling networks in head and neck cancer cell lines and tumors with worse prognosis
Authors: Cheng Hui , Yang Xinping , Si Han , Saleh Anthony , Xiao Wenming , Coupar Jamie , Gollin Susanne M. , Ferris Robert L. , Issaeva Natalia , Yarbrough Wendell G. , Prince Mark E. , Carey Thomas E. , Waes Carter Van , Chen Zhong
Published: August 2018

Human cancer cell lines have been important tools for biological and preclinical investigation, and establishing their relationship to genomic alterations and subtypes found in tumors could further accelerate functional and therapeutic discoveries. We conducted an integrated analysis of the genomic and transcriptomic profiles of 15 human papillomavirus negative (HPV−) and 11 HPV(+) head and neck squamous cell carcinoma (HNSCC) lines, to identify models of important molecular subtypes uncovered among 279 HNSCC tumors from The Cancer Genome Atlas (TCGA). We developed analytic approaches to detect copy number alterations (CNAs) driving altered expression and predict deleterious mutations in HNSCC lines for comparison with TCGA. Strikingly, HNSCC lines displayed recurrent amplifications on chromosomes 3q22-29, 5p15, 11q13/22, and 8p11 that drive increased expression of a cluster of ~100 mRNAs encoding multiple known and understudied candidate oncogenes. These CNAs, together with loss and under-expression or mutations of putative tumor suppressor genes, recapitulate genomic alterations found in more aggressive HNSCC tumor subtypes. Among these, concurrent 3q26.3 amplification and TP53 mutation in HPV(−) HNSCCs is associated with worse overall survival. Common and distinctive CNAs, transcriptome, and mutations converge on biologically and therapeutically important signal pathways and functions in HNSCCs differing in HPV status, including PI3K, Hippo, TGF-β, Wnt/β-catenin, TP63, TP53/death, cell cycle/mitosis, stemness/differentiation, chromatin remodelling/DNA replication, post-transcriptional regulation, and mitochondrial biosynthesis. Our findings elucidate and validate genomic alterations underpinning numerous discoveries made with historic and recently derived HNSCC lines, and provide valuable models for future preclinical and therapeutic studies in subsets of HNSCCs with worse prognosis.

Supported by NIDCD/NIH intramural projects ZIA-DC-000073, ZIA-DC-000074.

This work utilized the computational resources of the NIH HPC Biowulf cluster. (http://hpc.nih.gov)

Citation Format: Hui Cheng, Xinping Yang, Han Si, Anthony Saleh, Wenming Xiao, Jamie Coupar, Susanne M. Gollin, Robert L. Ferris, Natalia Issaeva, Wendell G. Yarbrough, Mark E. Prince, Thomas E. Carey, Carter Van Waes, Zhong Chen. Recurrent genomic copy alterations deregulate the transcriptome and key signaling networks in head and neck cancer cell lines and tumors with worse prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5346.
Abstract 535: The impact on transcriptome diversity after oncogenic transformation of human mammary epithelial cells
Authors: Tran Anthony
Published: August 2018

Breast cancer is a leading cause of cancer-related morbidity and mortality worldwide. In the USA, one out of eight women will be diagnosed with breast cancer over the course of their lifetime. A major obstacle hindering the treatment of breast cancers is intratumor heterogeneity since cytotoxic drug sensitivities among different clonal populations may vary. Previously, we have shown that cancer cells display an increased repertoire and abundance of all transcripts within a cell (termed transcriptome diversity) compared to normal cells. The driving mechanism(s) of cellular intratumor heterogeneity has yet to be fully elucidated. In this study, we utilize immortalized human mammary epithelial cells (MCF10A) transformed with an array of doxycycline-inducible lentiviral vectors encoding known genetic drivers of breast tumorigenesis (TP53 mutant, BRCA1 mutant, PIK3CA mutant, shPTEN and c-MYC) alone and in combination to determine their impact on transcriptome diversity based on RNA-seq. Our strategy enables strict temporal control and reversibility of gene expression alterations via the doxycycline-inducible promoter. Transcriptome diversity will also be interrogated using single-cell RNA sequencing to determine how individual cellular transcriptional profiles contribute to the overall population-based transcriptional landscape. These results will be compared to patient tumor samples' transcriptome diversity and correlated with their respective clinicopathologic characteristics. Advancing our understanding of cellular transcriptome diversity will enable new avenues of treatment for breast cancers resistant to current clinical interventions such as metastatic and triple negative breast cancers, both of which are characterized by high transcriptome diversity.

Citation Format: Anthony Tran. The impact on transcriptome diversity after oncogenic transformation of human mammary epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 535.
Abstract 5355: Multiple mutations to the same gene are selected for and cooperate to drive cancer
Authors: Gorelick Alexander N. , Reznik Ed , Cai Yanyan , Bielski Craig , Bandlamudi Chaitanya , Penson Alexander , Jonsson Philip , La Konnor , Scaltriti Maurizio , Schultz Nikolaus , Taylor Barry S.
Published: August 2018

Cancers accumulate oncogenic mutations whose biochemical impact depends upon other germline and somatic variants in the cell. It stands to reason that the consequence of a somatic mutation is mediated by the presence of additional genetic variants within the same gene, and by the allele on which they arise. We have undertaken integrative analyses of 27,534 human tumors, including 19,640 prospectively sequenced advanced and metastatic cancers, and revealed a startling rate of multiple non-synonymous somatic mutations in the same cancer gene and tumor, hereafter referred to as multiple mutations. Overall, 26% of primary and metastatic tumors had at least one cancer gene with two or more somatic mutations. A minority of multiple mutations arose from somatic hypermutation or as secondary mutations driving resistance to molecularly targeted therapy. Clonality analysis further indicated that the majority of multiple mutations were present in the same cell. Multiple cancer genes were enriched for a greater burden of multiple mutations than would be expected in the absence of selection, including APC, B2M, EGFR, and TERT. The allelic configuration of these mutations indicated that while multiple mutations in trans arose predominantly in tumor suppressor genes, consistent with the selective pressure for biallelic inactivation, the majority of phaseable mutations arose in cis in both tumor suppressors and oncogenes, implying a selective pressure exists for a biochemical function distinct from individual driver mutations in the same gene. Collectively, these data argue that multiple genetic variants within a gene and their allelic configurations can interact to drive cancers.

Citation Format: Alexander N. Gorelick, Ed Reznik, Yanyan Cai, Craig Bielski, Chaitanya Bandlamudi, Alexander Penson, Philip Jonsson, Konnor La, Maurizio Scaltriti, Nikolaus Schultz, Barry S. Taylor. Multiple mutations to the same gene are selected for and cooperate to drive cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5355.
Abstract 5356: Robust gene fusion detection in formalin-fixed tissue sample with QIAseq RNAscan Oncology Panel
Authors: Falk Jeffrey , Sitlani Parth , Orosco Claire , Panjikaran Maya , Weiner Dana , Tian Song , Samara Raed , DiCarlo John , Wang Yexun , Lader Eric , Reinecke Frank
Published: August 2018

Introduction: Gene fusions are frequently associated with tumorigenesismalignant tumors. Highly sensitive and reproducible detection of gene fusions in clinical samples, especially formalin-fixed paraffin-embedded (FFPE) specimens, is important for diagnosis, prognosis, and treatment guidance. Although many clinical tests utilize next-generation-sequencing (NGS) for detection of genetic alterations, reliable detection of gene fusions by NGS in FFPE samples remains a challenge.

Methods: Five FFPE non-small cell lung cancer samples confirmed by FISH to contain EML4-ALK or KIF5B-RET fusions were selected for testing along with the Seraseq™ FFPE Tumor Fusion RNA Reference Material, v1, which evaluates forcontains 12 known fusions. Four operators prepared NGS libraries for each sample (89-250ng input) using the commercially available QIAseq RNAscan Oncology Panel, which targets 223 fusion gene pairs or 576 unique breakpoints. The resulting libraries were sequenced on an Illumina® NextSeq 500 sequencer. Demultiplexed FASTQ files were analyzed using cloud-based QIAseq RNAscan Analysis pipeline v1.7.20.2. Detected fusions that are on the panel's target list were reported as curated gene fusions and assigned a score based on unique molecules supporting the transcript.

Results: For the Seraseq™ FFPE Tumor Fusion RNA Reference v1 sample, all 12 expectedknown fusions were detected in each of the libraries generated by four different operators. The analysis pipeline correctly called the expected fusion in all four replicates of the five clinical FFPE samples tested, which varied in both input quantityamount and quality. Reproducibility was evaluated by comparing the score values across replicate libraries for each sample; expected fusion detection was 100% consistent between users, and the average correlation coefficient for the fusion score was 0.995.

Conclusions: The commercially available QIAseq RNAscan Oncology panel is a highly sensitive and robust product for detection of gene fusions in FFPE samples. QIAseq RNAscan methodology provides a useful tool for studying gene fusions in tumor samples and with optimization, customization, and validation can further fit the specific needs for of clinical laboratories.

Citation Format: Jeffrey Falk, Parth Sitlani, Claire Orosco, Maya Panjikaran, Dana Weiner, Song Tian, Raed Samara, John DiCarlo, Yexun Wang, Eric Lader, Frank Reinecke. Robust gene fusion detection in formalin-fixed tissue sample with QIAseq RNAscan Oncology Panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5356.
Abstract 536: Targeting PRPK and TOPK for skin cancer prevention and therapy
Authors: Roh Eunmiri , Lee Mee-Hyun , Zykova Tatyana A. , Zhu Feng , Kim Hong-Gyum , Bae Ki Beom , Cho Yong Yeon , Bode Ann M. , Dong Zigang
Published: August 2018

Solar ultraviolet (sUV) irradiation is a major environmental carcinogen that can cause inflammation and skin cancer. The costs and morbidity associated with skin cancer are increasing, thus identifying molecules that can help prevent skin carcinogenesis is important. In this study, we identified the p53-related protein kinase (PRPK) as a novel oncogenic protein that is phosphorylated by the T-LAK cell-originated protein kinase (TOPK). Knockdown of TOPK inhibited PRPK phosphorylation and conferred resistance to solar simulated light (SSL)-induced skin carcinogenesis in mouse models. In the clinic, acute SSL irradiation significantly increased epidermal thickness as well as total protein and phosphorylation levels of TOPK and PRPK in human skin tissues. We identified two PRPK inhibitors, FDA-approved rocuronium bromide (Zemuron®) or betamethasone 17-valerate (Betaderm®) that could attenuate TOPK-dependent PRPK signaling. Importantly, topical application of either rocuronium or betamethasone attenuated SSL-induced epidermal hyperplasia, neovascularization and cutaneous squamous cell carcinoma (cSCC) development in SKH1 (Crl: SKH1-Hrhr) hairless mice by inhibiting PRPK activation, and also reduced expression of the proliferation and oncogenesis markers COX-2, cyclin D1 and MMP-9. This study is the first to demonstrate that PRPK- targeted therapy could be useful against sUV-induced cSCC.

Citation Format: Eunmiri Roh, Mee-Hyun Lee, Tatyana A. Zykova, Feng Zhu, Hong-Gyum Kim, Ki Beom Bae, Yong Yeon Cho, Ann M. Bode, Zigang Dong. Targeting PRPK and TOPK for skin cancer prevention and therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 536.
Abstract 5361: Spatial genome organization as a framework for somatic alterations in human cancer
Authors: Akdemir Kadir C. , Futreal Andrew
Published: August 2018

Genomic material within the nucleus is folded into successive layers in order to package and organize the long string of linear DNA. This hierarchical level of folding is closely associated with transcriptional regulation and DNA replication. Recent chromosome conformation studies have revealed that mammalian chromosomes are structured into tissue-invariant topologically associating domains (TADs) where the DNA within a given domain interacts more frequently together than with regions in other domains. Genes within the same TADs represent similar expression and histone-modification profiles. Therefore, regions separating different TADs (boundaries) have important roles in reinforcing the stability of these domain-wide features. Indeed, TAD boundary disruptions in human genetic disorders or human cancers lead to misregulation of certain genes, due to de novo enhancer exposure to promoters. Here, to understand effects and distributions of somatic structural variations across TADs, we utilized single nucleotide variations and genomic rearrangements from 2658 high-coverage whole genome sequencing data across various cancer types with paired normal samples. Our analysis revealed that deletions between repressed and active TADs result in up-regulation of genes on the repressed end of the deletions, whereas active domain genes remain unaffected. Interestingly, we further identified a strong correlation between the mutational distributions in human cancers and the spatial organization of the genome. Transcriptionally active TADs contain less mutation burden compared to inactive TADs, as a result regional mutation rates are drastically different around the boundaries delineating epigenetically distinct domains. However, mutation rates remain similar around the boundaries for samples with the DNA mismatch repair deficiency. Taken together, our analyses reveal new insights about genome architecture, aberrant gene expression and mutational distributions in human cancers.

Citation Format: Kadir C. Akdemir, Andrew Futreal. Spatial genome organization as a framework for somatic alterations in human cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5361.
Abstract 5372: The mutational landscape of primary cutaneous melanoma
Authors: Chen Sofia Y. , Mamunur Rashid , Laye Jon , Bishop D. Timothy , Newton-Bishop Julia A. , Adams David J.
Published: August 2018

Large-scale melanoma genome profiling studies to date have mainly focused on metastatic tumors. To better understand the link between genomic changes and outcome, primary tumors must be studied.

We have designed a comprehensive targeted genomic panel to study genetic alterations in melanoma, and applied this to a large collection of 536 primary melanomas, part of the Leeds Melanoma Cohort. Patients were invited to participate 3 months after diagnosis of primary melanoma. 1% received targeted therapies or immunotherapy and thus, our analysis is reflective of the landscape of primary melanoma in the treatment naïve setting. The sequencing panel allowed us to study genetic alterations in over 500 genes, including more than 150 genes frequently mutated in melanoma and an additional 250 genes linked to other solid tumor types. Both tumor and germline DNA were analyzed for most samples.

The average somatic mutation rates we observed was 15 mutations/MB (0 to 236 mutations/MB), while the nonsynonymous mutational load ranged from 0 to 57 mutations/MB (average 4 mutations/MB). We found that a high mutational burden (highest 20%, >45 nonsynonymous mutations/Mb) positively correlated with better survival (Cox proportional hazards model with age, sex and AJCC stage as additional covariates). Among the top recurrently mutated genes were well established melanoma driver genes such as BRAF (44%), NRAS (28%), NF1 (10%), CDKN2A (15%), TP53 (11%) and ARID2 (8%). We also found hotspot mutations in less well documented melanoma genes, including RQCD1 p.P131L (4.5%).

Altogether, our preliminary data shows a strong correlation between survival and high mutational load in primary melanomas. Our data also suggests a similar landscape of driver mutations in primary and metastatic melanoma, with some variants/genes possibly reflecting the differences in disease stage.

We will further investigate the mutational landscape in our cohort of primary melanomas, including analyses of gene co-occurrence and mutual exclusivity. Additionally, we will use extensive clinical parameters and transcriptomics to examine the possibility of predicting survival and other clinically relevant parameters in our cohort based on patient mutational profiles.

Citation Format: Sofia Y. Chen, Rashid Mamunur, Jon Laye, D. Timothy Bishop, Julia A. Newton-Bishop, David J. Adams. The mutational landscape of primary cutaneous melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5372.
Abstract 5398: Companion diagnostic for predicting the efficacy of mTOR inhibitor in neuroendocrine tumor
Authors: Liu I-Hua , Chang Jia-Ming
Published: August 2018

Neuroendocrine tumor (NET) is having both characterizations of hormone and neurotransmitter secretion. The mTOR, a serine-threonine kinase inhibitor, was used for treating the NET tumors by affecting angiogeneic blood vascular vessels as a disrupting agent and killing the tumor cells by inhibiting the mTOR signalling. Everolimus is a U.S. FDA-approved drug for treating advanced breast cancer, which is investigated for use in NET treatment. The efficacy will be evaluated by exosome reflecting the tumor microenvironment secreted into blood circulation. NCI-H727 cells are a kind of NET tumor that show the secretion of chromogranin A (CgA) and serotonin. By profiling of exosome with miRNA, the efficacy may be predicted by the level of miRNA. Here, we demonstrated the pattern of miRNA profile in everolimus-treated NCI-H727 cells. MIR192 and MIR375 were consistently secreted in exosomes with a high level. A panel of miRNA, MIR24-2, MIR3131, and MIR708, was increased and showed a change greater than 0.5 fold compared with untreated cells. In conclusion, by analyzing the pattern of miRNA in exosomes, the efficacy of drug can be monitored during the treatment. A new therapeutic strategy can be tailored according to the miRNA pattern.

Citation Format: I-Hua Liu, Jia-Ming Chang. Companion diagnostic for predicting the efficacy of mTOR inhibitor in neuroendocrine tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5398.
Abstract 5400: A comprehensive analysis of the interactome of miR-21, an established oncomir, by Argonaute-CLIP analysis identifies novel conserved and species-specific targets of miR-21 in human liver and hepatocellular carcinoma
Authors: Koenig Aaron B. , Barajas Juan M. , Ghoshal Kalpana
Published: August 2018

MicroRNAs are ~22 nucleotide RNAs that regulate gene expression at the post-transcriptional level by binding messenger RNA transcripts. MicroRNA (miR)-21 participates in carcinogenesis in hepatocellular carcinoma (HCC) and other malignancies. Here we analyze the miR-21 interactome in HCC by high-throughput sequencing of RNA isolated by Argonaute cross-linking immunoprecipitation (Argonaute-CLIP) in nine HCC cases with matched livers. Argonaute-CLIP identified miR-21 bound to 580 target sites on coding transcripts, of which 332 were located in the coding sequences, 214 in the 3'-untranslated region, and 34 in the 5'-untranslated region, introns or downstream sequences. Overall, 403 target sites (69.5%) enriched for miR-21 in HCCs relative to liver. We compared expression of miR-21 targets in 377 patients with liver cancer registered in The Cancer Genome Atlas. Ago-CLIP miR-21 enrichment score in HCC distinguished expression of miR-21 targets by their correlation with miR-21 expression. Comparison of the miR-21 interactome in mouse and human livers identified common and species-specific targets. Among targets of miR-21, 27.6% were downregulated in HCC. The miR-21 interactome was predicted to regulate tumor metabolism by inhibiting PPAR alpha/RXR alpha and LXR/RXR signaling. To identify targets of miR-21, we matched Ago-CLIP targets to genes previously reported as aberrantly expressed after anti-miR-21 overexpression in HCC. RMND5A, encoding an E3 ubiquitin ligase, was identified as a potential target of miR-21 regulation and was variably expressed in HCC. Three predicted miR-21 targets, CAMSAP1, DDX1 and MARCKSL1, correlated with HCC patient survival. Collectively, our analysis biochemically identified novel targets of miR-21 likely to play a causal role in hepatocarcinogenesis.

Citation Format: Aaron B. Koenig, Juan M. Barajas, Kalpana Ghoshal. A comprehensive analysis of the interactome of miR-21, an established oncomir, by Argonaute-CLIP analysis identifies novel conserved and species-specific targets of miR-21 in human liver and hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5400.
Abstract 5403: Discovery of high metastatic potential microRNAs in human colorectal cancer
Authors: Lee Jee Hyun , Kim Gyeonghwa , Kim Hye Jin , Choi Gyu-Seog , Hur Keun
Published: August 2018

Background and Aim: Colorectal cancer (CRC) is the third most common cancer worldwide. More than half of the CRC patients have liver metastasis at the time of diagnosis, which is the major cause of cancer-related death in CRC. MicroRNAs (miRNAs) have been identified as modulators of the epithelial-mesenchymal transition (EMT)-mesenchymal to epithelial transition (MET) process by regulating transcription factors. However, it is not clear which specific miRNAs are critical drivers of CRC metastasis development. The aim of this study was to discovery novel high metastatic potential miRNAs in matched CRC and metastasis tissues, serum-exosome, and CRC cells with high metastasis property.

Materials and Methods: We isolated total RNAs from pairs of normal colon (NC), primary CRC (pCRC), liver metastasis (LM), normal liver (NL) tissue specimens, and pre-OP/post-OP serum-exosome sample from 15 each CRC patients. We also prepared total RNAs from 4 CRC cell lines (SW480, LS174T, COLO 205, and EMT-induced SW480) as well as exosome from their culture medium. To induce EMT process, epithelial phenotype CRC cell (SW480) was treated with epidermal growth factor (EGF). Next, miRNAs discovery step was conducted via NanoString analysis. Further miRNAs expression was determined by quantitative real-time PCR (qRT-PCR), and miRNAs expression was normalized relative to U6 and cel-miR-39 expression for tissue and serum-exosome samples, respectively.

Results: We successfully generated miRNAs expression profiles to distinguish NC vs. pCRC, pCRC vs. LM, LM vs. NL, and epithelial phenotype cells vs. high metastatic phenotype cells. Interestingly, a subset of miRNAs, including miRNA-100-5p, -339-3p, -549a, -1304-5p, and -1972, was commonly enhanced in LM, EMT-induced SW480, and high metastatic phenotype CRC cells compared to pCRC, SW480, and low metastatic phenotype CRC cells. In our further miRNAs validation analysis using pairs of pCRC and LM tissues from 15 CRC patients, miRNA-100-5p (P<0.0001), miR-339-3p (P=0.0022), and miR-1972 (P<0.0001) were significantly upregulated in pCRC than matched LM tissues. We also observed discordance expression patterns of miRNAs between CRC tissues and serum-exosome specimens.

Conclusions: Our findings suggest that a unique subset of miRNAs is involved in CRC metastasis development, which may associate with EMT process and acquiring of high metastatic potential in CRC cells. Moreover, our metastasis specific miRNAs profile might be useful for development of markers predicting and/or treatment of CRC patients with metastasis.

Citation Format: Jee Hyun Lee, Gyeonghwa Kim, Hye Jin Kim, Gyu-Seog Choi, Keun Hur. Discovery of high metastatic potential microRNAs in human colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5403.
Abstract 5412: miR155 and miR9 expression in human prostate cancer cell lines and prostate cancer tissue
Authors: Benedetti Ines , Rebollo Juan , Reyes Niradiz
Published: August 2018

Background: Differential expression of miRNAs between malignant, precancerous lesions, and nonmalignant prostate tissues may indicate that these molecules play a role in cancer biology. Several miRNAs have been commonly reported to be differentially expressed in prostate cancer, compared to benign prostate tissue, but some results have been contradictory. Expression patterns of specific miRNAs across prostate cancer, precancerous lesions, and benign tissue have not been determined.

Design: The expression patterns of 20 miRNAs were determined in the metastatic prostate cancer cells lines LNCaP and PC3, using the nontumorigenic prostate cell line PWR-1E as reference. Differentially expressed miR-9 and miR-155 were subsequently evaluated in epithelial cells obtained by laser capture microdissection from cancerous lesions, high-grade prostatic intraepithelial neoplasia, proliferative inflammatory atrophy, and benign tissue from radical prostatectomy and transurethral prostatectomy tissue specimens, from patients diagnosed with prostate cancer. Total RNA was extracted from the cell lines and microdissected epithelial cells and expression of miR-9 and miR-155 was evaluated by qPCR; miRNA levels in individual samples were normalized to corresponding RNU62 levels. Fold-change values were calculated, and p value < 0.05 was considered statistically significant. The Ethical Review Board of the academic institution approved this study.

Results: Differential expression of several miRNAs was found between cell lines. Four miRNAs showed a similar expression profile in the cancer cell lines, two were overexpressed in metastatic cell lines LNCaP and PC3 compared to the nontumorigenic PWR-1E cells (hsa-miR-195, hsa-miR-9), and two were underexpressed (hsa-miR-143, hsa-miR-155). Evaluation of miRNA expression in laser capture microdissected epithelial cells showed a trend towards higher expression of miR-9, and lower expression of miR-155 in microdissected epithelial cells derived from prostate tissue with cancer and proliferative inflammatory atrophy compared to epithelial cells from benign tissue.

Conclusions: Our results are in agreement with the description of miR-9 as oncomiRNA. miR-155 was underexpressed in LNCaP and PC3 cells in relation to nontumorigenic PWR-1E cells. Also, this miRNA showed a trend towards underexpression in epithelial cells microdissected from prostate tissue with cancer and proliferative inflammatory atrophy compared to epithelial cells from benign tissue. Further studies of these deregulated miRNAs will help clarify their role in prostate tumorigenesis.

Citation Format: Ines Benedetti, Juan Rebollo, Niradiz Reyes. miR155 and miR9 expression in human prostate cancer cell lines and prostate cancer tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5412.
Abstract 5422: TMPRSS2-ERG fusions confers efficacy of enzalutamide in an in vivo bone tumor growth model
Authors: Chinni Sreenivasa R. , Semaan Louie , Cher Michael
Published: August 2018

Castrate Resistant Prostate Cancer (CRPC) is an advanced disease resistant to systemic anti-androgen therapies and resistance is primarily attributed to reactivation of AR through multiple mechanisms. TMPRSS2-ERG fusions have been shown to regulate AR signaling, interfere with pro-differentiation functions, and mediate oncogenic signaling. In fact, cooperation between AR and ERG drives invasive adenocarcinoma even in the castrate environment. We have recently shown that ERG regulates intra-tumoral androgen synthesis thereby facilitates AR function in CRPC disease. We hypothesize that enzalutamide treatment will be more effective in cells/tumors with TMPRSS2-ERG translocations because these tumors have increased AR signaling. In other words, AR blockade is likely to induce a greater treatment response in tumors with ERG gene fusions than in tumors without such fusions. ERG knockdown was performed with VCaP cells using lentiviral infections to generate VCaP ERGshRNA cells and control VCaP scr cells with scrambled shRNA. Cell-growth analysis was performed to determine the effect of enzalutamide. Luciferase tagged VCaP scr and shRNA infected cells were used in intra-tibial animal model for bone tumor growth analysis and enzalutamide treatment used to inhibit AR signaling in bone tumors. Reverse transcription, quantitative real-time PCR (RT-qPCR) was used to determine the expression of AR responsive genes and androgen biosynthetic enzyme genes; Western blotting (WB) samples, for ERG, AR and AKR1C3 in VCaP bone tumors. Enzalutamide inhibited VCaP scr more effectively than shERG cells. Analysis of AR responsive genes show that Enzalutamide treatment at 5 micro molar concentration inhibited 85-90% in VCaP Scr cells whereas these genes inhibited to lesser extent in VCaP shERG cells. In bone tumor growth experiment, VCaP ERG shRNA cells grown at slower than VCaP scr shRNA cells. Enzalutamide treatment resulted in a sever growth inhibition in VCaP scr shRNA cells compared to VCaP shERG cells. Androgen biosynthetic enzyme expression is lower VCaP shERG bone tumors compared to VCaP scr shRNA bone tumors and enzalutamide inhibited the enzyme expression in both types of tumors. These data suggest that ERG transcription factor regulates androgen biosynthetic enzyme expression and enzalutamide treatment is effective against VCaP bone tumors with an intact ERG expression, and knocking down ERG in VCaP cells leads lesser response for enzalutamide therapy.

Citation Format: Sreenivasa R. Chinni, Louie Semaan, Michael Cher. TMPRSS2-ERG fusions confers efficacy of enzalutamide in an in vivo bone tumor growth model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5422.
Abstract 5429: Targeting Nrf2 anti-oxidative pathway as a novel strategy to suppress IDH1-mutated cancer
Authors: Liu Yang
Published: August 2018

Background: Reactive oxygen species are recently recognized as a second messenger that affects many aspects in cell biology. In cancer cells, ROS has been proof closely related to metabolic reprogramming, tumor proliferation, progression and metastasis. In tumors with isocitrate dehydrogenase (IDH) mutations, the neomorphic enzyme results in unusual accumulation of ROS in cancer cells, suggesting distinctive vulnerabilities may be established in these types of cancer. However, the biologic function of ROS in IDH1-mutated cancers remains elusive.

Methods: In this study, we explored the ROS homeostasis in IDH1 mutated glioma. We investigated the correlation between ROS scavenging genes and overall survival in 530 IDH1-mutated glioma cases. Mechanistically, we focused on nuclear factor-erythroid 2-related factor 2 (Nrf2) pathway and seek for novel therapeutic strategy by targeting ROS burden in cancer cells. We further investigated the therapeutic value of Nrf2 inhibitor, Brusatol, in IDH1 mutated cancer in vitro and in vivo.

Results: We found IDH1 mutation leads to substantial reprogramming in ROS homeostasis, highlighted with prompted ROS generation and detoxification. Stronger expression of ROS scavenging gene predicts drug resistance and poor disease outcome. Enhanced Nrf2-associated scavenging pathway was found essential to maintain reasonable intracellular ROS level during cancer progression. Targeting Nrf2 scavenging pathway not only led to ROS overload, DNA/protein oxidative damage, but also reduced tumor cell proliferation and xenograft growth in vivo.

Conclusions: IDH1 mutant glioma highly depend on Nrf2 scavenging pathway to maintain ROS homeostasis. Targeting ROS scavenging might be a novel approach to treat gliomas with IDH1 mutation.

Citation Format: Yang Liu. Targeting Nrf2 anti-oxidative pathway as a novel strategy to suppress IDH1-mutated cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5429.
Abstract 5438: XPNPEP3: A novel transcriptional target of canonical Wnt/β-catenin signalling
Authors: Kumar Raju , Naz Ashmala , Kotapalli Viswakalyan , Gowrishankar Swarnalata , Rao Satish , Pollack Jonathan R. , Bashyam Murali Dharan
Published: August 2018

Canonical Wnt/β-catenin signalling plays pivotal roles during embryonic development and adult tissue regeneration. Its aberrant activation however drives expression of a panoply of genes to facilitate colorectal tumorigenesis. Hence, it is imperative to delineate the complete β-catenin transcriptome. We performed genome-wide mRNA profiling of sporadic rectal cancer samples stratified by Wnt status. Results revealed significant up-regulation of XPNPEP3 transcript levels along with that of canonical Wnt targets AXIN2 and EPHB2 in Wnt+ samples. The differential expression of XPNPEP3 was further validated by quantitative PCR (Q-PCR) in additional samples. Nuclear stabilization of β-catenin achieved through LiCl treatment in three colorectal cancer (CRC) cell lines followed by Q-PCR and promoter-luciferase assays confirmed up-regulation of XPNPEP3. XPNPEP3 encodes X-prolyl aminopeptidase 3 which functions to remove the penultimate N-terminal Proline residue from nascent proteins and appears to play a role in ciliary function. Immunohistochemistry based expression analysis using a CRC tissue microarray revealed significant correlation between XPNPEP3 levels and β-catenin nuclear localization as well as increased XPNPEP3 expression in tumor compared to matched normal samples. Survival analysis of The Cancer Genome Atlas (TCGA) breast invasive carcinoma, skin cutaneous melanoma and lung adenocarcinoma data sets revealed poor survival among patients having perturbed XPNPEP3 expression. Characterization of possible oncogenic function of XPNPEP3 in CRC cells and in mice tumor xenografts is currently underway. Altogether, our results suggest XPNPEP3 to be a novel transcriptional target of Wnt/β-catenin signalling having a possible significance in CRC tumorigenesis.

Citation Format: Raju Kumar, Ashmala Naz, Viswakalyan Kotapalli, Swarnalata Gowrishankar, Satish Rao, Jonathan R. Pollack, Murali Dharan Bashyam. XPNPEP3: A novel transcriptional target of canonical Wnt/β-catenin signalling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5438.
Abstract 544: Characterization of serine/threonine kinase LASK2 as a biomarker and therapeutic target for lung cancer
Authors: Daigo Yataro , Takano Atsushi , Nakamura Yusuke
Published: August 2018

As the number of lung cancer patients responding well to standard therapies is still small, further development of new anti-cancer drugs with minimum risk of adverse event and highly sensitive cancer biomarkers is urgently awaited. We have been developing new molecular therapies targeting oncoproteins with their companion biomarkers by screening system as follows; i) To identify up-regulated genes in 120 lung cancers by the gene expression microarray representing 27,648 genes, ii) To verify the candidate genes for their low expression in 23 normal tissues, iii) To validate the clinicopathological significance of their protein expression by tissue microarray covering hundreds of non-small cell lung cancers (NSCLCs), iv) To verify whether they are essential for the growth/invasion of cancer cells by siRNAs. During this process, we selected dozens of druggable oncoproteins with various enzymatic activities, and identified activation of serine/threonine kinase LASK2 (lung cancer-associated kinase 2) in the majority of various histological types of lung cancers, but not in normal tissues except testis. Immunohistochemical analysis showed that strong LASK2 positivity was an independent prognostic factor for patients with NSCLC (P<0.0001). Suppression of LASK2 expression with its siRNAs inhibited growth of lung cancer cells. The enhanced cellular proliferation by introduction of LASK2 in mammalian cells also supported its oncogenic function in vitro and in mice model. Induction of LASK2 appeared to increase the levels of phosphorylation of oncogenic signal proteins for lung cancer such as MAPK. The data suggest that LASK2 is a candidate prognostic biomarker and possible therapeutic target for lung cancers.

Citation Format: Yataro Daigo, Atsushi Takano, Yusuke Nakamura. Characterization of serine/threonine kinase LASK2 as a biomarker and therapeutic target for lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 544.
Abstract 5440: Role of tyrosine phosphorylation of β-catenin in EGFR-mutant lung cancer
Authors: Fujii Masanori , Nakayama Sohei , Shimizu Kohei , Takei Hisashi , Ando Mariko , Heo Eunyoung , Kobayashi ikei , Pan Gilbert , Inuzuka Hiroyuki , Kobayashi Susumu
Published: August 2018

Wnt/ β-catenin signaling plays a key role in the pathogenesis of colon and other cancers. Emerging evidence indicates that oncogenic β-catenin regulates several biological processes essential for cancer initiation and progression. The role of β-catenin in lung cancer with epidermal growth factor receptor (EGFR) activating mutations has not been fully understood; however, recent studies suggest that co-occurring genetic alterations in CTNNB1 might cooperate with mutant EGFR in promoting tumor progression and treatment resistance to EGFR-tyrosine kinase inhibitors (EGFR-TKIs). This sheds new light on this pathway in EGFR-mutant lung cancer. We previously demonstrated that β-catenin plays an essential role in lung tumorigenesis driven by EGFR mutants, particularly EGFR-T790M. We also found that β-catenin is activated through tyrosine-phosphorylation by EGFR mutants. In this study, we identified five tyrosine phosphorylation sites (Y5) of β-catenin by mass spectrometry. Tyrosine phosphorylation at these sites may be critical in β-catenin stability, nuclear translocation and its role as a transcriptional switch in oncogenesis. Firstly, we demonstrated that tyrosine phosphorylation of β-catenin disrupts the binding of a main ubiquitin ligase β-Trcp1, leading to an escape from degradation. Secondly, in contrast to known transcriptional activity with TCF/LEF, β-catenin that is tyrosine phosphorylated by mutant EGFR was found to form a complex with a transcriptional regulator, YAP1, and a transcriptional factor, TBX5. Immunoprecipitation experiments suggested Y5 tyrosine phosphorylation of β-catenin plays a critical role in the interaction between β-catenin and TBX5. Moreover, this complex may regulate anti-apoptotic genes, including BCL2L1, which encodes Bcl-xL. Combination treatment with osimertinib, a 3rd generation EGFR-TKI, and dasatinib suppressed Y5 tyrosine phosphorylation of β-catenin, leading to reduced Bcl-xL expression. Subsequent TBX5 knockdown in vitro decreased Bcl-xL expression while Bcl2l1 knockout in vivo mouse models suppressed lung tumor development. These observations suggest that β-catenin-YAP1-TBX5 complex contributes to EGFR-T790M lung cancer and may serve to explain the underlying mechanism for EGFR-TKIs resistance and for the effectiveness of combination therapy with osimertinib and dasatinib.

Citation Format: Masanori Fujii, Sohei Nakayama, Kohei Shimizu, Hisashi Takei, Mariko Ando, Eunyoung Heo, ikei Kobayashi, Gilbert Pan, Hiroyuki Inuzuka, Susumu Kobayashi. Role of tyrosine phosphorylation of β-catenin in EGFR-mutant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5440.
Abstract 5441: Regulation of AKT phosphorylation by GSK3β and PTEN to control chemoresistance in breast cancer
Authors: Gao Chunyi , Wang Guohua , Jiang Zhenglin
Published: August 2018

Background Chemotherapy is an important element in the treatment paradigm for breast cancers. However, the resistance of cancer cells to chemotherapeutic agents frequently results in the subsequent recurrence and metastasis. AKT phosphorylation is highly expressed or over-expressed in chemoresistant tumor samples. However, the precise molecular mechanism involved in AKT phosphorylation-related chemoresistance in breast cancer remains unknown. The aim of the present study was to assess whether the role of AKT phosphorylation in the cell viability and chemoresistance of breast cancer. Methodology/Principal Findings We developed two taxol resisted breast cancer cells: TAX Resis HepG2 and TAX Resis HepG2 SMMC7721. Western blot and immunofluorescence analysis indicated that glycogen synthase kinase 3 beta (GSK3β), phosphorylated phosphatase and tension homologue (p-PTEN) and phosphorylation of AKT (p-AKT) were highly expressed in taxol resisted HepG2 and SMMC7721 cells. The increase of GSK3β phosphorylated and inactivated PTEN, thereby enhanced phosphatidylinositide 3-kinases (PI3K)/Akt signaling. The increase in GSK3β, p-PTEN and p-AKT was associated with cell viability by MTT assay. Annexin-V-PI assay and transwell analysis were indicated that GSK3β knockdown with lentiviral shRNA (shRNA-GSK3β) promoted the apoptosis and suppressed the migration ability of Taxol resisted HepG2 and SMMC7721 cells, and both effects were reversed by activating p-AKT via PTEN inhibitor bpV(pic). Conclusions In conclusion, AKT phosphorylation manipulated by GSK3β and PTEN were correlated with cell viability, migration and apoptosis in Taxol resisted HepG2 and SMMC7721 cells, which may promote chemoresistance of breast cancer. Furthermore, functions of GSK3β can modulate cell viability via the PTEN/PI3K/Akt signaling pathway and induce chemoresistance, serving as a valuable molecular target for treatment of breast cancer.

Citation Format: Chunyi Gao, Guohua Wang, Zhenglin Jiang. Regulation of AKT phosphorylation by GSK3β and PTEN to control chemoresistance in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5441.