Citations

Abstract Neuroblastoma, an embryonic tumor of peripheral sympathetic nervous system (PSNS), accounts for 10% of all childhood cancer deaths. We recently developed a robust zebrafish model of neuroblastoma and demonstrated that activated ALK synergizes with MYCN by inhibiting a developmentally-timed apoptotic response that is otherwise induced by MYCN. Genomic studies show that PTPN11 (encoding SHP2) is the second most frequently mutated genes in high-risk neuroblastoma. We have now used our zebrafish model to ask whether mutationally activated SHP2 functions as an oncogene in neuroblastoma. We developed a transgenic line in which ptpn11E69K is overexpressed in the PSNS under control of the dopamine-beta-hydroxylase promoter. Interestingly, ptpn11E69K synergized with MYCN to accelerate the onset of neuroblastoma in the interrenal gland (IRG), the zebrafish analogue of the adrenal medulla. Tumors began to appear at 15 weeks in transgenic fish overexpressing MYCN alone, whereas latency was shortened to 7 weeks and the penetrance was increased more than four-fold in transgenic fish coexpressing MYCN and ptpn11E69K. Coexpression of ptpn11E69K and MYCN also induced ganglioneuroma in the sympathetic ganglia, an outcome that has not been observed in transgenic fish overexpressing MYCN and activated ALK. In addition, coexpression of ptpn11E69K and MYCN induced adrenal neuroblastic hyperplasia in the IRG of all the transgenic fish at 5 weeks of age, a phenotype that has only been observed in about 50% of transgenic fish overexpressing activated ALK and MYCN or MYCN alone. Thus, these results suggest that activated SHP2 can collaborate with MYCN in neuroblastoma tumorigenesis via mechanisms different from those of activated ALK. Thus, zebrafish appears to provide a robust model system for functional genomic analysis and for the investigation of the mechanisms and pathways underlying genetic alterations identified in integrative genomic studies. Citation Format: Xiaoling Zhang, Guang Yang, A.Thomas Look, Benjamin G. Neel, Shizhen (Jane) Zhu. Activated SHP2 collaborates with MYCN in neuroblastoma tumorigenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 80. doi:10.1158/1538-7445.AM2014-80

Abstract PURPOSE: Cell free circulating microvesicles (in particular, exosomes) contain proteins and nuclei acids that may serve as biomarkers for disease diagnosis and prognosis. The goal of this study was to identify exosomal microRNAs that may predict clinical outcome of patients with castrate resistant prostate cancer (CRPC). EXPERIMENTAL DESIGN: In discovery stage, we performed RNA sequencing using plasma exosomal RNAs derived from 36 patients with CRPC. We mapped the sequence reads to known miRbase (Release 19, 2043 entries) and normalized the miRNA abundance by sequence counts per million mappable reads. We applied Cox regression analysis to identify the miRNAs that were associated with overall survival of CRPC. In validation stage, we first examined an exosomal small RNA sequencing dataset consisting of 192 individuals with various health conditions. We used Normfinder and Bestkeeper to select most stably expressed miRNAs as candidates for normalization references. We then applied real-time qRT-PCR assays to test selected candidate reference miRNAs and survival-related miRNAs in additional 100 CRPC patients. From validated miRNAs, we constructed multivariate models to predict overall survival for this group of patients. RESULTS RNA sequencing generated over 6 million mappable reads per patient in the initial discovery cohort. Among these reads, ∼45% were mapped to known miRNAs for a total of 483 known and 275 novel miRNAs with normalized read counts ≥ 5. The median follow-up time for the 36 CRPC patients was 35.6 months during which 10 patients had died. Cox regression analysis identified four microRNAs (miR-1290, -1246, -375 and a predicted miRNA at chromosome 12) that were associated with overall survival (FDR<0.05). Of six selected candidate miRNAs, miR-30a/e-5p performed the best in their stability as endogenous references for real-time qRT-PCR. When normalized by these internal controls, we confirmed two of the three known miRs (miR-1290 and -375) showing significant association with overall survival in the validation cohort (p<0.001) with a median follow up time of 12.5 (range: 1-41) months at which time 28 patients had died. The median overall survival for patients with high (N=21) and low (N=40) expression in both miR-1290 and -375 was 7.2 (1-26.7) months and 15.3 (1-41) months, respectively (p<0.05). The miR-1290/-375-based prediction model consistently showed better predictive performance with AUC=72% than clinical variable-based model with AUC=64%. CONCLUSIONS: Plasma exosomal miRNAs provide an easily accessible resource for biomarker development in prognosis of advanced prostate cancer. Exosomal miR-1290 and miR-375 are associated with overall survival in CRPC patients. miR-30a/e-5p, especially the geometric mean of miR-30a/e-5p, are qualified endogenous references for real-time qPCR. Further confirmation of these findings is needed for prognostic and predictive biomarker in development of CRPC stage. Citation Format: Xiaoyi Huang, Tiezheng Yuan, Meihua Liang, Meijun Du, Shu Xia, Rachel Louise Dittmar, Zhifu Sun, Yan Lu, Stephen N. Thibodeau, Lisa Boardman, Manish Kohli, Liang Wang. Exosomal miR-1290 and miR-375 as prognostic markers in metastatic castrate resistant prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 574. doi:10.1158/1538-7445.AM2014-574

Abstract Carney's triad (CTr) is a non-hereditary condition, primarily seen in young women, characterized by gastrointestinal stromal tumors (GIST), extra-adrenal paragangliomas and pulmonary chondromas. Most CTr patients present with GIST and pulmonary chondroma (incomplete CTr). A marked decrease in the enzymatic activity of succinate dehydrogenase (SDH) has been detected in these tumors, but the presence or absence of SDH mutations in CTr is controversial. A related disease, known as Carney-Stratakis Syndrome (CSS), has no female predisposition and presents with extra-adrenal paragangliomas and GIST tumors, without pulmonary chondromas. In distinction to CTr, CSS is hereditary due to germline SDH mutations in the enzyme's subunits (SDHA, SDHB, SDHC and SDHD) with corresponding decreased SDH activity in associated tumors. We have investigated 64 patients with CTr for germline mutations and/or deletions in the SDH subunit genes; four patients were found to have germline mutations in SDHB or SDHC. All four patients had multifocal gastric GIST and pulmonary chondromas at diagnosis; two subsequently developed paragangliomas, confirmed by biopsy. One of the patients with CTr and a SDHB mutation had a nephew with the same mutation and a neuroblastoma, confirming a previously reported association of neuroblastoma with gist (JMG 2009; 46:215, and AJMG 2010; 152A: 1531). We conclude that few CTr patients maybe more correctly classified as having CSS; the genetic distinction of CTr from CSS needs further study. [S.A.B. and P.X. should be regarded as joint first authors.] Citation Format: Sosipatros A. Boikos, Paraskevi Xekouki, Fabio R. Faucz, Karel Pacak, Margarita Raygada, Karen Adams, Evan Szarek, Evan Ball, Su Young Kim, Elena Fumagalli, Lee J. Helman, J Aidan Carney, Constantine A. Stratakis. Few Carney's Triad patients have mutations in two subunits of the succinate dehydrogenase enzyme (SDHB, SDHC). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 568. doi:10.1158/1538-7445.AM2014-568

Abstract Introduction: Triple negative breast cancers (TNBC) are characterized as lacking estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) expression and TNBC patients have higher rates of recurrence and death compared with other breast cancer subtypes. For TNBC patients who fail standard chemotherapy, there are a lack of novel drug therapies, given the absence of well-defined molecular targets. Recently, a microarray meta-analysis identified 7 triple negative subtypes, including the validation of the luminal androgen receptor (LAR) positive subtype [Lehmann, 2011]. However, microarray technology is dependent on probe-target specificity and the 7 subtypes have yet to be validated using RNA sequencing data, and the presences of recurrent genomic alterations in the 7 subtypes are unknown. METHODS: We obtained 1106 breast cancer RNA-Seq bam files from The Cancer Genome Atlas (TCGA) and aligned with Tophat v1.3. The PAM50 intrinsic gene signature was used to extract a cohort of 128 TNBC samples. Consensus clustering of genes, greater than 75th percentile of variance, was performed using Kmeans clustering in Spearman's correlation space. A nearest centroid prediction model was developed from genes differentially expressed among the clusters. Eighty independent TNBC RNA sequencing samples were obtained (British Colombia; BC) [Shah, 2012] which were calibrated to our TNBC conditional quantile normalized cohort and sub-typed by our model. RESULTS: Using RNA-Seq gene expression count data, we identified 5 clusters, all of which were stable, including the LAR cluster. Signaling pathway impact analysis (SPIA) implicated cytokine-cytokine receptor interaction, leukocyte transendothelial migration, and regulation of actin cytoskeleton pathways commonly altered in the non-LAR TNBC subtypes. In contrast, cell cycle, ECM-receptor interaction, endocrine regulated calcium reabsorption, and insulin signaling pathways were altered in the LAR versus non-LAR subtypes. Neuroactive ligand-receptor interactions were observed to be altered commonly between all sub-types. We then applied our model to the Shah, et al cohort. In this cohort, the LAR subtype was consistent with Shah's classification of ‘other’ TNBC and contained no basal samples by PAM50 intrinsic modeling. Analysis of sub-type specific mutation data from the BC cohort demonstrates an increased mutational load in ECM-related proteins, particularly the myosins, along with increased TP53 clonality in the non-LAR subtypes. CONCLUSIONS: Using TCGA RNASeq data, we have confirmed the presence of 5 major TNBC subtypes, including the LAR; which was negligible in basal composition by PAM50 intrinsic modeling. SPIA pathway analysis indicates a core set of pathways demonstrating altered expression across the TNBC sub-types and the identification of molecular targets within each subtype is ongoing. Citation Format: Kevin J. Thompson, Xiaojia Tang, Zhifu Sun, Jason P. Sinnwell, Hugues Sicotte, Douglas W. Mahoney, Steven Hart, Peter T. Vedell, Poulami Barman, Jeanette E. Eckel Passow, Eric D. Wieben, James N. Ingle, Judy C. Boughey, Liewei Wang, Richard Weinshilboum, Krishna R. Kalari, Matthew P. Goetz. Molecular classification of triple negative breast cancer via RNA-sequencing data. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5592. doi:10.1158/1538-7445.AM2014-5592

Abstract Background: Fusion genes, transcripts, and proteins are key drivers of hematopoietic oncogenesis and can serve as effective therapeutic targets. Among peripheral T-cell lymphomas (PTCLs), little is known about fusion genes except for those involving ALK. Discovery of fusion genes may provide therapeutic targets for PTCLs, which have poor outcomes with conventional therapy. We have developed methods for detecting candidate fusions using (1) mate-pair DNA sequencing (MPseq), an approach that spans the entire genome at a fraction of the cost of traditional whole-genome sequencing, and (2) RNA sequencing (RNAseq). Each technique has strengths, limitations, and false discovery rates. Here, we integrated results of both methods to discover and orthogonally validate expressed fusion genes in PTCLs. Methods: DNA and RNA were extracted from 49 frozen, OCT-embedded clinical PTCL specimens, including 25 anaplastic large cell lymphomas; 16 PTCLs, not otherwise specified; and 8 other PTCLs. MPseq and RNAseq were performed using Illumina library protocols and a HiSeq 2000. Detection of fusion genes and transcripts followed our published methods (Blood 2012;120:2280 and Nucleic Acids Res 2011;39:e100, respectively). Functional annotation of genes involved in fusions was performed using DAVID. Results: Of 2818 candidate chromosomal rearrangements identified by MPseq and 90 candidate fusion transcripts identified by RNAseq, 45 events were present in both datasets (mean/case, 0.9; range, 0-7). Fusions were inter-chromosomal in 16 and intra-chromosomal in 29. Annotation clusters with the highest enrichment scores related to SH2 domain-containing proteins and tyrosine kinases (including FER and MAP2K3). Seven genes were recurrently involved in fusions, including known fusion partners such as ALK and previously unreported fusion partners such as PPP1R8, a phosphatase inhibitor important for the activity of Polycomb group proteins such as EZH2. Detection of candidate events only by MPseq could be explained in part by breakpoints mapping to non-genic regions (79% of events). Detection only by RNAseq could be explained in part by unannotated transcripts spanning neighboring named genes (median intra-chromosomal distance, 0.09 MB vs. 12.7 MB for intra-chromosomal candidates identified by MPseq; p<0.0001, Wilcoxon test). Conclusions: Integrated DNA/RNA sequencing is an effective, clinically feasible tool for simultaneous discovery and orthogonal validation of expressed fusion genes. This approach yielded fusions in PTCLs involving genes with key functions in lymphocytes, including novel and recurrent fusions, some of which might be targetable with compounds currently in clinical trial. Candidate intra-chromosomal fusion transcripts not identified by MPseq may represent unrecognized isoforms or the results of novel read-through mechanisms, and merit further study. Citation Format: Andrew L. Feldman, George Vasmatzis, Yan W. Asmann, Sarah H. Johnson, Bruce W. Eckloff, Sumit Middha, Jaime I. Davila, Paul J. Kurtin, Brian K. Link, Stephen M. Ansell, James R. Cerhan. Integrated DNA/RNA sequencing for discovery and orthogonal validation of expressed fusion genes in peripheral T-cell lymphomas. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5585. doi:10.1158/1538-7445.AM2014-5585

Abstract Background: The standard treatment for epithelial ovarian cancer (EOC) patients with advanced disease is initial debulking surgery followed by carboplatin-paclitaxel combination therapy. Unfortunately, even with modern chemotherapy, most patients with advanced disease relapse and die of EOC. One of the biggest challenges in the treatment of EOC is the large inter-patient variation in clinical response and toxicity observed for taxane and platinum therapies. Purpose: To determine pharmacogenomic markers related to carboplatin-paclitaxel therapy with 33 Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) derived from EOC patients for which genome-wide genetic information exists. Methods: The 33 LCLs were treated with increasing concentrations of carboplatin and/or paclitaxel, followed by MTT cytotoxicity and Caspase3/7 assays. Using the measurements of MTT absorbance or Caspase3/7 fluorescence, dose response curves were fit to estimate the in vitro drug response (MTT or caspase3/7) for each LCL and treatment (paclitaxel, carboplatin, and combination) using the inflection point of the fitted curve (i.e.., the MTT IC50 or effective dose that kills 50% of the cells). The six in vitro phenotypes where then associated with genome-wide SNP data, imputed up to the markers in the 1000 Genomes Project. Results: Genetic association analysis of carboplatin, paclitaxel and combination therapy cell viability, as measured by MTT, found one SNP, rs202167095 within HS3ST4, in common with all three phenotypes (p < 0.0001). HS3ST4 is regulated by TRF2 and activates natural killer cells. Furthermore, TRF2 maintains telomere integrity and is involved in activating DNA damage response (DDR) pathway.. Similarly, three SNPs were found to be associated with the three Caspase3/7 activities: SNPs on chromosome 3 (rs13098237 and rs13098239), and a SNP on chromosome 10 (rs138004421 within LINC00858). Lastly, SNPs in the following genes were associated with carboplatin IC50 with p < 1x10-6 (i.e., the top associated SNPs with any drug response phenotype): JAKMIP3 (p=2.3x10-7), TSHZ3 (p = 4.9x10-7) and TGFA (p=3.6x10-7). JAKMIP3 has been implicated in some cancers and interacts with other janus kinases and JAK-STAT pathways, while TSHZ3 inhibits the expression of CASP4, thus limiting cell apoptosis. Lastly, TGFA codes for a growth factor that is a ligand for epidermal growth factor receptor, which activates a signaling pathway for cell proliferation, differentiation and development. Conclusions: Identifying genetic loci associated with response to platinum-taxane therapies will ultimately improve clinicians' ability to tailor therapy decisions for EOC patients. This research discovered novel candidate genes for which further research is needed to understand the mechanism by which they impact clinical response. Citation Format: Brooke L. Fridley, Taraswi M. Ghosh, Alice Wang, Ellen L. Goode, Jatinder Lamba. In vitro pharmacogenomic study of ovarian cancer finds novel genetic variants associated with response to platinum and taxane therapies. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5565. doi:10.1158/1538-7445.AM2014-5565

Abstract Background: Genome wide association studies (GWAS) have recently identified 8 loci identified with multiple myeloma (MM) susceptibility. We hypothesized that germ line genetic variants may also affect MM progression. We performed the first GWAS of MM survival, by conducting a meta-analysis of two existing studies at University of California San Francisco (UCSF) and the Mayo Clinic, and replicating findings in the International Multiple Myeloma rESEarch (IMMEnSE) consortium. Methods: The UCSF study included 353 MM patients genotyped on an Illumina Omni5 and Illumina 660 array. The Mayo clinic study included 239 MM patients genotyped on an Affymetrix 6.0 array. We imputed missing genotypes using the 1000 Genomes dataset and performed a GWAS for survival using proportional hazards models adjusting for age and gender and genetic ancestry using principal components analysis. We conducted a meta-analysis of the results from the two GWAS. We replicated the top SNPs in the IMMEnSE cohort which included 772 patients with survival data from 7 European countries and one North American site. We used the dataset from Grundberg et al (Nat Genetics 2012) to test for an association between SNPs associated with survival and gene expression in immortalized lymphocytes. We used gene expression data from Zhan et al (Blood 2006) to analyze the association between expression and survival. Results: In meta-analysis, we found a genome wide significant association between SNPs on a region at 16p13 and survival (rs72773978; p=2.9x10e-10). Patients with the minor allele were at increased risk for mortality (HR 2.73; 95% CI: 1.99 - 3.73). The top associated SNPs were all in strong linkage disequilibrium and were centered over the gene FOPNL. We replicated the association in the IMMEnSE cohort and found a significant association between the top SNP from the discovery dataset (rs72773978 p=0.037). We used previously published data to determine the association between gene expression and the top associated SNPs from the GWAS. The top SNP (rs72773978) was not in previously published eQTL databases, so we used rs7201759 which was also associated with survival in our data (p=3.8x10e-10) as a proxy. The minor allele for this SNP was associated with increased levels of expression of FOPNL (p=9x10e-5), but not with expression of any other genes within a 1 megabase region. Finally, we also observed an association between increased expression of FOPNL and shorter survival (HR: 2.62 per standard deviation.; 95% CI: 1.08 - 6.32). Conclusion: Germ line variants at 16p13 near the FOPNL gene are associated with survival among MM patients. FOPNL is thought to be involved in centrosomal function, and centrosomal activity has previously been associated with survival in MM patients. Our results support this previous observation. Furthermore, they suggest that germ line variants could also be useful in assessing prognosis for patients with MM. Citation Format: Elad Ziv, Eric Dean, Donglei Hu, Alessandro Martino, Daniel Serie, Daniele Campa, Blake Aftab, Paige Bracci, Gabriele Buda, Jennifer Caswell, Charles Dumontet, Marek Dudziński, Laura Fejerman, Alexandra Greenberg, Scott Hunstman, Artur Jurczyszyn, Krzysztof Jamroziak, Shaji Kumar, Herlander Marques, Thomas Martin, Joaquin Martinez-Lopez, Vincent Rajkumar, Juan Sainz, Annette Juul Vangsted, Marzena Watek, Jeffrey Wolf, Susan Slager, Federico Canzian, Celine Vachon. Genome wide association study identifies variants at 16p13 associated with survival in multiple myeloma patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5078. doi:10.1158/1538-7445.AM2014-5078

Abstract Progression from adenoma to colon cancer is a multi-step process and the role of microRNAs in this transformation is not completely understood. We used both in vitro and in vivo approaches to demonstrate the role of miRNAs in the transformation of adenoma to adenocarcinoma. Reporter assays were used to show the direct interaction of miRNAs to target gene. A Tet-inducible TripZ system and miRzips constructs were used in the in vitro function and xenograft studies. Kaplan-Meier survival curves and Cox regression were used to analyze the survival data in colon cancer patients. Here, we show that the combination of miR-503 and miR-182 contributes to the transformation of colon adenoma to adenocarcinoma by cooperatively regulating the tumor suppressor gene, FBXW7. We found that miR-182 was upregulated in both colon adenoma and adenocarcinoma, whereas miR-503 was upregulated only in adenocarcinoma, indicating a potential hierarchical and stepwise expression of these miRNAs in the regulation of FBXW7. Furthermore, we showed that colon adenoma derived non-tumorigenic AAC1 cells were transformative and tumorigenic in mice when expressing Tet-inducible miR-503. Finally, the combination of miR-503 and miR-182 transcript levels was predictive of poor outcome in colon cancer patients. We conclude that a step-wise expression of miR-182 and miR-503 in benign adenoma synergistically regulates the driver gene FBXW7, thus contributing to the progression of colon adenoma to adenocarcinoma. Citation Format: Lihua Li, Aaron Sarver, Rohini Khatri, Praveensingh Hajeri, Iris Kamenev, Stephen Thibodeau, Clifford J. Steer, Subbaya Subramanian. MicroRNAs miR-503 and -182 regulate FBXW7 contributing to the malignant transformation to colon adenocarcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4368. doi:10.1158/1538-7445.AM2014-4368

Abstract The three-dimensional (3D) structure of the cell and its nucleus is intricately associated with cellular function. Aberrations and heterogeneity in cellular and nuclear morphology serve as diagnostically important cues to identify malignant transformation. However, current cytopathology practice is predominantly based on a qualitative, 2D assessment of cellular morphology that may bias the diagnosis. We utilized the Cell-CT® platform to perform single-cell, optical tomography imaging and generate 3D cell images with isotropic, sub-micron spatial resolution. We developed custom image analysis tools to accurately quantify 3D cell and nuclear morphology. We used these measures to characterize the morphological heterogeneity within and among epithelial cell populations, and to identify morphological descriptors that are reliably predictive of cell state. We assessed the efficacy of our approach relative to conventional 2D assessment (at 40x magnification) to detect malignant transformation in immortalized and primary normal-cancer cell line pairs from human esophagus and breast epithelia. We observed the 3D method of assessment to provide a consistently superior performance (sensitivity and specificity) in predicting malignant transformation. Further, some widely used diagnostic parameters, such as nuclear size or nucleus-to-cytoplasm ratio, did not always exhibit the highest predictive power in 3D space. The availability of 3D morphological information also provided novel insights on intra-population morphological heterogeneity in both normal and cancer cell populations. Our results emphasize the need to incorporate 3D morphological information into standard pathological practice. Citation Format: Vivek Nandakumar, Stephanie Helland, Jessica H. Han, Geriann Davis, Brian A. Ashcroft, Thai H. Tran, Ting Li, Karen S. Anderson, Rahul Pannala, Joseph R. Mikhael, David E. Fleischer, Roger H. Johnson, Kimberly J. Bussey, Deirdre R. Meldrum. Quantifying three-dimensional cellular morphology and its heterogeneity in epithelial cancers by single-cell optical tomography. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4297. doi:10.1158/1538-7445.AM2014-4297

Abstract INTRODUCTION Next generation sequencing (NGS) of patients has significantly changed our ways to study cancer genomics as it provides precise estimates of gene expression, fusion transcripts, expressed single nucleotide variants (eSNVs), splice variants and copy number variants. The Breast Cancer Genome Guided Therapy (BEAUTY) is an ongoing clinical study in which RNA sequencing (RNAseq) and whole exome sequencing (WES) are performed prior to, during and after neoadjuvant chemotherapy. Here we report the use of these sequencing technologies to investigate gene expression levels and mutational profiles in a triple negative breast cancer (TNBC) patient enrolled in BEAUTY whose disease did not respond to neoadjuvant paclitaxel and anthracycline/cycphosphamide. METHODS Computational approaches were used to integrate WES and RNAseq data obtained before therapy (V1T), after 12 weekly paclitaxel treatments (V2T) and after anthracycline-based regimen at surgical resection (V3T) to study a single patient with persistent TNBC disease after neoadjuvant chemotherapy. RESULTS Using RNA-Seq data, we identified an inter-chromosomal fusion transcript between chromosome 20 and 22 (GNAS-TTC38) that was highly expressed at V1T, V2T and V3T. We also identified intra-chromosomal fusion transcripts that were expressed at two time points, such as fusion transcript (KANSL1-ARL17A) on chromosome 17 for V1T and V2T and fusion transcript (RBM12B-LINC00535) on chromosome 8 for V2T and V3T time points. Several gene expression changes were also observed. Gene expression analysis of V1T, V2T and V3T tumors was performed. Differential temporal gene expression profiles of 9884 genes that were significant and varying at different time points were obtained for pathway analysis. Pathway analysis of 9884 genes identified up regulation and down regulation of several transcription factors with a fold change of 2x or more. When compared to blood, DNA tumor and RNA-Seq data, we identified 81 common somatic eSNVs that were expressed in both V1T and V2T time points and we are in the process of investigating V3T data. We found alterations of key transporter domains (CD225, Coatamer_beta_C, DUF2435, Dynamitin, EI24, GLTP, LMF1, Porin_3, V-ATPase_C) in our V1T and V2T SNV data. Similar to gene expression analysis, we are in the process of obtaining the list of mutations at various time points to identify driver and passenger mutation candidate genes for this specific TNBC patient. CONCLUSIONS Our initial time-series analysis of eSNV, fusion transcripts and gene expression data demonstrate that intensive analysis for individual patients is feasible. Further investigation of drug transporters and transcription regulators may help develop personalized treatment strategies for patients with disease resistant to current regimens. Citation Format: Krishna R. Kalari, Xiaojia Tang, Kevin J. Thompson, Douglas W. Mahoney, Poulami Barman, Jason P. Sinnwell, Hugues Sicotte, Peter Vedell, Steven N. Hart, Travis J. Dockter, Katie N. Jones, Amy L. Conners, Ann M. Moyer, Daniel W. Visscher, Jia Yu, Bowen Gao, Sarah A. McLaughlin, John A. Copland, Alvaro Moreno-Aspitia, Donald W. Northfelt, Richard J. Gray, Vera J. Suman, Jeanette E. Eckel Passow, Jean-Pierre A. Kocher, Eric D. Wieben, Gianrico Farrugia, Cloann G. Schultz, James N. Ingle, Richard Weinshilboum, Matthew P. Goetz, Liewei Wang, Judy C. Boughey. Analysis of sequencing data to identify potential drug targets for an individual newly diagnosed with basal breast cancer who failed to respond to current standard neoadjuvant chemotherapy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4185. doi:10.1158/1538-7445.AM2014-4185