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Yi-Mi Wu,
Fengyun Su,
Shanker Kalyana-Sundaram,
Nick Khazanov,
Bushra Ateeq, Xuhong Cao,
Robert J Lonigro,
Pankaj Vats,
Rui Wang,
Su-Fang Lin, [......],
Seth Sadis,
Sameek Roychowdhury,
Maha Hussain,
Felix Y Feng,
Mark M Zalupski,
Moshe Talpaz,
Kenneth J Pienta,
Daniel R Rhodes,
Dan R Robinson,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Through a prospective clinical sequencing program for advanced cancers, four index cases were identified which harbor gene rearrangements of FGFR2 including patients with cholangiocarcinoma, breast cancer, and prostate cancer. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, we identified additional FGFR gene fusions with intact kinase domains in lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins induced cell proliferation. Two bladder cancer cell lines that harbor FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Due to the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts which incorporate transcriptome analysis for gene fusions are poised to identify rare, targetable FGFR fusions across diverse cancer types.
Cancer discovery. 04/2013;
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Vishal Kothari,
Iris Wei,
Sunita Shankar,
Shanker Kalyana-Sundaram,
Lidong Wang,
Linda W. Ma,
Pankaj Vats,
Catherine S. Grasso,
Dan R. Robinson,
Yi-Mi Wu, Xuhong Cao,
Diane M. Simeone,
Arul M. Chinnaiyan,
and Chandan Kumar-Sinha
[show abstract]
[hide abstract]
ABSTRACT: Protein kinases represent the most effective class of therapeutic targets in cancer; therefore, determination of kinase aberrations is a major focus of cancer genomic studies. Here, we analyzed transcriptome sequencing data from a compendium of 482 cancer and benign samples from 25 different tissue types, and defi ned distinct "outlier kinases" in individual breast and pancreatic cancer samples, based on highest levels of absolute and differential expression. Frequent outlier kinases in breast cancer included therapeutic targets like ERBB2 and FGFR4 , distinct from MET , AKT2 , and PLK2 in pancreatic cancer. Outlier kinases imparted sample-specifi c depend-encies in various cell lines, as tested by siRNA knockdown and/or pharmacologic inhibition. Outlier expression of polo-like kinases was observed in a subset of KRAS -dependent pancreatic cancer cell lines, and conferred increased sensitivity to the pan-PLK inhibitor BI-6727. Our results suggest that outlier kinases represent effective precision therapeutic targets that are readily identifi able through RNA sequencing of tumors. SIGNIFICANCE: Various breast and pancreatic cancer cell lines display sensitivity to knockdown or pharmacologic inhibition of sample-specifi c outlier kinases identifi ed by high-throughput transcrip-tome sequencing. Outlier kinases represent personalized therapeutic targets that could improve
Cancer Discovery 02/2013;
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Dan R Robinson,
Yi-Mi Wu,
Shanker Kalyana-Sundaram, Xuhong Cao,
Robert J Lonigro,
Yun-Shao Sung,
Chun-Liang Chen,
Lei Zhang,
Rui Wang,
Fengyun Su, [......],
Sameek Roychowdhury,
Javed Siddiqui,
Kenneth J Pienta,
Lakshmi P Kunju,
Moshe Talpaz,
Juan Miguel Mosquera,
Samuel Singer,
Scott M Schuetze,
Cristina R Antonescu,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: A 44-year old woman with recurrent solitary fibrous tumor (SFT)/hemangiopericytoma was enrolled in a clinical sequencing program including whole-exome and transcriptome sequencing. A gene fusion of the transcriptional repressor NAB2 with the transcriptional activator STAT6 was detected. Transcriptome sequencing of 27 additional SFTs identified the presence of a NAB2-STAT6 gene fusion in all tumors. Using RT-PCR and sequencing, we detected this fusion in all 51 SFTs, indicating high levels of recurrence. Expression of NAB2-STAT6 fusion proteins was confirmed in SFT, and the predicted fusion products harbor the early growth response (EGR)-binding domain of NAB2 fused to the activation domain of STAT6. Overexpression of the NAB2-STAT6 gene fusion induced proliferation in cultured cells and activated the expression of EGR-responsive genes. These studies establish NAB2-STAT6 as the defining driver mutation of SFT and provide an example of how neoplasia can be initiated by converting a transcriptional repressor of mitogenic pathways into a transcriptional activator.
Nature Genetics 01/2013; · 35.53 Impact Factor
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Irfan A Asangani,
Bushra Ateeq,
Qi Cao,
Lois Dodson,
Mithil Pandhi,
Lakshmi P Kunju,
Rohit Mehra,
Robert J Lonigro,
Javed Siddiqui,
Nallasivam Palanisamy,
Yi-Mi Wu, Xuhong Cao,
Jung H Kim,
Meng Zhao,
Zhaohui S Qin,
Mathew K Iyer,
Christopher A Maher,
Chandan Kumar-Sinha,
Sooryanarayana Varambally,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Histone methyltransferases (HMTases), as chromatin modifiers, regulate the transcriptomic landscape in normal development as well in diseases such as cancer. Here, we molecularly order two HMTases, EZH2 and MMSET, that have established genetic links to oncogenesis. EZH2, which mediates histone H3K27 trimethylation and is associated with gene silencing, was shown to be coordinately expressed and function upstream of MMSET, which mediates H3K36 dimethylation and is associated with active transcription. We found that the EZH2-MMSET HMTase axis is coordinated by a microRNA network and that the oncogenic functions of EZH2 require MMSET activity. Together, these results suggest that the EZH2-MMSET HMTase axis coordinately functions as a master regulator of transcriptional repression, activation, and oncogenesis and may represent an attractive therapeutic target in cancer.
Molecular cell 11/2012; · 14.61 Impact Factor
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Shanker Kalyana-Sundaram,
Chandan Kumar-Sinha,
Sunita Shankar,
Dan R Robinson,
Yi-Mi Wu, Xuhong Cao,
Irfan A Asangani,
Vishal Kothari,
John R Prensner,
Robert J Lonigro,
Matthew K Iyer,
Terrence Barrette,
Achiraman Shanmugam,
Saravana M Dhanasekaran,
Nallasivam Palanisamy,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Pseudogene transcripts can provide a novel tier of gene regulation through generation of endogenous siRNAs or miRNA-binding sites. Characterization of pseudogene expression, however, has remained confined to anecdotal observations due to analytical challenges posed by the extremely close sequence similarity with their counterpart coding genes. Here, we describe a systematic analysis of pseudogene "transcription" from an RNA-Seq resource of 293 samples, representing 13 cancer and normal tissue types, and observe a surprisingly prevalent, genome-wide expression of pseudogenes that could be categorized as ubiquitously expressed or lineage and/or cancer specific. Further, we explore disease subtype specificity and functions of selected expressed pseudogenes. Taken together, we provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression, especially in light of the recently described ceRNA networks. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.
Cell 06/2012; 149(7):1622-34. · 32.40 Impact Factor
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Catherine S Grasso,
Yi-Mi Wu,
Dan R Robinson, Xuhong Cao,
Saravana M Dhanasekaran,
Amjad P Khan,
Michael J Quist,
Xiaojun Jing,
Robert J Lonigro,
J Chad Brenner, [......],
John R Prensner,
Nallasivam Palanisamy,
Gregory A Ryslik,
Fabio Vandin,
Benjamin J Raphael,
Lakshmi P Kunju,
Daniel R Rhodes,
Kenneth J Pienta,
Arul M Chinnaiyan,
Scott A Tomlins
[show abstract]
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ABSTRACT: Characterization of the prostate cancer transcriptome and genome has identified chromosomal rearrangements and copy number gains and losses, including ETS gene family fusions, PTEN loss and androgen receptor (AR) amplification, which drive prostate cancer development and progression to lethal, metastatic castration-resistant prostate cancer (CRPC). However, less is known about the role of mutations. Here we sequenced the exomes of 50 lethal, heavily pre-treated metastatic CRPCs obtained at rapid autopsy (including three different foci from the same patient) and 11 treatment-naive, high-grade localized prostate cancers. We identified low overall mutation rates even in heavily treated CRPCs (2.00 per megabase) and confirmed the monoclonal origin of lethal CRPC. Integrating exome copy number analysis identified disruptions of CHD1 that define a subtype of ETS gene family fusion-negative prostate cancer. Similarly, we demonstrate that ETS2, which is deleted in approximately one-third of CRPCs (commonly through TMPRSS2:ERG fusions), is also deregulated through mutation. Furthermore, we identified recurrent mutations in multiple chromatin- and histone-modifying genes, including MLL2 (mutated in 8.6% of prostate cancers), and demonstrate interaction of the MLL complex with the AR, which is required for AR-mediated signalling. We also identified novel recurrent mutations in the AR collaborating factor FOXA1, which is mutated in 5 of 147 (3.4%) prostate cancers (both untreated localized prostate cancer and CRPC), and showed that mutated FOXA1 represses androgen signalling and increases tumour growth. Proteins that physically interact with the AR, such as the ERG gene fusion product, FOXA1, MLL2, UTX (also known as KDM6A) and ASXL1 were found to be mutated in CRPC. In summary, we describe the mutational landscape of a heavily treated metastatic cancer, identify novel mechanisms of AR signalling deregulated in prostate cancer, and prioritize candidates for future study.
Nature 05/2012; 487(7406):239-43. · 36.28 Impact Factor
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Sameek Roychowdhury,
Matthew K Iyer,
Dan R Robinson,
Robert J Lonigro,
Yi-Mi Wu, Xuhong Cao,
Shanker Kalyana-Sundaram,
Lee Sam,
O Alejandro Balbin,
Michael J Quist, [......],
Christopher J Logothetis,
Jeffrey W Innis,
David C Smith,
Christopher D Lao,
Scott Y Kim,
J Scott Roberts,
Stephen B Gruber,
Kenneth J Pienta,
Moshe Talpaz,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Individual cancers harbor a set of genetic aberrations that can be informative for identifying rational therapies currently available or in clinical trials. We implemented a pilot study to explore the practical challenges of applying high-throughput sequencing in clinical oncology. We enrolled patients with advanced or refractory cancer who were eligible for clinical trials. For each patient, we performed whole-genome sequencing of the tumor, targeted whole-exome sequencing of tumor and normal DNA, and transcriptome sequencing (RNA-Seq) of the tumor to identify potentially informative mutations in a clinically relevant time frame of 3 to 4 weeks. With this approach, we detected several classes of cancer mutations including structural rearrangements, copy number alterations, point mutations, and gene expression alterations. A multidisciplinary Sequencing Tumor Board (STB) deliberated on the clinical interpretation of the sequencing results obtained. We tested our sequencing strategy on human prostate cancer xenografts. Next, we enrolled two patients into the clinical protocol and were able to review the results at our STB within 24 days of biopsy. The first patient had metastatic colorectal cancer in which we identified somatic point mutations in NRAS, TP53, AURKA, FAS, and MYH11, plus amplification and overexpression of cyclin-dependent kinase 8 (CDK8). The second patient had malignant melanoma, in which we identified a somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C. The STB identified the CDK8 amplification and Ras mutation as providing a rationale for clinical trials with CDK inhibitors or MEK (mitogen-activated or extracellular signal-regulated protein kinase kinase) and PI3K (phosphatidylinositol 3-kinase) inhibitors, respectively. Integrative high-throughput sequencing of patients with advanced cancer generates a comprehensive, individual mutational landscape to facilitate biomarker-driven clinical trials in oncology.
Science translational medicine 11/2011; 3(111):111ra121. · 7.80 Impact Factor
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Dan R Robinson,
Shanker Kalyana-Sundaram,
Yi-Mi Wu,
Sunita Shankar, Xuhong Cao,
Bushra Ateeq,
Irfan A Asangani,
Matthew Iyer,
Christopher A Maher,
Catherine S Grasso, [......],
Xiaojun Jing,
Thomas J Giordano,
Michael S Sabel,
Celina G Kleer,
Nallasivam Palanisamy,
Rachael Natrajan,
Maryou B Lambros,
Jorge S Reis-Filho,
Chandan Kumar-Sinha,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Breast cancer is a heterogeneous disease that has a wide range of molecular aberrations and clinical outcomes. Here we used paired-end transcriptome sequencing to explore the landscape of gene fusions in a panel of breast cancer cell lines and tissues. We observed that individual breast cancers have a variety of expressed gene fusions. We identified two classes of recurrent gene rearrangements involving genes encoding microtubule-associated serine-threonine kinase (MAST) and members of the Notch family. Both MAST and Notch-family gene fusions have substantial phenotypic effects in breast epithelial cells. Breast cancer cell lines harboring Notch gene rearrangements are uniquely sensitive to inhibition of Notch signaling, and overexpression of MAST1 or MAST2 gene fusions has a proliferative effect both in vitro and in vivo. These findings show that recurrent gene rearrangements have key roles in subsets of carcinomas and suggest that transcriptome sequencing could identify individuals with rare, targetable gene fusions.
Nature medicine 11/2011; 17(12):1646-51. · 27.14 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: The research community at large is expending considerable resources to sequence the coding region of the genomes of tumors and other human diseases using targeted exome capture (i.e., "whole exome sequencing"). The primary goal of targeted exome sequencing is to identify nonsynonymous mutations that potentially have functional consequences. Here, we demonstrate that whole-exome sequencing data can also be analyzed for comprehensively monitoring somatic copy number alterations (CNAs) by benchmarking the technique against conventional array CGH. A series of 17 matched tumor and normal tissues from patients with metastatic castrate-resistant prostate cancer was used for this assessment. We show that targeted exome sequencing reliably identifies CNAs that are common in advanced prostate cancer, such as androgen receptor (AR) gain and PTEN loss. Taken together, these data suggest that targeted exome sequencing data can be effectively leveraged for the detection of somatic CNAs in cancer.
Neoplasia (New York, N.Y.) 11/2011; 13(11):1019-25. · 5.48 Impact Factor
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Qi Cao,
Ram-Shankar Mani,
Bushra Ateeq,
Saravana M Dhanasekaran,
Irfan A Asangani,
John R Prensner,
Jung H Kim,
J Chad Brenner,
Xiaojun Jing, Xuhong Cao, [......],
Mithil Pandhi,
Robert J Lonigro,
Yi-Mi Wu,
Scott A Tomlins,
Nallasivam Palanisamy,
Zhaohui Qin,
Jindan Yu,
Christopher A Maher,
Sooryanarayana Varambally,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Polycomb Repressive Complexes (PRC1 and PRC2)-mediated epigenetic regulation is critical for maintaining cellular homeostasis. Members of Polycomb Group (PcG) proteins including EZH2, a PRC2 component, are upregulated in various cancer types, implicating their role in tumorigenesis. Here, we have identified several microRNAs (miRNAs) that are repressed by EZH2. These miRNAs, in turn, regulate the expression of PRC1 proteins BMI1 and RING2. We found that ectopic overexpression of EZH2-regulated miRNAs attenuated cancer cell growth and invasiveness, and abrogated cancer stem cell properties. Importantly, expression analysis revealed an inverse correlation between miRNA and PRC protein levels in cell culture and prostate cancer tissues. Taken together, our data have uncovered a coordinate regulation of PRC1 and PRC2 activities that is mediated by miRNAs.
Cancer cell 08/2011; 20(2):187-99. · 25.29 Impact Factor
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Jung H Kim,
Saravana M Dhanasekaran,
John R Prensner, Xuhong Cao,
Daniel Robinson,
Shanker Kalyana-Sundaram,
Christina Huang,
Sunita Shankar,
Xiaojun Jing,
Matthew Iyer, [......],
Lee Sam,
Catherine Grasso,
Christopher A Maher,
Nallasivam Palanisamy,
Rohit Mehra,
Hal D Kominsky,
Javed Siddiqui,
Jindan Yu,
Zhaohui S Qin,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value < 2 × 10(-16)). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.
Genome Research 07/2011; 21(7):1028-41. · 13.61 Impact Factor
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Ram-Shankar Mani,
Matthew K Iyer,
Qi Cao,
J Chad Brenner,
Lei Wang,
Aparna Ghosh, Xuhong Cao,
Robert J Lonigro,
Scott A Tomlins,
Sooryanarayana Varambally,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Recurrent gene fusions involving ETS family genes are a distinguishing feature of human prostate cancers, with TMPRSS2-ERG fusions representing the most common subtype. The TMPRSS2-ERG fusion transcript and its splice variants are well characterized in prostate cancers; however, not much is known about the levels and regulation of wild-type ERG. By employing an integrative approach, we show that the TMPRSS2-ERG gene fusion product binds to the ERG locus and drives the overexpression of wild-type ERG in prostate cancers. Knockdown of TMPRSS2-ERG in VCaP cells resulted in the downregulation of wild-type ERG transcription, whereas stable overexpression of TMPRSS2-ERG in the gene fusion-negative PC3 cells was associated with the upregulation of wild-type ERG transcript. Further, androgen signaling-mediated upregulation of TMPRSS2-ERG resulted in the concomitant upregulation of wild-type ERG transcription in VCaP cells. The loss of wild-type ERG expression was associated with a decrease in the invasive potential of VCaP cells. Importantly, 38% of clinically localized prostate cancers and 27% of metastatic prostate cancers harboring the TMPRSS2-ERG gene fusions exhibited overexpression of wild-type ERG. Taken together, these results provide novel insights into the regulation of ERG in human prostate cancers.
Cancer Research 06/2011; 71(16):5387-92. · 7.86 Impact Factor
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Rohit Mehra,
Chandan Kumar-Sinha,
Sunita Shankar,
Robert J Lonigro,
Xiaojun Jing,
Neena E Philips,
Javed Siddiqui,
Bo Han, Xuhong Cao,
David C Smith,
Rajal B Shah,
Arul M Chinnaiyan,
Kenneth J Pienta
[show abstract]
[hide abstract]
ABSTRACT: Bone is the most common metastatic site for prostate cancer, and osseous metastases are the leading cause of morbidity from this disease. Recent autopsy studies prove that 100% of men who die of prostate cancer have bone involvement. Understanding the biology of prostate cancer and its evolution to an incurable androgen-independent phenotype requires an understanding of the genetic and cellular alterations that lead to the seeding and proliferation of tumor foci in bone, as well as the microenvironment in which these metastases arise. No intensive studies, however, have been conducted on osseous metastatic tissues from patients with metastatic prostate cancer due to lack of access to such tissues for profiling and other research.
We show, for the first time, a reproducible methodology to obtain high quality clinical tumor tissues metastatic to the bone. This technique allowed the procurement of viable metastatic tumor tissue from involved bones in 13 recent autopsies conducted at the University of Michigan and analyzed the gene expression of these tissues using real-time PCR and microarrays.
We present here the discovery of nonossified bone metastases from multiple patients with advanced prostate cancer and their subsequent characterization and comparison to nonosseous metastases from the same patients.
This represents a versatile and practical approach that may be employed to characterize the steps in metastasis and the phenotypic characteristics of osseous metastasis of prostate cancer and to profile RNA, DNA, and cDNA from tumor samples metastatic to the bone.
Clinical Cancer Research 06/2011; 17(12):3924-32. · 7.74 Impact Factor
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Xiao-Song Wang,
Sunita Shankar,
Saravana M Dhanasekaran,
Bushra Ateeq,
Atsuo T Sasaki,
Xiaojun Jing,
Daniel Robinson,
Qi Cao,
John R Prensner,
Anastasia K Yocum, [......],
Gilbert S Omenn,
Dorothee Pflueger,
Anuradha Gopalan,
Victor E Reuter,
Emily Rose Kahoud,
Lewis C Cantley,
Mark A Rubin,
Nallasivam Palanisamy,
Sooryanarayana Varambally,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Using an integrative genomics approach called amplification breakpoint ranking and assembly analysis, we nominated KRAS as a gene fusion with the ubiquitin-conjugating enzyme UBE2L3 in the DU145 cell line, originally derived from prostate cancer metastasis to the brain. Interestingly, analysis of tissues revealed that 2 of 62 metastatic prostate cancers harbored aberrations at the KRAS locus. In DU145 cells, UBE2L3-KRAS produces a fusion protein, a specific knockdown of which attenuates cell invasion and xenograft growth. Ectopic expression of the UBE2L3-KRAS fusion protein exhibits transforming activity in NIH 3T3 fibroblasts and RWPE prostate epithelial cells in vitro and in vivo. In NIH 3T3 cells, UBE2L3-KRAS attenuates MEK/ERK signaling, commonly engaged by oncogenic mutant KRAS, and instead signals via AKT and p38 mitogen-activated protein kinase (MAPK) pathways. This is the first report of a gene fusion involving the Ras family, suggesting that this aberration may drive metastatic progression in a rare subset of prostate cancers. SIGNIFICANCE: This is the first description of an oncogenic gene fusion of KRAS, one of the most studied proto-oncogenes. KRAS rearrangement may represent the driving mutation in a rare subset of metastatic prostate cancers, emphasizing the importance of RAS-RAF-MAPK signaling in this disease.
Cancer discovery. 06/2011; 1(1):35-43.
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J Chad Brenner,
Bushra Ateeq,
Yong Li,
Anastasia K Yocum,
Qi Cao,
Irfan A Asangani,
Sonam Patel,
Xiaoju Wang,
Hallie Liang,
Jindan Yu, [......],
Jun Yang,
Scott A Tomlins,
Christopher A Maher,
Kojo S J Elenitoba-Johnson,
Maha Hussain,
Nora M Navone,
Kenneth J Pienta,
Sooryanarayana Varambally,
Felix Y Feng,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Recurrent fusions of ETS genes are considered driving mutations in a diverse array of cancers, including Ewing's sarcoma, acute myeloid leukemia, and prostate cancer. We investigate the mechanisms by which ETS fusions mediate their effects, and find that the product of the predominant ETS gene fusion, TMPRSS2:ERG, interacts in a DNA-independent manner with the enzyme poly (ADP-ribose) polymerase 1 (PARP1) and the catalytic subunit of DNA protein kinase (DNA-PKcs). ETS gene-mediated transcription and cell invasion require PARP1 and DNA-PKcs expression and activity. Importantly, pharmacological inhibition of PARP1 inhibits ETS-positive, but not ETS-negative, prostate cancer xenograft growth. Finally, overexpression of the TMPRSS2:ERG fusion induces DNA damage, which is potentiated by PARP1 inhibition in a manner similar to that of BRCA1/2 deficiency.
Cancer cell 05/2011; 19(5):664-78. · 25.29 Impact Factor
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Bushra Ateeq,
Scott A Tomlins,
Bharathi Laxman,
Irfan A Asangani,
Qi Cao, Xuhong Cao,
Yong Li,
Xiaoju Wang,
Felix Y Feng,
Kenneth J Pienta,
Sooryanarayana Varambally,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Gene fusions involving ETS (erythroblastosis virus E26 transformation-specific) family transcription factors are found in ~50% of prostate cancers and as such can be used as a basis for the molecular subclassification of prostate cancer. Previously, we showed that marked overexpression of SPINK1 (serine peptidase inhibitor, Kazal type 1), which encodes a secreted serine protease inhibitor, defines an aggressive molecular subtype of ETS fusion-negative prostate cancers (SPINK1+/ETS⁻, ~10% of all prostate cancers). Here, we examined the potential of SPINK1 as an extracellular therapeutic target in prostate cancer. Recombinant SPINK1 protein (rSPINK1) stimulated cell proliferation in benign RWPE as well as cancerous prostate cells. Indeed, RWPE cells treated with either rSPINK1 or conditioned medium from 22RV1 prostate cancer cells (SPINK1+/ETS⁻) significantly increased cell invasion and intravasation when compared with untreated cells. In contrast, knockdown of SPINK1 in 22RV1 cells inhibited cell proliferation, cell invasion, and tumor growth in xenograft assays. 22RV1 cell proliferation, invasion, and intravasation were attenuated by a monoclonal antibody (mAb) to SPINK1 as well. We also demonstrated that SPINK1 partially mediated its neoplastic effects through interaction with the epidermal growth factor receptor (EGFR). Administration of antibodies to SPINK1 or EGFR (cetuximab) in mice bearing 22RV1 xenografts attenuated tumor growth by more than 60 and 40%, respectively, or ~75% when combined, without affecting PC3 xenograft (SPINK1⁻/ETS⁻) growth. Thus, this study suggests that SPINK1 may be a therapeutic target in a subset of patients with SPINK1+/ETS⁻ prostate cancer. Our results provide a rationale for both the development of humanized mAbs to SPINK1 and evaluation of EGFR inhibition in SPINK1+/ETS⁻ prostate cancers.
Science translational medicine 03/2011; 3(72):72ra17. · 7.80 Impact Factor
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[show abstract]
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ABSTRACT: The second wave of next generation sequencing technologies, referred to as single-molecule sequencing (SMS), carries the promise of profiling samples directly without employing polymerase chain reaction steps used by amplification-based sequencing (AS) methods. To examine the merits of both technologies, we examine mRNA sequencing results from single-molecule and amplification-based sequencing in a set of human cancer cell lines and tissues. We observe a characteristic coverage bias towards high abundance transcripts in amplification-based sequencing. A larger fraction of AS reads cover highly expressed genes, such as those associated with translational processes and housekeeping genes, resulting in relatively lower coverage of genes at low and mid-level abundance. In contrast, the coverage of high abundance transcripts plateaus off using SMS. Consequently, SMS is able to sequence lower- abundance transcripts more thoroughly, including some that are undetected by AS methods; however, these include many more mapping artifacts. A better understanding of the technical and analytical factors introducing platform specific biases in high throughput transcriptome sequencing applications will be critical in cross platform meta-analytic studies.
PLoS ONE 01/2011; 6(3):e17305. · 4.09 Impact Factor
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John R Prensner,
Matthew K Iyer,
O Alejandro Balbin,
Saravana M Dhanasekaran,
Qi Cao,
J Chad Brenner,
Bharathi Laxman,
Irfan A Asangani,
Catherine S Grasso,
Hal D Kominsky, Xuhong Cao,
Xiaojun Jing,
Xiaoju Wang,
Javed Siddiqui,
John T Wei,
Daniel Robinson,
Hari K Iyer,
Nallasivam Palanisamy,
Christopher A Maher,
Arul M Chinnaiyan
[show abstract]
[hide abstract]
ABSTRACT: Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer-associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA(+) RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the Polycomb Repressive Complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1-repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.
Nature Biotechnology 01/2011; 29(8):742-9. · 29.50 Impact Factor
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Dorothee Pflueger,
Stéphane Terry,
Andrea Sboner,
Lukas Habegger,
Raquel Esgueva,
Pei-Chun Lin,
Maria A Svensson,
Naoki Kitabayashi,
Benjamin J Moss,
Theresa Y MacDonald, Xuhong Cao,
Terrence Barrette,
Ashutosh K Tewari,
Mark S Chee,
Arul M Chinnaiyan,
David S Rickman,
Francesca Demichelis,
Mark B Gerstein,
Mark A Rubin
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ABSTRACT: Half of prostate cancers harbor gene fusions between TMPRSS2 and members of the ETS transcription factor family. To date, little is known about the presence of non-ETS fusion events in prostate cancer. We used next-generation transcriptome sequencing (RNA-seq) in order to explore the whole transcriptome of 25 human prostate cancer samples for the presence of chimeric fusion transcripts. We generated more than 1 billion sequence reads and used a novel computational approach (FusionSeq) in order to identify novel gene fusion candidates with high confidence. In total, we discovered and characterized seven new cancer-specific gene fusions, two involving the ETS genes ETV1 and ERG, and four involving non-ETS genes such as CDKN1A (p21), CD9, and IKBKB (IKK-beta), genes known to exhibit key biological roles in cellular homeostasis or assumed to be critical in tumorigenesis of other tumor entities, as well as the oncogene PIGU and the tumor suppressor gene RSRC2. The novel gene fusions are found to be of low frequency, but, interestingly, the non-ETS fusions were all present in prostate cancer harboring the TMPRSS2-ERG gene fusion. Future work will focus on determining if the ETS rearrangements in prostate cancer are associated or directly predispose to a rearrangement-prone phenotype.
Genome Research 10/2010; 21(1):56-67. · 13.61 Impact Factor
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Arun Sreekumar,
Laila M Poisson,
Thekkelnaycke M Rajendiran,
Amjad P Khan,
Qi Cao,
Jindan Yu,
Bharathi Laxman,
Rohit Mehra,
Robert J Lonigro,
Yong Li, [......],
Gilbert S Omenn,
Debashis Ghoshd,
Subramaniam Pennathur,
Danny C Alexander,
Alvin Berger,
Jeffrey R Shuster,
John T Wei,
Sooryanarayana Varambally,
Christopher Beecher,
Arul M Chinnaiyan
European urology 09/2010; 58(3):e29-30; author reply e31-2. · 7.67 Impact Factor
