Showing papers by "Todd R. Golub published in 2014"
TL;DR: It is found that large-scale genomic analysis can identify nearly all known cancer genes in these cancer types and 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis.
Abstract: Although a few cancer genes are mutated in a high proportion of tumours of a given type (.20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600– 5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics. Comprehensive knowledge of the genes underlying human cancers is a critical foundation for cancer diagnostics, therapeutics, clinical-trial design and selection of rational combination therapies. It is now possible to use genomic analysis to identify cancer genes in an unbiased fashion, based on the presence of somatic mutations at a rate significantly higher than the expected background level. Systematic studies have revealed many new cancer genes, as well as new classes of cancer genes 1,2 . They have also made clear that, although some cancer genes are mutated at high frequencies, most cancer genes in most patients occur at intermediate frequencies (2–20%) or lower. Accordingly, a complete catalogue of mutations in this frequency class will be essential for recognizing dysregulated pathways and optimal targets for therapeutic intervention. However, recent work suggests major gaps in our knowledge of cancer genes of intermediate frequency. For example, a study of 183 lung adenocarcinomas 3 found that 15% of patients lacked even a single mutation affecting any of the 10 known hallmarks of cancer, and 38% had 3 or fewer such mutations. In this paper, we analysed somatic point mutations (substitutions and small insertion and deletions) in nearly 5,000 human cancers and their matched normal-tissue samples (‘tumour–normal pairs’) across 21 tumour types. The questions that we examine here are: first, whether large-scale genomic analysis across tumour types can reliably identify all known cancer genes; second, whether it will reveal many new candidate cancer genes; and third, how far we are from having a complete catalogue of cancer genes (at least those of intermediate frequency). We used rigorous statistical methods to enumerate candidate cancer genes and then carefully inspected each gene to identify those with strong biological connections to cancer and mutational patterns consistent with the expected function. The analysis reveals nearly all known cancer genes and revealed 33 novel candidates, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Importantly, the data show that the
2,565 citations
TL;DR: This article performed massively parallel sequencing of paired tumor/normal samples from 203 multiple myeloma (MM) patients and identified significantly mutated genes and copy number alterations and discovered putative tumor suppressor genes by determining homozygous deletions and loss of heterozygosity.
827 citations
TL;DR: In this paper, whole-exome sequencing of circulating tumor cells enables accurate and powered calling of somatic point mutations, and the authors propose a method to identify the source of the point mutations.
Abstract: Whole-exome sequencing of circulating tumor cells enables accurate and powered calling of somatic point mutations.
459 citations
TL;DR: Next-generation sequencing of Ewing sarcoma found remarkably few mutations, however, it was discovered that loss of STAG2 expression occurs in 15% of tumors and is associated with metastatic disease, suggesting a potential genetic vulnerability in Ewing Sarcoma.
Abstract: Pediatric Ewing sarcoma is characterized by the expression of chimeric fusions of EWS and ETS family transcription factors, representing a paradigm for studying cancers driven by transcription factor rearrangements. In this study, we describe the somatic landscape of pediatric Ewing sarcoma. These tumors are among the most genetically normal cancers characterized to date, with only EWS – ETS rearrangements identified in the majority of tumors. STAG2 loss, however, is present in more than 15% of Ewing sarcoma tumors; occurs by point mutation, rearrangement, and likely nongenetic mechanisms; and is associated with disease dissemination. Perhaps the most striking finding is the paucity of mutations in immediately targetable signal transduction pathways, highlighting the need for new therapeutic approaches to target EWS – ETS fusions in this disease.
Significance: We performed next-generation sequencing of Ewing sarcoma, a pediatric cancer involving bone, characterized by expression of EWS – ETS fusions. We found remarkably few mutations. However, we discovered that loss of STAG2 expression occurs in 15% of tumors and is associated with metastatic disease, suggesting a potential genetic vulnerability in Ewing sarcoma. Cancer Discov; 4(11); 1326–41. ©2014 AACR .
This article is highlighted in the In This Issue feature, [p. 1243][1]
[1]: /lookup/volpage/4/1243?iss=11
405 citations
TL;DR: These studies identify unique combinations of genetic alterations in discrete LBCL subtypes and subtype-selective bases for targeted therapy and characterize their recurrent somatic mutations, chromosomal rearrangements, copy number alterations (CNAs), and associated driver genes.
386 citations
TL;DR: This dataset facilitates the linkage of genetic dependencies with specific cellular contexts (e.g., gene mutations or cell lineage) and developed and provided a bioinformatics tool to identify linear and nonlinear correlations between these features.
Abstract: Using a genome-scale, lentivirally delivered shRNA library, we performed massively parallel pooled shRNA screens in 216 cancer cell lines to identify genes that are required for cell proliferation and/or viability. Cell line dependencies on 11,000 genes were interrogated by 5 shRNAs per gene. The proliferation effect of each shRNA in each cell line was assessed by transducing a population of 11M cells with one shRNA-virus per cell and determining the relative enrichment or depletion of each of the 54,000 shRNAs after 16 population doublings using Next Generation Sequencing. All the cell lines were screened using standardized conditions to best assess differential genetic dependencies across cell lines. When combined with genomic characterization of these cell lines, this dataset facilitates the linkage of genetic dependencies with specific cellular contexts (e.g., gene mutations or cell lineage). To enable such comparisons, we developed and provided a bioinformatics tool to identify linear and nonlinear correlations between these features.
372 citations
TL;DR: In this paper, the authors examined 59 tumor/normal pairs by whole-exome, whole-genome, and RNA-sequencing, and found that only the TP53 gene was mutated at significant frequency across all samples.
Abstract: Osteosarcoma is the most common primary bone tumor, yet there have been no substantial advances in treatment or survival in three decades. We examined 59 tumor/normal pairs by whole-exome, whole-genome, and RNA-sequencing. Only the TP53 gene was mutated at significant frequency across all samples. The mean nonsilent somatic mutation rate was 1.2 mutations per megabase, and there was a median of 230 somatic rearrangements per tumor. Complex chains of rearrangements and localized hypermutation were detected in almost all cases. Given the intertumor heterogeneity, the extent of genomic instability, and the difficulty in acquiring a large sample size in a rare tumor, we used several methods to identify genomic events contributing to osteosarcoma survival. Pathway analysis, a heuristic analytic algorithm, a comparative oncology approach, and an shRNA screen converged on the phosphatidylinositol 3-kinase/mammalian target of rapamycin (PI3K/mTOR) pathway as a central vulnerability for therapeutic exploitation in osteosarcoma. Osteosarcoma cell lines are responsive to pharmacologic and genetic inhibition of the PI3K/mTOR pathway both in vitro and in vivo.
349 citations
01 Jan 2014
TL;DR: In this paper, the authors explored the feasibility of creating a comprehensive catalogue of cancer genes by analyzing exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types and found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types.
Abstract: Although a few cancer genes are mutated in a high proportion of tumours of a given type (.20%), most are mutated at intermediate frequencies (2–20%). To explore the feasibility of creating a comprehensive catalogue of cancer genes, we analysed somatic point mutations in exome sequences from 4,742 human cancers and their matched normal-tissue samples across 21 cancer types. We found that large-scale genomic analysis can identify nearly all known cancer genes in these tumour types. Our analysis also identified 33 genes that were not previously known to be significantly mutated in cancer, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Down-sampling analysis indicates that larger sample sizes will reveal many more genes mutated at clinically important frequencies. We estimate that near-saturation may be achieved with 600– 5,000 samples per tumour type, depending on background mutation frequency. The results may help to guide the next stage of cancer genomics. Comprehensive knowledge of the genes underlying human cancers is a critical foundation for cancer diagnostics, therapeutics, clinical-trial design and selection of rational combination therapies. It is now possible to use genomic analysis to identify cancer genes in an unbiased fashion, based on the presence of somatic mutations at a rate significantly higher than the expected background level. Systematic studies have revealed many new cancer genes, as well as new classes of cancer genes 1,2 . They have also made clear that, although some cancer genes are mutated at high frequencies, most cancer genes in most patients occur at intermediate frequencies (2–20%) or lower. Accordingly, a complete catalogue of mutations in this frequency class will be essential for recognizing dysregulated pathways and optimal targets for therapeutic intervention. However, recent work suggests major gaps in our knowledge of cancer genes of intermediate frequency. For example, a study of 183 lung adenocarcinomas 3 found that 15% of patients lacked even a single mutation affecting any of the 10 known hallmarks of cancer, and 38% had 3 or fewer such mutations. In this paper, we analysed somatic point mutations (substitutions and small insertion and deletions) in nearly 5,000 human cancers and their matched normal-tissue samples (‘tumour–normal pairs’) across 21 tumour types. The questions that we examine here are: first, whether large-scale genomic analysis across tumour types can reliably identify all known cancer genes; second, whether it will reveal many new candidate cancer genes; and third, how far we are from having a complete catalogue of cancer genes (at least those of intermediate frequency). We used rigorous statistical methods to enumerate candidate cancer genes and then carefully inspected each gene to identify those with strong biological connections to cancer and mutational patterns consistent with the expected function. The analysis reveals nearly all known cancer genes and revealed 33 novel candidates, including genes related to proliferation, apoptosis, genome stability, chromatin regulation, immune evasion, RNA processing and protein homeostasis. Importantly, the data show that the
347 citations
TL;DR: The data indicate that MPN patients, regardless of diagnosis or JAK2 mutational status, are characterized by a distinct gene expression signature with upregulation of JAK-STAT target genes, demonstrating the central importance of the Jak-STAT pathway in MPN pathogenesis.
322 citations
TL;DR: Data suggest that EGFR inhibition using Food and Drug Administration‐approved inhibitors provides a promising therapeutic approach for reduction of fibrogenesis and prevention of HCC in high‐risk cirrhosis patients who can be identified and monitored by gene expression signatures.
269 citations
TL;DR: LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data.
Abstract: For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene expression signatures using the L1000 technology have been produced. The L1000 technology is a costeffective method to profile gene expression in large scale. LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered canvases, one to visualize clustered L1000 expression data, and the other to display enrichment analysis results using 30 different gene set libraries. Clicking on an experimental condition highlights gene-sets enriched for the differentially expressed genes from the selected experiment. A search interface allows users to input gene lists and query them against over 100 000 conditions to find the top matching experiments. The tool integrates many resources for an unprecedented potential for new discoveries in systems biology and systems pharmacology. The LCB application is available at http://www.maayanlab.net/LINCS/LCB. Customized versions will be made part of the http:// lincscloud.org and http://lincs.hms.harvard.edu websites.
TL;DR: The original version of this Data Descriptor contained a typographical error in the spelling of the author Terence C. Wong, which was incorrectly given as Terrence C Wong as discussed by the authors.
Abstract: Scientific Data 1:140035 doi: 10.1038/sdata.2014.35 (2014); Published 30 September 2014; Updated 11 November 2014 The original version of this Data Descriptor contained a typographical error in the spelling of the author Terence C. Wong, which was incorrectly given as Terrence C. Wong. This has now been corrected in the PDF and HTML versions of the Data Descriptor.
TL;DR: This study explores a cost-effective way of rapidly assessing the biological performance diversity of a screening collection in a single assay by simultaneously measuring a large number of cellular features, unbiased profiling assays can distinguish compound effects with high resolution and thus measure performance diversity.
Abstract: High-throughput screening has become a mainstay of small-molecule probe and early drug discovery. The question of how to build and evolve efficient screening collections systematically for cell-based and biochemical screening is still unresolved. It is often assumed that chemical structure diversity leads to diverse biological performance of a library. Here, we confirm earlier results showing that this inference is not always valid and suggest instead using biological measurement diversity derived from multiplexed profiling in the construction of libraries with diverse assay performance patterns for cell-based screens. Rather than using results from tens or hundreds of completed assays, which is resource intensive and not easily extensible, we use high-dimensional image-based cell morphology and gene expression profiles. We piloted this approach using over 30,000 compounds. We show that small-molecule profiling can be used to select compound sets with high rates of activity and diverse biological performance.
TL;DR: EnPlex, an efficient, high-throughput method for simultaneously assessing inhibitor potency and specificity, is reported and followed-up of a series of dipeptidyl peptidase 4 (DPP4) inhibitors showed that EnPlex indeed predicted efficacy and safety in animal models, and suggest such profiling can be incorporated into the earliest stages of drug discovery.
Abstract: The selectivity of an enzyme inhibitor is a key determinant of its usefulness as a tool compound or its safety as a drug. Yet selectivity is never assessed comprehensively in the early stages of the drug discovery process, and only rarely in the later stages, because technical limitations prohibit doing otherwise. Here, we report EnPlex, an efficient, high-throughput method for simultaneously assessing inhibitor potency and specificity, and pilot its application to 96 serine hydrolases. EnPlex analysis of widely used serine hydrolase inhibitors revealed numerous previously unrecognized off-target interactions, some of which may help to explain previously confounding adverse effects. In addition, EnPlex screening of a hydrolase-directed library of boronic acid- and nitrile-containing compounds provided structure-activity relationships in both potency and selectivity dimen - sions from which lead candidates could be more effectively prioritized. Follow-up of a series of dipeptidyl peptidase 4 inhibitors showed that EnPlex indeed predicted efficacy and safety in animal models. These results demonstrate the feasibility and value of high-throughput, superfamily-wide selectivity profiling and suggest that such profiling can be incorporated into the earliest stages of drug discovery.
TL;DR: A spectrum of kinase genes whose overexpression can overcome NSCLC cells’ reliance on EGFR are identified and their convergence on the PI3K-AKT and MEK-ERK signaling axes in sustaining EGFR-independent survival is underscored.
Abstract: Lung adenocarcinomas harboring activating mutations in the epidermal growth factor receptor (EGFR) represent a common molecular subset of non-small cell lung cancer (NSCLC) cases. EGFR mutations predict sensitivity to EGFR tyrosine kinase inhibitors (TKIs) and thus represent a dependency in NSCLCs harboring these alterations, but the genetic basis of EGFR dependence is not fully understood. Here, we applied an unbiased, ORF-based screen to identify genetic modifiers of EGFR dependence in EGFR-mutant NSCLC cells. This approach identified 18 kinase and kinase-related genes whose overexpression can substitute for EGFR in EGFR-dependent PC9 cells, and these genes include seven of nine Src family kinase genes, FGFR1, FGFR2, ITK, NTRK1, NTRK2, MOS, MST1R, and RAF1. A subset of these genes can complement loss of EGFR activity across multiple EGFR-dependent models. Unbiased gene-expression profiling of cells overexpressing EGFR bypass genes, together with targeted validation studies, reveals EGFR-independent activation of the MEK-ERK and phosphoinositide 3-kinase (PI3K)-AKT pathways. Combined inhibition of PI3K-mTOR and MEK restores EGFR dependence in cells expressing each of the 18 EGFR bypass genes. Together, these data uncover a broad spectrum of kinases capable of overcoming dependence on EGFR and underscore their convergence on the PI3K-AKT and MEK-ERK signaling axes in sustaining EGFR-independent survival.
TL;DR: Together, these results identify and characterize a new role for miR425, miR1,miR125, and miR150 in promoting radioresistance in glioblastomas and provide insight into the therapeutic application of TGFβ inhibitors in radiotherapy.
Abstract: Theefficacyofradiotherapyinmanytumortypesislimitedbynormaltissuetoxicityandbyintrinsicoracquired radioresistance. Therefore, it is essential to understand the molecular network responsible for regulating radiosensitivity/resistance. Here, an unbiased functional screen identified four microRNAs (miR1, miR125a, miR150,andmiR425)thatinduceradioresistance.Consideringtheclinicalimportanceofradiotherapyforpatients withglioblastoma,theimpactofthesemiRNAsonglioblastomaradioresistancewasinvestigated.Overexpressionof miR1, miR125a, miR150, and/or miR425 in glioblastoma promotes radioresistance through upregulation of the cell-cycle checkpoint response. Conversely, antagonizing with antagomiRs sensitizes glioblastoma cells to irradiation, suggesting their potential as targets for inhibiting therapeutic resistance. Analysis of glioblastoma datasetsfromTheCancerGenomeAtlas(TCGA)revealedthatthesemiRNAsareexpressedinglioblastomapatient specimensandcorrelatewithTGFbsignaling.Finally,itisdemonstratedthatexpressionofmiR1andmiR125acan be induced by TGFb and antagonized by a TGFb receptor inhibitor. Together, these results identify and characterizeanewroleformiR425,miR1,miR125,andmiR150inpromotingradioresistanceinglioblastomasand provide insight into the therapeutic application of TGFb inhibitors in radiotherapy. Implications: Systematic identification of miRs that cause radioresistance in gliomas is important for uncovering predictive markers for radiotherapy or targets for overcoming radioresistance. Mol Cancer Res; 12(12); 1767–78. � 2014 AACR.
TL;DR: Routine use of the EGFR inhibitor gefitinib as a single agent for advanced AML is not appropriate because of pre-clinical activity and anecdotal cases of response to EGFR inhibitors.
TL;DR: A direct binding screen of 100 000 sp(3)-rich molecules identified a single diastereomer of a macrolactam core that binds specifically to myeloid cell leukemia 1 (MCL1).
Abstract: A direct binding screen of 100 000 sp3-rich molecules identified a single diastereomer of a macrolactam core that binds specifically to myeloid cell leukemia 1 (MCL1). A comprehensive toolbox of biophysical methods was applied to validate the original hit and subsequent analogues and also established a binding mode competitive with NOXA BH3 peptide. X-ray crystallography of ligand bound to MCL1 reveals a remarkable ligand/protein shape complementarity that diverges from previously disclosed MCL1 inhibitor costructures.
TL;DR: It is found that the CXCR4 pathway might constitute a novel susceptibility pathway associated with family history of melanoma in first-degree relatives.
Abstract: Purpose
Genetic predisposition plays a major role in the etiology of melanoma, but known genetic markers only account for a limited fraction of family-history-associated melanoma cases. Expression microarrays have offered the opportunity to identify further genomic profiles correlated with family history of melanoma. We aimed to distinguish mRNA expression signatures between melanoma cases with and without a family history of melanoma.
TL;DR: Pathway analysis, a heuristic analytic algorithm, a comparative oncology approach and a genome-wide, pooled short hairpin RNA (shRNA) screen all point to the PI3K/mTOR pathway as a potential central vulnerability for therapeutic exploitation in osteosarcoma.
Abstract: Osteosarcoma is the most common primary bone tumor and yet there have been no substantial advances in treatment or survival in over 2 decades. We examined 59 tumor/normal pairs by whole-genome, whole-exome and RNA-Sequencing. Only TP53 was mutated at significant frequency across the 59 samples. The mean non-silent somatic mutation rate was 1.2 mutation per megabase and there were a median of 231 somatic rearrangements per tumor. Complex chains of rearrangements and localized hypermutation were detected in almost all cases. Given the inter-tumor heterogeneity, the extent of genomic instability and the difficulty in acquiring a large sample size in a rare tumor we used several methods to identify genomic events contributing to osteosarcoma proliferation and survival. Pathway analysis, a heuristic analytic algorithm, a comparative oncology approach and a genome-wide, pooled short hairpin RNA (shRNA) screen all point to the PI3K/mTOR pathway as a potential central vulnerability for therapeutic exploitation in osteosarcoma. Osteosarcoma cell lines are responsive to pharmacologic and genetic inhibition of the PI3K/mTOR pathway both in vitro and in vivo. Citation Format: Adam Kiezun, Jennifer Perry, Peter Tonzi, Eliezer Van Allen, Scott L. Carter, Sylvan Baca, Ami Bhatt, Michael Lawrence, Loren Walensky, Nikhil Wagle, Jaume Mora, Carmen deTorres, Cinzia Lavarino, Liliana Velasco-Hidalgo, Rocio Cardenas-Cardos, Simone dos Santos Aguiar, Jose A. Yunes, Gabriela Mercado, Jorge Melendez-Zajgla, Charles Roberts, Levi Garraway, Carlos Rodriguez-Galindo, Todd Golub, Stuart Orkin, Gad Getz, Katherine Janeway. Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A41.
TL;DR: Efforts to pilot such a “Target Accelerator” will be presented, with particular emphasis on use of the Connectivity Map/Library of integrated cellular signatures (LINCS) resource to systematically connect mutant alleles to pathways and to potential therapeutic strategies.
TL;DR: The feasibility of CTC sequencing and the ability to confidently call somatic mutations are demonstrated, and CTCs may represent a non-invasive window into the mutational landscape of metastatic cancer, and may have utility for genomics in clinical practice.
Abstract: Comprehensive analysis of cancer genomes in clinical settings holds the promise to inform prognoses and guide the deployment of precise cancer treatments A major barrier, however, is the inaccessibility of adequate metastatic tissue for accurate genomic analysis The recognition that circulating tumor cells (CTCs) are present in many advanced cancer patients suggests an exciting opportunity to overcome this challenge For instance, if CTCs could be comprehensively sequenced, it would be possible to obtain an orthogonal sample of the tumor burden_including subsets of transiting cells bound for metastatic colonization_potentially yielding new insights to complement the static sampling of resected or biopsied lesions We report an integrated process to isolate, qualify, and sequence whole exomes of CTCs with high fidelity, using a census-based sequencing strategy We isolated CTCs by magnetic bead purification (Illumina MagSweeper) from the blood of patients with prostate cancer, and integrated a nanowell platform to automatically image and recover candidate single CTCs We then developed a strategy to qualify individual CTC-derived libraries for DNA sequencing after whole genome amplification, and established an analytical framework for accurate calling of mutations using census-based sequencing and MuTect Whole exome sequencing was performed on 20 single CTCs, obtained from a patient with advanced prostate cancer We validated our sequencing process by comparing CTC-derived mutations to mutations found in a lymph node metastasis and nine separate cores of the primary tumor 51 of 73 CTC mutations (70%) were observed in the metastasis or the primary tumor Moreover, we identified 9 early trunk mutations and 56 metastatic trunk mutations in the non-CTC tumor samples and found 100% and 73% of these, respectively, in CTC exomes Our work demonstrates the feasibility of CTC sequencing and the ability to confidently call somatic mutations CTCs may therefore represent a non-invasive window into the mutational landscape of metastatic cancer, and may have utility for genomics in clinical practice Citation Format: Viktor A Adalsteinsson, Jens G Lohr, Kristian Cibulskis, Atish D Choudhury, Mara Rosenberg, Peter Cruz-Gordillo, Joshua Francis, ChengZhong Zhang, Alexander K Shalek, Rahul Satija, John T Trombetta, Diana Lu, Naren Tallapragada, Narmin T Tahirova, Sora Kim, Brendan Blumenstiel, Carrie Sougnez, Daniel Auclair, Eliezer M Van Allen, Mari Nakabayashi, Rosina T Lis, Gwo-Shu M Lee, Tiantian Li, Matthew S Chabot, Mary-Ellen Taplin, Thomas E Clancy, Massimo Loda, Aviv Regev, Matthew Meyerson, William C Hahn, Philip W Kantoff, Todd R Golub, Gad Getz, Jesse S Boehm, J Christopher Love Whole exome sequencing of CTCs as a window into metastatic 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 993 doi:101158/1538-7445AM2014-993
TL;DR: Crompton et al. as mentioned in this paper performed whole-exome sequencing of 96 Ewing sarcoma tumors and 11 Ewing SARcoma cell lines, as well as whole-genome sequencing, transcriptome sequencing and copy-number analysis of a subset of these samples.
Abstract: The sequencing of aggressive pediatric solid tumors is revealing remarkably stable genomes. In the cases of malignant rhabdoid and retinoblastoma, there is a paucity of recurrently mutated genes, and oncogenesis appears to be driven, at least in part, by epigenetic deregulation. It has been suggested that pediatric tumors characterized by oncogenic fusions will exhibit relatively few additional somatic driver aberrancies. Ewing sarcoma, the second most common pediatric bone tumor, is characterized by rearrangements of the EWS gene and ETS-family transcription factor genes, most commonly FLI and ERG. In experimental models, Ewing sarcoma demonstrates dependency on the expression of the resulting chimeric fusion products. As such, Ewing sarcoma represents a paradigm for studying the genomic landscape of fusion-driven cancers. To this end, we performed whole-exome sequencing of 96 Ewing sarcoma tumors and 11 Ewing sarcoma cell lines, as well as whole-genome sequencing, transcriptome sequencing, and copy-number analysis of a subset of these samples. We found that Ewing sarcoma is one of the most genetically normal cancers sequenced to date, but that treatment, which generally employs genotoxic chemotherapy and radiation, is associated with an increase in mutation rate and single nucleotide substitutions associated with DNA damage. There was a marked absence of recurrent mutations in immediately druggable targets, such as tyrosine kinases, calling into question the feasibility of utilizing tumor sequencing to nominate targeted therapies for patients with Ewing sarcoma. Rather, these results highlight the importance of directly targeting the EWS/ETS fusion events or identifying synthetic lethal dependencies. To this end, we clarified a number of outstanding questions regarding the EWS/ETS fusions. We found that reciprocal ETS/EWS fusions are not expressed in Ewing sarcoma and therefore unlikely to play a role in Ewing pathogenesis as is seen with reciprocal fusions of PML-RARα in acute promyelocytic leukemia. We also found that wild-type FLI and wild-type ERG are not expressed in Ewing sarcoma tumors. However, there appears to be a role for ETS gene deregulation in this disease beyond the expression of EWS/ETS fusion proteins because we found recurrent somatic events in ERF and ETS1. We also identified a small number of other recurrently mutated genes that likely collaborate with EWS/ETS fusions in a minority of cases and confirmed that loss of STAG2 occurs in approximately 15% of Ewing sarcoma tumors. Thus, massively parallel sequencing of a large collection of Ewing sarcoma tumors supports the notion that fusion-driven pediatric malignancies bear quiet genomes, underscores the importance of identifying new treatment approaches targeting EWS/ETS fusions, and also identifies new genetic abnormalities that warrant further biological validation. Citation Format: Brian Crompton, Chip Stewart, Amaro Taylor-Weiner, Gabriela Alexa, Kyle Kurek, Monica Calicchio, Adam Kiezun, Scott Carter, Sachet Shukla, Swapnil Mehta, Aaron Thorner, Carmen de Torres, Cinzia Lavarino, Mariona Sunol, Aaron McKenna, Andrey Sivachenko, Kristian Cibulskis, Michael Lawrence, Lauren Ambrogio, Daniel Auclair, Ivan Rosshandler, Angela Schwarz-Cruz y Celis, Miguel Rivera, Carlos Rodriguez-Galindo, Mark Fleming, Todd Golub, Gad Getz, Jaume Mora, Kimberly Stegmaier. The genomic landscape of pediatric Ewing sarcoma. [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 999. doi:10.1158/1538-7445.AM2014-999
Patent•
04 Dec 2014TL;DR: The invention provides a culture system that reproduces the cachetic process in cells in vitro, which facilitates the screening and identification of therapeutic agents useful for disrupting the progression of pre-cachexia to refractory cachexia.
Abstract: The invention provides markers indicative of pre-cachexia, compositions and methods for identifying patients with a molecular signature indicative of pre-cachexia; a culture system that reproduces the cachetic process in cells in vitro, which facilitates the screening and identification of therapeutic agents useful for disrupting (slowing, reducing, reversing, or preventing) the progression of pre-cachexia to refractory cachexia; as well as therapeutic agents identified using the culture system of the invention.