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1.
Nat Genet ; 2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38890488

RESUMO

Tumor genomic profiling is increasingly seen as a prerequisite to guide the treatment of patients with cancer. To explore the value of whole-genome sequencing (WGS) in broadening the scope of cancers potentially amenable to a precision therapy, we analysed whole-genome sequencing data on 10,478 patients spanning 35 cancer types recruited to the UK 100,000 Genomes Project. We identified 330 candidate driver genes, including 74 that are new to any cancer. We estimate that approximately 55% of patients studied harbor at least one clinically relevant mutation, predicting either sensitivity or resistance to certain treatments or clinical trial eligibility. By performing computational chemogenomic analysis of cancer mutations we identify additional targets for compounds that represent attractive candidates for future clinical trials. This study represents one of the most comprehensive efforts thus far to identify cancer driver genes in the real world setting and assess their impact on informing precision oncology.

2.
iScience ; 26(7): 107059, 2023 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-37360684

RESUMO

To address the limitation associated with degron based systems, we have developed iTAG, a synthetic tag based on IMiDs/CELMoDs mechanism of action that improves and addresses the limitations of both PROTAC and previous IMiDs/CeLMoDs based tags. Using structural and sequence analysis, we systematically explored native and chimeric degron containing domains (DCDs) and evaluated their ability to induce degradation. We identified the optimal chimeric iTAG(DCD23 60aa) that elicits robust degradation of targets across cell types and subcellular localizations without exhibiting the well documented "hook effect" of PROTAC-based systems. We showed that iTAG can also induce target degradation by murine CRBN and enabled the exploration of natural neo-substrates that can be degraded by murine CRBN. Hence, the iTAG system constitutes a versatile tool to degrade targets across the human and murine proteome.

3.
Nucleic Acids Res ; 51(D1): D1212-D1219, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36624665

RESUMO

canSAR (https://cansar.ai) is the largest public cancer drug discovery and translational research knowledgebase. Now hosted in its new home at MD Anderson Cancer Center, canSAR integrates billions of experimental measurements from across molecular profiling, pharmacology, chemistry, structural and systems biology. Moreover, canSAR applies a unique suite of machine learning algorithms designed to inform drug discovery. Here, we describe the latest updates to the knowledgebase, including a focus on significant novel data. These include canSAR's ligandability assessment of AlphaFold; mapping of fragment-based screening data; and new chemical bioactivity data for novel targets. We also describe enhancements to the data and interface.


Assuntos
Antineoplásicos , Descoberta de Drogas , Bases de Conhecimento , Pesquisa Translacional Biomédica , Humanos , Algoritmos , Neoplasias/tratamento farmacológico , Neoplasias/genética
4.
Nucleic Acids Res ; 49(D1): D1074-D1082, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33219674

RESUMO

canSAR (http://cansar.icr.ac.uk) is the largest, public, freely available, integrative translational research and drug discovery knowledgebase for oncology. canSAR integrates vast multidisciplinary data from across genomic, protein, pharmacological, drug and chemical data with structural biology, protein networks and more. It also provides unique data, curation and annotation and crucially, AI-informed target assessment for drug discovery. canSAR is widely used internationally by academia and industry. Here we describe significant developments and enhancements to the data, web interface and infrastructure of canSAR in the form of the new implementation of the system: canSARblack. We demonstrate new functionality in aiding translation hypothesis generation and experimental design, and show how canSAR can be adapted and utilised outside oncology.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Descoberta de Drogas/métodos , Bases de Conhecimento , Neoplasias/genética , Pesquisa Translacional Biomédica/métodos , Antineoplásicos/química , Antineoplásicos/uso terapêutico , Mineração de Dados/métodos , Genômica/métodos , Humanos , Internet , Oncologia/métodos , Estrutura Molecular , Neoplasias/metabolismo , Proteômica/métodos , Interface Usuário-Computador
5.
Nucleic Acids Res ; 47(D1): D917-D922, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30496479

RESUMO

canSAR (http://cansar.icr.ac.uk) is a public, freely available, integrative translational research and drug discovery knowlegebase. canSAR informs researchers to help solve key bottlenecks in cancer translation and drug discovery. It integrates genomic, protein, pharmacological, drug and chemical data with structural biology, protein networks and unique, comprehensive and orthogonal 'druggability' assessments. canSAR is widely used internationally by academia and industry. Here we describe major enhancements to canSAR including new and expanded data. We also describe the first components of canSARblack-an advanced, responsive, multi-device compatible redesign of canSAR with a question-led interface.


Assuntos
Antineoplásicos , Bases de Dados de Produtos Farmacêuticos , Descoberta de Drogas , Bases de Conhecimento , Antineoplásicos/química , Antineoplásicos/uso terapêutico , Humanos , Neoplasias/tratamento farmacológico , Neoplasias/genética , Conformação Proteica , Mapeamento de Interação de Proteínas , Pesquisa Translacional Biomédica , Interface Usuário-Computador
6.
Nucleic Acids Res ; 44(D1): D938-43, 2016 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-26673713

RESUMO

canSAR (http://cansar.icr.ac.uk) is a publicly available, multidisciplinary, cancer-focused knowledgebase developed to support cancer translational research and drug discovery. canSAR integrates genomic, protein, pharmacological, drug and chemical data with structural biology, protein networks and druggability data. canSAR is widely used to rapidly access information and help interpret experimental data in a translational and drug discovery context. Here we describe major enhancements to canSAR including new data, improved search and browsing capabilities, new disease and cancer cell line summaries and new and enhanced batch analysis tools.


Assuntos
Antineoplásicos/farmacologia , Descoberta de Drogas , Bases de Conhecimento , Neoplasias/metabolismo , Animais , Linhagem Celular Tumoral , Ensaios Clínicos como Assunto , Expressão Gênica , Humanos , Proteínas de Neoplasias/química , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Neoplasias/genética
7.
PLoS Comput Biol ; 11(12): e1004597, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26699810

RESUMO

The interaction environment of a protein in a cellular network is important in defining the role that the protein plays in the system as a whole, and thus its potential suitability as a drug target. Despite the importance of the network environment, it is neglected during target selection for drug discovery. Here, we present the first systematic, comprehensive computational analysis of topological, community and graphical network parameters of the human interactome and identify discriminatory network patterns that strongly distinguish drug targets from the interactome as a whole. Importantly, we identify striking differences in the network behavior of targets of cancer drugs versus targets from other therapeutic areas and explore how they may relate to successful drug combinations to overcome acquired resistance to cancer drugs. We develop, computationally validate and provide the first public domain predictive algorithm for identifying druggable neighborhoods based on network parameters. We also make available full predictions for 13,345 proteins to aid target selection for drug discovery. All target predictions are available through canSAR.icr.ac.uk. Underlying data and tools are available at https://cansar.icr.ac.uk/cansar/publications/druggable_network_neighbourhoods/.


Assuntos
Antineoplásicos/administração & dosagem , Modelos Biológicos , Proteínas de Neoplasias/metabolismo , Neoplasias/tratamento farmacológico , Neoplasias/metabolismo , Mapeamento de Interação de Proteínas/métodos , Algoritmos , Simulação por Computador , Sistemas de Liberação de Medicamentos/métodos , Descoberta de Drogas/métodos , Quimioterapia Assistida por Computador/métodos , Humanos , Terapia de Alvo Molecular/métodos , Proteínas de Neoplasias/antagonistas & inibidores , Transdução de Sinais/efeitos dos fármacos
8.
Cancer Discov ; 4(3): 304-17, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24520024

RESUMO

To interrogate the complex mechanisms involved in the later stages of cancer metastasis, we designed a functional in vivo RNA interference (RNAi) screen combined with next-generation sequencing. Using this approach, we identified the sialyltransferase ST6GalNAc2 as a novel breast cancer metastasis suppressor. Mechanistically, ST6GalNAc2 silencing alters the profile of O-glycans on the tumor cell surface, facilitating binding of the soluble lectin galectin-3. This then enhances tumor cell retention and emboli formation at metastatic sites leading to increased metastatic burden, events that can be completely blocked by galectin-3 inhibition. Critically, elevated ST6GALNAC2, but not galectin-3, expression in estrogen receptor-negative breast cancers significantly correlates with reduced frequency of metastatic events and improved survival. These data demonstrate that the prometastatic role of galectin-3 is regulated by its ability to bind to the tumor cell surface and highlight the potential of monitoring ST6GalNAc2 expression to stratify patients with breast cancer for treatment with galectin-3 inhibitors.


Assuntos
Neoplasias da Mama/genética , Galectina 3/metabolismo , Neoplasias Pulmonares/genética , Sialiltransferases/genética , Animais , Neoplasias da Mama/patologia , Linhagem Celular , Feminino , Regulação Neoplásica da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Células Endoteliais da Veia Umbilical Humana , Humanos , Neoplasias Pulmonares/patologia , Neoplasias Pulmonares/secundário , Neoplasias Mamárias Experimentais , Camundongos , Camundongos Endogâmicos BALB C , Interferência de RNA , Sialiltransferases/metabolismo
9.
J Pathol ; 232(5): 553-65, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24395524

RESUMO

Micropapillary carcinoma (MPC) is a rare histological special type of breast cancer, characterized by an aggressive clinical behaviour and a pattern of copy number aberrations (CNAs) distinct from that of grade- and oestrogen receptor (ER)-matched invasive carcinomas of no special type (IC-NSTs). The aims of this study were to determine whether MPCs are underpinned by a recurrent fusion gene(s) or mutations in 273 genes recurrently mutated in breast cancer. Sixteen MPCs were subjected to microarray-based comparative genomic hybridization (aCGH) analysis and Sequenom OncoCarta mutation analysis. Eight and five MPCs were subjected to targeted capture and RNA sequencing, respectively. aCGH analysis confirmed our previous observations about the repertoire of CNAs of MPCs. Sequencing analysis revealed a spectrum of mutations similar to those of luminal B IC-NSTs, and recurrent mutations affecting mitogen-activated protein kinase family genes and NBPF10. RNA-sequencing analysis identified 17 high-confidence fusion genes, eight of which were validated and two of which were in-frame. No recurrent fusions were identified in an independent series of MPCs and IC-NSTs. Forced expression of in-frame fusion genes (SLC2A1-FAF1 and BCAS4-AURKA) resulted in increased viability of breast cancer cells. In addition, genomic disruption of CDK12 caused by out-of-frame rearrangements was found in one MPC and in 13% of HER2-positive breast cancers, identified through a re-analysis of publicly available massively parallel sequencing data. In vitro analyses revealed that CDK12 gene disruption results in sensitivity to PARP inhibition, and forced expression of wild-type CDK12 in a CDK12-null cell line model resulted in relative resistance to PARP inhibition. Our findings demonstrate that MPCs are neither defined by highly recurrent mutations in the 273 genes tested, nor underpinned by a recurrent fusion gene. Although seemingly private genetic events, some of the fusion transcripts found in MPCs may play a role in maintenance of a malignant phenotype and potentially offer therapeutic opportunities.


Assuntos
Biomarcadores Tumorais/genética , Neoplasias da Mama/genética , Carcinoma Papilar/genética , Regulação Neoplásica da Expressão Gênica , Fusão Gênica , Mutação , Biomarcadores Tumorais/metabolismo , Neoplasias da Mama/metabolismo , Neoplasias da Mama/patologia , Carcinoma Papilar/metabolismo , Carcinoma Papilar/patologia , Estudos de Casos e Controles , Linhagem Celular Tumoral , Proliferação de Células , Hibridização Genômica Comparativa , Variações do Número de Cópias de DNA , Análise Mutacional de DNA , Feminino , Dosagem de Genes , Predisposição Genética para Doença , Humanos , Invasividade Neoplásica , Análise de Sequência com Séries de Oligonucleotídeos , Fenótipo , Análise de Sequência de RNA , Fatores de Tempo
10.
Breast Cancer Res Treat ; 139(3): 907-21, 2013 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-23756628

RESUMO

Given the steady increase in breast cancer rates in both the developed and developing world, there has been a concerted research effort undertaken worldwide to understand the molecular mechanisms underpinning the disease. The data generated from numerous clinical trials and experimental studies shed light on different aspects of the disease. We present a new version of the ROCK database (rock.icr.ac.uk), which integrates such diverse data types allowing unique analyses of published breast cancer experimental data. We have added several new data types and analysis modules to ROCK, which allow the user to interactively query and research the huge amounts of available experimental data and perform complex correlations across studies and data types such as gene expression, genomic copy number aberrations, micro RNA expression, RNA interference, survival analysis, clinical annotation and signalling protein networks. We present the recent and major functional updates and enhancements to the ROCK resource, including new analysis modules and microRNA and NGS data integration, and illustrate how ROCK can be used to confirm known experimental results as well as generate novel leads and new experimental hypotheses using the Wnt signalling cell surface receptor FZD7 and the Myc oncogene. ROCK provides a unique breast cancer analysis platform of integrated experimental datasets at the genomic, transcriptomic and proteomic level. This paper presents how ROCK has transitioned from being simply a database to an interactive resource useful to the broader breast cancer research community in our effort to facilitate research into the underlying molecular mechanisms of breast cancer.


Assuntos
Neoplasias da Mama , Neoplasias da Mama/genética , Neoplasias da Mama/metabolismo , Neoplasias da Mama/mortalidade , Mineração de Dados/métodos , Bases de Dados de Compostos Químicos , Bases de Dados Factuais , Bases de Dados Genéticas , Feminino , Receptores Frizzled/genética , Receptores Frizzled/metabolismo , Dosagem de Genes , Perfilação da Expressão Gênica , Genes myc , Humanos , MicroRNAs , Oncogenes , Interferência de RNA , Análise de Sobrevida , Via de Sinalização Wnt
11.
Nat Genet ; 44(11): 1182-4, 2012 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-23001122

RESUMO

We conducted a genome-wide association study of male breast cancer comprising 823 cases and 2,795 controls of European ancestry, with validation in independent sample sets totaling 438 cases and 474 controls. A SNP in RAD51B at 14q24.1 was significantly associated with male breast cancer risk (P = 3.02 × 10(-13); odds ratio (OR) = 1.57). We also refine association at 16q12.1 to a SNP within TOX3 (P = 3.87 × 10(-15); OR = 1.50).


Assuntos
Neoplasias da Mama Masculina/genética , Proteínas de Ligação a DNA/genética , Estudo de Associação Genômica Ampla , Cromossomos Humanos Par 14 , Predisposição Genética para Doença , Humanos , Masculino , Polimorfismo de Nucleotídeo Único , Fatores de Risco , População Branca
12.
Pigment Cell Melanoma Res ; 25(4): 488-92, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22578220

RESUMO

Acral melanoma is a rare melanoma subtype with distinct epidemiological, clinical and genetic features. To determine if acral melanoma cell lines are representative of this melanoma subtype, six lines were analysed by whole-exome sequencing and array comparative genomic hybridisation. We demonstrate that the cell lines display a mutation rate that is comparable to that of published primary and metastatic acral melanomas and observe a mutational signature suggestive of UV-induced mutagenesis in two of the cell lines. Mutations were identified in oncogenes and tumour suppressors previously linked to melanoma including BRAF, NRAS, KIT, PTEN and TP53, in cancer genes not previously linked to melanoma and in genes linked to DNA repair such as BRCA1 and BRCA2. Our findings provide strong circumstantial evidence to suggest that acral melanoma cell lines and acral tumours share genetic features in common and that these cells are therefore valuable tools to investigate the biology of this aggressive melanoma subtype. Data are available at: http://rock.icr.ac.uk/collaborations/Furney_et_al_2012/.


Assuntos
Genoma Humano/genética , Melanoma/classificação , Melanoma/genética , Neoplasias Cutâneas/classificação , Neoplasias Cutâneas/genética , Linhagem Celular Tumoral , Exoma/genética , Humanos , Repetições de Microssatélites/genética , Mutação/genética , Polimorfismo de Nucleotídeo Único/genética
13.
Breast Cancer Res Treat ; 135(1): 79-91, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22535017

RESUMO

Cancer is caused by mutations in oncogenes and tumor suppressor genes, resulting in the deregulation of processes fundamental to the normal behavior of cells. The identification and characterization of oncogenes and tumor suppressors has led to new treatment strategies that have significantly improved cancer outcome. The advent of next generation sequencing has allowed the elucidation of the fine structure of cancer genomes, however, the identification of pathogenic changes is complicated by the inherent genomic instability of cancer cells. Therefore, functional approaches for the identification of novel genes involved in the initiation and development of tumors are critical. Here we report the first whole human genome in vivo RNA interference screen to identify functionally important tumor suppressor genes. Using our novel approach, we identify previously validated tumor suppressor genes including TP53 and MNT, as well as several novel candidate tumor suppressor genes including leukemia inhibitory factor receptor (LIFR). We show that LIFR is a key novel tumor suppressor, whose deregulation may drive the transformation of a significant proportion of human breast cancers. These results demonstrate the power of genome wide in vivo RNAi screens as a method for identifying novel genes regulating tumorigenesis.


Assuntos
Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Neoplasias da Mama/genética , Genes Supressores de Tumor , Subunidade alfa de Receptor de Fator Inibidor de Leucemia/genética , Proteínas Repressoras/genética , Proteína Supressora de Tumor p53/genética , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/metabolismo , Linhagem Celular Tumoral , Feminino , Genes p53 , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Interferência de RNA , RNA Interferente Pequeno
14.
PLoS One ; 7(3): e32617, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22403682

RESUMO

Next generation DNA sequencing (NGS) technologies have revolutionized the pace at which whole genome and exome sequences can be generated. However, despite these advances, many of the methods for targeted resequencing, such as the generation of high-depth exome sequences, are somewhat limited by the relatively large amounts of starting DNA that are normally required. In the case of tumour analysis this is particularly pertinent as many tumour biopsies often return submicrogram quantities of DNA, especially when tumours are microdissected prior to analysis. Here, we present a method for exome capture and resequencing using as little as 50 ng of starting DNA. The sequencing libraries generated by this minimal starting amount (MSA-Cap) method generate datasets that are comparable to standard amount (SA) whole exome libraries that use three micrograms of starting DNA. This method, which can be performed in most laboratories using commonly available reagents, has the potential to enhance large scale profiling efforts such as the resequencing of tumour exomes.


Assuntos
DNA/genética , Exoma/genética , Análise de Sequência de DNA/métodos , Linhagem Celular , DNA/isolamento & purificação , Feminino , Biblioteca Gênica , Genômica , Genótipo , Humanos , Laboratórios , Reação em Cadeia da Polimerase
15.
Proc Natl Acad Sci U S A ; 109(8): 2730-5, 2012 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-21482774

RESUMO

Therapies that target estrogen signaling have made a very considerable contribution to reducing mortality from breast cancer. However, resistance to tamoxifen remains a major clinical problem. Here we have used a genome-wide functional profiling approach to identify multiple genes that confer resistance or sensitivity to tamoxifen. Combining whole-genome shRNA screening with massively parallel sequencing, we have profiled the impact of more than 56,670 RNA interference reagents targeting 16,487 genes on the cellular response to tamoxifen. This screen, along with subsequent validation experiments, identifies a compendium of genes whose silencing causes tamoxifen resistance (including BAP1, CLPP, GPRC5D, NAE1, NF1, NIPBL, NSD1, RAD21, RARG, SMC3, and UBA3) and also a set of genes whose silencing causes sensitivity to this endocrine agent (C10orf72, C15orf55/NUT, EDF1, ING5, KRAS, NOC3L, PPP1R15B, RRAS2, TMPRSS2, and TPM4). Multiple individual genes, including NF1, a regulator of RAS signaling, also correlate with clinical outcome after tamoxifen treatment.


Assuntos
Genes Neoplásicos/genética , Testes Genéticos/métodos , Genoma Humano/genética , Interferência de RNA/efeitos dos fármacos , Tamoxifeno/farmacologia , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/genética , Linhagem Celular Tumoral , Resistencia a Medicamentos Antineoplásicos/efeitos dos fármacos , Resistencia a Medicamentos Antineoplásicos/genética , Ensaios de Seleção de Medicamentos Antitumorais , Feminino , Humanos , Reprodutibilidade dos Testes , Transdução de Sinais/efeitos dos fármacos
16.
Genome Res ; 22(2): 196-207, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22183965

RESUMO

Next generation sequencing has enabled systematic discovery of mutational spectra in cancer samples. Here, we used whole genome sequencing to characterize somatic mutations and structural variation in a primary acral melanoma and its lymph node metastasis. Our data show that the somatic mutational rates in this acral melanoma sample pair were more comparable to the rates reported in cancer genomes not associated with mutagenic exposure than in the genome of a melanoma cell line or the transcriptome of melanoma short-term cultures. Despite the perception that acral skin is sun-protected, the dominant mutational signature in these samples is compatible with damage due to ultraviolet light exposure. A nonsense mutation in ERCC5 discovered in both the primary and metastatic tumors could also have contributed to the mutational signature through accumulation of unrepaired dipyrimidine lesions. However, evidence of transcription-coupled repair was suggested by the lower mutational rate in the transcribed regions and expressed genes. The primary and the metastasis are highly similar at the level of global gene copy number alterations, loss of heterozygosity and single nucleotide variation (SNV). Furthermore, the majority of the SNVs in the primary tumor were propagated in the metastasis and one nonsynonymous coding SNV and one splice site mutation appeared to arise de novo in the metastatic lesion.


Assuntos
Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala , Melanoma/genética , Idoso , Variações do Número de Cópias de DNA , Análise Mutacional de DNA , Exoma , Humanos , Perda de Heterozigosidade , Masculino , Melanoma/patologia , Taxa de Mutação , Metástase Neoplásica , Polimorfismo de Nucleotídeo Único
17.
BMC Med Genomics ; 4: 75, 2011 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-22032724

RESUMO

BACKGROUND: Gene fusions arising from chromosomal translocations have been implicated in cancer. However, the role of gene fusions in BRCA1-related breast cancers is not well understood. Mutations in BRCA1 are associated with an increased risk for breast cancer (up to 80% lifetime risk) and ovarian cancer (up to 50%). We sought to identify putative gene fusions in the transcriptomes of these cancers using high-throughput RNA sequencing (RNA-Seq). METHODS: We used Illumina sequencing technology to sequence the transcriptomes of five BRCA1-mutated breast cancer cell lines, three BRCA1-mutated primary tumors, two secretory breast cancer primary tumors and one non-tumorigenic breast epithelial cell line. Using a bioinformatics approach, our initial attempt at discovering putative gene fusions relied on analyzing single-end reads and identifying reads that aligned across exons of two different genes. Subsequently, latter samples were sequenced with paired-end reads and at longer cycles (producing longer reads). We then refined our approach by identifying misaligned paired reads, which may flank a putative gene fusion junction. RESULTS: As a proof of concept, we were able to identify two previously characterized gene fusions in our samples using both single-end and paired-end approaches. In addition, we identified three novel in-frame fusions, but none were recurrent. Two of the candidates, WWC1-ADRBK2 in HCC3153 cell line and ADNP-C20orf132 in a primary tumor, were confirmed by Sanger sequencing and RT-PCR. RNA-Seq expression profiling of these two fusions showed a distinct overexpression of the 3' partner genes, suggesting that its expression may be under the control of the 5' partner gene's regulatory elements. CONCLUSIONS: In this study, we used both single-end and paired-end sequencing strategies to discover gene fusions in breast cancer transcriptomes with BRCA1 mutations. We found that the use of paired-end reads is an effective tool for transcriptome profiling of gene fusions. Our findings suggest that while gene fusions are present in some BRCA1-mutated breast cancers, they are infrequent and not recurrent. However, private fusions may still be valuable as potential patient-specific biomarkers for diagnosis and treatment.


Assuntos
Proteína BRCA1/genética , Neoplasias da Mama/patologia , Perfilação da Expressão Gênica/métodos , Fusão Gênica/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Mutação , Análise de Sequência de RNA/métodos , Sequência de Bases , Neoplasias da Mama/genética , Linhagem Celular Tumoral , Pontos de Quebra do Cromossomo , Variações do Número de Cópias de DNA/genética , Estudos de Viabilidade , Feminino , Humanos , Dados de Sequência Molecular , RNA Mensageiro/genética
18.
Sci Transl Med ; 3(98): 98ra82, 2011 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-21885404

RESUMO

Integrating transcriptomic sequencing with conventional cytogenetics, we identified WWTR1 (WW domain-containing transcription regulator 1) (3q25) and CAMTA1 (calmodulin-binding transcription activator 1) (1p36) as the two genes involved in the t(1;3)(p36;q25) chromosomal translocation that is characteristic of epithelioid hemangioendothelioma (EHE), a vascular sarcoma. This WWTR1/CAMTA1 gene fusion is under the transcriptional control of the WWTR1 promoter and encodes a putative chimeric transcription factor that joins the amino terminus of WWTR1, a protein that is highly expressed in endothelial cells, in-frame to the carboxyl terminus of CAMTA1, a protein that is normally expressed only in brain. Thus, CAMTA1 expression is activated inappropriately through a promoter-switch mechanism. The gene fusion is present in virtually all EHEs tested but is absent from all other vascular neoplasms, demonstrating it to be a disease-defining genetic alteration. A sensitive and specific break-apart fluorescence in situ hybridization assay was also developed to detect the translocation and will assist in the evaluation of this diagnostically challenging neoplasm. The chimeric WWTR1/CAMTA1 transcription factor may represent a therapeutic target for EHE and offers the opportunity to shed light on the functions of two poorly characterized proteins.


Assuntos
Fusão Gênica/genética , Hemangioendotelioma Epitelioide/genética , Proteínas de Ligação ao Cálcio/genética , Proteínas de Ligação ao Cálcio/metabolismo , Quebra Cromossômica , Análise Citogenética , Perfilação da Expressão Gênica , Genoma Humano/genética , Hemangioendotelioma Epitelioide/patologia , Humanos , Imuno-Histoquímica , Hibridização in Situ Fluorescente , Peptídeos e Proteínas de Sinalização Intracelular/genética , Reação em Cadeia da Polimerase , Transativadores/genética , Transativadores/metabolismo , Fatores de Transcrição , Proteínas com Motivo de Ligação a PDZ com Coativador Transcricional
19.
Breast Cancer Res ; 13(4): R79, 2011 Aug 11.
Artigo em Inglês | MEDLINE | ID: mdl-21834968

RESUMO

INTRODUCTION: The mammary primordium forms during embryogenesis as a result of inductive interactions between its constitutive tissues, the mesenchyme and epithelium, and represents the earliest evidence of commitment to the mammary lineage. Previous studies of embryonic mouse mammary epithelium indicated that, by mid-gestation, these cells are determined to a mammary cell fate and that a stem cell population has been delimited. Mammary mesenchyme can induce mammary development from simple epithelium even across species and classes, and can partially restore features of differentiated tissue to mouse mammary tumours in co-culture experiments. Despite these exciting properties, the molecular identity of embryonic mammary cells remains to be fully characterised. METHODS: Here, we define the transcriptome of the mammary primordium and the two distinct cellular compartments that comprise it, the mammary primordial bud epithelium and mammary mesenchyme. Pathway and network analysis was performed and comparisons of embryonic mammary gene expression profiles to those of both postnatal mouse and human mammary epithelial cell sub-populations and stroma were made. RESULTS: Several of the genes we have detected in our embryonic mammary cell signatures were previously shown to regulate mammary cell fate and development, but we also identified a large number of novel candidates. Additionally, we determined genes that were expressed by both embryonic and postnatal mammary cells, which represent candidate regulators of mammary cell fate, differentiation and progenitor cell function that could signal from mammary lineage inception during embryogenesis through postnatal development. Comparison of embryonic mammary cell signatures with those of human breast cells identified potential regulators of mammary progenitor cell functions conserved across species. CONCLUSIONS: These results provide new insights into genetic regulatory mechanisms of mammary development, particularly identification of novel potential regulators of mammary fate and mesenchymal-epithelial cross-talk. Since cancers may represent diseases of mesenchymal-epithelial communications, we anticipate these results will provide foundations for further studies into the fundamental links between developmental, stem cell and breast cancer biology.


Assuntos
Perfilação da Expressão Gênica , Glândulas Mamárias Animais/citologia , Glândulas Mamárias Animais/embriologia , Animais , Animais Recém-Nascidos , Linhagem da Célula , Células Epiteliais/fisiologia , Receptor alfa de Estrogênio , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Humanos , Glândulas Mamárias Animais/crescimento & desenvolvimento , Glândulas Mamárias Animais/metabolismo , Glândulas Mamárias Humanas/citologia , Mesoderma/citologia , Camundongos , Camundongos Endogâmicos , Transdução de Sinais , Células Estromais/metabolismo
20.
PLoS One ; 6(7): e21639, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21750719

RESUMO

Capan-1 is a well-characterised BRCA2-deficient human cell line isolated from a liver metastasis of a pancreatic adenocarcinoma. Here we report a genome-wide assessment of structural variations and high-depth exome characterization of single nucleotide variants and small insertion/deletions in Capan-1. To identify potential somatic and tumour-associated variations in the absence of a matched-normal cell line, we devised a novel method based on the analysis of HapMap samples. We demonstrate that Capan-1 has one of the most rearranged genomes sequenced to date. Furthermore, small insertions and deletions are detected more frequently in the context of short sequence repeats than in other genomes. We also identify a number of novel mutations that may represent genetic changes that have contributed to tumour progression. These data provide insight into the genomic effects of loss of BRCA2 function.


Assuntos
Proteína BRCA2/genética , Genoma Humano/genética , Genômica/métodos , Análise de Sequência de DNA/métodos , Adenocarcinoma/genética , Adenocarcinoma/patologia , Proteína BRCA2/deficiência , Linhagem Celular Tumoral , Mapeamento Cromossômico , Hibridização Genômica Comparativa , Humanos , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/patologia
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