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1.
Am J Hum Genet ; 107(4): 622-635, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-32946763

RESUMO

Quantifying the functional effects of complex disease risk variants can provide insights into mechanisms underlying disease biology. Genome-wide association studies have identified 39 regions associated with risk of epithelial ovarian cancer (EOC). The vast majority of these variants lie in the non-coding genome, where they likely function through interaction with gene regulatory elements. In this study we first estimated the heritability explained by known common low penetrance risk alleles for EOC. The narrow sense heritability (hg2) of EOC overall and high-grade serous ovarian cancer (HGSOCs) were estimated to be 5%-6%. Partitioned SNP heritability across broad functional categories indicated a significant contribution of regulatory elements to EOC heritability. We collated epigenomic profiling data for 77 cell and tissue types from Roadmap Epigenomics and ENCODE, and from H3K27Ac ChIP-seq data generated in 26 ovarian cancer and precursor-related cell and tissue types. We identified significant enrichment of risk single-nucleotide polymorphisms (SNPs) in active regulatory elements marked by H3K27Ac in HGSOCs. To further investigate how risk SNPs in active regulatory elements influence predisposition to ovarian cancer, we used motifbreakR to predict the disruption of transcription factor binding sites. We identified 469 candidate causal risk variants in H3K27Ac peaks that are predicted to significantly break transcription factor (TF) motifs. The most frequently broken motif was REST (p value = 0.0028), which has been reported as both a tumor suppressor and an oncogene. Overall, these systematic functional annotations with epigenomic data improve interpretation of EOC risk variants and shed light on likely cells of origin.


Assuntos
Carcinoma Epitelial do Ovário/genética , Proteínas Correpressoras/genética , Cistadenocarcinoma Seroso/genética , Elementos Facilitadores Genéticos , Histonas/genética , Proteínas do Tecido Nervoso/genética , Neoplasias Ovarianas/genética , Alelos , Sítios de Ligação , Carcinoma Epitelial do Ovário/diagnóstico , Carcinoma Epitelial do Ovário/patologia , Mapeamento Cromossômico , Proteínas Correpressoras/metabolismo , Cistadenocarcinoma Seroso/diagnóstico , Cistadenocarcinoma Seroso/patologia , Feminino , Predisposição Genética para Doença , Genoma Humano , Estudo de Associação Genômica Ampla , Histonas/metabolismo , Humanos , Padrões de Herança , Proteínas do Tecido Nervoso/metabolismo , Neoplasias Ovarianas/diagnóstico , Neoplasias Ovarianas/patologia , Penetrância , Polimorfismo de Nucleotídeo Único , Risco
2.
Nat Commun ; 11(1): 2020, 2020 04 24.
Artigo em Inglês | MEDLINE | ID: mdl-32332753

RESUMO

The functional consequences of somatic non-coding mutations in ovarian cancer (OC) are unknown. To identify regulatory elements (RE) and genes perturbed by acquired non-coding variants, here we establish epigenomic and transcriptomic landscapes of primary OCs using H3K27ac ChIP-seq and RNA-seq, and then integrate these with whole genome sequencing data from 232 OCs. We identify 25 frequently mutated regulatory elements, including an enhancer at 6p22.1 which associates with differential expression of ZSCAN16 (P = 6.6 × 10-4) and ZSCAN12 (P = 0.02). CRISPR/Cas9 knockout of this enhancer induces downregulation of both genes. Globally, there is an enrichment of single nucleotide variants in active binding sites for TEAD4 (P = 6 × 10-11) and its binding partner PAX8 (P = 2×10-10), a known lineage-specific transcription factor in OC. In addition, the collection of cis REs associated with PAX8 comprise the most frequently mutated set of enhancers in OC (P = 0.003). These data indicate that non-coding somatic mutations disrupt the PAX8 transcriptional network during OC development.


Assuntos
Carcinoma Epitelial do Ovário/genética , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes , Neoplasias Ovarianas/genética , Fator de Transcrição PAX8/metabolismo , Adulto , Idoso , Sítios de Ligação/genética , Carcinoma Epitelial do Ovário/patologia , Sequenciamento de Cromatina por Imunoprecipitação , Proteínas de Ligação a DNA/metabolismo , Elementos Facilitadores Genéticos , Epigênese Genética , Epigenômica , Feminino , Técnicas de Inativação de Genes , Humanos , Fatores de Transcrição Kruppel-Like/genética , Pessoa de Meia-Idade , Proteínas Musculares/metabolismo , Mutação , Neoplasias Ovarianas/patologia , Ovário/patologia , Polimorfismo de Nucleotídeo Único , RNA-Seq , Proteínas Repressoras/genética , Fatores de Transcrição/metabolismo , Sequenciamento Completo do Genoma
3.
Cancer Res ; 80(13): 2722-2736, 2020 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-32332020

RESUMO

Gastrointestinal adenocarcinomas (GIAC) of the tubular gastrointestinal (GI) tract including esophagus, stomach, colon, and rectum comprise most GI cancers and share a spectrum of genomic features. However, the unified epigenomic changes specific to GIAC are poorly characterized. Using 907 GIAC samples from The Cancer Genome Atlas, we applied mathematical algorithms to large-scale DNA methylome and transcriptome profiles to reconstruct transcription factor (TF) networks and identify a list of functionally hyperactive master regulator (MR) TF shared across different GIAC. The top candidate HNF4A exhibited prominent genomic and epigenomic activation in a GIAC-specific manner. A complex interplay between the HNF4A promoter and three distal enhancer elements was coordinated by GIAC-specific MRTF including ELF3, GATA4, GATA6, and KLF5. HNF4A also self-regulated its own promoter and enhancers. Functionally, HNF4A promoted cancer proliferation and survival by transcriptional activation of many downstream targets, including HNF1A and factors of interleukin signaling, in a lineage-specific manner. Overall, our study provides new insights into the GIAC-specific gene regulatory networks and identifies potential therapeutic strategies against these common cancers. SIGNIFICANCE: These findings show that GIAC-specific master regulatory transcription factors control HNF4A via three distal enhancers to promote GIAC cell proliferation and survival. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/13/2722/F1.large.jpg.


Assuntos
Adenocarcinoma/patologia , Biomarcadores Tumorais/metabolismo , Epigenômica , Neoplasias Gastrointestinais/patologia , Regulação Neoplásica da Expressão Gênica , Fator 4 Nuclear de Hepatócito/metabolismo , Fatores de Transcrição/metabolismo , Adenocarcinoma/genética , Adenocarcinoma/metabolismo , Animais , Apoptose , Biomarcadores Tumorais/genética , Proliferação de Células , Neoplasias Gastrointestinais/genética , Neoplasias Gastrointestinais/metabolismo , Redes Reguladoras de Genes , Genômica , Fator 4 Nuclear de Hepatócito/genética , Humanos , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Nus , Prognóstico , Regiões Promotoras Genéticas , Taxa de Sobrevida , Fatores de Transcrição/genética , Transcriptoma , Células Tumorais Cultivadas , Ensaios Antitumorais Modelo de Xenoenxerto
4.
Gut ; 69(4): 630-640, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31409603

RESUMO

OBJECTIVE: While oesophageal squamous cell carcinoma remains infrequent in Western populations, the incidence of oesophageal adenocarcinoma (EAC) has increased sixfold to eightfold over the past four decades. We aimed to characterise oesophageal cancer-specific and subtypes-specific gene regulation patterns and their upstream transcription factors (TFs). DESIGN: To identify regulatory elements, we profiled fresh-frozen oesophageal normal samples, tumours and cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematical modelling was performed to establish (super)-enhancers landscapes and interconnected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs were investigated by ChIP-Seq, circularised chromosome conformation capture sequencing and luciferase assay. Biological functions of candidate factors were evaluated both in vitro and in vivo. RESULTS: We found widespread and pervasive alterations of the (super)-enhancer reservoir in both subtypes of oesophageal cancer, leading to transcriptional activation of a myriad of novel oncogenes and signalling pathways, some of which may be exploited pharmacologically (eg, leukemia inhibitory factor (LIF) pathway). Focusing on EAC, we bioinformatically reconstructed and functionally validated an interconnected circuitry formed by four master TFs-ELF3, KLF5, GATA6 and EHF-which promoted each other's expression by interacting with each super-enhancer. Downstream, these master TFs occupied almost all EAC super-enhancers and cooperatively orchestrated EAC transcriptome. Each TF within the transcriptional circuitry was highly and specifically expressed in EAC and functionally promoted EAC cell proliferation and survival. CONCLUSIONS: By establishing cancer-specific and subtype-specific features of the EAC epigenome, our findings promise to transform understanding of the transcriptional dysregulation and addiction of EAC, while providing molecular clues to develop novel therapeutic modalities against this malignancy.


Assuntos
Adenocarcinoma/genética , Neoplasias Esofágicas/genética , Carcinoma de Células Escamosas do Esôfago/genética , Redes Reguladoras de Genes/fisiologia , Fatores de Transcrição/genética , Adenocarcinoma/patologia , Estudos de Casos e Controles , Linhagem Celular Tumoral , Proliferação de Células , Proteínas de Ligação a DNA/genética , Neoplasias Esofágicas/patologia , Carcinoma de Células Escamosas do Esôfago/patologia , Fator de Transcrição GATA6/genética , Humanos , Fatores de Transcrição Kruppel-Like/genética , Proteínas Proto-Oncogênicas c-ets/genética
5.
Cancer Res ; 80(2): 219-233, 2020 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-31551365

RESUMO

ZFP36L1 is a tandem zinc-finger RNA-binding protein that recognizes conserved adenylate-uridylate-rich elements (ARE) located in 3'untranslated regions (UTR) to mediate mRNA decay. We hypothesized that ZFP36L1 is a negative regulator of a posttranscriptional hub involved in mRNA half-life regulation of cancer-related transcripts. Analysis of in silico data revealed that ZFP36L1 was significantly mutated, epigenetically silenced, and downregulated in a variety of cancers. Forced expression of ZFP36L1 in cancer cells markedly reduced cell proliferation in vitro and in vivo, whereas silencing of ZFP36L1 enhanced tumor cell growth. To identify direct downstream targets of ZFP36L1, systematic screening using RNA pull-down of wild-type and mutant ZFP36L1 as well as whole transcriptome sequencing of bladder cancer cells {plus minus} tet-on ZFP36L1 was performed. A network of 1,410 genes was identified as potential direct targets of ZFP36L1. These targets included a number of key oncogenic transcripts such as HIF1A, CCND1, and E2F1. ZFP36L1 specifically bound to the 3'UTRs of these targets for mRNA degradation, thus suppressing their expression. Dual luciferase reporter assays and RNA electrophoretic mobility shift assays showed that wild-type, but not zinc-finger mutant ZFP36L1, bound to HIF1A 3'UTR and mediated HIF1A mRNA degradation, leading to reduced expression of HIF1A and its downstream targets. Collectively, our findings reveal an indispensable role of ZFP36L1 as a posttranscriptional safeguard against aberrant hypoxic signaling and abnormal cell-cycle progression. SIGNIFICANCE: RNA-binding protein ZFP36L1 functions as a tumor suppressor by regulating the mRNA stability of a number of mRNAs involved in hypoxia and cell-cycle signaling.


Assuntos
Neoplasias da Mama/genética , Fator 1 de Resposta a Butirato/metabolismo , Regulação Neoplásica da Expressão Gênica , Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Neoplasias da Bexiga Urinária/genética , Regiões 3' não Traduzidas/genética , Animais , Neoplasias da Mama/mortalidade , Neoplasias da Mama/patologia , Fator 1 de Resposta a Butirato/genética , Carcinogênese/genética , Ciclo Celular/genética , Hipóxia Celular/genética , Linhagem Celular Tumoral , Ciclina D1/genética , Fator de Transcrição E2F1/genética , Epigênese Genética , Feminino , Técnicas de Silenciamento de Genes , Humanos , Camundongos , Mutação , Processamento Pós-Transcricional do RNA , Estabilidade de RNA , RNA Mensageiro/metabolismo , RNA Interferente Pequeno/metabolismo , Neoplasias da Bexiga Urinária/patologia , Ensaios Antitumorais Modelo de Xenoenxerto , Dedos de Zinco/genética
6.
BMC Genomics ; 20(1): 745, 2019 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-31619158

RESUMO

BACKGROUND: The development of next generation sequencing (NGS) methods led to a rapid rise in the generation of large genomic datasets, but the development of user-friendly tools to analyze and visualize these datasets has not developed at the same pace. This presents a two-fold challenge to biologists; the expertise to select an appropriate data analysis pipeline, and the need for bioinformatics or programming skills to apply this pipeline. The development of graphical user interface (GUI) applications hosted on web-based servers such as Shiny can make complex workflows accessible across operating systems and internet browsers to those without programming knowledge. RESULTS: We have developed GENAVi (Gene Expression Normalization Analysis and Visualization) to provide a user-friendly interface for normalization and differential expression analysis (DEA) of human or mouse feature count level RNA-Seq data. GENAVi is a GUI based tool that combines Bioconductor packages in a format for scientists without bioinformatics expertise. We provide a panel of 20 cell lines commonly used for the study of breast and ovarian cancer within GENAVi as a foundation for users to bring their own data to the application. Users can visualize expression across samples, cluster samples based on gene expression or correlation, calculate and plot the results of principal components analysis, perform DEA and gene set enrichment and produce plots for each of these analyses. To allow scalability for large datasets we have provided local install via three methods. We improve on available tools by offering a range of normalization methods and a simple to use interface that provides clear and complete session reporting and for reproducible analysis. CONCLUSION: The development of tools using a GUI makes them practical and accessible to scientists without bioinformatics expertise, or access to a data analyst with relevant skills. While several GUI based tools are currently available for RNA-Seq analysis we improve on these existing tools. This user-friendly application provides a convenient platform for the normalization, analysis and visualization of gene expression data for scientists without bioinformatics expertise.


Assuntos
Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos , Software , Interpretação Estatística de Dados , Visualização de Dados , Internet , Reprodutibilidade dos Testes , Interface Usuário-Computador
7.
Cell Syst ; 9(1): 24-34.e10, 2019 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-31344359

RESUMO

We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)-mRNA and miRNA expression, single nucleotide variants, DNA methylation and copy number alterations-comprehensive sample, gene, and probe-level studies were performed, towards quantifying the degree of similarity between the 'legacy' GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as 'harmonized' by the Genomic Data Commons. We offer gene lists to elucidate differences that remained after controlling for confounders, and strategies to mitigate their impact on biological interpretation. Our results demonstrate that the hg19 and hg38 TCGA datasets are very highly concordant, promote informed use of either legacy or harmonized omics data, and provide a rubric that encourages similar comparisons as new data emerge and reference data evolve.


Assuntos
Genoma/genética , MicroRNAs/genética , Neoplasias/genética , Software , Estudos Controlados Antes e Depois , Conjuntos de Dados como Assunto , Perfilação da Expressão Gênica , Genoma Humano , Genômica , Troca de Informação em Saúde , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Anotação de Sequência Molecular , Reprodutibilidade dos Testes
8.
J Proteome Res ; 18(5): 2270-2278, 2019 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-30990720

RESUMO

Protein citrullination (or deimination), an irreversible post-translational modification, has been implicated in several physiological and pathological processes, including gene expression regulation, apoptosis, rheumatoid arthritis, and Alzheimer's disease. Several research studies have been carried out on citrullination under many conditions. However, until now, challenges in sample preparation and data analysis have made it difficult to confidently identify a citrullinated protein and assign the citrullinated site. To overcome these limitations, we generated a mouse hyper-citrullinated spectral library and set up coordinates to confidently identify and validate citrullinated sites. Using this workflow, we detect a four-fold increase in citrullinated proteome coverage across six mouse organs compared with the current state-of-the art techniques. Our data reveal that the subcellular distribution of citrullinated proteins is tissue-type-dependent and that citrullinated targets are involved in fundamental physiological processes, including the metabolic process. These data represent the first report of a hyper-citrullinated library for the mouse and serve as a central resource for exploring the role of citrullination in this organism.


Assuntos
Citrulina/metabolismo , Redes e Vias Metabólicas/fisiologia , Biblioteca de Peptídeos , Peptídeos/metabolismo , Processamento de Proteína Pós-Traducional , Sequência de Aminoácidos , Animais , Encéfalo/metabolismo , Cromatografia Líquida , Biologia Computacional/métodos , Rim/química , Rim/metabolismo , Fígado/química , Fígado/metabolismo , Pulmão/química , Pulmão/metabolismo , Masculino , Espectrometria de Massas , Camundongos , Camundongos Endogâmicos C57BL , Muramidase/química , Músculo Esquelético/química , Músculo Esquelético/metabolismo , Miocárdio/química , Miocárdio/metabolismo , Especificidade de Órgãos , Peptídeos/química , Desiminases de Arginina em Proteínas/química
9.
Bioinformatics ; 35(11): 1974-1977, 2019 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-30364927

RESUMO

MOTIVATION: DNA methylation has been used to identify functional changes at transcriptional enhancers and other cis-regulatory modules (CRMs) in tumors and other disease tissues. Our R/Bioconductor package ELMER (Enhancer Linking by Methylation/Expression Relationships) provides a systematic approach that reconstructs altered gene regulatory networks (GRNs) by combining enhancer methylation and gene expression data derived from the same sample set. RESULTS: We present a completely revised version 2 of ELMER that provides numerous new features including an optional web-based interface and a new Supervised Analysis mode to use pre-defined sample groupings. We show that Supervised mode significantly increases statistical power and identifies additional GRNs and associated Master Regulators, such as SOX11 and KLF5 in Basal-like breast cancer. AVAILABILITY AND IMPLEMENTATION: ELMER v.2 is available as an R/Bioconductor package at http://bioconductor.org/packages/ELMER/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Redes Reguladoras de Genes , Transcriptoma , Metilação de DNA , Software
10.
Nucleic Acids Res ; 47(3): 1255-1267, 2019 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-30496486

RESUMO

As the second most common malignant bone tumor in children and adolescents, Ewing sarcoma is initiated and exacerbated by a chimeric oncoprotein, most commonly, EWS-FLI1. In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. Through integrative analysis, we identify MEIS1 as a super-enhancer-driven oncogene, which co-operates with EWS-FLI1 in transcriptional regulation, and plays a key pro-survival role in Ewing sarcoma. Moreover, APCDD1, another super-enhancer-associated gene, acting as a downstream target of both MEIS1 and EWS-FLI1, is also characterized as a novel tumor-promoting factor in this malignancy. These data delineate super-enhancer-mediated transcriptional deregulation in Ewing sarcoma, and uncover numerous candidate oncogenes which can be exploited for further understanding of the molecular pathogenesis for this disease.


Assuntos
Peptídeos e Proteínas de Sinalização Intracelular/genética , Proteínas de Membrana/genética , Proteína Meis1/genética , Sarcoma de Ewing/genética , Transcrição Genética , Apoptose/genética , Linhagem Celular Tumoral , Proliferação de Células/genética , Elementos Facilitadores Genéticos , Regulação Neoplásica da Expressão Gênica , Humanos , Motivos de Nucleotídeos/genética , Proteínas de Fusão Oncogênica/genética , Proteína Proto-Oncogênica c-fli-1/genética , Proteína EWS de Ligação a RNA/genética , Sarcoma de Ewing/patologia , Transdução de Sinais/genética
11.
Sci Adv ; 4(12): eaav8550, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30555922

RESUMO

As part of PsychENCODE, we developed a three-dimensional (3D) epigenomic map of primary cultured neuronal cells derived from olfactory neuroepithelium (CNON). We mapped topologically associating domains and high-resolution chromatin interactions using Hi-C and identified regulatory elements using chromatin immunoprecipitation and nucleosome positioning assays. Using epigenomic datasets from biopsies of 63 living individuals, we found that epigenetic marks at distal regulatory elements are more variable than marks at proximal regulatory elements. By integrating genotype and metadata, we identified enhancers that have different levels corresponding to differences in genetic variation, gender, smoking, and schizophrenia. Motif searches revealed that many CNON enhancers are bound by neuronal-related transcription factors. Last, we combined 3D epigenomic maps and gene expression profiles to predict enhancer-target gene interactions on a genome-wide scale. This study not only provides a framework for understanding individual epigenetic variation using a primary cell model system but also contributes valuable data resources for epigenomic studies of neuronal epithelium.


Assuntos
Epigênese Genética , Epigenômica , Regulação da Expressão Gênica , Neurônios Receptores Olfatórios/metabolismo , Sítios de Ligação , Imunoprecipitação da Cromatina , Mapeamento Cromossômico , Biologia Computacional/métodos , Elementos Facilitadores Genéticos , Epigenômica/métodos , Perfilação da Expressão Gênica , Variação Genética , Heterocromatina/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Motivos de Nucleotídeos , Ligação Proteica , Sequências Reguladoras de Ácido Nucleico , Fatores de Transcrição/metabolismo , Transcriptoma , Fluxo de Trabalho
12.
Science ; 362(6413)2018 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-30361341

RESUMO

We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy.


Assuntos
Cromatina/metabolismo , Regulação Neoplásica da Expressão Gênica , Predisposição Genética para Doença , Neoplasias/genética , Neoplasias/metabolismo , Sequências Reguladoras de Ácido Nucleico , Cromatina/genética , Pegada de DNA , Elementos Facilitadores Genéticos , Loci Gênicos , Humanos , Imunidade/genética , Fatores de Transcrição/metabolismo , Transposases/metabolismo
13.
Nat Commun ; 9(1): 3619, 2018 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-30190462

RESUMO

Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that master transcription factors (TFs) TP63 and SOX2 exhibited overlapping genomic occupancy in SCCs. However, functional consequence of their frequent co-localization at super-enhancers remains incompletely understood. Here, epigenomic profilings of different types of SCCs reveal that TP63 and SOX2 cooperatively and lineage-specifically regulate long non-coding RNA (lncRNA) CCAT1 expression, through activation of its super-enhancers and promoter. Silencing of CCAT1 substantially reduces cellular growth both in vitro and in vivo, phenotyping the effect of inhibiting either TP63 or SOX2. ChIRP analysis shows that CCAT1 forms a complex with TP63 and SOX2, which regulates EGFR expression by binding to the super-enhancers of EGFR, thereby activating both MEK/ERK1/2 and PI3K/AKT signaling pathways. These results together identify a SCC-specific DNA/RNA/protein complex which activates TP63/SOX2-CCAT1-EGFR cascade and promotes SCC tumorigenesis, advancing our understanding of transcription dysregulation in cancer biology mediated by master TFs and super-enhancers.


Assuntos
Carcinoma de Células Escamosas/genética , Elementos Facilitadores Genéticos , RNA Longo não Codificante/genética , Fatores de Transcrição SOXB1/genética , Fatores de Transcrição/genética , Proteínas Supressoras de Tumor/genética , Animais , Carcinoma de Células Escamosas/patologia , Linhagem Celular Tumoral , Receptores ErbB/genética , Receptores ErbB/metabolismo , Regulação Neoplásica da Expressão Gênica , Humanos , MAP Quinase Quinase Quinases/genética , MAP Quinase Quinase Quinases/metabolismo , Camundongos Endogâmicos NOD , Fosfatidilinositol 3-Quinases/genética , Fosfatidilinositol 3-Quinases/metabolismo , Regiões Promotoras Genéticas , Proteínas Proto-Oncogênicas c-akt/genética , Proteínas Proto-Oncogênicas c-akt/metabolismo , Fatores de Transcrição SOXB1/metabolismo , Fatores de Transcrição/metabolismo , Proteínas Supressoras de Tumor/metabolismo , Ensaios Antitumorais Modelo de Xenoenxerto
14.
Phys Med Biol ; 63(17): 175006, 2018 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-30101756

RESUMO

Extracting coronary artery calcium (CAC) scores from contrast-enhanced computed tomography (CT) images using dual-energy (DE) based material decomposition has been shown feasible, mainly through patient studies. However, the quantitative performance of such DE-based CAC scores, particularly per stenosis, is underexamined due to lack of reference standard and repeated scans. In this work we conducted a comprehensive quantitative comparative analysis of CAC scores obtained with DE and compare to conventional unenhanced single-energy (SE) CT scans through phantom studies. Synthetic vessels filled with iodinated blood mimicking material and containing calcium stenoses of different sizes and densities were scanned with a third generation dual-source CT scanner in a chest phantom using a DE coronary CT angiography protocol with three exposures/CTDIvol: auto-mAs/8 mGy (automatic exposure), 160 mAs/20 mGy and 260 mAs/34 mGy and 10 repeats. As a control, a set of vessel phantoms without iodine was scanned using a standard SE CAC score protocol (3 mGy). Calcium volume, mass and Agatston scores were estimated for each stenosis. For DE dataset, image-based three-material decomposition was applied to remove iodine before scoring. Performance of DE-based calcium scores were analyzed on a per-stenosis level and compared to SE-based scores. There was excellent correlation between the DE- and SE-based scores (correlation coefficient r: 0.92-0.98). Percent bias for the calcium volume and mass scores varied as a function of stenosis size and density for both modalities. Precision (coefficient of variation) improved with larger and denser stenoses for both DE- and SE-based calcium scores. DE-based scores (20 mGy and 34 mGy) provided comparable per-stenosis precision to SE-based (3 mGy). Our findings suggest that on a per-stenosis level, DE-based CAC scores from contrast-enhanced CT images can achieve comparable quantification performance to conventional SE-based scores. However, DE-based CAC scoring required more dose compared with SE for high per-stenosis precision so some caution is necessary with clinical DE-based CAC scoring.


Assuntos
Angiografia por Tomografia Computadorizada/métodos , Doença da Artéria Coronariana/diagnóstico por imagem , Tomógrafos Computadorizados/normas , Calcificação Vascular/diagnóstico por imagem , Angiografia por Tomografia Computadorizada/instrumentação , Vasos Coronários/diagnóstico por imagem , Humanos , Imagens de Fantasmas , Reprodutibilidade dos Testes
15.
Proc Natl Acad Sci U S A ; 115(22): E5086-E5095, 2018 05 29.
Artigo em Inglês | MEDLINE | ID: mdl-29764999

RESUMO

Competitive BET bromodomain inhibitors (BBIs) targeting BET proteins (BRD2, BRD3, BRD4, and BRDT) show promising preclinical activities against brain cancers. However, the BET protein-dependent glioblastoma (GBM)-promoting transcriptional network remains elusive. Here, with mechanistic exploration of a next-generation chemical degrader of BET proteins (dBET6), we reveal a profound and consistent impact of BET proteins on E2F1- dependent transcriptional program in both differentiated GBM cells and brain tumor-initiating cells. dBET6 treatment drastically reduces BET protein genomic occupancy, RNA-Pol2 activity, and permissive chromatin marks. Subsequently, dBET6 represses the proliferation, self-renewal, and tumorigenic ability of GBM cells. Moreover, dBET6-induced degradation of BET proteins exerts superior antiproliferation effects compared to conventional BBIs and overcomes both intrinsic and acquired resistance to BBIs in GBM cells. Our study reveals crucial functions of BET proteins and provides the rationale and therapeutic merits of targeted degradation of BET proteins in GBM.


Assuntos
Antineoplásicos/farmacologia , Fator de Transcrição E2F1 , Glioblastoma , Proteínas Serina-Treonina Quinases , Proteínas de Ligação a RNA , Proteínas de Ciclo Celular , Linhagem Celular Tumoral , Sistemas de Liberação de Medicamentos , Fator de Transcrição E2F1/antagonistas & inibidores , Fator de Transcrição E2F1/metabolismo , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Glioblastoma/metabolismo , Glioblastoma/patologia , Humanos , Proteínas Nucleares/antagonistas & inibidores , Proteínas Nucleares/metabolismo , Domínios Proteicos , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas de Ligação a RNA/antagonistas & inibidores , Proteínas de Ligação a RNA/metabolismo , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/metabolismo
16.
Sci Rep ; 8(1): 6294, 2018 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-29662153

RESUMO

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

17.
Nat Genet ; 50(4): 591-602, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29610480

RESUMO

DNA methylation loss occurs frequently in cancer genomes, primarily within lamina-associated, late-replicating regions termed partially methylated domains (PMDs). We profiled 39 diverse primary tumors and 8 matched adjacent tissues using whole-genome bisulfite sequencing (WGBS) and analyzed them alongside 343 additional human and 206 mouse WGBS datasets. We identified a local CpG sequence context associated with preferential hypomethylation in PMDs. Analysis of CpGs in this context ('solo-WCGWs') identified previously undetected PMD hypomethylation in almost all healthy tissue types. PMD hypomethylation increased with age, beginning during fetal development, and appeared to track the accumulation of cell divisions. In cancer, PMD hypomethylation depth correlated with somatic mutation density and cell cycle gene expression, consistent with its reflection of mitotic history and suggesting its application as a mitotic clock. We propose that late replication leads to lifelong progressive methylation loss, which acts as a biomarker for cellular aging and which may contribute to oncogenesis.


Assuntos
Divisão Celular/genética , Metilação de DNA , Envelhecimento/genética , Envelhecimento/metabolismo , Animais , Ilhas de CpG , Replicação do DNA , DNA de Neoplasias/genética , DNA de Neoplasias/metabolismo , Desenvolvimento Embrionário/genética , Feminino , Humanos , Masculino , Camundongos , Mitose/genética , Neoplasias/genética , Neoplasias/metabolismo , Gravidez , Sequenciamento Completo do Genoma
18.
Sci Rep ; 8(1): 4505, 2018 03 14.
Artigo em Inglês | MEDLINE | ID: mdl-29540744

RESUMO

Interstitial cystitis (IC) is a chronic urinary tract disease that is characterized by unpleasant sensations, such as persistent pelvic pain, in the absence of infection or other identifiable causes. We previously performed comprehensive metabolomics profiling of urine samples from IC patients using nuclear magnetic resonance and gas-chromatography/mass spectrometry and found that urinary α-oxoglutarate (α-OG), was significantly elevated. α-OG, a tricarboxylic acid (TCA) cycle intermediate, reportedly functions to suppress the proliferation of immortalized normal human bladder epithelial cells. Here, we identified AT-rich interactive domain 1 A (ARID1A), a key chromatin remodeler, as being hypomethylated and upregulated by α-OG treatment. This was done through EPIC DNA methylation profiling and subsequent biochemical approaches, including quantitative RT-PCR and western blot analyses. Furthermore, we found that α-OG almost completely suppresses ten-eleven translocation (TET) activity, but does not affect DNA methyltransferase (DNMT) activity. Altogether, our studies reveal the potential role of α-OG in epigenetic remodeling through its effects on ARID1A and TET expression in the bladder. This may provide a new possible therapeutic strategy in treating IC.

19.
Gut ; 67(10): 1769-1779, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-28860350

RESUMO

OBJECTIVES: Oesophageal squamous cell carcinoma (OSCC) and adenocarcinoma (OAC) are distinct cancers in terms of a number of clinical and epidemiological characteristics, complicating the design of clinical trials and biomarker developments. We analysed 1048 oesophageal tumour-germline pairs from both subtypes, to characterise their genomic features, and biological and clinical significance. DESIGN: Previously exome-sequenced samples were re-analysed to identify significantly mutated genes (SMGs) and mutational signatures. The biological functions of novel SMGs were investigated using cell line and xenograft models. We further performed whole-genome bisulfite sequencing and chromatin immunoprecipitation (ChIP)-seq to characterise epigenetic alterations. RESULTS: OSCC and OAC displayed nearly mutually exclusive sets of driver genes, indicating that they follow independent developmental paths. The combined sample size allowed the statistical identification of a number of novel subtype-specific SMGs, mutational signatures and prognostic biomarkers. Particularly, we identified a novel mutational signature similar to Catalogue Of Somatic Mutations In Cancer (COSMIC)signature 16, which has prognostic value in OSCC. Two newly discovered SMGs, CUL3 and ZFP36L2, were validated as important tumour-suppressors specific to the OSCC subtype. We further identified their additional loss-of-function mechanisms. CUL3 was homozygously deleted specifically in OSCC and other squamous cell cancers (SCCs). Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; DNA hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancer-associated SCC suppressor. CONCLUSIONS: These data comprehensively contrast differences between OSCC and OAC at both genomic and epigenomic levels, and reveal novel molecular features for further delineating the pathophysiological mechanisms and treatment strategies for these cancers.


Assuntos
Adenocarcinoma/genética , Carcinoma de Células Escamosas/genética , Proteínas Culina/genética , Neoplasias Esofágicas/genética , Fatores de Transcrição/genética , Adenocarcinoma/patologia , Animais , Carcinoma de Células Escamosas/patologia , Linhagem Celular Tumoral , Proliferação de Células/genética , Metilação de DNA , Neoplasias Esofágicas/patologia , Carcinoma de Células Escamosas do Esôfago , Humanos , Mutação com Perda de Função , Prognóstico
20.
Immunity ; 47(5): 890-902.e4, 2017 11 21.
Artigo em Inglês | MEDLINE | ID: mdl-29166589

RESUMO

Granulocyte-monocyte progenitors (GMPs) and monocyte-dendritic cell progenitors (MDPs) produce monocytes during homeostasis and in response to increased demand during infection. Both progenitor populations are thought to derive from common myeloid progenitors (CMPs), and a hierarchical relationship (CMP-GMP-MDP-monocyte) is presumed to underlie monocyte differentiation. Here, however, we demonstrate that mouse MDPs arose from CMPs independently of GMPs, and that GMPs and MDPs produced monocytes via similar but distinct monocyte-committed progenitors. GMPs and MDPs yielded classical (Ly6Chi) monocytes with gene expression signatures that were defined by their origins and impacted their function. GMPs produced a subset of "neutrophil-like" monocytes, whereas MDPs gave rise to a subset of monocytes that yielded monocyte-derived dendritic cells. GMPs and MDPs were also independently mobilized to produce specific combinations of myeloid cell types following the injection of microbial components. Thus, the balance of GMP and MDP differentiation shapes the myeloid cell repertoire during homeostasis and following infection.


Assuntos
Células Dendríticas/fisiologia , Células Precursoras de Granulócitos/fisiologia , Monócitos/fisiologia , Células Progenitoras Mieloides/fisiologia , Animais , Antígenos Ly/análise , Diferenciação Celular , Leucossialina/análise , Camundongos , Análise de Sequência de RNA , Transcriptoma
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