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1.
PLoS Comput Biol ; 16(11): e1008332, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33166276

RESUMO

The tumor mutational burden (TMB) is increasingly recognized as an emerging biomarker that predicts improved outcomes or response to immune checkpoint inhibitors in cancer. A multitude of technical and biological factors make it difficult to compare TMB values across platforms, histologies, and treatments. Here, we present a mechanistic model that explains the association between panel size, histology, and TMB threshold with panel performance and survival outcome and demonstrate the limitations of existing methods utilized to harmonize TMB across platforms.

2.
Accid Anal Prev ; 148: 105799, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33080377

RESUMO

Pedestrian protection is an important component of road safety. Intersections are dangerous locations for pedestrians with mixed traffic. This paper aims to predict potential traffic conflicts between pedestrians and vehicles at signalized intersections. Using detection and tracking techniques in computer vision, pedestrians' and vehicles' features are extracted from video data. An LSTM (Long Short-term Memory) neural network is proposed to predict the pedestrian-vehicle conflicts 2 s ahead. The established model reaches an accuracy of 88.5 % at one signalized intersection. It is further tested at a new intersection, reaching the accuracy of 84.9 %, while the new data merely takes up 30 % of the training data set. This indicates that the proposed model is promising to be implemented at different locations. Moreover, the proposed model can also be applied to develop collision warning systems under the Connected Vehicles' environment.

3.
Accid Anal Prev ; 148: 105844, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33125922

RESUMO

Pedestrian safety plays an important role in the transportation system. Intersections are dangerous locations for pedestrians with mixed traffic. This paper aims to predict the near-accident events between pedestrians and vehicles at signalized intersections using PET (Post Encroachment Time) and TTC (Time to Collision). With automated computer vision techniques, mobility features of pedestrians and vehicles are generated. Extreme Value Theory (EVT) is used to model PET and minimum TTC values to select the most appropriate threshold values to label pedestrians' near-accident events. A Gated Recurrent Unit (GRU) neural network is further used to predict these events. The established model reaches an AUC (Area Under the Curve) value of 0.865 on the test data set. Moreover, the proposed model can also be applied to develop collision warning systems under the Connected Vehicle environment.

4.
Clin Cancer Res ; 24(22): 5673-5684, 2018 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-29784674

RESUMO

Purpose: High-risk neuroblastoma is an aggressive disease. DNA sequencing studies have revealed a paucity of actionable genomic alterations and a low mutation burden, posing challenges to develop effective novel therapies. We used RNA sequencing (RNA-seq) to investigate the biology of this disease, including a focus on tumor-infiltrating lymphocytes (TIL).Experimental Design: We performed deep RNA-seq on pretreatment diagnostic tumors from 129 high-risk and 21 low- or intermediate-risk patients with neuroblastomas. We used single-sample gene set enrichment analysis to detect gene expression signatures of TILs in tumors and examined their association with clinical and molecular parameters, including patient outcome. The expression profiles of 190 additional pretreatment diagnostic neuroblastomas, a neuroblastoma tissue microarray, and T-cell receptor (TCR) sequencing were used to validate our findings.Results: We found that MYCN-not-amplified (MYCN-NA) tumors had significantly higher cytotoxic TIL signatures compared with MYCN-amplified (MYCN-A) tumors. A reported MYCN activation signature was significantly associated with poor outcome for high-risk patients with MYCN-NA tumors; however, a subgroup of these patients who had elevated activated natural killer (NK) cells, CD8+ T cells, and cytolytic signatures showed improved outcome and expansion of infiltrating TCR clones. Furthermore, we observed upregulation of immune exhaustion marker genes, indicating an immune-suppressive microenvironment in these neuroblastomas.Conclusions: This study provides evidence that RNA signatures of cytotoxic TIL are associated with the presence of activated NK/T cells and improved outcomes in high-risk neuroblastoma patients harboring MYCN-NA tumors. Our findings suggest that these high-risk patients with MYCN-NA neuroblastoma may benefit from additional immunotherapies incorporated into the current therapeutic strategies. Clin Cancer Res; 24(22); 5673-84. ©2018 AACR.


Assuntos
Citotoxicidade Imunológica/genética , Proteína Proto-Oncogênica N-Myc/genética , Neuroblastoma/genética , Neuroblastoma/imunologia , Receptores de Antígenos de Linfócitos T/genética , Linfócitos T/imunologia , Linfócitos T/metabolismo , Linhagem Celular Tumoral , Pré-Escolar , Biologia Computacional/métodos , Amplificação de Genes , Regulação Neoplásica da Expressão Gênica , Humanos , Lactente , Recém-Nascido , Estadiamento de Neoplasias , Neuroblastoma/patologia , Transcriptoma
5.
Pigment Cell Melanoma Res ; 31(1): 73-81, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28786531

RESUMO

To determine the feasibility of liquid biopsy for monitoring of patients with advanced melanoma, cell-free DNA was extracted from plasma for 25 Stage III/IV patients, most (84.0%) having received previous therapy. DNA concentrations ranged from 0.6 to 390.0 ng/ml (median = 7.8 ng/ml) and were positively correlated with tumor burden as measured by imaging (Spearman rho = 0.5435, p = .0363). Using ultra-deep sequencing for a 61-gene panel, one or more mutations were detected in 12 of 25 samples (48.0%), and this proportion did not vary significantly for patients on or off therapy at the time of blood draw (52.9% and 37.5% respectively; p = .673). Sixteen mutations were detected in eight different genes, with the most frequent mutations detected in BRAF, NRAS, and KIT. Allele fractions ranged from 1.1% to 63.2% (median = 29.1%). Among patients with tissue next-generation sequencing, nine of 11 plasma mutations were also detected in matched tissue, for a concordance of 81.8%.


Assuntos
Biomarcadores Tumorais/genética , Ácidos Nucleicos Livres/genética , Melanoma/diagnóstico , Mutação , Neoplasias Cutâneas/diagnóstico , Biomarcadores Tumorais/sangue , Ácidos Nucleicos Livres/sangue , Estudos de Viabilidade , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Melanoma/sangue , Melanoma/genética , Pessoa de Meia-Idade , Projetos Piloto , Neoplasias Cutâneas/sangue , Neoplasias Cutâneas/genética
6.
Clin Cancer Res ; 23(18): 5648-5656, 2017 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-28536309

RESUMO

Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy.Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care.Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did (P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF (P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03).Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR.


Assuntos
Biomarcadores Tumorais , DNA Tumoral Circulante , Sequenciamento de Nucleotídeos em Larga Escala , Neoplasias/diagnóstico , Neoplasias/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Testes Genéticos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequenciamento de Nucleotídeos em Larga Escala/normas , Humanos , Masculino , Pessoa de Meia-Idade , Mutação , Neoplasias/mortalidade , Prognóstico , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
7.
Clin Cancer Res ; 22(15): 3810-20, 2016 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-26994145

RESUMO

PURPOSE: We undertook a multidimensional clinical genomics study of children and adolescent young adults with relapsed and refractory cancers to determine the feasibility of genome-guided precision therapy. EXPERIMENTAL DESIGN: Patients with non-central nervous system solid tumors underwent a combination of whole exome sequencing (WES), whole transcriptome sequencing (WTS), and high-density single-nucleotide polymorphism array analysis of the tumor, with WES of matched germline DNA. Clinically actionable alterations were identified as a reportable germline mutation, a diagnosis change, or a somatic event (including a single nucleotide variant, an indel, an amplification, a deletion, or a fusion gene), which could be targeted with drugs in existing clinical trials or with FDA-approved drugs. RESULTS: Fifty-nine patients in 20 diagnostic categories were enrolled from 2010 to 2014. Ages ranged from 7 months to 25 years old. Seventy-three percent of the patients had prior chemotherapy, and the tumors from these patients with relapsed or refractory cancers had a higher mutational burden than that reported in the literature. Thirty patients (51% of total) had clinically actionable mutations, of which 24 (41%) had a mutation that was currently targetable in a clinical trial setting, 4 patients (7%) had a change in diagnosis, and 7 patients (12%) had a reportable germline mutation. CONCLUSIONS: We found a remarkably high number of clinically actionable mutations in 51% of the patients, and 12% with significant germline mutations. We demonstrated the clinical feasibility of next-generation sequencing in a diverse population of relapsed and refractory pediatric solid tumors. Clin Cancer Res; 22(15); 3810-20. ©2016 AACR.


Assuntos
Genômica , Neoplasias/genética , Neoplasias/terapia , Medicina de Precisão , Adolescente , Adulto , Biomarcadores Tumorais , Criança , Pré-Escolar , Resistencia a Medicamentos Antineoplásicos , Feminino , Genômica/métodos , Mutação em Linhagem Germinativa , Humanos , Lactente , Masculino , Terapia de Alvo Molecular , Mutação , Neoplasias/diagnóstico , Polimorfismo de Nucleotídeo Único , Medicina de Precisão/métodos , Recidiva , Sequenciamento Completo do Exoma , Adulto Jovem
8.
Cancer Lett ; 371(2): 214-24, 2016 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-26683771

RESUMO

The molecular mechanisms underlying the aggressive behavior of MYCN driven neuroblastoma (NBL) is under intense investigation; however, little is known about the impact of this family of transcription factors on the splicing program. Here we used high-throughput RNA sequencing to systematically study the expression of RNA isoforms in stage 4 MYCN-amplified NBL, an aggressive subtype of metastatic NBL. We show that MYCN-amplified NBL tumors display a distinct gene splicing pattern affecting multiple cancer hallmark functions. Six splicing factors displayed unique differential expression patterns in MYCN-amplified tumors and cell lines, and the binding motifs for some of these splicing factors are significantly enriched in differentially-spliced genes. Direct binding of MYCN to promoter regions of the splicing factors PTBP1 and HNRNPA1 detected by ChIP-seq demonstrates that MYCN controls the splicing pattern by direct regulation of the expression of these key splicing factors. Furthermore, high expression of PTBP1 and HNRNPA1 was significantly associated with poor overall survival of stage4 NBL patients (p ≤ 0.05). Knocking down PTBP1, HNRNPA1 and their downstream target PKM2, an isoform of pro-tumor-growth, result in repressed growth of NBL cells. Therefore, our study reveals a novel role of MYCN in controlling global splicing program through regulation of splicing factors in addition to its well-known role in the transcription program. These findings suggest a therapeutically potential to target the key splicing factors or gene isoforms in high-risk NBL with MYCN-amplification.


Assuntos
Processamento Alternativo , Biomarcadores Tumorais/genética , Neuroblastoma/genética , Proteínas Nucleares/genética , Proteínas Oncogênicas/genética , RNA Neoplásico/genética , Sítios de Ligação , Biomarcadores Tumorais/metabolismo , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Linhagem Celular Tumoral , Proliferação de Células , Imunoprecipitação da Cromatina , Amplificação de Genes , Regulação Neoplásica da Expressão Gênica , Ribonucleoproteína Nuclear Heterogênea A1 , Ribonucleoproteínas Nucleares Heterogêneas Grupo A-B/genética , Ribonucleoproteínas Nucleares Heterogêneas Grupo A-B/metabolismo , Ribonucleoproteínas Nucleares Heterogêneas/genética , Ribonucleoproteínas Nucleares Heterogêneas/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Proteína Proto-Oncogênica N-Myc , Estadiamento de Neoplasias , Neuroblastoma/metabolismo , Neuroblastoma/mortalidade , Proteínas Nucleares/metabolismo , Proteínas Oncogênicas/metabolismo , Proteína de Ligação a Regiões Ricas em Polipirimidinas/genética , Proteína de Ligação a Regiões Ricas em Polipirimidinas/metabolismo , Regiões Promotoras Genéticas , Interferência de RNA , RNA Neoplásico/metabolismo , Fatores de Risco , Hormônios Tireóideos/genética , Hormônios Tireóideos/metabolismo , Transcrição Genética , Transfecção
9.
Nature ; 528(7582): 418-21, 2015 Dec 17.
Artigo em Inglês | MEDLINE | ID: mdl-26560027

RESUMO

Neuroblastoma is a paediatric malignancy that typically arises in early childhood, and is derived from the developing sympathetic nervous system. Clinical phenotypes range from localized tumours with excellent outcomes to widely metastatic disease in which long-term survival is approximately 40% despite intensive therapy. A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility and oncogenic addiction to LMO1 in the tumour cells. Here we investigate the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation and transcription factor binding sites. We show that SNP rs2168101 G>T is the most highly associated variant (combined P = 7.47 × 10(-29), odds ratio 0.65, 95% confidence interval 0.60-0.70), and resides in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G allele that is associated with tumour formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P = 0.028) in neuroblastoma primary tumours, and ablates GATA3 binding (P < 0.0001). We demonstrate allelic imbalance favouring the G-containing strand in tumours heterozygous for this SNP, as demonstrated both by RNA sequencing (P < 0.0001) and reporter assays (P = 0.002). These findings indicate that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumour cells.


Assuntos
Proteínas de Ligação a DNA/genética , Elementos Facilitadores Genéticos/genética , Predisposição Genética para Doença/genética , Proteínas com Domínio LIM/genética , Neuroblastoma/genética , Polimorfismo de Nucleotídeo Único/genética , Fatores de Transcrição/genética , Acetilação , Alelos , Desequilíbrio Alélico , Sítios de Ligação , Epigenômica , Fator de Transcrição GATA3/metabolismo , Regulação Neoplásica da Expressão Gênica/genética , Estudo de Associação Genômica Ampla , Genótipo , Histonas/química , Histonas/metabolismo , Humanos , Íntrons/genética , Lisina/metabolismo , Especificidade de Órgãos , Reprodutibilidade dos Testes
10.
Oncotarget ; 6(34): 35247-62, 2015 Nov 03.
Artigo em Inglês | MEDLINE | ID: mdl-26497213

RESUMO

Despite advances in multimodal treatment, neuroblastoma (NB) is often fatal for children with high-risk disease and many survivors need to cope with long-term side effects from high-dose chemotherapy and radiation. To identify new therapeutic targets, we performed an siRNA screen of the druggable genome combined with a small molecule screen of 465 compounds targeting 39 different mechanisms of actions in four NB cell lines. We identified 58 genes as targets, including AURKB, in at least one cell line. In the drug screen, aurora kinase inhibitors (nine molecules) and in particular the AURKB-selective compound, barasertib, were the most discriminatory with regard to sensitivity for MYCN-amplified cell lines. In an expanded panel of ten NB cell lines, those with MYCN-amplification and wild-type TP53 were the most sensitive to low nanomolar concentrations of barasertib. Inhibition of the AURKB kinase activity resulted in decreased phosphorylation of the known target, histone H3, and upregulation of TP53 in MYCN-amplified, TP53 wild-type cells. However, both wild-type and TP53 mutant MYCN-amplified cell lines arrested in G2/M phase upon AURKB inhibition. Additionally, barasertib induced endoreduplication and apoptosis. Treatment of MYCN-amplified/TP53 wild-type neuroblastoma xenografts resulted in profound growth inhibition and tumor regression. Therefore, aurora B kinase inhibition is highly effective in aggressive neuroblastoma and warrants further investigation in clinical trials.


Assuntos
Aurora Quinase B/antagonistas & inibidores , Neuroblastoma/enzimologia , Neuroblastoma/terapia , Animais , Apoptose/fisiologia , Aurora Quinase B/genética , Aurora Quinase B/metabolismo , Linhagem Celular Tumoral , Feminino , Técnicas de Silenciamento de Genes , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Camundongos , Camundongos Endogâmicos NOD , Camundongos SCID , Terapia de Alvo Molecular , Neuroblastoma/genética , Neuroblastoma/metabolismo , Inibidores de Proteínas Quinases/farmacologia , Interferência de RNA , Bibliotecas de Moléculas Pequenas/farmacologia , Ensaios Antitumorais Modelo de Xenoenxerto
11.
PLoS One ; 10(8): e0135583, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26295157

RESUMO

BACKGROUND: An important attribute of the traditional impact factor was the controversial 2-year citation window. So far, several scholars have proposed using different citation time windows for evaluating journals. However, there is no confirmation whether a longer citation time window would be better. How did the journal evaluation effects of 3IF, 4IF, and 6IF comparing with 2IF and 5IF? In order to understand these questions, we made a comparative study of impact factors with different citation time windows with the peer-reviewed scores of ophthalmologic journals indexed by Science Citation Index Expanded (SCIE) database. METHODS: The peer-reviewed scores of 28 ophthalmologic journals were obtained through a self-designed survey questionnaire. Impact factors with different citation time windows (including 2IF, 3IF, 4IF, 5IF, and 6IF) of 28 ophthalmologic journals were computed and compared in accordance with each impact factor's definition and formula, using the citation analysis function of the Web of Science (WoS) database. An analysis of the correlation between impact factors with different citation time windows and peer-reviewed scores was carried out. RESULTS: Although impact factor values with different citation time windows were different, there was a high level of correlation between them when it came to evaluating journals. In the current study, for ophthalmologic journals' impact factors with different time windows in 2013, 3IF and 4IF seemed the ideal ranges for comparison, when assessed in relation to peer-reviewed scores. In addition, the 3-year and 4-year windows were quite consistent with the cited peak age of documents published by ophthalmologic journals. RESEARCH LIMITATIONS: Our study is based on ophthalmology journals and we only analyze the impact factors with different citation time window in 2013, so it has yet to be ascertained whether other disciplines (especially those with a later cited peak) or other years would follow the same or similar patterns. ORIGINALITY/ VALUE: We designed the survey questionnaire ourselves, specifically to assess the real influence of journals. We used peer-reviewed scores to judge the journal evaluation effect of impact factors with different citation time windows. The main purpose of this study was to help researchers better understand the role of impact factors with different citation time windows in journal evaluation.


Assuntos
Bibliometria , Fator de Impacto de Revistas , Oftalmologia , Bases de Dados Bibliográficas , Humanos , Revisão da Pesquisa por Pares , Publicações Periódicas como Assunto , Projetos de Pesquisa , Inquéritos e Questionários , Fatores de Tempo
12.
Opt Express ; 23(14): 17805-14, 2015 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-26191842

RESUMO

Terahertz (THz) time domain spectroscopy (THz-TDS) of a CoCr2O4 single crystal has been performed under magnetic fields up to 8 Tesla. The magnetic field dependences of inter-sublattice exchange resonance at different temperatures have been investigated. Benefiting from the phase and polarization sensitive detection technique in THz-TDS, the circular absorption dichroism and Faraday ellipticity in the THz frequency region are observed and are found to be tunable by the external magnetic field. The complex indices of refraction are obtained under different magnetic field, which present distinct rotatory dispersions arising from the exchange magnetic resonance.

13.
Nat Genet ; 47(8): 864-71, 2015 08.
Artigo em Inglês | MEDLINE | ID: mdl-26121087

RESUMO

The majority of patients with neuroblastoma have tumors that initially respond to chemotherapy, but a large proportion will experience therapy-resistant relapses. The molecular basis of this aggressive phenotype is unknown. Whole-genome sequencing of 23 paired diagnostic and relapse neuroblastomas showed clonal evolution from the diagnostic tumor, with a median of 29 somatic mutations unique to the relapse sample. Eighteen of the 23 relapse tumors (78%) showed mutations predicted to activate the RAS-MAPK pathway. Seven of these events were detected only in the relapse tumor, whereas the others showed clonal enrichment. In neuroblastoma cell lines, we also detected a high frequency of activating mutations in the RAS-MAPK pathway (11/18; 61%), and these lesions predicted sensitivity to MEK inhibition in vitro and in vivo. Our findings provide a rationale for genetic characterization of relapse neuroblastomas and show that RAS-MAPK pathway mutations may function as a biomarker for new therapeutic approaches to refractory disease.


Assuntos
Sistema de Sinalização das MAP Quinases/genética , Proteínas Quinases Ativadas por Mitógeno/genética , Mutação , Recidiva Local de Neoplasia/genética , Neuroblastoma/genética , Proteínas ras/genética , Quinase do Linfoma Anaplásico , Animais , Benzimidazóis/farmacologia , Western Blotting , Linhagem Celular Tumoral , Criança , Pré-Escolar , Aberrações Cromossômicas , Inibidor p16 de Quinase Dependente de Ciclina/genética , Inibidor p16 de Quinase Dependente de Ciclina/metabolismo , Feminino , Regulação Neoplásica da Expressão Gênica , Células HEK293 , Humanos , Lactente , Masculino , Camundongos SCID , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Neuroblastoma/tratamento farmacológico , Neuroblastoma/patologia , Fosforilação/efeitos dos fármacos , Receptores Proteína Tirosina Quinases/genética , Receptores Proteína Tirosina Quinases/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Ensaios Antitumorais Modelo de Xenoenxerto , Proteínas ras/metabolismo
14.
Cancer Res ; 75(15): 3155-66, 2015 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-26100672

RESUMO

Chromosome 6p22 was identified recently as a neuroblastoma susceptibility locus, but its mechanistic contributions to tumorigenesis are as yet undefined. Here we report that the most highly significant single-nucleotide polymorphism (SNP) associations reside within CASC15, a long noncoding RNA that we define as a tumor suppressor at 6p22. Low-level expression of a short CASC15 isoform (CASC15-S) associated highly with advanced neuroblastoma and poor patient survival. In human neuroblastoma cells, attenuating CASC15-S increased cellular growth and migratory capacity. Gene expression analysis revealed downregulation of neuroblastoma-specific markers in cells with attenuated CASC15-S, with concomitant increases in cell adhesion and extracellular matrix transcripts. Altogether, our results point to CASC15-S as a mediator of neural growth and differentiation, which impacts neuroblastoma initiation and progression.


Assuntos
Cromossomos Humanos Par 6/genética , Genes Supressores de Tumor , Neuroblastoma/genética , Polimorfismo de Nucleotídeo Único , RNA Longo não Codificante/genética , Diferenciação Celular/genética , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Neuroblastoma/mortalidade , Neuroblastoma/patologia , Reprodutibilidade dos Testes
15.
Cancer Discov ; 5(4): 380-95, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25637275

RESUMO

UNLABELLED: Regulation of mRNA splicing, a critical and tightly regulated cellular function, underlies the majority of proteomic diversity and is frequently disrupted in disease. Using an integrative genomics approach, we combined both genomic data and exon-level transcriptome data in two somatic tissues (cerebella and peripheral ganglia) from a transgenic mouse model of neuroblastoma, a tumor that arises from the peripheral neural crest. Here, we describe splicing quantitative trait loci associated with differential splicing across the genome that we use to identify genes with previously unknown functions within the splicing pathway and to define de novo intronic splicing motifs that influence splicing from hundreds of bases away. Our results show that these splicing motifs represent sites for functional recurrent mutations and highlight novel candidate genes in human cancers, including childhood neuroblastoma. SIGNIFICANCE: Somatic mutations with predictable downstream effects are largely relegated to coding regions, which comprise less than 2% of the human genome. Using an unbiased in vivo analysis of a mouse model of neuroblastoma, we have identified intronic splicing motifs that translate into sites for recurrent somatic mutations in human cancers.


Assuntos
Regulação Neoplásica da Expressão Gênica , Neuroblastoma/genética , Processamento de RNA , Processamento Alternativo , Animais , Cerebelo/metabolismo , Modelos Animais de Doenças , Epistasia Genética , Éxons , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Genômica , Íntrons , Camundongos , Mutação , Neuroblastoma/metabolismo , Motivos de Nucleotídeos , Locos de Características Quantitativas , Isoformas de RNA , Especificidade da Espécie , Gânglio Cervical Superior/metabolismo
16.
Sci Rep ; 4: 4284, 2014 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-24594662

RESUMO

We report a new mechanism for the enhancement of porous-ZnO surface photovoltage (SPV) response to polychlorinated biphenyls (PCBs, a notorious class of persistent organic pollutants as global environmental hazard) based on copper phthalocyanine (CuPc) chemisorptive bonding on porous-ZnO. A new ZnO-CuPc composite is formed on the porous-ZnO surface due to the interaction between the surface ZnO and CuPc, with its valence band (VB) energy level being higher than that of the pristine porous-ZnO. So that the efficiency of the photogenerated-electron transfer from the composite VB to the adjacent ZnO's surface states is drastically increased due to the reduced energy gap between the transition states. As a result, the sensitivity of the PCB-orientated SPV sensor is much improved by showing amplified variation of the SPV-signals perturbed by PCBs adsorbed on the ZnO-CuPc@porous-ZnO sensitive material.

17.
Cancer Discov ; 4(2): 216-31, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24436047

RESUMO

UNLABELLED: Despite gains in survival, outcomes for patients with metastatic or recurrent rhabdomyosarcoma remain dismal. In a collaboration between the National Cancer Institute, Children's Oncology Group, and Broad Institute, we performed whole-genome, whole-exome, and transcriptome sequencing to characterize the landscape of somatic alterations in 147 tumor/normal pairs. Two genotypes are evident in rhabdomyosarcoma tumors: those characterized by the PAX3 or PAX7 fusion and those that lack these fusions but harbor mutations in key signaling pathways. The overall burden of somatic mutations in rhabdomyosarcoma is relatively low, especially in tumors that harbor a PAX3/7 gene fusion. In addition to previously reported mutations in NRAS, KRAS, HRAS, FGFR4, PIK3CA, and CTNNB1, we found novel recurrent mutations in FBXW7 and BCOR, providing potential new avenues for therapeutic intervention. Furthermore, alteration of the receptor tyrosine kinase/RAS/PIK3CA axis affects 93% of cases, providing a framework for genomics-directed therapies that might improve outcomes for patients with rhabdomyosarcoma. SIGNIFICANCE: This is the most comprehensive genomic analysis of rhabdomyosarcoma to date. Despite a relatively low mutation rate, multiple genes were recurrently altered, including NRAS, KRAS, HRAS, FGFR4, PIK3CA, CTNNB1, FBXW7, and BCOR. In addition, a majority of rhabdomyosarcoma tumors alter the receptor tyrosine kinase/RAS/PIK3CA axis, providing an opportunity for genomics-guided intervention.


Assuntos
Genômica , Proteínas de Fusão Oncogênica/genética , Rabdomiossarcoma/genética , Animais , Proteínas de Ciclo Celular/genética , Aberrações Cromossômicas , Classe I de Fosfatidilinositol 3-Quinases , Análise por Conglomerados , Variações do Número de Cópias de DNA , Exoma , Regulação Neoplásica da Expressão Gênica , Rearranjo Gênico , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Camundongos , Mutação , Proteínas de Fusão Oncogênica/metabolismo , Fatores de Transcrição Box Pareados/genética , Fatores de Transcrição Box Pareados/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Proteínas Proto-Oncogênicas p21(ras)/metabolismo , Receptores de Fatores de Crescimento de Fibroblastos/metabolismo , Rabdomiossarcoma/metabolismo , Transdução de Sinais
18.
Thorax ; 67(2): 122-31, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21940491

RESUMO

BACKGROUND: The mechanisms underlying chronic obstructive pulmonary disease (COPD) remain unclear. MicroRNAs (miRNAs or miRs) are small non-coding RNA molecules that modulate the levels of specific genes and proteins. Identifying expression patterns of miRNAs in COPD may enhance our understanding of the mechanisms of disease. A study was undertaken to determine if miRNAs are differentially expressed in the lungs of smokers with and without COPD. miRNA and mRNA expression were compared to enrich for biological networks relevant to the pathogenesis of COPD. METHODS: Lung tissue from smokers with no evidence of obstructive lung disease (n=9) and smokers with COPD (n=26) was examined for miRNA and mRNA expression followed by validation. We then examined both miRNA and mRNA expression to enrich for relevant biological pathways. RESULTS: 70 miRNAs and 2667 mRNAs were differentially expressed between lung tissue from subjects with COPD and smokers without COPD. miRNA and mRNA expression profiles enriched for biological pathways that may be relevant to the pathogenesis of COPD including the transforming growth factor ß, Wnt and focal adhesion pathways. miR-223 and miR-1274a were the most affected miRNAs in subjects with COPD compared with smokers without obstruction. miR-15b was increased in COPD samples compared with smokers without obstruction and localised to both areas of emphysema and fibrosis. miR-15b was differentially expressed within GOLD classes of COPD. Expression of SMAD7, which was validated as a target for miR-15b, was decreased in bronchial epithelial cells in COPD. CONCLUSIONS: miRNA and mRNA are differentially expressed in individuals with COPD compared with smokers without obstruction. Investigating these relationships may further our understanding of the mechanisms of disease.


Assuntos
Regulação da Expressão Gênica/genética , Redes Reguladoras de Genes/genética , MicroRNAs/genética , Doença Pulmonar Obstrutiva Crônica/genética , Idoso , Brônquios/metabolismo , Análise por Conglomerados , Células Epiteliais/metabolismo , Feminino , Perfilação da Expressão Gênica/métodos , Humanos , Pulmão/metabolismo , Masculino , MicroRNAs/biossíntese , Pessoa de Meia-Idade , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Doença Pulmonar Obstrutiva Crônica/metabolismo , RNA Mensageiro/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Proteína Smad7/biossíntese , Proteína Smad7/genética , Fumar/genética , Fumar/metabolismo , Fator de Crescimento Transformador beta/biossíntese , Fator de Crescimento Transformador beta/genética , Via de Sinalização Wnt/genética
19.
BMC Med Genomics ; 4: 8, 2011 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-21241464

RESUMO

BACKGROUND: The molecular pathways involved in the interstitial lung diseases (ILDs) are poorly understood. Systems biology approaches, with global expression data sets, were used to identify perturbed gene networks, to gain some understanding of the underlying mechanisms, and to develop specific hypotheses relevant to these chronic lung diseases. METHODS: Lung tissue samples from patients with different types of ILD were obtained from the Lung Tissue Research Consortium and total cell RNA was isolated. Global mRNA and microRNA were profiled by hybridization and amplification-based methods. Differentially expressed genes were compiled and used to identify critical signaling pathways and potential biomarkers. Modules of genes were identified that formed a regulatory network, and studies were performed on cultured cells in vitro for comparison with the in vivo results. RESULTS: By profiling mRNA and microRNA (miRNA) expression levels, we found subsets of differentially expressed genes that distinguished patients with ILDs from controls and that correlated with different disease stages and subtypes of ILDs. Network analysis, based on pathway databases, revealed several disease-associated gene modules, involving genes from the TGF-ß, Wnt, focal adhesion, and smooth muscle actin pathways that are implicated in advancing fibrosis, a critical pathological process in ILDs. A more comprehensive approach was also adapted to construct a putative global gene regulatory network based on the perturbation of key regulatory elements, transcription factors and microRNAs. Our data underscores the importance of TGF-ß signaling and the persistence of smooth muscle actin-containing fibroblasts in these diseases. We present evidence that, downstream of TGF-ß signaling, microRNAs of the miR-23a cluster and the transcription factor Zeb1 could have roles in mediating an epithelial to mesenchymal transition (EMT) and the resultant persistence of mesenchymal cells in these diseases. CONCLUSIONS: We present a comprehensive overview of the molecular networks perturbed in ILDs, discuss several potential key molecular regulatory circuits, and identify microRNA species that may play central roles in facilitating the progression of ILDs. These findings advance our understanding of these diseases at the molecular level, provide new molecular signatures in defining the specific characteristics of the diseases, suggest new hypotheses, and reveal new potential targets for therapeutic intervention.


Assuntos
Doenças Pulmonares Intersticiais/genética , MicroRNAs/metabolismo , RNA Mensageiro/metabolismo , Biologia de Sistemas , Adulto , Idoso , Estudos de Casos e Controles , Células Cultivadas , Feminino , Redes Reguladoras de Genes , Humanos , Doenças Pulmonares Intersticiais/metabolismo , Masculino , MicroRNAs/genética , Pessoa de Meia-Idade , RNA Mensageiro/análise , RNA Mensageiro/genética , Transdução de Sinais/genética , Software
20.
J Cell Physiol ; 226(6): 1479-88, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-20945389

RESUMO

The prostate stromal mesenchyme controls organ-specific development. In cancer, the stromal compartment shows altered gene expression compared to non-cancer. The lineage relationship between cancer-associated stromal cells and normal tissue stromal cells is not known. Nor is the cause underlying the expression difference. Previously, the embryonal carcinoma (EC) cell line, NCCIT, was used by us to study the stromal induction property. In the current study, stromal cells from non-cancer (NP) and cancer (CP) were isolated from tissue specimens and co-cultured with NCCIT cells in a trans-well format to preclude heterotypic cell contact. After 3 days, the stromal cells were analyzed by gene arrays for microRNA (miRNA) and mRNA expression. In co-culture, NCCIT cells were found to alter the miRNA and mRNA expression of NP stromal cells to one like that of CP stromal cells. In contrast, NCCIT had no significant effect on the gene expression of CP stromal cells. We conclude that the gene expression changes in stromal cells can be induced by diffusible factors synthesized by EC cells, and suggest that cancer-associated stromal cells represent a more primitive or less differentiated stromal cell type.


Assuntos
Células-Tronco de Carcinoma Embrionário/metabolismo , MicroRNAs/genética , Próstata/metabolismo , Próstata/patologia , Comunicação Celular , Linhagem Celular Tumoral , Forma Celular , Técnicas de Cocultura , Meios de Cultura , Citoplasma/genética , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , MicroRNAs/metabolismo , Neoplasias da Próstata/genética , Neoplasias da Próstata/patologia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Células Estromais/metabolismo , Células Estromais/patologia
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