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1.
Cell ; 163(7): 1611-27, 2015 Dec 17.
Artículo en Inglés | MEDLINE | ID: mdl-26686651

RESUMEN

Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes toward CTCF foci for coordinated transcription. Furthermore, we show that haplotype variants and allelic interactions have differential effects on chromosome configuration, influencing gene expression, and may provide mechanistic insights into functions associated with disease susceptibility. 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D genome strategy thus provides unique insights in the topological mechanism of human variations and diseases.


Asunto(s)
Cromatina/química , Genoma Humano , Proteínas Represoras/metabolismo , Transcripción Genética , Animales , Factor de Unión a CCCTC , Proteínas de Ciclo Celular/metabolismo , Línea Celular , Cromatina/genética , Cromatina/metabolismo , Proteínas Cromosómicas no Histona/metabolismo , Cromosomas/metabolismo , Empaquetamiento del ADN , Humanos , ARN Polimerasa II/metabolismo , Salamandridae , Cohesinas
2.
Mol Cell ; 81(11): 2428-2444.e6, 2021 06 03.
Artículo en Inglés | MEDLINE | ID: mdl-33882298

RESUMEN

Repair pathway "choice" at stalled mammalian replication forks is an important determinant of genome stability; however, the underlying mechanisms are poorly understood. FANCM encodes a multi-domain scaffolding and motor protein that interacts with several distinct repair protein complexes at stalled forks. Here, we use defined mutations engineered within endogenous Fancm in mouse embryonic stem cells to study how Fancm regulates stalled fork repair. We find that distinct FANCM repair functions are enacted by molecularly separable scaffolding domains. These findings define FANCM as a key mediator of repair pathway choice at stalled replication forks and reveal its molecular mechanism. Notably, mutations that inactivate FANCM ATPase function disable all its repair functions and "trap" FANCM at stalled forks. We find that Brca1 hypomorphic mutants are synthetic lethal with Fancm null or Fancm ATPase-defective mutants. The ATPase function of FANCM may therefore represent a promising "druggable" target for therapy of BRCA1-linked cancer.


Asunto(s)
Proteína BRCA1/genética , ADN Helicasas/genética , Reparación del ADN , Replicación del ADN , Células Madre Embrionarias de Ratones/metabolismo , Mutaciones Letales Sintéticas , Animales , Proteína BRCA1/metabolismo , Ciclo Celular/genética , Línea Celular , Células Clonales , ADN Helicasas/metabolismo , Proteína del Grupo de Complementación D2 de la Anemia de Fanconi/genética , Proteína del Grupo de Complementación D2 de la Anemia de Fanconi/metabolismo , Fibroblastos/citología , Fibroblastos/metabolismo , Humanos , Ratones , Células Madre Embrionarias de Ratones/citología , Ubiquitinación
3.
Cell ; 152(4): 859-72, 2013 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-23415232

RESUMEN

Histone modifications are key regulators of chromatin function. However, little is known to what extent histone modifications can directly impact on chromatin. Here, we address how a modification within the globular domain of histones regulates chromatin function. We demonstrate that H3K122ac can be sufficient to stimulate transcription and that mutation of H3K122 impairs transcriptional activation, which we attribute to a direct effect of H3K122ac on histone-DNA binding. In line with this, we find that H3K122ac defines genome-wide genetic elements and chromatin features associated with active transcription. Furthermore, H3K122ac is catalyzed by the coactivators p300/CBP and can be induced by nuclear hormone receptor signaling. Collectively, this suggests that transcriptional regulators elicit their effects not only via signaling to histone tails but also via direct structural perturbation of nucleosomes by directing acetylation to their lateral surface.


Asunto(s)
Regulación de la Expresión Génica , Código de Histonas , Histonas/metabolismo , Activación Transcripcional , Acetilación , Animales , Línea Celular Tumoral , Eucariontes/metabolismo , Fibroblastos/metabolismo , Humanos , Ratones , Modelos Moleculares , Nucleosomas/metabolismo , Receptores de Estrógenos/metabolismo , Schizosaccharomyces/metabolismo , Sitio de Iniciación de la Transcripción , Factores de Transcripción p300-CBP/metabolismo
4.
Cell ; 148(1-2): 84-98, 2012 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-22265404

RESUMEN

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.


Asunto(s)
Cromatina/metabolismo , Regulación de la Expresión Génica , Regiones Promotoras Genéticas , ARN Polimerasa II/metabolismo , Transcripción Genética , Línea Celular Tumoral , Inmunoprecipitación de Cromatina , Elementos de Facilitación Genéticos , Estudio de Asociación del Genoma Completo , Humanos
5.
Nature ; 551(7682): 590-595, 2017 11 30.
Artículo en Inglés | MEDLINE | ID: mdl-29168504

RESUMEN

Small, approximately 10-kilobase microhomology-mediated tandem duplications are abundant in the genomes of BRCA1-linked but not BRCA2-linked breast cancer. Here we define the mechanism underlying this rearrangement signature. We show that, in primary mammalian cells, BRCA1, but not BRCA2, suppresses the formation of tandem duplications at a site-specific chromosomal replication fork barrier imposed by the binding of Tus proteins to an array of Ter sites. BRCA1 has no equivalent role at chromosomal double-stranded DNA breaks, indicating that tandem duplications form specifically at stalled forks. Tandem duplications in BRCA1 mutant cells arise by a replication restart-bypass mechanism terminated by end joining or by microhomology-mediated template switching, the latter forming complex tandem duplication breakpoints. Solitary DNA ends form directly at Tus-Ter, implicating misrepair of these lesions in tandem duplication formation. Furthermore, BRCA1 inactivation is strongly associated with ~10 kilobase tandem duplications in ovarian cancer. This tandem duplicator phenotype may be a general signature of BRCA1-deficient cancer.


Asunto(s)
Reparación del ADN por Unión de Extremidades/genética , Replicación del ADN/genética , Secuencias Repetidas en Tándem/genética , Proteínas Supresoras de Tumor/deficiencia , Proteínas Supresoras de Tumor/genética , Animales , Proteína BRCA1 , Células Cultivadas , Roturas del ADN de Doble Cadena , Reparación del ADN , Células Madre Embrionarias , Femenino , Genes Reporteros , Recombinación Homóloga , Humanos , Ratones , Neoplasias Ováricas/genética , Eliminación de Secuencia , Proteínas Supresoras de Tumor/metabolismo
6.
Nat Methods ; 15(6): 455-460, 2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29713081

RESUMEN

Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( https://github.com/TheJacksonLaboratory/Picky ), to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation. Examination of genome-wide breakpoints at nucleotide resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with the propensity for interchromosomal connectivity and was found to be enriched in promoters and transcribed regions of the genome. Furthermore, we observed an over-representation of reciprocal translocations from chromosomal double-crossovers through phased SVs. We demonstrate that Picky analysis is an effective tool for comprehensive detection of SVs in cancer genomes from long-read data.


Asunto(s)
Regulación Neoplásica de la Expresión Génica , Variación Estructural del Genoma , Nanoporos , Línea Celular Tumoral , Análisis Mutacional de ADN/métodos , Genoma , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos
7.
Blood ; 131(17): 1931-1941, 2018 04 26.
Artículo en Inglés | MEDLINE | ID: mdl-29475961

RESUMEN

Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphomas (EBV+-DLBLs) tend to occur in immunocompromised patients, such as the elderly or those undergoing solid organ transplantation. The pathogenesis and genomic characteristics of EBV+-DLBLs are largely unknown because of the limited availability of human samples and lack of experimental animal models. We observed the development of 25 human EBV+-DLBLs during the engraftment of gastric adenocarcinomas into immunodeficient mice. An integrated genomic analysis of the human-derived EBV+-DLBLs revealed enrichment of mutations in Rho pathway genes, including RHPN2, and Rho pathway transcriptomic activation. Targeting the Rho pathway using a Rho-associated protein kinase (ROCK) inhibitor, fasudil, markedly decreased tumor growth in EBV+-DLBL patient-derived xenograft (PDX) models. Thus, alterations in the Rho pathway appear to contribute to EBV-induced lymphomagenesis in immunosuppressed environments.


Asunto(s)
Adenocarcinoma/metabolismo , Transformación Celular Viral , Infecciones por Virus de Epstein-Barr/metabolismo , Herpesvirus Humano 4/metabolismo , Linfoma de Células B Grandes Difuso/metabolismo , Transducción de Señal , Neoplasias Gástricas/metabolismo , Proteínas de Unión al GTP rho/metabolismo , Adenocarcinoma/genética , Adenocarcinoma/patología , Adenocarcinoma/virología , Animales , Infecciones por Virus de Epstein-Barr/genética , Infecciones por Virus de Epstein-Barr/patología , Herpesvirus Humano 4/genética , Linfoma de Células B Grandes Difuso/genética , Linfoma de Células B Grandes Difuso/patología , Linfoma de Células B Grandes Difuso/virología , Ratones , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Neoplasias Gástricas/genética , Neoplasias Gástricas/patología , Neoplasias Gástricas/virología , Proteínas de Unión al GTP rho/genética
8.
Genes Dev ; 26(7): 668-82, 2012 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-22431510

RESUMEN

The transcription factor Ebf1 is an important determinant of early B lymphopoiesis. To gain insight into the functions of Ebf1 at distinct stages of differentiation, we conditionally inactivated Ebf1. We found that Ebf1 is required for the proliferation, survival, and signaling of pro-B cells and peripheral B-cell subsets, including B1 cells and marginal zone B cells. The proliferation defect of Ebf1-deficient pro-B cells and the impaired expression of multiple cell cycle regulators are overcome by transformation with v-Abl. The survival defect of transformed Ebf1(fl/fl) pro-B cells can be rescued by the forced expression of the Ebf1 targets c-Myb or Bcl-x(L). In mature B cells, Ebf1 deficiency interferes with signaling via the B-cell-activating factor receptor (BAFF-R)- and B-cell receptor (BCR)-dependent Akt pathways. Moreover, Ebf1 is required for germinal center formation and class switch recombination. Genome-wide analyses of Ebf1-mediated gene expression and chromatin binding indicate that Ebf1 regulates both common and distinct sets of genes in early and late stage B cells. By regulating important components of transcription factor and signaling networks, Ebf1 appears to be involved in the coordination of cell proliferation, survival, and differentiation at multiple stages of B lymphopoiesis.


Asunto(s)
Linfocitos B/citología , Linfocitos B/metabolismo , Diferenciación Celular , Proliferación Celular , Transducción de Señal , Transactivadores/metabolismo , Animales , Linfocitos B/inmunología , Supervivencia Celular , Regulación de la Expresión Génica , Estudio de Asociación del Genoma Completo , Cadenas Pesadas de Inmunoglobulina/inmunología , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Transactivadores/genética , Transactivadores/inmunología , Transcripción Genética
9.
FASEB J ; 32(3): 1537-1549, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-29146734

RESUMEN

Establishment of an in vivo small animal model of human tumor and human immune system interaction would enable preclinical investigations into the mechanisms underlying cancer immunotherapy. To this end, nonobese diabetic (NOD).Cg- PrkdcscidIL2rgtm1Wjl/Sz (null; NSG) mice were transplanted with human (h)CD34+ hematopoietic progenitor and stem cells, which leads to the development of human hematopoietic and immune systems [humanized NSG (HuNSG)]. HuNSG mice received human leukocyte antigen partially matched tumor implants from patient-derived xenografts [PDX; non-small cell lung cancer (NSCLC), sarcoma, bladder cancer, and triple-negative breast cancer (TNBC)] or from a TNBC cell line-derived xenograft (CDX). Tumor growth curves were similar in HuNSG compared with nonhuman immune-engrafted NSG mice. Treatment with pembrolizumab, which targets programmed cell death protein 1, produced significant growth inhibition in both CDX and PDX tumors in HuNSG but not in NSG mice. Finally, inhibition of tumor growth was dependent on hCD8+ T cells, as demonstrated by antibody-mediated depletion. Thus, tumor-bearing HuNSG mice may represent an important, new model for preclinical immunotherapy research.-Wang, M., Yao, L.-C., Cheng, M., Cai, D., Martinek, J., Pan, C.-X., Shi, W., Ma, A.-H., De Vere White, R. W., Airhart, S., Liu, E. T., Banchereau, J., Brehm, M. A., Greiner, D. L., Shultz, L. D., Palucka, K., Keck, J. G. Humanized mice in studying efficacy and mechanisms of PD-1-targeted cancer immunotherapy.


Asunto(s)
Anticuerpos Monoclonales Humanizados/farmacología , Linfocitos T CD8-positivos/inmunología , Inmunidad Celular/efectos de los fármacos , Inmunoterapia , Neoplasias/terapia , Receptor de Muerte Celular Programada 1/inmunología , Animales , Linfocitos T CD8-positivos/patología , Línea Celular Tumoral , Femenino , Humanos , Ratones , Ratones Endogámicos NOD , Neoplasias/inmunología , Neoplasias/patología , Ensayos Antitumor por Modelo de Xenoinjerto
10.
Immunity ; 32(5): 714-25, 2010 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-20451411

RESUMEN

The transcription factor early B cell factor-1 (Ebf1) is a key determinant of B lineage specification and differentiation. To gain insight into the molecular basis of Ebf1 function in early-stage B cells, we combined a genome-wide ChIP sequencing analysis with gain- and loss-of-function transcriptome analyses. Among 565 genes that are occupied and transcriptionally regulated by Ebf1, we identified large sets involved in (pre)-B cell receptor and Akt signaling, cell adhesion, and migration. Interestingly, a third of previously described Pax5 targets was found to be occupied by Ebf1. In addition to Ebf1-activated and -repressed genes, we identified targets at which Ebf1 induces chromatin changes that poise the genes for expression at subsequent stages of differentiation. Poised chromatin states on specific targets could also be established by Ebf1 expression in T cells but not in NIH 3T3 cells, suggesting that Ebf1 acts as a "pioneer" factor in a hematopoietic chromatin context.


Asunto(s)
Linfocitos B/inmunología , Cromatina/genética , Redes Reguladoras de Genes , Activación de Linfocitos/inmunología , Factor de Transcripción PAX5/metabolismo , Animales , Linfocitos B/citología , Linfocitos B/metabolismo , Linaje de la Célula , Cromatina/química , Cromatina/metabolismo , Mapeo Cromosómico , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Ratones , Ratones Transgénicos , Células 3T3 NIH , Factor de Transcripción PAX5/genética , Regiones Promotoras Genéticas , Unión Proteica , Transducción de Señal
11.
Proc Natl Acad Sci U S A ; 113(17): E2373-82, 2016 Apr 26.
Artículo en Inglés | MEDLINE | ID: mdl-27071093

RESUMEN

Next-generation sequencing studies have revealed genome-wide structural variation patterns in cancer, such as chromothripsis and chromoplexy, that do not engage a single discernable driver mutation, and whose clinical relevance is unclear. We devised a robust genomic metric able to identify cancers with a chromotype called tandem duplicator phenotype (TDP) characterized by frequent and distributed tandem duplications (TDs). Enriched only in triple-negative breast cancer (TNBC) and in ovarian, endometrial, and liver cancers, TDP tumors conjointly exhibit tumor protein p53 (TP53) mutations, disruption of breast cancer 1 (BRCA1), and increased expression of DNA replication genes pointing at rereplication in a defective checkpoint environment as a plausible causal mechanism. The resultant TDs in TDP augment global oncogene expression and disrupt tumor suppressor genes. Importantly, the TDP strongly correlates with cisplatin sensitivity in both TNBC cell lines and primary patient-derived xenografts. We conclude that the TDP is a common cancer chromotype that coordinately alters oncogene/tumor suppressor expression with potential as a marker for chemotherapeutic response.


Asunto(s)
Neoplasias Endometriales/genética , Neoplasias Ováricas/genética , Duplicaciones Segmentarias en el Genoma/genética , Neoplasias de la Mama Triple Negativas/genética , Antineoplásicos/farmacología , Femenino , Genes Relacionados con las Neoplasias/genética , Marcadores Genéticos/genética , Humanos , Fenotipo
12.
Proc Natl Acad Sci U S A ; 112(40): 12492-7, 2015 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-26401016

RESUMEN

Gastric cancer (GC) is the third leading cause of cancer-related deaths worldwide. Recent high-throughput analyses of genomic alterations revealed several driver genes and altered pathways in GC. However, therapeutic applications from genomic data are limited, largely as a result of the lack of druggable molecular targets and preclinical models for drug selection. To identify new therapeutic targets for GC, we performed array comparative genomic hybridization (aCGH) of DNA from 103 patients with GC for copy number alteration (CNA) analysis, and whole-exome sequencing from 55 GCs from the same patients for mutation profiling. Pathway analysis showed recurrent alterations in the Wnt signaling [APC, CTNNB1, and DLC1 (deleted in liver cancer 1)], ErbB signaling (ERBB2, PIK3CA, and KRAS), and p53 signaling/apoptosis [TP53 and BCL2L1 (BCL2-like 1)] pathways. In 18.4% of GC cases (19/103), amplification of the antiapoptotic gene BCL2L1 was observed, and subsequently a BCL2L1 inhibitor was shown to markedly decrease cell viability in BCL2L1-amplified cell lines and in similarly altered patient-derived GC xenografts, especially when combined with other chemotherapeutic agents. In 10.9% of cases (6/55), mutations in DLC1 were found and were also shown to confer a growth advantage for these cells via activation of Rho-ROCK signaling, rendering these cells more susceptible to a ROCK inhibitor. Taken together, our study implicates BCL2L1 and DLC1 as potential druggable targets for specific subsets of GC cases.


Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Proteínas Activadoras de GTPasa/genética , Estudio de Asociación del Genoma Completo/métodos , Neoplasias Gástricas/tratamiento farmacológico , Neoplasias Gástricas/genética , Proteínas Supresoras de Tumor/genética , Proteína bcl-X/genética , Anciano , Anciano de 80 o más Años , Animales , Línea Celular Tumoral , Supervivencia Celular/genética , Hibridación Genómica Comparativa , Variaciones en el Número de Copia de ADN , Exoma/genética , Femenino , Proteínas Activadoras de GTPasa/metabolismo , Humanos , Subunidad gamma Común de Receptores de Interleucina/deficiencia , Subunidad gamma Común de Receptores de Interleucina/genética , Masculino , Ratones Endogámicos NOD , Ratones Noqueados , Ratones SCID , Persona de Mediana Edad , Mutación , Interferencia de ARN , Análisis de Secuencia de ADN/métodos , Neoplasias Gástricas/patología , Proteínas Supresoras de Tumor/metabolismo , Ensayos Antitumor por Modelo de Xenoinjerto , Proteína bcl-X/metabolismo
13.
Genome Res ; 24(10): 1559-71, 2014 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-25186909

RESUMEN

Chromosomal structural variations play an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural variations, we analyzed eight breast tumor samples with a focus on regions of gene amplification using mate-pair sequencing of long-insert genomic DNA with matched transcriptome profiling. We found that tandem duplications appear to be early events in tumor evolution, especially in the genesis of amplicons. In a detailed reconstruction of events on chromosome 17, we found large unpaired inversions and deletions connect a tandemly duplicated ERBB2 with neighboring 17q21.3 amplicons while simultaneously deleting the intervening BRCA1 tumor suppressor locus. This series of events appeared to be unusually common when examined in larger genomic data sets of breast cancers albeit using approaches with lesser resolution. Using siRNAs in breast cancer cell lines, we showed that the 17q21.3 amplicon harbored a significant number of weak oncogenes that appeared consistently coamplified in primary tumors. Down-regulation of BRCA1 expression augmented the cell proliferation in ERBB2-transfected human normal mammary epithelial cells. Coamplification of other functionally tested oncogenic elements in other breast tumors examined, such as RIPK2 and MYC on chromosome 8, also parallel these findings. Our analyses suggest that structural variations efficiently orchestrate the gain and loss of cancer gene cassettes that engage many oncogenic pathways simultaneously and that such oncogenic cassettes are favored during the evolution of a cancer.


Asunto(s)
Proteína BRCA1/genética , Neoplasias de la Mama/genética , Aberraciones Cromosómicas , Cromosomas Humanos Par 17/genética , Receptor ErbB-2/genética , Secuencia de Bases , Línea Celular Tumoral , Femenino , Amplificación de Genes , Duplicación de Gen , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Humanos , Células MCF-7 , Datos de Secuencia Molecular , Análisis de Secuencia de ADN
14.
Nucleic Acids Res ; 43(7): e44, 2015 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-25572314

RESUMEN

Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact.


Asunto(s)
Melanoma/genética , Algoritmos , Humanos , Melanoma/fisiopatología , Mutación , Medición de Riesgo , Análisis de Supervivencia
15.
Trends Genet ; 28(11): 550-9, 2012 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-22901976

RESUMEN

Next-generation sequencing (NGS) has enabled the comprehensive and precise identification of many somatic structural mutations in cancer. Analyses integrating point mutation information with data on rearrangements and copy number variation have revealed a higher-order organization of the seemingly random genetic events that lead to cancer. These meta-analyses provide a more refined view of the mutational mechanisms, genomic evolution, and combinations of mutations that contribute to tumorigenesis. Structural mutations, or genome-scale rearrangements of segments of DNA, may play a hitherto unappreciated role in cancer through their ability to move blocks of adjacent genes simultaneously, leading to concurrent oncogenic events. Moreover, whole-genome sequencing (WGS) data from tumors have revealed global rearrangements, such as those seen in the tandem duplicator phenotype and in chromothripsis, suggesting that massive rearrangements are a specific cancer phenotype. Taken together, the emerging data suggest that the chromosome structure itself functions as a systems oncogenic organizer.


Asunto(s)
Mutación , Neoplasias/genética , Animales , Genoma Humano , Humanos , Oncogenes
16.
Nat Rev Genet ; 10(1): 64-8, 2009 01.
Artículo en Inglés | MEDLINE | ID: mdl-19092836

RESUMEN

The precision of genome sequences, together with advanced computational approaches, allows complex, clinically relevant biological systems to be examined. Here, I describe the experiences of the Genome Institute of Singapore (GIS) in using genome-to-systems strategies to accelerate biomedical research. To maximize clinically relevant output, we have explored an organizational strategy that encourages coordinated experimentation among investigators with diverse skills and interests through building a culture of integrative science. Our experience suggests that systems biomedicine is a real and potentially fruitful strategy for translational research.


Asunto(s)
Biología de Sistemas/métodos , Animales , Investigación Biomédica , Humanos , Singapur , Transcripción Genética , Proteína p53 Supresora de Tumor/genética
17.
Nature ; 462(7269): 58-64, 2009 Nov 05.
Artículo en Inglés | MEDLINE | ID: mdl-19890323

RESUMEN

Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor alpha (ER-alpha) in the human genome. We found that most high-confidence remote ER-alpha-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-alpha functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.


Asunto(s)
Cromatina/genética , Cromatina/metabolismo , Receptor alfa de Estrógeno/metabolismo , Genoma Humano/genética , Sitios de Unión , Línea Celular , Inmunoprecipitación de Cromatina , Reactivos de Enlaces Cruzados , Formaldehído , Humanos , Regiones Promotoras Genéticas/genética , Unión Proteica , Reproducibilidad de los Resultados , Análisis de Secuencia de ADN , Transcripción Genética , Activación Transcripcional
18.
Nat Genet ; 38(6): 626-35, 2006 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-16645617

RESUMEN

Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.


Asunto(s)
Evolución Molecular , Regiones Promotoras Genéticas , Regiones no Traducidas 3' , Animales , Secuencia de Bases , ADN , Genoma , Proteoma , TATA Box
19.
BMC Genomics ; 15: 1013, 2014 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-25417144

RESUMEN

BACKGROUND: Structural mutations (SMs) play a major role in cancer development. In some cancers, such as breast and ovarian, DNA double-strand breaks (DSBs) occur more frequently in transcribed regions, while in other cancer types such as prostate, there is a consistent depletion of breakpoints in transcribed regions. Despite such regularity, little is understood about the mechanisms driving these effects. A few works have suggested that protein binding may be relevant, e.g. in studies of androgen receptor binding and active chromatin in specific cell types. We hypothesized that this behavior might be general, i.e. that correlation between protein-DNA binding (and open chromatin) and breakpoint locations is common across divergent cancers. RESULTS: We investigated this hypothesis by comprehensively analyzing the relationship among 457 ENCODE protein binding ChIP-seq experiments, 125 DnaseI and 24 FAIRE experiments, and 14,600 SMs from 8 diverse cancer datasets covering 147 samples. In most cancers, including breast and ovarian, we found enrichment of protein binding and open chromatin in the vicinity of SM breakpoints at distances up to 200 kb. Furthermore, for all cancer types we observed an enhanced enrichment in regions distant from genes when compared to regions proximal to genes, suggesting that the SM-induction mechanism is independent from the bias of DSBs to occur near transcribed regions. We also observed a stronger effect for sites with more than one protein bound. CONCLUSIONS: Protein binding and open chromatin state are associated with nearby SM breakpoints in many cancer datasets. These observations suggest a consistent mechanism underlying SM locations across different cancers.


Asunto(s)
Cromatina/metabolismo , Mutación/genética , Neoplasias/genética , Emparejamiento Base , Inmunoprecipitación de Cromatina , Roturas del ADN de Doble Cadena , Humanos , Masculino , Proteínas de Neoplasias/metabolismo , Oportunidad Relativa , Unión Proteica
20.
Genome Res ; 21(5): 676-87, 2011 May.
Artículo en Inglés | MEDLINE | ID: mdl-21467264

RESUMEN

Using a long-span, paired-end deep sequencing strategy, we have comprehensively identified cancer genome rearrangements in eight breast cancer genomes. Herein, we show that 40%-54% of these structural genomic rearrangements result in different forms of fusion transcripts and that 44% are potentially translated. We find that single segmental tandem duplication spanning several genes is a major source of the fusion gene transcripts in both cell lines and primary tumors involving adjacent genes placed in the reverse-order position by the duplication event. Certain other structural mutations, however, tend to attenuate gene expression. From these candidate gene fusions, we have found a fusion transcript (RPS6KB1-VMP1) recurrently expressed in ∼30% of breast cancers associated with potential clinical consequences. This gene fusion is caused by tandem duplication on 17q23 and appears to be an indicator of local genomic instability altering the expression of oncogenic components such as MIR21 and RPS6KB1.


Asunto(s)
Neoplasias de la Mama/metabolismo , Reordenamiento Génico , Genoma Humano/genética , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Proteínas Recombinantes de Fusión/metabolismo , Proteínas Quinasas S6 Ribosómicas/metabolismo , Transcripción Genética , Neoplasias de la Mama/genética , Línea Celular Tumoral , Mapeo Cromosómico , Cromosomas Humanos Par 17/genética , Femenino , Dosificación de Gen , Perfilación de la Expresión Génica , Inestabilidad Genómica , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Proteínas Recombinantes de Fusión/genética , Proteínas Quinasas S6 Ribosómicas/genética , Análisis de Secuencia de ADN
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