RESUMEN
Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a comprehensive integrated genomic study, including the most detailed analysis of BAP1 alterations to date. We identified histology-independent molecular prognostic subsets, and defined a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity. We also report strong expression of the immune-checkpoint gene VISTA in epithelioid MPM, strikingly higher than in other solid cancers, with implications for the immune response to MPM and for its immunotherapy. Our findings highlight new avenues for further investigation of MPM biology and novel therapeutic options. SIGNIFICANCE: Through a comprehensive integrated genomic study of 74 MPMs, we provide a deeper understanding of histology-independent determinants of aggressive behavior, define a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity, and discovered strong expression of the immune-checkpoint gene VISTA in epithelioid MPM.See related commentary by Aggarwal and Albelda, p. 1508.This article is highlighted in the In This Issue feature, p. 1494.
Asunto(s)
Biomarcadores de Tumor/genética , Neoplasias Pulmonares/genética , Mesotelioma/genética , Mutación , Neoplasias Pleurales/genética , Anciano , Femenino , N-Metiltransferasa de Histona-Lisina , Humanos , Estimación de Kaplan-Meier , Neoplasias Pulmonares/patología , Neoplasias Pulmonares/terapia , Masculino , Mesotelioma/patología , Mesotelioma/terapia , Persona de Mediana Edad , Neoplasias Pleurales/patología , Neoplasias Pleurales/terapia , Pronóstico , Proteína Metiltransferasas/genética , Proteínas Supresoras de Tumor/genética , Ubiquitina Tiolesterasa/genéticaRESUMEN
Comprehensive multiplatform analysis of 80 uveal melanomas (UM) identifies four molecularly distinct, clinically relevant subtypes: two associated with poor-prognosis monosomy 3 (M3) and two with better-prognosis disomy 3 (D3). We show that BAP1 loss follows M3 occurrence and correlates with a global DNA methylation state that is distinct from D3-UM. Poor-prognosis M3-UM divide into subsets with divergent genomic aberrations, transcriptional features, and clinical outcomes. We report change-of-function SRSF2 mutations. Within D3-UM, EIF1AX- and SRSF2/SF3B1-mutant tumors have distinct somatic copy number alterations and DNA methylation profiles, providing insight into the biology of these low- versus intermediate-risk clinical mutation subtypes.
Asunto(s)
Biomarcadores de Tumor/genética , Metilación de ADN , Regulación Neoplásica de la Expresión Génica , Melanoma/genética , Mutación , Neoplasias de la Úvea/genética , Variaciones en el Número de Copia de ADN , Factor 1 Eucariótico de Iniciación/genética , Humanos , Melanoma/clasificación , Monosomía , Fosfoproteínas/genética , Pronóstico , Factores de Empalme de ARN/genética , Factores de Empalme Serina-Arginina/genética , Proteínas Supresoras de Tumor/genética , Ubiquitina Tiolesterasa/genética , Neoplasias de la Úvea/clasificaciónAsunto(s)
Bases de Datos de Ácidos Nucleicos , Biología Computacional , Presentación de Datos , Bases de Datos de Ácidos Nucleicos/historia , Bases de Datos de Ácidos Nucleicos/tendencias , Procesamiento Automatizado de Datos , Historia del Siglo XX , Historia del Siglo XXI , Modelos Moleculares , Estructura Molecular , Conformación de Ácido Nucleico , Ácidos Nucleicos/químicaRESUMEN
The Nucleic Acid Database was established in 1991 as a resource to assemble and distribute structural information about nucleic acids. Over the years, the NDB has developed generalized software for processing, archiving, querying and distributing structural data for nucleic acid-containing structures. The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article.
Asunto(s)
Bases de Datos de Ácidos Nucleicos , Gráficos por Computador , Bases de Datos de Ácidos Nucleicos/normas , Almacenamiento y Recuperación de la Información , Internet , Interfaz Usuario-ComputadorRESUMEN
The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource.
