RESUMEN
Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs. Our analyses revealed gene expression and methylation subgroups and focused on dysregulated pathways, including those involved in neural crest development.
Asunto(s)
Regulación del Desarrollo de la Expresión Génica/genética , Tumor Rabdoide/genética , Línea Celular Tumoral , Proteínas Cromosómicas no Histona/genética , Metilación de ADN/genética , Proteínas de Unión al ADN/genética , Expresión Génica/genética , Histonas/genética , Humanos , MicroARNs/genética , Proteína SMARCB1 , Factores de Transcripción/genética , Transcriptoma/genéticaRESUMEN
Parathyroid carcinoma is a rare endocrine malignancy with an estimated incidence of less than 1 per million population. Excessive secretion of parathyroid hormone, extremely high serum calcium level, and the deleterious effects of hypercalcaemia are the clinical manifestations of the disease. Up to 60% of patients develop multiple disease recurrences and although long-term survival is possible with palliative surgery, permanent remission is rarely achieved. Molecular drivers of sporadic parathyroid carcinoma have remained largely unknown. Previous studies, mostly based on familial cases of the disease, suggested potential roles for the tumour suppressor MEN1 and proto-oncogene RET in benign parathyroid tumourigenesis, while the tumour suppressor HRPT2 and proto-oncogene CCND1 may also act as drivers in parathyroid cancer. Here, we report the complete genomic analysis of a sporadic and recurring parathyroid carcinoma. Mutational landscapes of the primary and recurrent tumour specimens were analysed using high-throughput sequencing technologies. Such molecular profiling allowed for identification of somatic mutations never previously identified in this malignancy. These included single nucleotide point mutations in well-characterized cancer genes such as mTOR, MLL2, CDKN2C, and PIK3CA. Comparison of acquired mutations in patient-matched primary and recurrent tumours revealed loss of PIK3CA activating mutation during the evolution of the tumour from the primary to the recurrence. Structural variations leading to gene fusions and regions of copy loss and gain were identified at a single-base resolution. Loss of the short arm of chromosome 1, along with somatic missense and truncating mutations in CDKN2C and THRAP3, respectively, provides new evidence for the potential role of these genes as tumour suppressors in parathyroid cancer. The key somatic mutations identified in this study can serve as novel diagnostic markers as well as therapeutic targets.
Asunto(s)
Biomarcadores de Tumor/genética , Perfilación de la Expresión Génica , Genómica , Recurrencia Local de Neoplasia/genética , Neoplasias de las Paratiroides/genética , Adulto , Secuencia de Bases , Calcio/sangre , Transformación Celular Neoplásica , Fosfatidilinositol 3-Quinasa Clase I , Inhibidor p18 de las Quinasas Dependientes de la Ciclina/genética , ADN de Neoplasias/química , ADN de Neoplasias/genética , Proteínas de Unión al ADN/genética , Dosificación de Gen , Fusión Génica , Humanos , Masculino , Datos de Secuencia Molecular , Mutación , Proteínas de Neoplasias/genética , Recurrencia Local de Neoplasia/patología , Recurrencia Local de Neoplasia/cirugía , Hormona Paratiroidea/metabolismo , Neoplasias de las Paratiroides/patología , Neoplasias de las Paratiroides/cirugía , Fosfatidilinositol 3-Quinasas/genética , Polimorfismo de Nucleótido Simple , Proto-Oncogenes Mas , ARN Neoplásico/genética , Serina-Treonina Quinasas TOR/genética , Factores de Transcripción/genéticaRESUMEN
Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-ß signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.
Asunto(s)
Neoplasias Cerebelosas/clasificación , Neoplasias Cerebelosas/genética , Genoma Humano/genética , Variación Estructural del Genoma/genética , Meduloblastoma/clasificación , Meduloblastoma/genética , Proteínas Portadoras/genética , Neoplasias Cerebelosas/metabolismo , Niño , Variaciones en el Número de Copia de ADN/genética , Duplicación de Gen/genética , Genes myc/genética , Genómica , Proteínas Hedgehog/metabolismo , Humanos , Meduloblastoma/metabolismo , FN-kappa B/metabolismo , Proteínas del Tejido Nervioso/genética , Proteínas de Fusión Oncogénica/genética , Proteínas/genética , ARN Largo no Codificante , Transducción de Señal , Factor de Crecimiento Transformador beta/metabolismo , Translocación Genética/genéticaRESUMEN
We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.
Asunto(s)
Biología Computacional/métodos , Perfilación de la Expresión Génica , Análisis de Secuencia de ADN/métodos , Animales , RatonesRESUMEN
MOTIVATION: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. RESULTS: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled approximately 194 million reads using ABySS into 66 921 contigs 100 bp or longer, with a maximum contig length of 10 951 bp, representing over 30 million base pairs of unique transcriptome sequence, or roughly 1% of the genome. AVAILABILITY AND IMPLEMENTATION: Source code and binaries of ABySS are freely available for download at http://www.bcgsc.ca/platform/bioinfo/software/abyss. Assembler tool is implemented in C++. The parallel version uses Open MPI. ABySS-Explorer tool is implemented in Java using the Java universal network/graph framework. CONTACT: ibirol@bcgsc.ca.