Rhabdomyosarcoma is a childhood tumor with features of aberrant muscle differentiation. We studied samples from 101 rhabdomyosarcoma patients to determine core gene expression signatures relevant in the disease.
Integrative Bayesian Analysis Identifies Rhabdomyosarcoma Disease Genes.
Sex, Age, Specimen partView Samples
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Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.
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Renal cell carcinoma (RCC) exhibits some unusual features and genes commonly mutated in cancer are rarely mutated in clear-cell RCC (ccRCC), the most common type. The most prevalent genetic alteration in ccRCC is the inactivation of the tumor suppressor gene VHL. Using whole-genome and exome sequencing we discovered BAP1 as a novel tumor suppressor in ccRCC that shows little overlap with mutations in PBRM1, another recent tumor suppressor. Whereas VHL was mutated in 81% of the patients (142/176), PBRM1 was lost in 58% and BAP1 in 15% of the patients analyzed. All these tumor suppressor genes are located in chromosome 3p, which is partially or completely lost in most ccRCC patients. However, BAP1 but not PBRM1 loss was associated with higher Fuhrman grade and, therefore, poorer outcome. Xenograft tumors (tumorgrafts) implanted orthotopically in mice exhibited similar gene expression profiling to corresponding primary tumors. Gene expression profiling of tumors and tumorgrafts displayed different signatures for BAP1- and PBRM1-deficient samples. Thus, after inactivation of VHL, the acquisition of a mutation in BAP1 or PBRM1 defines a different program that might alter the fate of the patient. Our results establish the foundation for an integrated pathological and molecular genetic classification of about 70% of ccRCC patients, paving the way for subtype-specific treatments exploiting genetic vulnerabilities.
BAP1 loss defines a new class of renal cell carcinoma.
Sex, Age, Specimen part, Disease, Disease stage, SubjectView Samples
The signaling pathways orchestrating both the evolution and development of language in the human brain remain unknown. To date, the transcription factor FOXP2 is the only gene implicated in Mendelian forms of human speech and language dysfunction1,2. It has been proposed, that the amino acid composition in the human variant of FOXP2 has undergone accelerated evolution, and this change occurred around the time of language emergence in humans3,4. However, this remains controversial, and whether the acquisition of these amino acids in human FOXP2 has any functional consequence in human neurons remains untested. Here, we demonstrate that these two amino acids confer new functionality in terms of differential transcriptional regulation, and extend these observations to in vivo brain, showing that several of the differential FOXP2 targets significantly overlap with genes different between human and chimpanzee brain. We also identify novel relationships among the differentially expressed genes with additional critical regulators of neuronal development. These data provide support for the functional relevance of changes that occur on the human lineage by showing that the two amino acids unique to human FOXP2 can lead to significant differences in gene expression patterns across brain evolution, with direct consequences for human brain development and disease. Since FOXP2 has an important role in the use of language in humans, the identified targets may have a critical function in the development and evolution of language circuitry in humans.
Human-specific transcriptional regulation of CNS development genes by FOXP2.
Specimen part, Cell lineView Samples
Gene expression profile studies have identified an interferon signature in whole blood or mononuclear cell samples from patients with systemic lupus erythematosus. This study was designed to determine whether specific lymphocyte and myeloid subsets freshly isolated from the blood of systemic lupus erythematosus patients demonstrated unique gene expression profiles compared to subsets isolated from healthy controls.
Combined deficiency of proapoptotic regulators Bim and Fas results in the early onset of systemic autoimmunity.
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The requirement of frozen tissues for microarray experiments limits the clinical usage of genome-wide expression profiling using microarray technology.
Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients.
Sex, Specimen part, RaceView Samples
Develop an EGFR mutation gene expression signature to aid in predicting response and clinical outcome and to identify genes associated with the EGFR-dependent phenotype
No associated publication
Sex, Age, Disease stage, RaceView Samples