This SuperSeries is composed of the SubSeries listed below.
A NOTCH3 transcriptional module induces cell motility in neuroblastoma.
Specimen part, Cell line
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Methylation of cancer-stem-cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients.
Sex, Age, Specimen part, Disease
View SamplesProfiling project of CRC patient material collected in the Academic Medical Center (AMC) in Amsterdam, The Netherlands. We focused on a set of 90 AJCC stage II patients that underwent intentionally curative surgery in the years 1997-2006 (AMC-AJCCII-90). Extensive medical records are kept from these patients and long-term clinical follow-up is available for the large majority. Both paraffin-embedded as well as fresh frozen tissue is available from all these patients for analysis.
Methylation of cancer-stem-cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients.
Sex, Age, Specimen part, Disease
View SamplesmRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGF pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.
Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes.
Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
A NOTCH feed-forward loop drives reprogramming from adrenergic to mesenchymal state in neuroblastoma.
Specimen part, Cell line, Time
View SamplesTo identify molecular subtypes of medulloblastoma we have profiled a series of 62 medulloblastoma tumors. Unsupervised hierarchical cluster analysis of these data identified 5 distinct molecular subtypes.
Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features.
Sex
View SamplesIn Rspondin-based 3D cultures, Lgr5 stem cells from multiple organs form ever-expanding epithelial organoids that retain their tissue identity. We report the establishment of tumor organoid cultures from 20 consecutive colorectal (CRC) patients. For most, organoids were also generated from adjacent normal tissue. The organoids closely resemble the original tumor. The spectrum of genetic changes observed within the 'living biobank' agrees well with previous large-scale mutational analyses of CRC. Gene expression analysis indicates that the major CRC molecular subtypes are represented. Tumor organoids are amenable to robotized, high-throughput drug screens allowing detection of gene-drug associations. As an example, a single organoid culture was exquisitely sensitive to Wnt secretion (porcupine) inhibitors and carried a mutation in the negative Wnt feedback regulator RNF43 (rather than in APC). Organoid technology may fill the gap between cancer genetics and patient trials, complement cell line- and xenograft-based drug studies and allow personalized therapy design.
Prospective derivation of a living organoid biobank of colorectal cancer patients.
Specimen part, Disease, Disease stage, Subject
View SamplesWhole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis
TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors.
Specimen part
View SamplesValidation of the RT-qPCR test by comparison with the 4-gene microarray test and the original random forest-based CMS (consensus molecular subtypes) classifier
No associated publication
Specimen part, Disease
View SamplesmRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 (http://r2.amc.nl) in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGF pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.
Deoxyhypusine synthase (DHPS) inhibitor GC7 induces p21/Rb-mediated inhibition of tumor cell growth and DHPS expression correlates with poor prognosis in neuroblastoma patients.
Specimen part, Cell line
View Samples