The genetic landscape of the childhood cancer medulloblastoma.

Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.
Science (Impact Factor: 31.48). 01/2011; 331(6016):435-9. DOI: 10.1126/science.1198056
Source: PubMed

ABSTRACT Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high-density microarrays and sequenced all known protein-coding genes and microRNA genes using Sanger sequencing in a set of 22 MBs. We found that, on average, each tumor had 11 gene alterations, fewer by a factor of 5 to 10 than in the adult solid tumors that have been sequenced to date. In addition to alterations in the Hedgehog and Wnt pathways, our analysis led to the discovery of genes not previously known to be altered in MBs. Most notably, inactivating mutations of the histone-lysine N-methyltransferase genes MLL2 or MLL3 were identified in 16% of MB patients. These results demonstrate key differences between the genetic landscapes of adult and childhood cancers, highlight dysregulation of developmental pathways as an important mechanism underlying MBs, and identify a role for a specific type of histone methylation in human tumorigenesis.

  • [Show abstract] [Hide abstract]
    ABSTRACT: Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers. We performed exome sequencing on 113 tumor-normal pairs, yielding a mean of 82 non-silent mutations per tumor, and 8 cell lines. The mutational profile of ESCC closely resembles those of squamous cell carcinomas of other tissues but differs from that of esophageal adenocarcinoma. Genes involved in cell cycle and apoptosis regulation were mutated in 99% of cases by somatic alternations of TP53 (93%), CCND1 (33%), CDKN2A (20%), NFE2L2 (10%) and RB1 (9%). Histone modifier genes were frequently mutated, including KMT2D (also called MLL2; 19%), KMT2C (MLL3; 6%), KDM6A (7%), EP300 (10%) and CREBBP (6%). EP300 mutations were associated with poor survival. The Hippo and Notch pathways were dysregulated by mutations in FAT1, FAT2, FAT3 or FAT4 (27%) or AJUBA (JUB; 7%) and NOTCH1, NOTCH2 or NOTCH3 (22%) or FBXW7 (5%), respectively. These results define the mutational landscape of ESCC and highlight mutations in epigenetic modulators with prognostic and potentially therapeutic implications.
    Nature Genetics 08/2014; · 29.65 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Gliomas, the most common primary brain tumors in adults, constitute clinically, histologically, and molecularly a most heterogeneous type of cancer. Owing to this, accurate clinical prognosis for short-term vs. long-term survival for patients with grade II or III glioma is currently nonexistent. A rigorous, multi-method bioinformatic approach was used to identify the top most differentially expressed genes as captured by mRNA sequencing of tumor tissue. Mathematical modeling was employed to develop the model, and three different and independent methods of validation were used to assess its performance. I present here a mathematical model that can identify with a high accuracy (sensitivity=92.9%, specificity=96.0%) those patients with glioma (grade II or III) who will experience short-term survival (≤ 1 year), as well as those with long-term survival (≥ 3 years), at the time of diagnosis and prior to surgery and adjuvant chemotherapy. The 5 gene input variables to the model are: FAM120AOS, PDLIM4, OCIAD2, PCDH15, and MXI1. MXI1, a transcriptional repressor, represents the top biomarker of survival and the most promising target for the development of a pharmacological treatment.
    American journal of cancer research. 01/2014; 4(6):862-73.
  • [Show abstract] [Hide abstract]
    ABSTRACT: SMARCA4 (BRG1) and SMARCB1 (INI1) are tumor suppressor genes that are crucially involved in the formation of malignant rhabdoid tumors, such as atypical teratoid/rhabdoid tumor (AT/RT). AT/RTs typically affect infants and occur at various sites of the CNS with a particular frequency in the cerebellum. Here, granule neurons and their progenitors represent the most abundant cell type and are known to give rise to a subset of medulloblastoma, a histologically similar embryonal brain tumor. To test how Smarc proteins influence the development of granule neurons and whether this population may serve as cellular origin for AT/RTs, we specifically deleted Smarca4 and Smarcb1 in cerebellar granule cell precursors. Respective mutant mice displayed severe ataxia and motor coordination deficits, but did not develop any tumors. In fact, they suffered from a severely hypoplastic cerebellum due to a significant inhibition of granule neuron precursor proliferation. Molecularly, this was accompanied by an enhanced activity of Wnt/β-catenin signaling that, by itself, is known to cause a nearly identical phenotype. We further used an hGFAP-cre allele, which deleted Smarcb1 much earlier and in a wider neural precursor population, but we still did not detect any tumor formation in the CNS. In summary, our results emphasize cell-type-dependent roles of Smarc proteins and argue against cerebellar granule cells and other progeny of hGFAP-positive neural precursors as the cellular origin for AT/RTs.
    Journal of Neuroscience 10/2014; · 6.75 Impact Factor


Available from
May 19, 2014