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Ena-DATASET-DKFZ-IBIOS-01-08-2014-15:53:49:885-84 - samples

ABSTRACT: Whole genome bisulfite sequencing data for 6 ependymomas plus 3 fetal controls (f1, f2, f4) and 3 adult controls (a2, a3, a4). See Mack, Witt et al. Nature 506(7489):445-50, 2014 (PMID: 24553142).

PROVIDER: EGAD00001000966 | EGA |

REPOSITORIES: EGA

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Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.

Mack S C SC Witt H H Piro R M RM Gu L L Zuyderduyn S S Stütz A M AM Wang X X Wang X X Gallo M M Garzia L L Zayne K K Zhang X X Ramaswamy V V Jäger N N Jones D T W DT Sill M M Pugh T J TJ Ryzhova M M Wani K M KM Shih D J H DJ Head R R Remke M M Bailey S D SD Zichner T T Faria C C CC Barszczyk M M Stark S S Seker-Cin H H Hutter S S Johann P P Bender S S Hovestadt V V Tzaridis T T Dubuc A M AM Northcott P A PA Peacock J J Bertrand K C KC Agnihotri S S Cavalli F M G FM Clarke I I Nethery-Brokx K K Creasy C L CL Verma S K SK Koster J J Wu X X Yao Y Y Milde T T Sin-Chan P P Zuccaro J J Lau L L Pereira S S Castelo-Branco P P Hirst M M Marra M A MA Roberts S S SS Fults D D Massimi L L Cho Y J YJ Van Meter T T Grajkowska W W Lach B B Kulozik A E AE von Deimling A A Witt O O Scherer S W SW Fan X X Muraszko K M KM Kool M M Pomeroy S L SL Gupta N N Phillips J J Huang A A Tabori U U Hawkins C C Malkin D D Kongkham P N PN Weiss W A WA Jabado N N Rutka J T JT Bouffet E E Korbel J O JO Lupien M M Aldape K D KD Bader G D GD Eils R R Lichter P P Dirks P B PB Pfister S M SM Korshunov A A Taylor M D MD

Nature 20140219 7489

Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants ...[more]

PMID: 24553142

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Project description:The dimethyl ester of bovine pancreatic ribonuclease-A (dimethyl RNAase-A), the initial product of esterification of RNAase-A in anhydrous methanolic HCl, was isolated in a homogeneous form. The two carboxy functions esterified in this derivative are those of glutamic acid-49 and aspartic acid-53. There were no changes in the u.v.-absorption spectral characteristics, the accessibility of the methionine residues, the resistance of the protein to proteolysis by trypsin and the antigenic behaviour of RNAase-A as a result of the esterification of these two carboxy groups. Dimethyl RNAase-A exhibited only 65% of the specific activity of RNAase-A, but still had the same K(m) value for both RNA and 2':3'-cyclic CMP. However, the V(max.) was decreased by about 35%. On careful hydrolysis of the methyl ester groups at pH9.5, dimethyl RNAase-A was converted back into RNAase-A. Limited proteolysis of dimethyl RNAase-A by subtilisin resulted in the formation of an active RNAase-S-type derivative, namely dimethyl RNAase-S, which was chromatographically distinct from dimethyl RNAase-A and had very nearly the same enzymic activity as dimethyl RNAase-A. Fractionation of dimethyl RNAase-S by trichloroacetic acid yielded dimethyl RNAase-S-protein and dimethyl RNAase-S-peptide, both of which were inactive by themselves but regenerated dimethyl RNAase-S when mixed together. Dimethyl RNAase-A-peptide was identical with RNAase-S-peptide. RNAase-S-protein could be generated from dimethyl RNAase-S-protein by careful hydrolysis of the methyl ester groups at pH9.5. The interaction of dimethyl RNAase-S-protein with RNAase-S-peptide appears to be about 4-fold weaker than that between the RNAase-S-protein and RNAase-S-peptide. Conceivably, the binding of the S-peptide ;tail' of dimethyl RNAase-A with the remainder of the molecule is similarly weaker than that in RNAase-A, and this brings about subtle changes in the geometrical orientation of the active-site amino acid residues of these modified methyl ester derivatives. It is suggested that these changes could be responsible for the generation of the catalytically less-efficient RNAase-A and RNAase-S molecules (dimethyl RNAase-A and dimethyl RNAase-S respectively).

Dataset Information

Ena-DATASET-DKFZ-IBIOS-01-08-2014-15:53:49:885-84 - samples

Publications

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.

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