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TMT10-TAILS investigation of the proteolytic landscape in B cell activation

ABSTRACT: The N-terminome in EBV-B cells from a human patient homozygous for an W580S mutation in MALT1 were analyzed by TMT10-plex TAILS and compared to EBV-B cells from heterozygous subjects under resting and PMA/ionomycin stimulation for 2 and 4 h.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Christopher M. Overall

PROVIDER: MSV000083027 | MassIVE | Thu Oct 11 16:31:00 BST 2018

SECONDARY ACCESSION(S): PXD006723

REPOSITORIES: MassIVE

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TMT10-TAILS investigation of the proteolytic landscape in B cell activation

Project description:The N-terminome in EBV-B cells from a human patient homozygous for an W580S mutation in MALT1 were analyzed by TMT10-plex TAILS and compared to EBV-B cells from heterozygous subjects under resting and PMA/ionomycin stimulation for 2 and 4 h.

2018-10-03 | PXD006723 | Pride

TMT10-TAILS for monitoring MALT1 substrate cleavage

Project description:We used TMT-TAILS to monitor MALT1 substrate cleavage in normal EBV B lymphocytes stimulated with PMA/ionomycin to evaluate kinetic profiles of MALT1 inhibitors

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TMT10-TAILS for monitoring MALT1 substrate cleavage

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A genotype directed dose-finding study of Irinotecan (CPT-11) by groups of Uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) polymorphisms in patients with advanced metastatic colorectal cancer and gastric cancer.

Project description:Interventions: Administraion of CPT-11 is twice for 4 weeks on days 1 and 15. CPT-11 is reconstituted in >=250 mL of normal saline or 5% dextrose in water and infuse 90min on day 1 for pharmacokinetics, and 90min over on day15. CPT-11 adjusted dosage is determined from 50,75,100,125 or 150mg/sqm in the heterozygous group and the homozygous group by continual reassessment method. CPT-11 dosage is fixed at 150mg/sqm in the wild group.Definision of UGT1A1 polymorphisms groups: The homozygous group is patient with homozygous genotype of UGT1A1*28/*28 or UGT1A1*6/*6, with combined heterozygous genotypes of UGT1A1*28 and UGT1A1*6. The heterozygous group is patient with heterozygous genotype of either UGT1A1*28 or UGT1A1*6. The wild group is patients with no UGT1A1*28 and UGT1A1*6 mutation. Primary outcome(s): Maximum tolerated dose for the heterozygous group and the homozygous group, respectively. Incidence rate of dose limiting toxicities for the wild group. Study Design: Single arm Non-randomized

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A feasibility study of Irinotecan (CPT-11) by groups of Uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) polymorphisms in patients with metastatic colorectal cancer.

Project description:Interventions: Patients receive FOLFIRI with bevacizumab fixed 5mg/kg. (Treatment will be continued unless the disease progression, unacceptable toxicity, or consent withdrawal.) Definision of UGT1A1 polymorphisms groups: The homozygous group is patient with homozygous genotype of UGT1A1*28/*28 or UGT1A1*6/*6, with combined heterozygous genotypes of UGT1A1*28 and UGT1A1*6. The heterozygous group is patient with heterozygous genotype of either UGT1A1*28 or UGT1A1*6. The wild group is patients with no UGT1A1*28 and UGT1A1*6 mutation. CPT-11 dosage is wild and heterozygous:CPT-11 150mg/m2 homozygous:CPT-11 100mg/m2 Primary outcome(s): 1)incidence of adverse events 2)frequency of severe toxicity Study Design: Single arm Non-randomized

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Bulk-RNA sequencing on Oryzias sakaizumii Kaga and Oryizas latipes Cab tails 13-14SS

Project description:Bulk-RNA sequencing was performed on Kaga and Cab tails at 13-14SS (3 replicates each)

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RNA-seq profiling of tissue from deer mouse embryo tails

Project description:We used RNA-seq to compare transcriptional profiles from the embryonic tails from E12.5–E15.5 Peromyscus maniculatus. Samples are from two ecotypes, forest (P.m.nubiterrae) and prairie (P.m.bairdii) with different numbers of caudal vertebrae.

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Histone N-tails modulate sequence-specific positioning of nucleosomes

Project description:The precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA remain unknown in detail. Existing algorithms, taking into account the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo. To uncover novel factors responsible for the nucleosome positioning, we analyzed potential involvement of the histone N-tails in this process. To this aim, we reconstituted the H2A/H4 N-tailless nucleosomes on human BRCA1 DNA (~100 kb) and compared their positions and sequences with those of the wild-type nucleosomes. In the case of H2A tailless nucleosomes, the AT content of DNA sequences is changed locally at superhelical location (SHL) ±4, while maintaining the same rotational setting as their wild-type counterparts. Conversely, the H4 tailless nucleosomes display widespread changes of the AT content near SHL ±1 and SHL ±2, where the H4 N-tails interact with DNA. Furthermore, a substantial number of H4 tailless nucleosomes exhibit rotational setting opposite to that of the wild-type nucleosomes. Thus, our findings strongly suggest that the histone N-tails are operative in selection of nucleosome positions, which may have wide-ranging implications for epigenetic modulation of chromatin states.

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Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization [Bisulfite-seq]

Project description:To determine what DNA methylation and gene expression changes occur following EBV transformation. B-cells were isolated from 3 donors. Resting, CD40 activated and EBV transfromed cells from each donor was analyzed. Each sample was assayed using Affymetrix expression arrays and whole genome bisulfite sequenicng. Additional time points during transformation and activation were sequenced as well, but not assayed for expression. B-cells were isolated from 3 donors. Resting, CD40 activated and EBV transfromed cells from each donor was analyzed. Additional B-cells were isolated from 2 additional donors and assay at days 16 and week 3 following CD40 activation and EBV infection. Only one donor contributed to the EBV timepoints.

2013-09-17 | E-GEOD-49627 | biostudies-arrayexpress

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