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87 results for “NSD2”

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zenodo40/100

Data files for manuscript "A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2"

#2022-02-21 #Summary This ZIP-file contains the data files used for all analyses for the manuscript "A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2". #File structure README.txt                                                                    This README file. File S02 ("FileS02_NSD2-clinical-information-and-variants.xlsx")            Clinical data of GoF and LoF inidviduals used for Table 1 and Table 2 and genetic variant data used for Figure 2. File S03 ("FileS03_NSD2-CCLE-analyses.xlsx")                                Tables containing information of the CCLE analyses and depmap results used for Figure 3A-D. File S04 ("FileS04_humanbase_global_1642958821189.tar.gz")                    Tar.gz file of the downlaoded humanbase result files used for Figure 3E. #Files and checksums 5FE613FC7646419C20153068E8D5F463    ./FileS02_NSD2-clinical-information-and-variants.xlsx AC53634E6044469BE42DBBE8F7503275    ./FileS03_NSD2-CCLE-analyses.xlsx 7AE58A28A4D1E1462521A37522BB78B6    ./FileS04_humanbase_global_1642958821189.tar.gz

opencc-by-4.0Feb 2022View details →

zenodo36/100

Chemoproteomic Analysis of an NSD2-PWWP1 Chemical Probe

Dataset details Project Title: Chemoproteomic Analysis of an NSD2-PWWP1 Chemical Probe Keywords: chemoproteomics, epigenetics, chemical probe, histone methyltransferase Project description: Here we use competitive chemoproteomics pulldowns followed by label-free quantitative LC-MS/MS to assess target engagement and selectivity profiles of UNC6934 and UNC7145, a chemical probe targeting the PWWP1 domain of NSD2 and its negative control counterpart, respectively. To this end, we used a biotinylated probe derivative (UNC7096) for streptavidin pulldowns from KMS-11 multiple myeloma cell lysates, including in the context of UNC7145 or UNC6934 competition. Methods: Chemical Proteomics  To prepare whole cell lysates, KMS11 cells were washed 2 times with 1x PBS, lysed by resuspension in high-salt lysis buffer (20 mM HEPES pH 7.5, 350 mM KCl, 1% Triton X-100 + a protease inhibitor cocktail containing aprotinin, leupeptin, pepstatin A, and E-64) and passed through a 25 gauge needle 5 times followed by a 20 min incubation on ice. Cell lysates were cleared by centrifugation at 18 000 x g for 20 minutes at 4°C. Cleared supernatant was diluted to 150 mM KCl and 0.4% Triton X-100 with 20mM HEPES pH7.5 including fresh protease inhibitors. Sample protein concentrations were determined using the BCA assay (ThermoScientific). For each pulldown, 3 mg of cell lysate was pre-incubated with either DMSO control, 20 µM UNC7145, or 20 µM UNC6934 (final concentration) for 1 hour with rotation at 4°C. For each sample, 25 µl of M270 Dynabeads (ThermoScientific) were prepared by washing three times in low salt wash buffer (10 mM Tris-HCl pH7.9, 100 mM NaCl, 0.1% NP-40), followed by incubation with 1 µM UNC7096 (biotinylated probe) for 1 hour at 4 °C. The unbound biotinylated compound was removed by 3 washes with low salt buffer. UNC7096 bound beads were then added to each sample followed by incubation 1 hour with rotation at 4oC. Beads were then washed 3 times with low-salt wash buffer followed by 2 washes with 50mM ammonium bicarbonate. On-bead digestion was performed by overnight incubation at 37°C with 2 µg of mass spectrometry grade trypsin (Promega). The following morning an additional 2 µg of trypsin was added to each sample and incubated at 37°C for 4-6 hours. The supernatant, containing digested peptides, was collected. Beads were then washed twice with water and supernatant pooled with digested peptides. Samples were then acidified with formic acid to a final concentration of 2% final concentration and flash frozen prior drying under vacuum before being run on a Thermo Scientific LTQ Orbitrap Velos. Label-free quantitative mass spectrometry data analysis  Raw MS/MS files were searched and quantified using Maxquant version 1.6.7.0 using the UP000005640 Uniprot human database (containing 20,605 protein entries, last modified November 5, 2019) with label-free quantification enabled and variable modifications oxidized methionine (+15.9949 Da) and deamidated asparagine (+0.9840) set. First search peptide tolerance and main search peptide tolerance were set at 30 and 6 ppm, respectively. For all other parameters default settings were used.  Differential enrichment analysis was performed using the DEP package (v1.8.0) in R (v3.5.1). Briefly, samples were filtered for proteins identified in 2 out of 3 replicates of at least one condition, normalized by variance stabilizing normalization and tested for differential enrichment relative to pulldowns competed with DMSO vehicle control.  Brief Description of Data Files: <ul> <li>.raw & .index files - raw proteomic data files - note: dataset has also been uploaded to ProteomeXchange Consortium via the PRIDE17 partner repository with the dataset identifier PXD017641. </li> <li>mqpar.xml - provides parameters used for quantification with Maxquant, which can be found in the combined folder. </li> <li>UP000005640_9606.fasta - UniProt reference used for Mazquant quantification of peptides</li> <li>NSD2_Chemoproteomics.Rproj & DEP_Analysis.R - R project & script file for differential analysis of Maxquant output with DEP. </li> <li>methods.docx - additional details covering experimental method</li> </ul>

opencc-by-4.0Aug 2021View details →

zenodo32/100

Diffraction images for PWWP1 domain of NSD2 in complex with MR837

A set of x-ray diffraction images collected at beam line 08ID of the Canadian Light Source.

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Dataset results

Data files for manuscript "A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2"

Chemoproteomic Analysis of an NSD2-PWWP1 Chemical Probe

Diffraction images for PWWP1 domain of NSD2 in complex with MR837

NSD2 targeting reverses plasticity and drug resistance in prostate cancer

The NSD2 p.E1099K Mutation is Enriched at Relapse and Confers Drug Resistance in a Cell Context Dependent Manner in Pediatric Acute Lymphoblastic Leukemia

Depletion of Nsd2-mediated histone H3K36 methylation impairs adipose tissue development and function

NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming [RNAi]

NSD2 targeting reverses lineage plasticity and drug resistance in advanced prostate cancer [multiome snRNA-seq]

NSD2 interacts with SMARCA2 and regulates expression of oncogenes CCND1 and PRL3 in t(4;14) multiple myeloma

SPT6 interacts with NSD2 and facilitates interferon-stimulated transcription

The C-terminal of NSD2 regulates transcription of cell adhesion genes in multiple myeloma

Epigenetic Activation and alteration of chromatin structure regulated by NSD2 in metastatic castration-resistant prostate cancer

Next Generation Sequencing of Wild Type and Nsd2 Treg cells conditional knock out Treg cells Transcriptomes

The NSD2 p.E1099K Mutation is Enriched at Relapse and Confers Drug Resistance in a Cell Context Dependent Manner in Pediatric Acute Lymphoblastic Leukemia (RNA-Seq)

NSD2 targeting reverses lineage plasticity and drug resistance in advanced prostate cancer [scRNA-seq]

Loss of NSD2 causes dysregulation of synaptic genes and altered H3K36 dimethylation in mice [RNA-seq]

NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming

Effects of NSD2 depletion on gene expression and H3K36me2 in a lung cancer cell line

Targeting steroid receptor co-activator 3 sensitizes myeloma cell to proteasome inhibitor treatment through NSD2-mediated phase separation and chromatin remodeling [RNA-Seq]

NSD2 amplifies oncogenic transcriptional output to promote lung adenocarcinoma pathogenesis

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