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EWSR1 protein, human

EWSR1 protein is a fusion protein involved in several types of cancer, including Ewing sarcoma.
It is characterized by the presence of the Ewing sarcoma breakpoint region 1 (EWSR1) gene, which can fuse with other genes to form oncogenic fusion proteins.
Understanding the role of EWSR1 protein in disease pathogenesis is crucial for developing effective treatments.
Researchers can use PubCompare.ai's AI-powered protocol optimization to identify the most accurate and effective protocols from literature, preprints, and patents, advancing their EWSR1 protein research with confidence.

Most cited protocols related to «EWSR1 protein, human»

FISH on interphase nuclei from paraffin embedded 4-micron sections was performed applying custom probes using bacterial artificial chromosomes (BAC), covering and flanking EWSR1 in 22q12, FUS in 16p11, PBX1 in 1q23, ZNF444 in 19q13 and POU5F1 in 6p21 (Fig. 1). BAC clones were chosen according to USCS genome browser (http://genome.uscs.edu). The BAC clones were obtained from BACPAC sources of Children's Hospital of Oakland Research Institute (CHORI) (Oakland, CA) (http://bacpac.chori.org). DNA from individual BACs was isolated according to the manufacturer’s instructions, labeled with different fluorochromes in a nick translation reaction, denatured, and hybridized to pretreated slides. Slides were then incubated, washed, and mounted with DAPI in an antifade solution, as previously described (Agaram et al., 2008 (link)). The genomic location of each BAC set was verified by hybridizing them to normal metaphase chromosomes. Two hundred successive nuclei were examined using a Zeiss fluorescence microscope (Zeiss Axioplan, Oberkochen, Germany), controlled by Isis 5 software (Metasystems). A positive score was interpreted when at least 20% of the nuclei showed a break-apart signal. Nuclei with incomplete set of signals were omitted from the score.
All cases were first tested with an EWSR1 probe. The EWSR1-rearranged tumors were then evaluated for break-apart signals using probes for PBX1, ZNF444, and POU5F1. The EWSR1 negative tumors were then tested for FUS break-apart, since FUS may substitute for the EWSR1 gene in certain translocation-associated sarcomas. In selective cases, two-color FISH was applied using probe-sets centromerically flanking one gene and telomerically flanking the partner gene, in order to confirm the fusion between EWSR1 and the partner genes. In one case a G-banded karyotype was obtained after short term culture.
Publication 2010
Bacterial Artificial Chromosomes Cell Nucleus Chromosomes Clone Cells DAPI EWSR1 protein, human Fishes Fluorescent Dyes Genes Genome Interphase Karyotyping Metaphase Microscopy, Fluorescence Neoplasms Paraffin pbx1 protein, human POU5F1 protein, human Sarcoma Translocation, Chromosomal
Formalin-fixed paraffin-embedded tissues were available in each case for FISH analysis. FISH for EWSR1 was performed on all cases and followed by subsequent FISH for various fusion partners, including CREM, CREB1, and ATF1. FISH was performed on 4 μm-thick formalin-fixed paraffin-embedded (FFPE) tissue sections. Custom probes were made by bacterial artificial chromosomes (BAC) clones (Supplementary Table 2) flanking the target genes, according to UCSC genome browser (http://genome.ucsc.edu) and obtained from BACPAC sources of Children’s Hospital of Oakland Research Institute (Oakland, CA; http://bacpac.chori.org). DNA from each BACs was isolated according to the manufacturer’s instructions. The BAC clones were labeled with fluorochromes by nick translation and validated on normal metaphase chromosomes. The slides were deparaffinized, pretreated, and hybridized with denatured probes. After overnight incubation, the slides were washed, stained with DAPI, mounted with an antifade solution, and then examined on a Zeiss fluorescence microscope (Zeiss Axioplan, Oberkochen, Germany) controlled by Isis 5 software (Metasystems).
Publication 2016
Bacterial Artificial Chromosomes Child Chromosomes Clone Cells DAPI EWSR1 protein, human Fishes Fluorescent Dyes Formalin Genes Genome Metaphase Microscopy, Fluorescence Paraffin Paraffin Embedding Tissues
The validation of the MSK-Fusion Solid panel was performed according to NYS DOH standard requirements. The panel was fully approved by NYS DOH for use in our clinical laboratory. In brief, the accuracy study included 132 unique tumor RNA samples from formalin-fixed paraffin-embedded sections. These samples were previously profiled in our clinical laboratory and were confirmed to be positive for fusions by alternate methods. The assay called 99% of the expected fusions with high confidence. The reproducibility and precision studies included 8 samples positive for known fusions sequenced in triplicate within the same and across 3 separate runs; 100% of the expected calls were made. Finally, the analytical sensitivity of the assay was determined using 3 cell lines harboring 3 different fusions: A673 (EWSR1-FLI1), SYO1 (SS18-SSX2) and H3122 (EML4-ALK). Serial dilutions were prepared by mixing each positive sample with RNA from a normal sample previously characterized as fusion negative. The sensitivity results demonstrated that gene fusion detection sensitivity of the assay is at approximately 3% positive tumor RNA. This assay sensitivity should be viewed as an estimate, recognizing that it can also affected by differences in the expression levels of different fusions.
Publication 2018
Biological Assay Cell Lines Clinical Laboratory Services EWSR1 protein, human Formalin Gene Fusion Hypersensitivity Paraffin Embedding RNA, Neoplasm Technique, Dilution
Our discovery cohort comprised 112 patients with Ewing sarcoma; both tumor and germline samples underwent whole-genome sequencing. All tumors selected for WGS were predicted to contain a large proportion of tumor cells based on pathology reports, previous CGH or SNP arrays, and/or a low Ct (cycle threshold) of EWSR1–ETS fusion assessed by RT-QPCR. Eighteen Ewing sarcomas were obtained from the St. Jude tissue resource core facility for genome sequence analysis with St Jude Institutional Review Board (IRB) approval for the Pediatric Cancer Genome Project (PCGP). The remaining cases were those referred to Institut Curie from all over France for molecular diagnosis of Ewing sarcoma. Samples were stored in a tumor bank at the Institut Curie. The genetic study was approved by the Institutional Review Board of the Institut Curie (Paris, France) and by the Comité de Protection de Personnes Ile-de-France I (regional ethics committee; GenEwing n° IC 2009-02); specific informed consent was provided. Most patients were treated according to the EuroEwing protocol (47 (link)). An anonymization procedure was performed before compilation of clinical, histologic, and biological information in a secure database with restricted access. All tumors included in this study were positive for the EWSR1–ETS fusion. Detailed clinicopathologic and sequencing information is provided in Fig. 1 and Supplementary Table S1.
The follow-up set comprising 199 tumor DNAs from EWSR1–ETS-positive Ewing sarcomas was distinct from the discovery set and consisted of patients treated according to the EuroEwing99 protocol.
Publication 2014
Biopharmaceuticals Cells DNA, Neoplasm Ethics Committees, Research EWSR1 protein, human Genome Germ Line Malignant Neoplasms Molecular Diagnostics Neoplasms Patients Regional Ethics Committees Tissues
RNA was extracted at five time points—0 h, 18 h, 36 h, 53 h, 72 h—and subjected to microarray analysis where 0 h marks the time point when doxycycline was added, and 18 h the time point when modulation of EWSR1/FLI1 protein was first observed as determined by immunoblot analysis. RNA was hybridized to Affymetrix GeneChip Human Genome U133A 2.0 Arrays. cRNA target synthesis and GeneChip processing were performed according to standard protocols (Affymetrix). Processing of CEL files, normalizing, and filtering were done in the R statistical environment using Bioconductor packages (Wu et al. 2004 ). Each time point was replicated at least twice.
Affymetrix CEL files were read into the R statistical environment and normalized using the “gcrma” algorithm (Wu et al. 2004 ). Probe sets with very low expression values across all samples (R package “panp”) were filtered out. Subsequently, probe sets associated with the same gene identifier were averaged and merged to one symbol, yielding 12,928 unique genes. Principal component analysis was performed using the GNU scientific library Singular Value Decomposition routines. Pearson correlation coefficients with |r| > 0.8 of comparing individual genes with the first three principal components were used to identify significantly correlated genes.
Publication 2013
Anabolism Complementary RNA DNA Library Doxycycline EWSR1 protein, human Gene Chips Genes Genome, Human Immunoblotting Maritally Unattached Microarray Analysis

Most recents protocols related to «EWSR1 protein, human»

To establish the (AID-EWSR1/AID-EWSR1) DLD-1 cell line, CRISPR/Cas9 system was employed to tag the 5’ end of EWSR1 gene with mini-AID (mAID).
The donor plasmid of mAID was generated by following the procedure of the previous report with a minor modification (Hassebroek et al., 2020 (link)). First, the homology arms (left/up and right/down) that targets the EWSR1 locus were amplified from genomic DNA extracted from DLD-1 using following primers, respectively. Note that mutations were introduced in PAM sequences on the homology arms to avoid the Cas9 dependent degradation of the donor plasmid. The PCR products for the homology arms were inserted into the donor plasmid (containing hygromycin resistant gene/P2A sequence and 3x mini-AID and 3X Flag sequence) using PciI/SalI and SpeI/NotI sites, respectively (Hassebroek et al., 2020 (link)).
The guide RNA sequence was designed using the CRISPR Design Tool; Zhang laboratory, MIT. The suggested guide RNA sequences are listed below.

- EWSR1 gRNA1 F: ATG​GCG​TCC​ACG​GGT​GAG​TA

- EWSR1 gRNA1 R: TAC​TCA​CCC​GTG​GAC​GCC​AT

- EWSR1 gRNA2 F: AGT​TCC​ACC​ATA​CTC​ACC​CG

- EWSR1 gRNA2 R: CGG​GTG​AGT​ATG​GTG​GAA​CT

The oligonucleotides (synthesized by Integrated DNA technologies, IDT) were annealed, inserted into pX330 at its BbsI site (Addgene, #42230), and its sequence was confirmed by the DNA sequencing (ACGT Inc.).
The EWSR1-mCherry and EWSR1:R565A-mCherry DNA constructs that targets the AAVS1 locus of the (AID-EWSR1/AID-EWSR1) DLD-1 cell line are generated as described below. The mCherry, hEWSR1,hEWSR1:R565A genes were individually amplified using pCDNA4-His-maxC-mCherry, pSG5-2XFLAG-hEWSR1 or pSG5-2XFLAG-hEWSR1:R565A plasmids as a template using the following primers (Park et al., 2014 (link)).

- MluI-hEWS F: 5′-GAT​ACG​CGT​ATG​GCT​GCC​ACG​GAT​TAC-3′

- NotInostop3′huEWS 1965to1945hEWS R: 5′-CTG​CGG​CCG​CGT​AGG​GCC​GAT​CTC​TGC-3′

- NotI mChe F: 5′-GCG​GCC​GCA​GGC​GCT​GG-3′

- SalI stop mChe R: 5′-CTT​GTC​GAC​TTA​CTT​GTA​CAG​CTC​GTC​C-3′

The PCR products of hEWSR1, hEWSR1:R565A and mCherry were inserted to SalI and MluI sites of pMK243 that had been modified at its multicloning sites in the previous study (Tet-OSTIR1-PURO) (Natsume et al., 2016 (link); Hassebroek et al., 2020 (link); Park et al., 2021 (link)).
Publication 2023
Arm, Upper Cell Lines Clustered Regularly Interspaced Short Palindromic Repeats EWSR1 protein, human fluorinated trisacryl conjugate Genes Genome Homologous Sequences hygromycin A Mutation Oligonucleotide Primers Oligonucleotides Plasmids Tissue Donors
Targeted sequencing results from primary or metastatic tumors profiled with our clinical NGS-panel, OncoKids®, were reviewed for 26 cases34 (link). The LP-WGS data from the LB samples were assessed to determine whether the same mutations could be detected. For mutations identified by OncoKids®, we used GetBaseCountsMultisample, to verify the presence of a mutation in LP-WGS (https://github.com/mskcc/GetBaseCountsMultiSample). We further verified the presence of mutations by LP-WGS using Integrative Genomics Viewer (IGV)39 .
For detection of the EWSR1 and FOXO1 fusions in Ewing sarcoma and ARMS patients, respectively, we designed a custom panel to test in tumor DNA using a hybridization-based capture method (Twist Bioscience, South San Francisco, CA). Since UMIs only help with correcting PCR and chemistry artifacts when detecting point mutations, we trimmed the UMIs using the Dragen 3.7.3 aligner and realigned the reads to build 37 of the human reference genome. This increased the sensitivity to detect fusions. We used Illumina Manta (version 1.6.0) in the “targeted” mode (Manta">https://github.com/Illumina/Manta) to detect structural variants. All statistical analysis was carried out using R version 4.0.4.
Publication 2023
Arm, Upper Crossbreeding DNA, Neoplasm Ewings Sarcoma EWSR1 protein, human Genome, Human Hypersensitivity Mutation Neoplasm Metastasis Patients Point Mutation
Protein extraction was performed using gentle hypotonic lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 2 mM EDTA, 0.5% Triton-X-100) supplemented with 1 × complete protease inhibitor (Roche). After 30 min incubation on ice, the NaCl concentration was adjusted to 150 mM, followed by another 5 min incubation on ice. The lysate was cleared by centrifugation at 16000xg for 15 min at 4 °C. Western blot analyses were performed according to the already published protocol from our laboratory16 (link). Briefly, 30 μg of proteins were separated by SDS–polyacrylamide gel electrophoresis, transferred to polyvinylidene difluoride (PVDF) membranes (Millipore), blocking was done with 5% skim milk diluted in PBS or TBS with 0.1% Tween-20 (PBS-T or TBS-T), and then incubated for 1.5–2 h at room temperature (RT) with anti-FUS (Santa Cruz, 4H11, 1:3000 dilution in PBS-T), home-made polyclonal rabbit anti-FUS9 (link), anti-actin (MP Biomedicals, 691,001, 1:25,000 dilution in PBS-T), anti-FBL (Santa Cruz, sc-25397, 1:500 dilution in TBS-T), anti-NOP56 (Santa Cruz, sc-23701, 1:500 dilution in TBS-T), anti-EWSR1 (Santa Cruz, sc-48404, 1:500 dilution in TBS-T) primary antibodies. After washing, the membrane was incubated for 1 h at RT with species-specific horseradish peroxidase (HRP)-coupled secondary antibody (Santa Cruz, sc-2005, goat anti-mouse; Santa Cruz, sc-2357, mouse anti-rabbit; Santa Cruz, sc-2020, monkey anti-goat; 1:3000 dilution in PBS-T). The signal was detected using the enhanced chemiluminescence method (ECL, GE Healthcare) and quantified using Image J software. Immunofluorescence was performed according to the protocol described in16 (link). Images were acquired using an Olympus Fluoview 1200 IX83 confocal scanning microscope with a 60 × oil-immersion objective. Two channels were used to acquire images with the following excitation parameters: 488 nm for Alexa Fluor 488 and 405 nm for DAPI. The obtained images were analyzed using ImageJ software.
Publication 2023
Actins alexa fluor 488 Antibodies Buffers Centrifugation Chemiluminescence DAPI Edetic Acid EWSR1 protein, human Goat Horseradish Peroxidase Immunofluorescence Immunoglobulins Microscopy, Confocal, Laser Scanning Milk, Cow's Monkeys Mus polyvinylidene fluoride Proteins Rabbits SDS-PAGE SERPINA1 protein, human Sodium Chloride Submersion Technique, Dilution Tissue, Membrane Triton X-100 Tromethamine Tween 20 Western Blot
To assess EWSR1::FLI1 protein levels, cells were harvested in 2X SDS-loading buffer with 2-mercaptoethanol and boiled. To assess proteins enriched by immunoprecipitation, eluted proteins were diluted 1:1 in 2X SDS-loading buffer with 2-mercaptoethanol and incubated at 95°C for 5 min. For all western blots, proteins were resolved by SDS/PAGE (BioRad) and were transferred onto a nitrocellulose membrane (BioRad). After blocking in 5% BSA in PBS, membranes were probed using the appropriate primary antibody (Table 3) and fluorescent secondary antibodies (LiCor). Quantification was performed using Image Studio Lite (LiCor, version 5.2).
Publication 2023
2-Mercaptoethanol Buffers Cells EWSR1 protein, human Fluorescent Antibody Technique Immunoglobulins Immunoprecipitation Nitrocellulose Proteins SDS-PAGE Tissue, Membrane Western Blot
The retrospective patient population is derived from the Department of Pathology at the University of Debrecen, from the period of January 2015–December 2022. Cases diagnosed as “atypical Ewing sarcoma” without EWSR1 rearrangement being detected by FISH were investigated. Due to its rarity, we found only one case that met these criteria.
For research purposes, this patient consented and agreed, according to the ethical guidelines of the University of Debrecen, to the use of tissue blocks and clinical information for this report. All protocols have been approved by the authors’ respective Institutional Review Boards for human subjects (IRB reference number: 60355-2/2016/EKU and IV/8465-3/2021/EKU). This study was managed according to the Declaration of Helsinki.
Publication 2023
Ewings Sarcoma EWSR1 protein, human Fishes Patients Tissues

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More about "EWSR1 protein, human"

The EWSR1 protein is a critical player in various types of cancer, including the devastating Ewing sarcoma.
This fusion protein, characterized by the presence of the EWSR1 gene, can combine with other genes to form potent oncogenic fusion proteins.
Understanding the complex role of EWSR1 in disease pathogenesis is crucial for developing effective treatments.
Researchers can leverage the power of PubCompare.ai's AI-powered protocol optimization to identify the most accurate and effective protocols from literature, preprints, and patents.
This advanced tool can help advance EWSR1 protein research with confidence.
When studying the EWSR1 protein, researchers may utilize techniques like fluorescence microscopy, which can visualize the subcellular localization of the protein using fluorescent labels.
Cell culture experiments with EWSR1-expressing cell lines may involve the use of Isis 5 software for data analysis, FBS for cell growth, TRIzol reagent for RNA extraction, and Puromycin for selecting transfected cells.
To further understand the EWSR1 fusion partners and their impact, the TruSight RNA Fusion Panel can be employed to detect and characterize fusion transcripts.
Transfection of EWSR1-related constructs into cells may be facilitated by Lipofectamine 2000, a common transfection reagent.
Maintaining a healthy cell environment is crucial, and the use of Penicillin/Streptomycin can help prevent bacterial contamination.
Antibodies, such as Ab54708, may be utilized to detect and quantify the EWSR1 protein.
By combining the insights gained from the MeSH term description and the Metadescription, researchers can confidently navigate the complexities of EWSR1 protein research and unlock new possibilities for advancing cancer treatments.