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  1. Article: A Rapid, Functional sgRNA Screening Method for Generating Murine RET and NTRK1 Fusion Oncogenes.

    Schubert, Laura / Le, Anh T / Hinz, Trista K / Navarro, Andre / Nelson-Taylor, Sarah K / Nemenoff, Raphael A / Heasley, Lynn E / Doebele, Robert C

    bioRxiv : the preprint server for biology

    2023  

    Abstract: CRISPR/Cas9 gene editing technology is an indispensable and powerful tool in the field of cancer biology. To conduct successful CRISPR-based experiments, it is crucial that sgRNAs generate their designed alterations. Here, we describe a simple and ... ...

    Abstract CRISPR/Cas9 gene editing technology is an indispensable and powerful tool in the field of cancer biology. To conduct successful CRISPR-based experiments, it is crucial that sgRNAs generate their designed alterations. Here, we describe a simple and efficient sgRNA screening method for validating sgRNAs that generate oncogenic gene rearrangements. We used IL3-independence in Ba/F3 cells as an assay to identify sgRNA pairs that generate fusion oncogenes involving the
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.06.535912
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Single cell RNA-sequencing of Ewing sarcoma tumors demonstrates transcriptional heterogeneity and clonal evolution.

    Goodspeed, Andrew / Bodlak, Avery / Nelson-Taylor, Sarah / Oike, Naoki / Porfilio, Timothy / Shirai, Ryota / Walker, Deandra / Treece, Amy / Black, Jennifer / Donaldson, Nathan / Cost, Carrye / Garrington, Tim / Greffe, Brian / Luna-Fineman, Sandra / Demedis, Jenna / Lake, Jessica / Danis, Etienne / Verneris, Michael / Hayashi, Masanori

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Ewing sarcoma is the second most common bone cancer in children, accounting for 2% of pediatric cancer diagnoses. Patients who present with metastatic disease at the time of diagnosis have a dismal prognosis, compared to the >70% 5-year survival of those ...

    Abstract Ewing sarcoma is the second most common bone cancer in children, accounting for 2% of pediatric cancer diagnoses. Patients who present with metastatic disease at the time of diagnosis have a dismal prognosis, compared to the >70% 5-year survival of those with localized disease. Here, we utilized single cell RNA-sequencing to characterize the transcriptional landscape of primary Ewing sarcoma tumors and surrounding tumor microenvironment (TME). Copy-number analysis identified subclonal evolution within patients even prior to treatment. Primary tumor samples demonstrate a heterogenous transcriptional landscape with several conserved gene expression programs, including those composed of genes related to proliferation and EWS targets. We also were able to identify the composition of the TME and molecularly dissect the transcriptional profile of circulating tumor cells in peripheral blood at the time of diagnosis.
    Language English
    Publishing date 2024-01-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.18.576251
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: A functional sgRNA-CRISPR screening method for generating murine RET and NTRK1 rearranged oncogenes.

    Schubert, Laura / Le, Anh T / Hinz, Trista K / Navarro, Andre C / Nelson-Taylor, Sarah K / Nemenoff, Raphael A / Heasley, Lynn E / Doebele, Robert C

    Biology open

    2023  Volume 12, Issue 8

    Abstract: CRISPR/Cas9 gene editing represents a powerful tool for investigating fusion oncogenes in cancer biology. Successful experiments require that sgRNAs correctly associate with their target sequence and initiate double stranded breaks which are subsequently ...

    Abstract CRISPR/Cas9 gene editing represents a powerful tool for investigating fusion oncogenes in cancer biology. Successful experiments require that sgRNAs correctly associate with their target sequence and initiate double stranded breaks which are subsequently repaired by endogenous DNA repair systems yielding fusion chromosomes. Simple tests to ensure sgRNAs are functional are not generally available and often require single cell cloning to identify successful CRISPR-editing events. Here, we describe a novel method relying on acquisition of IL3-independence in Ba/F3 cells to identify sgRNA pairs that generate oncogenic gene rearrangements of the Ret and Ntrk1 tyrosine kinases. The rearrangements were confirmed with PCR, RT-PCR and sequencing and Ba/F3 cells harboring Ret or Ntrk1 rearrangements acquired sensitivity to RET and TRK inhibitors, respectively. Adenoviruses encoding Cas9 and sgRNA pairs inducing the Kif5b-Ret and Trim24-Ret rearrangements were intratracheally instilled into mice and yielded lung adenocarcinomas. A cell line (TR.1) established from a Trim24-Ret positive tumor exhibited high in vitro sensitivity to the RET inhibitors LOXO-292 and BLU-667 and orthotopic TR.1 cell-derived tumors underwent marked shrinkage upon LOXO-292 treatment. Thus, the method offers an efficient means to validate sgRNAs that successfully target their intended loci for the generation of novel, syngeneic murine oncogene-driven tumor models.
    MeSH term(s) Animals ; Mice ; RNA, Guide, CRISPR-Cas Systems ; Oncogenes ; Protein Kinase Inhibitors/pharmacology
    Chemical Substances RNA, Guide, CRISPR-Cas Systems ; Protein Kinase Inhibitors
    Language English
    Publishing date 2023-08-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2632264-X
    ISSN 2046-6390 ; 2046-6390
    ISSN (online) 2046-6390
    ISSN 2046-6390
    DOI 10.1242/bio.059994
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Resistance to RET-Inhibition in RET-Rearranged NSCLC Is Mediated By Reactivation of RAS/MAPK Signaling.

    Nelson-Taylor, Sarah K / Le, Anh T / Yoo, Minjae / Schubert, Laura / Mishall, Katie M / Doak, Andrea / Varella-Garcia, Marileila / Tan, Aik-Choon / Doebele, Robert C

    Molecular cancer therapeutics

    2017  Volume 16, Issue 8, Page(s) 1623–1633

    Abstract: Oncogenic rearrangements ... ...

    Abstract Oncogenic rearrangements in
    MeSH term(s) Carcinoma, Non-Small-Cell Lung/drug therapy ; Carcinoma, Non-Small-Cell Lung/enzymology ; Carcinoma, Non-Small-Cell Lung/genetics ; Carcinoma, Non-Small-Cell Lung/pathology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Drug Resistance, Neoplasm/drug effects ; Drug Resistance, Neoplasm/genetics ; ErbB Receptors/metabolism ; GTP Phosphohydrolases/metabolism ; Gene Rearrangement/genetics ; Humans ; Imidazoles/pharmacology ; Imidazoles/therapeutic use ; Lung Neoplasms/drug therapy ; Lung Neoplasms/enzymology ; Lung Neoplasms/genetics ; Lung Neoplasms/pathology ; MAP Kinase Signaling System/drug effects ; Membrane Proteins/metabolism ; Mutation/genetics ; Oncogenes ; Phosphatidylinositol 3-Kinases/metabolism ; Proto-Oncogene Proteins/antagonists & inhibitors ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins c-ret/antagonists & inhibitors ; Proto-Oncogene Proteins c-ret/metabolism ; Pyridazines/pharmacology ; Pyridazines/therapeutic use ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors ; Receptor Protein-Tyrosine Kinases/metabolism
    Chemical Substances Imidazoles ; Membrane Proteins ; Proto-Oncogene Proteins ; Pyridazines ; ponatinib (4340891KFS) ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; ErbB Receptors (EC 2.7.10.1) ; Proto-Oncogene Proteins c-ret (EC 2.7.10.1) ; RET protein, human (EC 2.7.10.1) ; Receptor Protein-Tyrosine Kinases (EC 2.7.10.1) ; axl receptor tyrosine kinase (EC 2.7.10.1) ; GTP Phosphohydrolases (EC 3.6.1.-) ; NRAS protein, human (EC 3.6.1.-)
    Language English
    Publishing date 2017-05-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2063563-1
    ISSN 1538-8514 ; 1535-7163
    ISSN (online) 1538-8514
    ISSN 1535-7163
    DOI 10.1158/1535-7163.MCT-17-0008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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