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  1. 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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  2. Article ; Online: ddPCR Analysis Reveals BRAF V600E Mutations Are Infrequent in Isolated Pituitary Langerhans Cell Histiocytosis Patients.

    Nellan, Anandani / Bodlak, Avery / Mirsky, David M / Mulcahy Levy, Jean / Garrington, Timothy P / Foreman, Nicholas K / Gilani, Ahmed / Hayashi, Masanori

    Journal of neuropathology and experimental neurology

    2020  Volume 79, Issue 12, Page(s) 1313–1319

    Abstract: Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia with a highly variable clinical presentation affecting people of all ages. Mutations in BRAF V600E are the most identifiable molecular alteration in LCH although its incidence in ... ...

    Abstract Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia with a highly variable clinical presentation affecting people of all ages. Mutations in BRAF V600E are the most identifiable molecular alteration in LCH although its incidence in pediatric patients with isolated pituitary stalk involvement is not well described. Pediatric patients with LCH and isolated pituitary stalk involvement typically present with central diabetes insipidus. Diagnosis requires a transcranial biopsy which often yields scant tissue. We sought to determine the prevalence of BRAF V600E mutations in patients with isolated pituitary stalk LCH using digital droplet polymerase chain reaction because this method requires minimal tumor DNA. We identified 8 patients with isolated pituitary stalk thickening who underwent a biopsy at Children's Hospital Colorado from January 2001 to December 2019, as well as 6 patients with systemic LCH diagnosed by biopsy in the same period as a comparison. Only one out of the 8 patients with isolated thickened pituitary stalk was found to have a detectable BRAF V600E mutation. Five out of the 6 patients with systemic LCH had a detectable BRAF V600E mutation. In our series, BRAF V600E mutations are rare in pediatric patients with LCH and isolated pituitary stalk involvement.
    MeSH term(s) Child ; Child, Preschool ; Female ; Histiocytosis, Langerhans-Cell/genetics ; Histiocytosis, Langerhans-Cell/pathology ; Humans ; Male ; Mutation ; Pituitary Diseases/genetics ; Pituitary Diseases/pathology ; Pituitary Gland/pathology ; Polymerase Chain Reaction ; Proto-Oncogene Proteins B-raf/genetics
    Chemical Substances BRAF protein, human (EC 2.7.11.1) ; Proto-Oncogene Proteins B-raf (EC 2.7.11.1)
    Language English
    Publishing date 2020-10-14
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 3088-0
    ISSN 1554-6578 ; 0022-3069
    ISSN (online) 1554-6578
    ISSN 0022-3069
    DOI 10.1093/jnen/nlaa091
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  3. Article ; Online: Circulating Plasma Tumor DNA Is Superior to Plasma Tumor RNA Detection in Ewing Sarcoma Patients: ptDNA and ptRNA in Ewing Sarcoma.

    Bodlak, Avery / Chang, Kyle / Channel, Jessica / Treece, Amy L / Donaldson, Nathan / Cost, Carrye R / Garrington, Timothy P / Greffe, Brian / Luna-Fineman, Sandra / Sopfe, Jenna / Loeb, David M / Hayashi, Masanori

    The Journal of molecular diagnostics : JMD

    2021  Volume 23, Issue 7, Page(s) 872–881

    Abstract: The detection of tumor-specific nucleic acids from blood increasingly is being used as a method of liquid biopsy and minimal residual disease detection. However, achieving high sensitivity and high specificity remains a challenge. Here, we perform a ... ...

    Abstract The detection of tumor-specific nucleic acids from blood increasingly is being used as a method of liquid biopsy and minimal residual disease detection. However, achieving high sensitivity and high specificity remains a challenge. Here, we perform a direct comparison of two droplet digital PCR (ddPCR)-based detection methods, circulating plasma tumor RNA and circulating plasma tumor DNA (ptDNA), in blood samples from newly diagnosed Ewing sarcoma patients. First, we developed three specific ddPCR-based assays to detect EWS-FLI1 or EWS-ERG fusion transcripts, which naturally showed superior sensitivity to DNA detection on in vitro control samples. Next, we identified the patient-specific EWS-FLI1 or EWS-ERG breakpoint from five patient tumor samples and designed ddPCR-based, patient-specific ptDNA assays for each patient. These patient-specific assays show that although plasma tumor RNA can be detected in select newly diagnosed patients, positive results are low and statistically unreliable compared with ptDNA assays, which reproducibly detect robust positive results across most patients. Furthermore, the unique disease biology of Ewing sarcoma enabled us to show that most cell-free RNA is not tumor-derived, although cell-free-DNA burden is affected strongly by tumor-derived DNA burden. Here, we conclude that, even with optimized highly sensitive and specific assays, tumor DNA detection is superior to RNA detection in Ewing sarcoma patients.
    MeSH term(s) Adolescent ; Biomarkers, Tumor/blood ; Biomarkers, Tumor/genetics ; Child ; Circulating Tumor DNA/blood ; Circulating Tumor DNA/genetics ; Circulating Tumor DNA/isolation & purification ; Female ; Humans ; Male ; Oncogene Proteins, Fusion/blood ; Oncogene Proteins, Fusion/genetics ; Polymerase Chain Reaction/methods ; Proto-Oncogene Protein c-fli-1/blood ; Proto-Oncogene Protein c-fli-1/genetics ; RNA, Neoplasm/blood ; RNA, Neoplasm/genetics ; RNA, Neoplasm/isolation & purification ; RNA-Binding Protein EWS/blood ; RNA-Binding Protein EWS/genetics ; Reproducibility of Results ; Sarcoma, Ewing/blood ; Sarcoma, Ewing/genetics ; Transcription Factors/blood ; Transcription Factors/genetics ; Translocation, Genetic
    Chemical Substances Biomarkers, Tumor ; Circulating Tumor DNA ; EWS-ERG fusion protein, human ; EWS-FLI fusion protein ; Oncogene Proteins, Fusion ; Proto-Oncogene Protein c-fli-1 ; RNA, Neoplasm ; RNA-Binding Protein EWS ; Transcription Factors
    Language English
    Publishing date 2021-04-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2000060-1
    ISSN 1943-7811 ; 1525-1578
    ISSN (online) 1943-7811
    ISSN 1525-1578
    DOI 10.1016/j.jmoldx.2021.04.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5146: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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