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  • 1
    Online Resource
    Online Resource
    American Society of Hematology ; 2015
    In:  Blood Vol. 126, No. 23 ( 2015-12-03), p. 4969-4969
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 4969-4969
    Abstract: Introduction Despite the discovery of new genetic alterations the cytogenetically normal acute myeloid leukemia (CN-AML) subset is still insufficiently characterized. As mRNA-sequencing (RNA-seq) is becoming more accessible, sequencing of the transcriptome could reveal not only information regarding deregulated expression patterns in leukemias, but also enable mutational evaluation of expressed alleles. To address this issue we performed RNA-seq of 5 AML patients from diagnostic bone marrow aspirates to assess the validity of the following: 1) remission samples can be used as control, 2) concordance between standard clinical laboratory analysis and RNA-seq data, and 3) implementation of existing microarray data repository to infer expected mutational status of the sequenced samples based on expression patterns. Methods Diagnostic samples were selected among patients with high leukemic blast fraction (mean of 75%) and paired remission samples with very low, or no detectable, molecular minimal residual disease. A panel of recurrent somatic mutations was assessed by means of quantitative PCR (qPCR) and fragment analysis for sequencing comparisons. Sequencing was performed on single HiSeq lane aimed at minimum 66 million reads per sample (AROS Applied Biotechnology, Aarhus, Denmark). Biomedical Genomics Workbench 2 was employed for alignment, mutation calling and analysis of differential expression (Robinson-Smyth exact test, Bonferroni corrected). R and Mathematica were used for comparison of expression patterns from the individual samples in conjunction with CN-AML (251) and control bone marrow (73) data from microarray repositories (Gene Expression Omnibus, GSE15434 and GSE13159). Results 259 genes were differentially expressed as defined by the following thresholds: normalized fold-change 〉 2, expression range values 〉 10 RPKM and p 〈 0.05. Of these, 41 genes were upregulated in AML samples (p 〈 0.01 subset heatmap is shown in fig. 1A). Supervised clustering of the samples on the basis of differential expression patterns efficiently divided the data into 2 groups according to diagnosis and remission status (fig. 1A, dendrogram). A median of 61 mutations per sample was observed (35 to 675). Thirty-four mutations occurred twice or more (fig. 1B, size reflects transcript fraction of mutated allele). A close correlation between routine molecular diagnostics and sequencing data was found. As expected, routine minimal residual disease marker WT1 was in agreement and found to be clearly expressed at diagnosis, but not at time of remission. By comparing patient expression patterns with NPM1, FLT3 or CEPBA mutation specific microarray expression signatures we were largely able to deduce expected mutational status for each patient (fig. 1C, showing the individual matching fraction of mutation specific gene expression signature in terms of upregulated or downregulated) in favor of qPCR analysis shown in table 1. Table 1. Comparison of mutational status from qPCR/RNA-seq FLT3 mut NPM1 mut IDH1 mut WT1 mut CEBPA mut KIT mut #1 +/+ +/+ +/+ -/- -/- -/- #2 +/+ +/+ -/- -/- -/- -/- #3 +/+ +/- -/- -/- -/- -/- #4 -/- +/- +/+ +/- -/- -/- #5 +/+ -/- -/- -/- -/- -/- Conclusions This approach serves as a proof of the concept that RNA-sequencing can be directly implemented in the routine laboratory. Moreover, transcriptome data such as these can extend the molecular survey in a dynamic manner by aiding in therapy-related decision-making for the application of targeted therapy and for delineating the reasons for treatment. While publicly available repositories of RNA-seq data are being generated for referencing, it is possible to include microarray data to support molecular classification of the individual patients, as is shown here. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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  • 2
    In: BioMed Research International, Hindawi Limited, Vol. 2016 ( 2016), p. 1-14
    Abstract: MicroRNAs have the potential to be useful biomarkers in the development of individualized treatment since they are easy to detect, are relatively stable during sample handling, and are important determinants of cellular processes controlling pathogenesis, progression, and response to treatment of several types of cancers including B-cell malignancies. miR-155 is an oncomiR with a crucial role in tumor initiation and development of several B-cell malignancies. The present review elucidates the potential of miR-155 as a diagnostic, prognostic, or predictive biomarker in B-cell malignancies using a systematic search strategy to identify relevant literature. miR-155 was upregulated in several malignancies compared to nonmalignant controls and overexpression of miR-155 was further associated with poor prognosis. Elevated expression of miR-155 shows potential as a diagnostic and prognostic biomarker in diffuse large B-cell lymphoma and chronic lymphocytic leukemia. Additionally, in vitro and in vivo studies suggest miR-155 as an efficient therapeutic target, supporting its oncogenic function. The use of inhibiting anti-miR structures indicates promising potential as novel anticancer therapeutics. Reports from 53 studies prove that miR-155 has the potential to be a molecular tool in personalized medicine.
    Type of Medium: Online Resource
    ISSN: 2314-6133 , 2314-6141
    Language: English
    Publisher: Hindawi Limited
    Publication Date: 2016
    detail.hit.zdb_id: 2698540-8
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  • 3
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 1529-1529
    Abstract: Introduction: Therapy-related myeloid neoplasms (tMN) are high-risk conditions evolved after exposure to a number of agents, including cytotoxic therapy, and include myelodysplastic syndrome (MDS), acute myeloid leukemia (AML) and myeloproliferative neoplasms (MPN). As such cytoreduction as part of autologous stem cell transplantation (ASCT) increases the risk of developing tMN. Importantly, both the use of ASCT and the incidence of tMN are rising. The recent characterization of clonal hematopoiesis of indeterminate potential (CHIP) has, in preliminary reports, been shown to increase the risk of developing de novo hematological disease as well as tMN. We hypothesized that patients with non-myeloid primary disease who develop tMN after ASCT, had detectable myeloid mutations at time of transplantation, and that these may represent a risk factor in the development of tMN. This study characterizes tMN patients previously subjected to ASCT and investigates whether CHIP mutations are present in hematopoietic stem cells at time of ASCT. Methods: The cohort of this observational study consists of patients treated with ASCT at the Department of Hematology, Aarhus University Hospital (Denmark) from 1989 to 2016. Cases were identified via the Danish Pathology Registry and all tMN diagnoses were verified by the same experienced hemopathologist (GBK). Only cases from patients with non-myeloid primary disease, who were diagnosed with tMN after being treated with ASCT (minimum latency being 90 days) were included. 36 cases with available leukapheresis products were identified out of a cohort of 1130 patients. Samples collected from leukapheresis prior to ASCT were subjected to targeted next-generation sequencing (NGS), using the commercially available panel "Myeloid Solution" (Sophia Genetics, Saint Sulpice, Switzerland), covering 30 genes relevant for myeloid neoplasms, joined with a bioinformatics pipeline from Sophia Genetics. Samples from 31 patients have been subjected to NGS. Variants residing in or within ± 25 nucleotides of coding exons and with coverage 〉 5000 at the variant site were reported. Indels present in polynucleotide stretches were excluded. Data for continuous variables age, latency to tMN and survival were analyzed as one sample from a normal distribution based on the Students t-test. Normality was assessed via Q-Q plot. Estimates are reported with a 95% confidence intervals (Stata, version 15.1, StataCorp LLC, TX, USA). Results: The cohort consisted of 25 males (80.7%) and 6 females (19.3%), with an estimated median age at ASCT of 58 years (CI 95% 54;63). Estimated median time to tMN was 3.7 years (CI 95% 2.5;5.4) and estimated median survival after tMN diagnosis was 132 days (CI 95% 71;246). At time of tMN diagnosis, 14 patients had a poor risk karyotype and 9 patients had intermediate risk karyotype (hereof 4 normal karyotype). Karyotype was not evaluated in 8 patients. CHIP mutations were detected in stem cell enriched leukapheresis products from 21 patients (67.7%). Of these, we found multiple mutations in 14 patients (66%) and in one patient as many as 6 CHIP mutations. Point mutations were frequently found in the DNMT3A gene and was present in 16 out of 21 patients (76%). Six patients had more than one DNMT3A mutation, one of which had 5 separate DNMT3A mutations. Other mutations detected were TP53 (6/21), TET2 (5/21), ASXL1 (4/21), EZH2 (1/21), WT1 (1/21), JAK2 (1/21), NRAS (1/21), HRAS (1/21), BRAF (1/21), CSF3R (1/21), SF3B1 (1/21), ZRSR2 (1/21), CALR (1/21), SRSF2 (1/21). Conclusion: We found that CHIP mutations can be detected at time of ASCT in patients being treated for non-myeloid diseases. We hypothesize that presence of CHIP mutations at ASCT may predict the development of tMN and as such serve as a biomarker in this setting. We speculate that high-dose cytotoxic therapy may provide an evolutionary advantage for hematopoietic clones containing CHIP mutations. On the other hand, we cannot rule out that the cytoreduction administered prior at ASCT may be a main contributor to the tMN development. To address this as well as the development of tMN in the post-ASCT phase, a nested case-control study will be necessary. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 4
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2019
    In:  Current Treatment Options in Oncology Vol. 20, No. 4 ( 2019-4)
    In: Current Treatment Options in Oncology, Springer Science and Business Media LLC, Vol. 20, No. 4 ( 2019-4)
    Type of Medium: Online Resource
    ISSN: 1527-2729 , 1534-6277
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2090563-4
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