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  • 1
    In: Leukemia, Springer Science and Business Media LLC, Vol. 34, No. 8 ( 2020-08), p. 2113-2124
    Type of Medium: Online Resource
    ISSN: 0887-6924 , 1476-5551
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2008023-2
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  • 2
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 4043-4043
    Abstract: Introduction - Targeted therapy of chronic myeloid leukemia (CML) using tyrosine kinase inhibitors (TKI) very effectively suppresses the growth of leukemic clone to a clinically safe level of the disease. Therefore sensitive monitoring of molecular response (MR) based on standardized measurements of BCR-ABL1 transcript levels plays an important role for prediction either of optimal response or progression. Thus, its sensitive and accurate detection is very important for the individualized therapy, especially for a TKI stopping treatment management in patients achieving long-term deep MR. While the transcript levels may not exactly correspond to the number of leukemic cells, BCR-ABL1 quantification at the DNA level using patient-specific assays may bring more accurate information about residual disease. Moreover, BCR-ABL1 DNA quantification may contribute to a stratification of patients for whom the cessation of TKI therapy may be safe. Objectives - This work is focused on the comparison of BCR-ABL1 quantity at DNA and mRNA level in CML patients after TKI initiation until the MR achievement, and after TKI discontinuation within the EURO-SKI clinical trial (Europe Stops TKI in CML), respectively, and on determination of differences on BCR-ABL1 positivity/negativity of samples analyzed. Additionally, the BCR-ABL1 DNA data obtained from the measurements by qPCR and droplet digital PCR (ddPCR) were compared. Methods - Our study included analyses of 232 samples of 13 patients with CML in chronic phase (CP), who achieved deep MR during TKI treatment. Four of 13 patients (total of 85 samples analyzed) discontinued the treatment within the EURO-SKI study. The levels of BCR-ABL1 mRNA were determined by standardized RT-qPCR method and DNA levels were detected by qPCR with developed patient-specific qPCR assays after BCR-ABL1 genomic fusions characterization. The ddPCR method was performed on 72 samples using QX-200 Droplet Digital PCR System (Bio-Rad). The determined ratios of BCR-ABL1/GUSB (mRNA) and BCR-ABL1/albumin (DNA level) of follow-up samples of every patient were related to the diagnostic sample (considered as 100% level) for the most appropriate comparison of mRNA and DNA levels. Results - Standardized RT-qPCR and patient-specific qPCRs were able to detect the mRNA and DNA BCR-ABL1 levels, respectively, reduced by more than 5 logs from the levels at the time of diagnosis. We observed a significant correlation between the mRNA and DNA levels by comparing 148 paired BCR-ABL1 positive results (correlation coefficient r2=0.9055; P˂0.0001). When comparing the frequency of the BCR-ABL1 negative/positive results at the DNA vs. mRNA levels, BCR-ABL1 positivity at DNA level was found in 21 samples which were BCR-ABL1-negative at mRNA level. BCR-ABL1 mRNA was found either negative or positive at MR5.0 in 3/4 EURO-SKI patients within the period between MR achievement until the TKI discontinuation (19 samples analyzed). The level of BCR-ABL1 DNA was continuously positive in this period before the TKI cessation. The molecular relapse (i.e. MMR loss) was observed in all those 3 patients several months after the therapy cessation. The levels of BCR-ABL1 DNA detected by ddPCR method correlated with DNA qPCR results (r2=0.9684; P˂0.0001) and the obtained values were not significantly different. Conclusion - The levels of the BCR-ABL1 mRNA and DNA in peripheral blood (PB) correlated significantly, thus both consistently reflecting the course of CP-CML at the molecular level. Although much more patients with TKI cessation need to be tested for the presence of BCR-ABL1 DNA, our data suggest that quantification at the DNA level appears to be (at least in some cases) more sensitive method for detection of residual leukemic cells in PB in comparison to the mRNA quantification. The BCR-ABL1 DNA measurement may have a potential prognostic significance in deciding for eventual withdrawal of TKI therapy, which is currently being investigated within the clinical trials. Digital PCR enables absolute quantification without a need of patient-specific calibration curves and with the potentially higher sensitivity and accuracy for BCR-ABL1 DNA quantification. This work was supported by the project 15-31540A of the Czech Health Research Council, GAUK 554214 and EURO-SKI Research Consortium. Disclosures Klamova: Novartis: Consultancy, Honoraria, Research Funding; Bristol Myers-Squibb: Consultancy, Honoraria, Research Funding. Saussele:ARIAD: Honoraria; Pfizer: Honoraria, Other: Travel grant; BMS: Honoraria, Other: Travel grant, Research Funding; Novartis Pharma: Honoraria, Other: Travel grant, Research Funding. Mahon:Pfizer: Consultancy, Research Funding; BMS: Consultancy, Research Funding; Ariad: Consultancy, Research Funding; Novartis: Consultancy, Research Funding. Machova Polakova:Bristol Myers-Squibb: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 3
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 1743-1743
    Abstract: Introduction: In chronic myeloid leukemia (CML) resistant to tyrosine kinase inhibitors (TKI), detection of mutations in the BCR-ABL1 kinase domain (KD) is routinely performed on transcript level. To determine the level of BCR-ABL1 KD mutation is important to follow kinetics of resistant CML cells and therapeutically prevent progression. However, the mutation types and levels are not always reliable predictors of subsequent dynamics of mutation-bearing clones and of corresponding clinical consequences (Willis, 2005; Khorashad, 2006; Preuner, 2012). DNA analysis enables more precise quantification of (sub)clonal levels and thus might be more reliable approach to monitor dynamics of BCR-ABL1 KD mutations. Aim: To study clonal evolution of resistant CML cells using genomic quantification of mutated BCR-ABL1 KD by droplet digital PCR (ddPCR). Methods: BCR-ABL1 mutation analysis on transcript level was performed using next generation sequencing (NGS) (Nextera XT; Illumina) and on DNA level using allele-specific ddPCR assays detecting T315I, E255K and Y253H (Bio-Rad). The level of genomic BCR-ABL1 mutation was determined as a copy number of mutation divided by a copy number of genomic BCR-ABL1 fusion. Quantification of genomic BCR-ABL1 was performed by ddPCR using patient-specific primers and probes designed to detect individual fusions. ALB (albumin) quantification was used as a control of DNA load/cell numbers. For analyses, mRNA and DNA extracted from KCL-22 cell line resistant to imatinib (IM) and from leukocytes of a patient who developed T315I during TKI therapy were used. Results: KCL-22 cell line is characterized by 2 Ph chromosomes and by ability to develop resistance by acquisition of BCR-ABL1 mutations early after the exposure to IM. We repeatedly found, that during early cultivation in the presence of IM, BCR-ABL1-T315I transcript increased up to maximum of 50%. Subsequently, after 2 months, BCR-ABL1-E255K transcripts became detectable and increased over time to 100%, while T315I decreased to un-detectable levels. To study the observed kinetics, we isolated 4 clones resistant to 4 µM IM that expressed 1) 50% of T315I, 2) 50% of E255K and 3) 30% of Y253H. In the fourth clone, no BCR-ABL1 mutation was detected, but mutation acquisition was found in KRAS, RUNX1 and ATRX. The levels of mutated BCR-ABL1 transcripts in mutation bearing clones remained stable over time. DNA analyses confirmed the same level of mutated BCR-ABL1 and revealed that in all resistant clones, only 1 Ph chromosome carried the BCR-ABL1 mutation (T315I, E255K or Y253H). Based on quantification of genomic BCR-ABL1 fusion and albumin we found, that the un-mutated BCR-ABL1 fusion was duplicated in Y253H clone, explaining the 30% level of Y253H. To follow a clonal evolution, we mixed the 4 KCL-22 resistant clones and analyzed BCR-ABL1 KD mutations at both mRNA and DNA levels during exposition to IM. We found that T315I clone overgrew other 3 clones in the mixture over time and 1 Ph chromosome remained mutated. These data confirm the T315I mutation being the most resistant; however, the data from the original cell culture, where the 100% E255K clone overgrew the 50% T315I cells, demonstrate, that a less resistant mutation might dominate the culture if present on both Ph chromosomes (as revealed by DNA analysis). We compared mRNA and DNA approach in 14 samples collected during individualized treatment management of a CML patient, who developed T315I during TKI therapy. The first mutation detection was during warning response preceded by eight samples negative by mRNA-NGS approach; DNA ddPCR analysis reliably detected T315I mutation in 7 of these 8 samples. Six mRNA positive samples were positive by DNA approach, which showed the same level of T315I. Conclusions: Allele-specific ddPCR together with quantification of BCR-ABL1 genomic fusion represents highly sensitive and reliable method providing fast and precise quantification of BCR-ABL1 mutations. A single DNA analysis is able to uncover clinically relevant events including BCR-ABL1 amplification or additional mutation acquisition, which presumably influence fitness of leukemic cells and clonal evolution during therapeutic interventions. The information provided by DNA mutational analysis may thus refine prediction of mutation kinetics and consequently improve management of progressed CML and Ph+ ALL. Support GACR 18-18407S, MZCR 00023736, AZV 15-31540, AZV 16-30186A Disclosures Klamova: Novartis: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria. Ernst:Novartis: Research Funding. Soverini:Incyte Biosciences: Consultancy; Novartis: Consultancy; Bristol Myers Squibb: Consultancy. Machova:Bristol-Myers Squibb: Consultancy, Other: Educational grant funding; Incyte: Consultancy; Novartis: Consultancy.
    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
    In: Blood, American Society of Hematology, Vol. 136, No. Supplement 1 ( 2020-11-5), p. 23-24
    Abstract: Introduction: The clonal hematopoiesis with somatic mutations is age-related phenomenon with a frequency around 10% for population older than 65 years in contrast to population younger than 50 years with frequency of 1%. Mutations in genes involved in epigenetic modification and RNA splicing, which are recurrently mutated in myeloid neoplasms and associated with increased risk of hematologic cancer, seem to represent a premalignant condition. Generally, ASXL1 mutations are frequently found in myeloid malignancies. Patients with chronic myeloid leukemia (CML) diagnosed at the age of 15 to 39 years, also called adolescent and young adults (AYAs), have a worse prognosis and response to tyrosine kinase inhbitors (TKIs) compared to elderly patients. Little is known about the molecular background differing AYA from the common group of CML patients. Objectives: To determine, whether the worse prognosis and response to therapy of CML AYAs is associated with the clonal hematopoiesis with somatic mutations. Methods: Samples from 22 AYAs were retrospectively analyzed at the time of diagnosis (aged 18-37; Table 1). Of them, 20 patients failed on TKI or relapsed after allo-HSCT (allogeneic hematopoietic stem cells transplantation). In 6/20 AYAs, mutations in the kinase domain of BCR-ABL1 were detected at the time of TKI failure (M244V, T315I, E255K/V + Q252H, F317L + M351T, V379I, L284S). Two responders were included for comparison. Sequencing of custom myeloid panel (Roche), partly or fully covering 36 genes frequently mutated in myeloid malignancies, was performed on MiSeq (Illumina). Data was analyzed in NextGENe software (Softgenetics). The detected variants were characterized by open-source databases (VarSome, Ensembl, COSMIC, NCBI - dbSNP) and confirmed by Sanger sequencing and/or ASO-ddPCR. Results: At the time of diagnosis, somatic mutations were identified in ASXL1 (n=4), CSF3R (n=1), TET2 (n=1), PCDHA12 (n=1), SETD2 (n=1), ATRX (n=1), and SIRT1 (n=1) in 10/20 AYAs, who subsequently failed on treatment (Table 1). Overall, 6 missense, 3 frameshift mutations and one nonsense mutation were detected. In patients #21 and #22 with optimal response to TKIs, no mutations were detected at diagnosis. In patient #10, ASXL1 mutation E773X was confirmed at the time of TKI failure and also at the allo-HSCT relapse. In patient #6, G645delinsGWfs was found at the diagnosis and on the 3rd line nilotinib treatment. Another ASXL1 mutation, S795delinsCLfs, was found in a patient #1 only at diagnosis. In patient #19, ASXL1 mutation T1372delinsTCfs found at diagnosis will be followed during the TKI treatment. In patient #3, the CSF3R mutation A593V was found at diagnosis and confirmed 14 months after the imatinib initiation. In patient #8, who relapsed after 2nd allo-HSCT, the RUNX1 D198N was found in the same clone bearing BCR-ABL1 T315I, both confirmed by ASO-ddPCR also before 1st allo-HSCT. This clone was, in the follow-up treatment, responsible for the relapse to CNS and also the relapse even after 3rd allo-HSCT and patient died. Conclusions: The preliminary data of this work outlined that somatic mutations in the myeloid genes are frequently found in CML AYAs, who failed on the TKI or relapsed after allo-HSCT, alone or together with mutated BCR-ABL1. The most frequently mutated gene was ASXL1, which is in line with the work by Ernst et al. (2018) even though on younger patients including children. Despite the clonal hematopoiesis with somatic mutations is considered as age-related phenomenon, in AYA CML patients, it may represent a critical problem in achieving sustained molecular response on solo TKI therapy, or even worse, it may result in higher risk of therapy failure and disease progression. Supported by MZCR 00023736 Table Disclosures Stoklosa: Janssen: Honoraria. Machova:Incyte: Consultancy; Angelini: Consultancy.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2020
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 5
    In: Leukemia, Springer Science and Business Media LLC, Vol. 35, No. 8 ( 2021-08), p. 2419-2423
    Type of Medium: Online Resource
    ISSN: 0887-6924 , 1476-5551
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2008023-2
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  • 6
    In: HemaSphere, Ovid Technologies (Wolters Kluwer Health), Vol. 7, No. S3 ( 2023-08), p. e70530bf-
    Type of Medium: Online Resource
    ISSN: 2572-9241
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2023
    detail.hit.zdb_id: 2922183-3
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  • 7
    In: Leukemia, Springer Science and Business Media LLC, Vol. 36, No. 7 ( 2022-07), p. 1879-1886
    Abstract: Several studies have reported that chronic myeloid leukaemia (CML) patients expressing e14a2 BCR::ABL1 have a faster molecular response to therapy compared to patients expressing e13a2. To explore the reason for this difference we undertook a detailed technical comparison of the commonly used Europe Against Cancer (EAC) BCR::ABL1 reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assay in European Treatment and Outcome Study (EUTOS) reference laboratories ( n  = 10). We found the amplification ratio of the e13a2 amplicon was 38% greater than e14a2 ( p  = 0.015), and the amplification efficiency was 2% greater ( P  = 0.17). This subtle difference led to measurable transcript-type dependent variation in estimates of residual disease which could be corrected by (i) taking the qPCR amplification efficiency into account, (ii) using alternative RT-qPCR approaches or (iii) droplet digital PCR (ddPCR), a technique which is relatively insensitive to differences in amplification kinetics. In CML patients, higher levels of BCR :: ABL1/GUSB were identified at diagnosis for patients expressing e13a2 ( n  = 67) compared to e14a2 ( n  = 78) when analysed by RT-qPCR ( P  = 0.0005) but not ddPCR ( P  = 0.5). These data indicate that widely used RT-qPCR assays result in subtly different estimates of disease depending on BCR::ABL1 transcript type; these differences are small but may need to be considered for optimal patient management.
    Type of Medium: Online Resource
    ISSN: 0887-6924 , 1476-5551
    RVK:
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2008023-2
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  • 8
    In: Journal of Proteomics, Elsevier BV, Vol. 132 ( 2016-01), p. 13-20
    Type of Medium: Online Resource
    ISSN: 1874-3919
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2016
    detail.hit.zdb_id: 2400835-7
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  • 9
    Online Resource
    Online Resource
    Palacky University Olomouc ; 2017
    In:  Bohemica Olomucensia Vol. 9, No. 2 ( 2017-6-1), p. 172-179
    In: Bohemica Olomucensia, Palacky University Olomouc, Vol. 9, No. 2 ( 2017-6-1), p. 172-179
    Type of Medium: Online Resource
    ISSN: 0231-634X
    Uniform Title: Substantivizace adjektiv jako problém strojové analýzy češtiny
    RVK:
    Language: cs
    Publisher: Palacky University Olomouc
    Publication Date: 2017
    detail.hit.zdb_id: 2585153-6
    SSG: 7,39
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  • 10
    Online Resource
    Online Resource
    Walter de Gruyter GmbH ; 2019
    In:  Journal of Linguistics/Jazykovedný casopis Vol. 70, No. 2 ( 2019-12-01), p. 370-379
    In: Journal of Linguistics/Jazykovedný casopis, Walter de Gruyter GmbH, Vol. 70, No. 2 ( 2019-12-01), p. 370-379
    Abstract: Part of speech transitions represent an interesting issue in terms of Automatic Morphological Analysis (AMA). In these cases, two parts of speech have to be considered: initial and final. However, their automatic recognition is complicated by the same form. This article presents the results of a corpus study aimed at mapping nominalized adjectives tagging with a focus on detecting candidates for nominalization among frequent adjectives. Analysis of the data obtained from the ČNK SYN v5 corpus shows different reasons for incorrect tagging. Taking into account these reasons, we propose three solutions for the improvement nominalized adjectives tagging.
    Type of Medium: Online Resource
    ISSN: 1338-4287 , 0021-5597
    RVK:
    Language: English
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2019
    detail.hit.zdb_id: 2253046-0
    SSG: 7,39
    SSG: 7,11
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