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  • 1
    In: Blood, American Society of Hematology, Vol. 122, No. 21 ( 2013-11-15), p. 519-519
    Abstract: The underlying molecular defects in myelodysplastic syndromes (MDS), which are a heterogeneous group of malignant clonal hematologic disorders, are not well understood. Recently, next generation sequencing (NGS) based whole genome and exome sequencing highlighted the oligoclonal nature of persistent MDS clones that are present already at early disease stages. The reconstruction of mutational hierarchies in MDS clones and distinction of primary founder from subsequently acquired lesions has yet to be thoroughly interrogated and is likely to aid dissecting the molecular pathogenesis of MDS. Methods An amplicon-based NGS assay using the Roche 454 GS Junior system was established within the IRON-II framework study in order to screen for 17 commonly mutated genes in MDS. Genomic DNA from purified mononuclear bone marrow (BM) cells of 23 MDS IPSS low/int1 risk subjects was screened for somatic mutations. Called variants were compared to dbSNP and COSMIC database entries to rule out germline polymorphisms. In addition, copy number variation analysis was performed by Affymetrix SNP 6.0 array profiling. Custom pyrosequencing assays and interphase-FISH were applied for sensitive quantification of lesion burdens in FACS-sorted myeloid, erythroid, lymphoid and stem/progenitor cells. These were isolated from patients’ primary BM as well as their long-term engrafted human xenotransplants using our recently established MDS xenograft model. Results In this work, we identified 12 oligoclonal BM samples with ≥2 molecular lesions. Of note, varying frequencies of individual mutations between different sorted cell subsets from primary or human xenografted BM support the notion that distinct MDS (sub-)clones from these subjects contributed to hematopoiesis simultaneously and lead to differential engraftment between xenografts. Comparison of variable subset-specific mutation burdens allowed deciphering the individual hierarchical architecture of the mutational landscape from 9 individuals. ASXL1, SF3B1 and SRSF2 were detected as a primary lesion for 2 patients each. In contrast, large-scale genomic alterations such as del(5q), del(RUNX1) or trisomy 8 occurred as late-end lesion or even defined distinct clones which coexist with others harboring different mutations as detected for 2 subjects. Surprisingly, CD19+ and CD3+ lymphocytes from primary and/or xenografted BM displayed significant mutational burden of at least 1 mutation in 50% of the MDS cohort (5/10). Moreover, mutations were detected simultaneously in lymphocytes (hCD19+) as well as myeloid (hCD33+) and erythroid (hCD235a+) cells from three xenografted samples indicating a potent multilineage engraftment capability of MDS hematopoietic stem cells. Interestingly, one individual presented with high RUNX1 mutational frequency in the primary early progenitor fraction (CD34+CD38+), which was absent in the stem-cell enriched fraction (CD34+CD38-), whereas TET2, ZRSR2 and ASXL1 mutations were detected in both fractions and their xenografts. Intriguingly, only xenotransplantation of primary CD34+38- BM cells lead to long-term engraftment of RUNX1 wild type human BM cells in mice, while CD34+CD38+ BM cells gave rise to short term engraftment of RUNX1 mutated human BM cells indicating that mutated RUNX1might originate in a more committed progenitor fraction with limited self-renewal potential. Conclusion Molecular characterization of oligoclonal mutation patterns in primary and xenograft BM allowed the establishment of individual mutational hierarchies and indicates a relatively random order in the mutational evolution of MDS clones, although spliceosome mutations appear as rather early events. Furthermore, our analysis revealed engraftment of independent MDS clones in different mice xenografted with the same subject material, which opens the door to the in vivo study of isolated clones with respect to their pathomechanisms and response to treatment. Our data also suggests that the occurrence of large-scale genomic aberrations is frequently preceded by small-scale gene mutations, emphasizing their potential role in disease diagnosis and risk stratification. Finally, detection of MDS specific mutations in the lymphocytic compartment might be involved in facilitating impaired immune functionality and needs to be investigated prospectively. Disclosures: Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Staller:MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment; Roche Diagnostics: Honoraria.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2013
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  • 2
    In: Blood, American Society of Hematology, Vol. 124, No. 21 ( 2014-12-06), p. 4604-4604
    Abstract: Background Myelodysplastic Syndromes (MDS) likely arise from an evolutionary process involving accumulation of somatic mutations and selection that occurs at the level of hematopoietic stem cells. Using next generation sequencing (NGS), several groups found recurrent somatic mutations to be associated with MDS. However, the history of stepwise molecular progression is still poorly defined. Likewise, little is known about patient-specific subclonal compositions, which may well contribute to the tremendous heterogeneity observed both in terms of clinical manifestations and response to treatment. Therefore, we sought to reconstruct patient-specific clonal hierarchies and decipher their dynamic evolution during long-term disease monitoring in order to better understand MDS pathogenesis and aid in adapting targeted therapeutic options in the future. Methods Bone marrow (BM) or CD34+ cells from patients with MDS were subjected to mutational screening by whole exome sequencing (WES, n=44) or targeted NGS (n=28) interrogating up to 17 recurrently mutated genes. Mesenchymal stromal cells (MSCs) were used as germline control. Allelic burdens were quantified with custom pyrosequencing assays and interphase-FISH in FACS purified myeloid, erythroid, lymphoid and stem cells isolated from both patients’ BM and corresponding xenografts in NSG mice. For unbiased follow up analysis, BM or CD34+ cells from two distant time points (median: 3 years, range 0.5-4.0 years) were analyzed for 13 patients using WES and these data were used to design patient-specific mutational panels. These panels contained amplicons representing mutational events uniquely present at one time point as well as others present at both time points. The panels were then subjected to ultra-deep-sequencing (UDS) to accurately quantify mutational burdens in all follow up (FU) samples. Results Integrative mutational data allowed us to reconstruct patient-specific mutational hierarchies in 35 cases, which revealed both linear and branching evolution in MDS. The data is also in support of the notion that potential founder lesions are highly enriched in genes involved in RNA splicing and epigenetic regulators, which we further show to be frequently detected in primary and/or xenografted lymphocytes. In contrast, we clearly demonstrate that large scale cytogenetic lesions (e.g. monosomy 7, trisomy 8, del(5q)) occur as late mutational events in at least 85% of the cases analyzed (n=17/20, 3 unresolved cases). Moreover, we could readily demonstrate the existence of subclonal heterogeneity in the patients’ BM, with variable contribution to different lineages and also cases showing lineage restriction of specific sub-clones. Most importantly, UDS analysis of FU samples from 13 independent patients (median FU 3.3 years, range FU 0.5-11.8 years and median of 5 samples per patient) with detailed clinical data revealed a highly dynamic clonal evolution during the course of the disease and dramatic shifts in the composition of mutational (sub-)clusters during therapy. Treatment often resulted in complete disappearance of specific sub-clones and most importantly, simultaneous outgrowth of previously undetectable subclones that subsequently dominated the marrow. Conclusion By reconstructing patient-specific mutational hierarchies we gained invaluable insights into the dynamic clonal composition and the molecular progression of human MDS. Our study shows that acquisition of large scale cytogenetic lesions appears to be a rather late event, which likely indicates that such lesions might not be tolerated by healthy stem cells. Most importantly, WES and subsequent deep sequencing analysis of FU samples demonstrated that patient-specific clonal diversity is highly dynamic and modulated during the course of the disease. This is especially true upon response to treatment, where concomitant disappearance and emergence of new pathogenic subclones was observed. Our work unravels two major paths of mutational acquisition by which MDS cells evade therapeutic pressure: (1) linear evolution of the previously sensitive subclone or (2) by branching evolution of an earlier independent founder clone. Our findings therefore strongly emphasize the importance of a genetically unbiased disease monitoring and the development of novel therapeutic strategies aiming at targeting founder lesions that are present in all ensuing subclones. Disclosures Nolte: Celgene Corp., Novartis Pharma: Honoraria, Research Funding. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2014
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  • 3
    In: Blood, American Society of Hematology, Vol. 122, No. 21 ( 2013-11-15), p. 100-100
    Abstract: Myelodysplastic syndromes (MDS) are clonal hematologic disorders characterized by ineffective hematopoiesis, dysplasia and increased risk of progression to acute myeloid leukemia. The development of targeted therapies for MDS has been lagging behind and remains a key clinical challenge that has been hampered, at least in part, by difficulties to establish in vivo model systems that recapitulate disease heterogeneity and complexity. Attempts to generate a xenograft model of lower risk MDS have only achieved low and often transient levels of engraftment. Recent evidence from mouse studies suggests that MDS is a disease in which both the hematopoietic system and the bone marrow microenvironment might be involved. Thus, we hypothesized that a specific MDS microenvironment might be required for the successful modeling of low risk MDS in mice, proposing a dependency of the “disease propagating cells“ on their corresponding niche cells in human MDS. Methods Our study is based on xenotransplantation of material from 19 MDS patients classified as follows: IPSS low risk (n=6), intermediate-1 risk (n=13), WHO 2008 classification: MDS 5q- (n=7), MDS RCMD (n=7), MDS RAEB I (n=3), MDS-U (n=1), MDS RARS (n=1). MDS CD34+ cells were co-injected with patient-derived mesenchymal stromal cells (MSCs) directly in the bone marrow cavity (i.f) of NOD.Cg-Prkdscid Il2rgtm1Wjl/Szj (NSG) or NSGS (NSG mice expressing human SCF, IL3 and GM-CSF) mice. Molecular tracking of MDS cells was carried out by copy number analysis (Affymetrix SNP 6.0 Arrays), metaphase cytogenetics, interphase FISH, Roche 454 deep sequencing and pyrosequencing of known mutations. Mice were analyzed after a minimum of 16 weeks post transplantation. Results We show that co-injection of MDS CD34+ cells with their corresponding MSCs leads to significant and long-term engraftment of over 77% of the MDS patients analyzed, both in NSG (10/13 patients, range hCD45+= 1-18%) and NSGS mice (7/8 patients, range hCD45+=2.2-74%). In contrast, absence of MSCs or co-injection of healthy age-matched MSCs only gave rise to limited engraftment in NSG mice (2/7 patients (hCD45+=1-3.8%) and 1/2 patients (hCD45+=2%), respectively). Transplanted samples exhibited a clear myeloid bias and significant engraftment of cells with progenitor (CD34+CD38+) and stem cell phenotype (CD34+CD38-) that could be serially transplanted. In addition, presence of morphologically dysplastic cells was readily detectable in NSGS mice. Importantly, molecular analysis of the engrafted cells confirmed their “diseased” origin as they carried identical lesions to the ones present in the original MDS patient. Furthermore, we could demonstrate that disease-propagating stem cells in lower risk MDS exclusively reside within the lin-CD34+CD38- stem cell fraction. Finally, RNA sequencing analysis comparing MDS and age-matched healthy control MSCs revealed altered expression of key genes involved in cellular adhesion, extra-cellular matrix (ECM) remodeling and cellular cross-talk in diseased MSCs, strongly supporting the notion of a complex interplay between MDS hematopoietic cells and their corresponding stroma. In addition, patient MSCs exhibited clear molecular features of fibrosis, a clinical feature often associated with MDS. Conclusion In this study we have identified patient-derived MSCs as a critical functional component of lower risk MDS. Together with MDS stem cells, these patient MSCs form a functional stem cell-niche unit, which allows the propagation of the disease in a xenograft recipient. The striking changed expression in diseased MSCs of genes involved in processes like cytokine-cytokine receptor interaction, cellular adhesion, ECM remodeling as well as hypoxia further suggests that diseased MDS cells might alter the function of the normal HSC niche into one that can support the requirement of MDS cells. Studying the interaction of MDS stem cells and MSCs at the cellular and molecular level will provide a platform for unraveling the molecular basis of clonal dominance in MDS as well as allow the design of targeted strategies aimed to disrupt the MDS stem cell-MSC niche interactions. 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: 2013
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 4
    In: Blood, American Society of Hematology, Vol. 128, No. 9 ( 2016-09-01), p. 1246-1259
    Abstract: Mutational trajectories are defined by complex patterns of molecular heterogeneity in MDS, including lower-risk cases. Therapeutic intervention dynamically reshapes mutational patterns often resulting in branched or independent evolution of MDS clones.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2016
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
    Location Call Number Limitation Availability
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  • 5
    In: Blood Advances, American Society of Hematology, Vol. 7, No. 6 ( 2023-03-28), p. 1011-1018
    Abstract: Acute myeloid leukemia (AML) is a heterogeneous disease characterized by high rate of relapse and mortality. Current chemotherapies whilst successful in eradicating blasts, are less effective in eliminating relapse-causing leukemic stem cells (LSCs). Although LSCs are usually identified as CD34+CD38- cells, there is significant heterogeneity in surface marker expression, and CD34- LSCs exist particularly in NPM1mut AMLs. By analyzing diagnostic primary DNMT3AmutNPM1mut AML samples, we suggest a novel flow cytometry sorting strategy particularly useful for CD34neg AML subtypes. To enrich for LSCs independently of CD34 status, positive selection for GPR56 and negative selection for NKG2D ligands are used. We show that the functional reconstitution capacity of CD34- and CD34+ LSCs as well as their transcriptomes are very similar which support phenotypic plasticity. Furthermore, we show that although CD34+ subpopulations can contain next to LSCs also normal and/or preleukemic hematopoietic stem cells (HSCs), this is not the case in CD34-GPR56+NKG2DL- enriched LSCs which thus can be isolated with high purity. Finally, we show that patients with AML, who retain at the time of diagnosis a reserve of normal and/or preleukemic HSCs in their bone marrow able to reconstitute immunocompromised mice, have significantly longer relapse-free and overall survival than patients with AML in whom functional HSCs are no longer detectable.
    Type of Medium: Online Resource
    ISSN: 2473-9529 , 2473-9537
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2023
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