bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allogeneic Hemopoietic Stem Transplant for Patients with Idiopathic Myelofibrosis Using a Reduced Intensity Thiotepa Based Conditioning Regimen.
Authors: Bacigalupo Andrea , Dominietto Alida , Pozzi Sarah , Piaggio Giovanna , van Lint Maria Teresa , Zupo Simonetta , Raiola Anna Maria , Gobbi Marco , Frassoni Francesco , De Stefano Francesco , Verdiani Simonetta , Barosi Giovanni 
Published: October 2019

Abstract
We are reporting the outcome of 39 patients with idiopathic myelofibrosis (IMF) who received an allogeneic hemopoietic stem cell transplant (HSCT) at a single Institution. Patients. The conditioning was a thiotepa - cyclophosphamide based reduced intensity regimen, and graft versus host disease (GvHD) prophylaxis was cyclosporin and methotrexate. 30 patients received marrow, 9 peripheral blood. The donor was an HLA identical sibling (ISD) (n=22) or an alternative related or unrelatd donor (UD) (n=17). The median age was 51 (32–67), the median interval diagnosis HSCT was 1015 days (225–7178) and the Lille risk score at the time of transplant was intermediate in 23 and high in 16 patients. Splenectomy was performed in 25 patients as a preparation for transplant. Results. The overall actuarial survival is 50% with a median follow up of 823 days (221– 4356). In univariate analysis favourable factors for survival were a Karnowsky score of 100% (93% vs 37%), an interval diagnosis transplant of less than 1 year (85% vs 55%), an HLA identical sibling donor (68% vs 47%) and splenectomy pre-transplant (60% vs 50%). When combined together, 17 and 22 patients has 0–1 or 2–3 favourable factors pre-transplant: their 4 year actuarial survival is respectively 0% vs 83% (p=.0001). Patients with 0–1 favourable factors, had higher transplant related mortality (41% vs 0%; p=0.009) and higher relapse related death (35% vs 4%, p=0.01). Conclusions. We conclude that allogeneic transplantation is a curative option for patients with idiopathic myelofibrosis. We have identified factors which predict a favourable outcome and may be used to select patients for this procedure.
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MicroRNA Profiling of Human Acute Myeloid Leukemia and Normal Hematopoietic Stem/Progenitor Cells Reveals a Leukemia Stem Cell Signature.
Authors: Park Christopher Y. , Wang Yulei , Prohaska Susan , Tseng Diane , Weissman Irving L. 
Published: October 2019

Abstract
While numerous studies have contributed important insights into the molecular origins of human acute myeloid leukemia (AML), many may not accurately reflect molecular pathways critical to AML development or maintenance because they ignore the inherent heterogeneity among AML blasts. One subset of blasts - leukemia stem cells (LSCs) - exhibits the unique ability to self-renew and to engraft disease in immunodeficient mouse hosts, suggesting that their elimination is critical to developing curative therapies. In addition, there is little information regarding the role of microRNAs (miRNAs) in regulating gene expression or biologic function in AML. In order to assess the potential contribution of miRNAs to AML LSC biology, we have evaluated the expression profile of 315 mature miRNAs in FACS-purified AML LSC and compared it to both non-LSC blasts as well as normal human bone marrow (BM) derived hematopoietic stem cells (HSC) and committed progenitors using a multiplexed TaqMan-based real-time PCR strategy. SAM analysis with stringent criteria (at least 25% samples with Ct <30, FDR <1%) reveals that AML LSC and non-LSC blasts are more similar to one another than to normal HSC or committed progenitors. Among the BM populations tested, AML LSC and non-LSC populations are most similar to the granulocyte-macrophage progenitor (GMP). A set of miRNAs distinguishes AML LSC and non-LSC from normal HSC and committed progenitors, including 35 miRNAs that are under-expressed and 33 miRNAs that are over-expressed in both AML fractions versus the normal populations; many of these differentially expressed miRNAs show a range of expression exceeding 3 orders of magnitude. Supervised clustering analysis of AML LSC and non-LSC blasts reveals an LSC signature composed of 89 miRNAs, with nearly all differentially expressed miRNAs (86/89) exhibiting lower expression levels in AML LSC than non-LSC blasts. Finally, supervised clustering identifies a “stem-cell” signature composed of 17 miRNAs that are over-expressed in AML LSC and HSC versus committed progenitors. This group of miRNAs does not include miRNAs previously described as being highly expressed in embryonic stem cells. Together, these studies represent the first direct comparison of miRNA expression in a human cancer stem cell to its normal counterpart, thereby identifying miRNAs that may regulate AML LSC and/or normal HSC/committed progenitor function. Initial functional studies in vivo using LNA knockdown strategies indicate that a subset of miRNAs highly expressed in HSC and LSC is important in regulating normal HSC function. We are currently expanding these studies to test the role of these miRNAs in maintaining engrafted AMLs in the xenotransplant setting.
The MLL Recombinome of Adult ALL - Results from the GMALL Study Group.
Authors: Burmeister Thomas , Meyer Claus , Schwartz Stefan , Hubert Daniela , Molkentin Mara , Kowarz Eric , Goekbuget Nicola , Hoelzer Dieter , Marschalek Rolf , Thiel Eckhard 
Published: October 2019

Abstract
The pro B and the CD10-negative pre B immunophenotypes are found in approximately 12% and 2–3% of adult acute lymphoblastic leukemia cases, respectively. Both are characterized by a high prevalence of MLL aberrations. MLL fusion genes define a high risk group of ALL patients and they have proven useful as target structures for assessing minimal residual disease. It has been a matter of debate whether MLL aberrations are of prognostic significance within the group of pro B ALL patients. To better characterize the MLL recombinome in adult ALL we have prospectively and retrospectively investigated BCR-ABL-negative pro B (N=152) and CD10-negative pre-B ALL (N=31) patient samples obtained within the framework of the GMALL study group between 2001 and 2007. We used RT-PCR to detect MLL-AF4, MLL-ENL and MLL-AF9 and other MLL fusion genes. An inverse long PCR method was used to identify the exact chromosomal breakpoints in the MLL gene or unknown MLL fusions.
Results: RT-PCR analysis revealed a MLL-AF4 fusion in 20/31 (64.5%) and a MLL-ENL fusion in 2/31 (6.5%) of CD10-negative pre-B cases. A MLL-AF4 fusion was detected in 101/151 (67.3%) and a MLL-ENL fusion in 9/151 (6.0%) of pro B cases. Additionally, two pro B patients showed a MLL-AF9 and MLL-CXXC6 fusion, respectively. The relative frequency of MLL aberrations was higher (50/68 = 73.5%) in those pro B patients with immunophenotypic coexpression of myeloid markers than in those without myeloid coexpression (41/84 = 48.8%). The chromosomal breakpoints in the MLL gene and the respective partner gene were determined on the genomic level in 91 patients. The distribution of chromosomal breakpoints in the MLL gene was the following: 1 in intron 7, 1 in intron 8, 33 in exon/intron 9, 27 in exon/intron 10, 28 in intron/exon 11, 1 in intron 12. These data illustrate the spectrum and relative frequency of MLL fusion genes in adult pro B and CD10-negative pre B ALL. The chromosomal breakpoint data provide insight into the molecular mechanisms leading to MLL aberrations in adult ALL. Chromosomal breakpoint sequences are powerful molecular markers for assessing MRD in individual patients as has been shown in the context of the GMALL MRD evaluation trials.
Three-Way Translocations and Insertions Are the Molecular Basis for Complex MLL Rearrangements.
Authors: Meyer Claus , Kowarz Eric , Hofmann Julia , Dingermann Theo , Klingebiel Thomas , Marschalek Rolf 
Published: October 2019

Abstract
The human MLL gene on 11q23 is frequently involved in chromosomal rearrangements including almost all human chromosomes. These rearrangements are associated with high-risk acute leukemias. Today more than 60 MLL fusion partner genes which represent the MLL recombinome have been characterized at the molecular level. Interestingly, more than 20% of all MLL translocations are highly complex. Here we distinguish between two types of complex rearrangements: Type I: A complex rearrangement is a genetic prerequisite due to the transcriptional orientation of the involved genes, for example t(10;11) with MLL and AF10, respectively; Type II: A complex rearrangement is not prerequisite, although identified in leukemia patients. More than 500 MLL rearrangements have been analyzed at the Diagnostic Center of Acute Leukemia so far and here, we present data on 60 complex translocations that were resolved at the molecular level. Three-way chromosomal translocations, insertions and combinations thereof are the molecular basis for most of these complex MLL rearrangements which in most cases create 3 or more fusions. However, type I is mainly based on insertions and type II is based on 3 way translocations. Within these complex rearrangements, the 5′ part of the MLL gene is in general fused in frame to one of the most frequent partner genes. But the 3′ part of the MLL gene is fused in 36 cases (60%) to a novel gene such as, for example, APBB1IP or CMAH. We defined this heterogeneous group of novel translocation partner genes as “reciprocal MLL fusion genes” as they had not been identified as fusion partners to the 5′ part of the MLL gene before. These fusions are only in frame in four cases; the remaining fusions are out of frame or the genes have an opposite transcriptional orientation. I.e. these genes show genetic haplo-insufficiency and thus may also cooperate in promoting leukemogenesis. For the remaining 40% the 3′ part of the MLL gene is fused to a chromosomal area which does not encode any gene. In many complex aberrations additional genes like for example RREB1 or OS9 are fused mostly out of frame to other genes or non-coding chromosomal areas of these complex rearrangements. These genes are also haplo-insufficient and may also contribute to the leukemogenic process. These results demonstrate that LDI-PCR is a potent tool to identify highly complex and cryptic rearrangements as both MLL fusion alleles are analyzed at the same time and reveal immediately if a balanced or more complex rearrangement is present. Whether the pathobiology of type II complex rearrangements is different in comparison to their not complex counterparts has still to be proven. Supported in part by grants Ma 1876/7-1, /8-1 and /9-1 from the DFG, grant N1KR-S12T13 from the BMBF and grant 102362 from the Deutsche Krebshilfe.
PAX5/TEL Causes Down Modulation of B-Lineage Specific Genes, and Enhances Migration to CXCL12 in preBI Cells.
Authors: Fazio Grazia , Palmi Chiara , Rolink Antonius G. , Cazzaniga Giovanni , Biondi Andrea 
Published: October 2019

Abstract
PAX5 is a transcription factor essential for B-cell development. Recently, it has been found as frequent target of abnormalities in childhood ALL (30% of B-cell precursor ALL cases), showing monoallelic loss, point mutations or chromosomal translocations. The role of these lesions is still poorly understood. We previously cloned the PAX5/TEL fusion gene in a patient affected by B-cell precursor ALL with t(9;12) translocation. We investigated the functional roles of PAX5/TEL protein in vitro, in murine wild type preBI cells, primary cells derived from a wild type mouse and positive for B220, cKIT and CD19 antigens.We demonstrated that the PAX5/TEL protein acts as a transcriptional repressor, down regulating not only CD19, but also other B-lineage specific genes, such as BLNK and MB-1. In addition, PAX5/TEL down regulates FLT3, B220 and μ heavy chain expression, and it does not activate MCSFR. Moreover in PAX5−/− preBI cells, PAX5/TEL did not restore CD19 expression. Comprehensively, these findings suggest that the fusion protein functions as a dominant repressor of transcription on many PAX5-target genes. It is known that CXCL12/SDF1 is a growth factor promoting B-cell progenitor proliferation, acting as a chemo attractant to the bone marrow. In several hematopoietic malignancies, tumor cells express CXCR4, and that the CXCL12-CXCR4 axis may influence the biology of tumor, favoring the metastasis process and the tumor proliferation. Indeed, we demonstrated that PAX5/TEL enhances cell migration towards CXCL12, with over-expression of CXCR4. These phenomena could indicate that leukemic cells carrying PAX5/TEL are able to access to niches that are normally restricted to progenitor cells, and thereby reside in a microenvironment that favours their growth and survival, although this finding must be proved in vivo. Together with previous evidences on the PAX5/TEL capacity to overcome IL7 withdrawal and to interfere with TGFbeta1 pathway, we conclude that PAX5/TEL induces resistance to apoptosis and interferes with the processes of B-cell differentiation and migration. Taken together, these phenomena likely represent key events in the process of B-cell transformation.
Cytogenetic and Molecular Genetic Aberrations in Bone Marrow Mesenchymal Stroma Cells from Patients with Myelodysplastic Syndrome and Acute Myeloid Leukemia.
Authors: Blau Olga , Hofmann Wolf-Karsten , Blau Igor W. , Baldus Claudia D. , Thiel Gundula , Nowak Verena , Schuemann Elke , Sindram Annette , Kuehne Korinna , Thiel Eckhard 
Published: October 2019

Abstract
Introduction : The biology of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) is heterogeneous. Ineffective hematopoiesis results from complex interactions between hematopoietic cells (HC) and the hematopoietic microenvironment. Bone marrow mesenchymal stroma cells (BMSC) are key components of the hematopoietic microenvironment. The question of whether BMSC from patients with hematological disorders have cytogenetic abnormalities is discussed controversially.
Methods: We performed standard cytogenetic analyses (G-banding), FISH, M-FISH, and FLT3 mutation examinations of both HC and BMSC from 56 patients (30 MDS and 26 AML) and 9 healthy individuals. For BMSC selection, mononuclear cells were isolated from fresh bone marrow aspirates at the time of initial diagnosis and were further expanded in cell culture.
Results: Clonal cytogenetic aberrations were observed in HC from 14 (46%) MDS and 14 (53%) AML patients. Cytogenetic analyses of BMSC were successfully performed in 50 of the 56 cases. Structural chromosomal aberrations, including t(1;7); t(1;3); t(1;10); t(4;7); t(7;9); t(7;19); i(1q); inv(X); del(1q); del(2q); del(3p); del(4p); del(11q); del(13q); del(17p), and others were detectable in BMSC from 42% of patients. The breakpoints of chromosomes in BMSC were typical for leukemia aberrations. Six patients showed clonal chromosomal markers: t(1;7), t(1;10), t(7;9), inv(X), del(17p), and monosomy 4. Interestingly, cytogenetic markers in BMSC differed to the aberrations in HC from the same individual. No deletions or monosomy of chromosomes 5 or 7 in BMSC (FISH, 500 cells) were found in BMSC, even in those patients, who showed these aberrations in HC. M-FISH confirmed chromosomal aberrations in BMSC. We have found cytogenetic abnormalities in BMSC from patients presenting with cytogenetic alterations in their HC as well as from those with normal karyotype. We did not find structural chromosomal alterations in BMSC cultures of healthy bone marrow donors. Fourteen percent of AML patients showed FLT3 mutations in HC, but no FLT3 mutations were found in BMSC.
Conclusion: We showed that BMSC from AML and especially from MDS patients are characterized by genetic instability. The breakpoints of chromosomes in BMSC were typical for leukemia aberrations. The fact that BMSC showed typical chromosomal changes may suggest enhanced genetic susceptibility and potential involvement in the pathophysiology of MDS. Characterization of BMSC may help us to better understand the biology of this disease.
CTCF and Nucleophosmin Participate in Long Distance Cyclin D1 Deregulation in Mantle Cell Lymphoma.
Authors: Epner Elliot M. , Huang Jing , Liu Hui , Wang Jin , Liang Shugiang , Fleming William H. 
Published: October 2019

Abstract
Cyclin D1 expression in B cells is deregulated by long distance chromosome translocations involving the immunoglobulin heavy chain (IgH) locus in mantle cell lymphoma (MCL). Ge. Using chromatin immunoprecipitation (ChIP) assays, we show that the cyclin D1 (CCND1) loci in MCL cell lines and MCL patient samples are packaged in chromatin containing CCCTC binding factor (CTCF) and nucleophosmin (NPM). Using allelic chromatin immunoprecipitation (ChIP) assays, we demonstrate that both the translocated and nontranslocated cyclin D1 alleles bind both CTCF and NPM, while RNA polymerase II is only bound to the translocated allele. Sequential ChIP assays demonstrated CTCF and NPM binding at the cyclin D1 loci in MCL cells. By immunoFISH, we demonstrate that the translocated and nontranslocated cyclin D1 loci colocalize at the nucleolus. CTCF and NPM are bound at the IgH 3′ regulatory elements only in MCL cell lines. NPM shRNA effects a specific growth arrest in these cells. These data demonstrate a role for CTCF and NPM in long distance cyclin D1 deregulation in mantle cell lymphoma.
A Novel Mechanism of Ig and Myc Translocations in AID-Deficient Mice.
Authors: Kovalchuk Alexander L. , Mushinski Elizabeth , Burkholder Brad , Qi Chen-Feng , Li Zhaoyang , Shin Dong-Mi , Morse Herbert , Potter Michael 
Published: October 2019

Abstract
Consistent with the role of activation induced cytidine deaminase (AID) as a major “catalyst” of aberrant translocations between the Ig switch regions and c-myc, AID-sufficient Bcl-xL transgenic mice rapidly develop transplantable plasmacytomas with classical T(12;15) translocations. Unexpectedly, we found that Bcl-xL transgenic BALB/cAn mice deficient for AID (designated pBxAicda−/− mice) also developed plasma cell tumors but with a lower frequency (24% vs. 62%) and with a longer mean latency (108 d vs. 36 d) than AID-sufficient controls. Six out of nine of primary tumors were shown by interphase FISH to contain a T(12;15) translocation and one other had a T(6;15). pBxAicda−/− tumors did not transplant well because they were presumably in early stages of neoplastic development or had not progressed to full malignancy including association with ascites. Nevertheless, two tumors (4885 and 4961) were successfully transplanted and established as stable cell lines. They exhibited mature plasma cell phenotype (CD45−, CD138+, PC-1+, CD19−, CD23−) and secreted IgM. Gene expression profiling showed no significant difference from control plasma cell tumors of AID-sufficient mice. Detailed molecular and cytogenetic analysis of 4885 uncovered an unusual unbalanced T(12;15) translocation with IgH Cμ and Pvt-1 in a head to tail orientation at the breakpoint, resulting in elevated c-myc expression as detected by qPCR. In contrast, 4961, a T(12;15) negative cell line, had elevated N-myc expression as a result of paracentric inversion of Chr. 12. These rearrangements had no direct association with RAG activity. We conclude that rapid development of malignant plasma cell tumors with reciprocal T(12;15) does require AID, and that in AID deficiency a novel less efficient mechanism can be utilized to bring c-myc and Ig genes into juxtaposition.
A Genome-Wide Map of Acquired Uniparental Disomy in Acute Myeloid Leukemia.
Authors: Gupta Manu , Raghavan Manoj , Gale Rosemary E. , Chelala Claude , Allen Christopher , Molloy Gael , Chaplin Tracy , Linch David C. , Cazier Jean-Baptiste , Young Bryan 
Published: October 2019

Abstract
The recent discovery of acquired uniparental disomy (aUPD) in acute myeloid leukemia (AML) has been linked to homozygosity for mutations in certain genes (Raghavan et al, Cancer Res. 2005, Fitzgibbon et al, Cancer Res. 2005). Although this phenomenon, which is undetectable by conventional cytogenetics, has been confirmed in subsequent small-scale studies, its extent and frequency remains uncertain. To determine the frequency and distribution of aUPD, DNA samples from 455 young adult AML patients entered in the UK Medical Research Council AML10 trial were analyzed using Mapping 10K 2.0 single nucleotide polymorphism (SNP) arrays (Affymetrix Inc.). Genomic DNA from blood samples of ten non-leukemic individuals was used as control to estimate the copy number values (control set I). We defined aUPD as 50 consecutive homozygous markers but allowed 2 heterozygous calls to accommodate contaminating normal tissue. Using this criterion a false positive rate of 3.3% was calculated from an available data of 90 independent controls (control set I). Overall, 120 regions of UPD were observed in 79 AML cases (17%), 87% of which involved at least one breakpoint, i.e. resulted from mitotic recombination, and 13% were whole chromosome aUPDs arising from chromosomal non-disjunction. They were the sole aberration, as detected by SNP arrays, in 61 samples (13%), and 84% of these had only a single region of aUPD. There was a non-random distribution across chromosomes; 13q (n=18 cases), 11p (n=8) and 11q (n=9) were the most frequently affected. Other chromosomes with regions of recurrent aUPD were 2p (n=7), 2q (n=6), 1p (n=5), 19q (n=4), 17q12–q21.2 (n=4), 21q (n=4), 9p (n=3), Xq (n=3), 6p (n=2), and 17p (n=2). Acquired UPDs were observed across all cytogenetic risk groups: in 25% of adverse risk patients, 11% of favorable risk, 19% of normal karyotype and 10% of the remaining intermediate risk patients. Samples with aUPD13q (5% of samples) belonged exclusively to the intermediate risk group. Chromosome 13 was the only chromosome to show recurrent whole chromosome aUPD. Fifteen samples with aUPD13q covered the region of the FLT3 gene at 13q12.2; all 15 had a FLT3-internal tandem duplication (ITD) and all cases with a high FLT3-ITD mutant level > 50% of total had 13q aUPD. Gains and losses were observed in 12% and 14% of the samples respectively. As expected, gains on chromosome 8 and losses on chromosomes 5 and 7 were common, confirming the general utility of this approach. No homozygous losses were observed. Comparison of arrays with cytogenetic analysis showed that additional information (aUPDs and/or copy number changes) was obtained in 23% of cases with a normal karyotype and 38% of cases without available cytogenetics. This study highlights the importance of aUPD in the development of AML and pinpoints regions that may contain novel mutational targets.